Studying Strangeness Production with HADES

NASA Astrophysics Data System (ADS)

Schuldes, Heidi

2018-02-01

The High-Acceptance DiElectron Spectrometer (HADES) operates in the 1 - 2A GeV energy regime in fixed target experiments to explore baryon-rich strongly interacting matter in heavy-ion collisions at moderate temperatures with rare and penetrating probes. We present results on the production of strange hadrons below their respective NN threshold energy in Au+Au collisions at 1.23A GeV ( = 2.4 GeV). Special emphasis is put on the enhanced feed-down contribution of ϕ mesons to the inclusive yield of K- and its implication on the measured spectral shape of K-. Furthermore, we investigate global properties of the system, confronting the measured hadron yields and transverse mass spectra with a Statistical Hadronization Model (SHM) and a blastwave parameterization, respectively. These supplement the world data of the chemical and kinetic freeze-out temperatures.

Coral Reef Early Warning System (CREWS) RPC Experiment

NASA Technical Reports Server (NTRS)

Estep, Leland; Spruce, Joseph P.; Hall, Callie

2007-01-01

This viewgraph document reviews the background, objectives, methodology, validation, and present status of the Coral Reef Early Warning System (CREWS) Rapid Prototyping Capability (RPC) experiment. The potential NASA contribution to CREWS Decision Support Tool (DST) centers on remotely sensed imagery products.

Accelerated time-of-flight (TOF) PET image reconstruction using TOF bin subsetization and TOF weighting matrix pre-computation.

PubMed

Mehranian, Abolfazl; Kotasidis, Fotis; Zaidi, Habib

2016-02-07

Time-of-flight (TOF) positron emission tomography (PET) technology has recently regained popularity in clinical PET studies for improving image quality and lesion detectability. Using TOF information, the spatial location of annihilation events is confined to a number of image voxels along each line of response, thereby the cross-dependencies of image voxels are reduced, which in turns results in improved signal-to-noise ratio and convergence rate. In this work, we propose a novel approach to further improve the convergence of the expectation maximization (EM)-based TOF PET image reconstruction algorithm through subsetization of emission data over TOF bins as well as azimuthal bins. Given the prevalence of TOF PET, we elaborated the practical and efficient implementation of TOF PET image reconstruction through the pre-computation of TOF weighting coefficients while exploiting the same in-plane and axial symmetries used in pre-computation of geometric system matrix. In the proposed subsetization approach, TOF PET data were partitioned into a number of interleaved TOF subsets, with the aim of reducing the spatial coupling of TOF bins and therefore to improve the convergence of the standard maximum likelihood expectation maximization (MLEM) and ordered subsets EM (OSEM) algorithms. The comparison of on-the-fly and pre-computed TOF projections showed that the pre-computation of the TOF weighting coefficients can considerably reduce the computation time of TOF PET image reconstruction. The convergence rate and bias-variance performance of the proposed TOF subsetization scheme were evaluated using simulated, experimental phantom and clinical studies. Simulations demonstrated that as the number of TOF subsets is increased, the convergence rate of MLEM and OSEM algorithms is improved. It was also found that for the same computation time, the proposed subsetization gives rise to further convergence. The bias-variance analysis of the experimental NEMA phantom and a clinical

Accelerated time-of-flight (TOF) PET image reconstruction using TOF bin subsetization and TOF weighting matrix pre-computation

NASA Astrophysics Data System (ADS)

Mehranian, Abolfazl; Kotasidis, Fotis; Zaidi, Habib

2016-02-01

Time-of-flight (TOF) positron emission tomography (PET) technology has recently regained popularity in clinical PET studies for improving image quality and lesion detectability. Using TOF information, the spatial location of annihilation events is confined to a number of image voxels along each line of response, thereby the cross-dependencies of image voxels are reduced, which in turns results in improved signal-to-noise ratio and convergence rate. In this work, we propose a novel approach to further improve the convergence of the expectation maximization (EM)-based TOF PET image reconstruction algorithm through subsetization of emission data over TOF bins as well as azimuthal bins. Given the prevalence of TOF PET, we elaborated the practical and efficient implementation of TOF PET image reconstruction through the pre-computation of TOF weighting coefficients while exploiting the same in-plane and axial symmetries used in pre-computation of geometric system matrix. In the proposed subsetization approach, TOF PET data were partitioned into a number of interleaved TOF subsets, with the aim of reducing the spatial coupling of TOF bins and therefore to improve the convergence of the standard maximum likelihood expectation maximization (MLEM) and ordered subsets EM (OSEM) algorithms. The comparison of on-the-fly and pre-computed TOF projections showed that the pre-computation of the TOF weighting coefficients can considerably reduce the computation time of TOF PET image reconstruction. The convergence rate and bias-variance performance of the proposed TOF subsetization scheme were evaluated using simulated, experimental phantom and clinical studies. Simulations demonstrated that as the number of TOF subsets is increased, the convergence rate of MLEM and OSEM algorithms is improved. It was also found that for the same computation time, the proposed subsetization gives rise to further convergence. The bias-variance analysis of the experimental NEMA phantom and a clinical

Early evolution of comet 67P studied with the RPC-LAP onboard Rosetta

NASA Astrophysics Data System (ADS)

Miloch, Wojciech; Edberg, Niklas J. T.; Eriksson, Anders I.; Yang, Lei; Paulsson, Joakim J. P.; Wedlund, Cyril Simon; Odelstad, Elias

2016-07-01

The Rosetta mission provides the in-situ measurements of a comet that are closest to a comet's aphelion ever made. The Rosetta Plasma Consortium (RPC) is a set of five instruments on board the spacecraft that specialise in the measurements of the plasma environment of comet 67P. One of the instruments is RPC-LAP, which consists of two Langmuir Probes and can measure the density, temperature, and flow speed of the plasma in the vicinity of the comet. At the early stage of the Rosetta mission, when the spacecraft is far from the nucleus of comet 67P, the ion part of the current-voltage characteristics of RPC-LAP1 is dominated by the photoemission current which surpasses the currents from the dilute solar wind plasma. As Rosetta starts orbiting around the nucleus in September 2014, LAP1 picks up signatures of local plasma density enhancements corresponding to variations of water-group ions observed in the vicinity of the comet. With the help of current-voltage characteristics and the spacecraft potential, we identify and characterise in space and time the entering of this coma-dominated plasma. In particular we determine the transition for entering the ion dominated region characterised by the 6-hour variations in the local plasma density due to the comet rotation. This transition manifests as a steep gradient in the density with respect to the distance to the comet nucleus. We discuss these RPC-LAP results together with the corresponding measurements by other instruments to provide a comprehensive picture of the transition.

77 FR 22799 - Royalty Policy Committee (RPC) Notice of Renewal

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-17

... DEPARTMENT OF THE INTERIOR Royalty Policy Committee (RPC) Notice of Renewal AGENCY: Office of Natural Resources Revenue, Interior. ACTION: Notice of renewal of the Royalty Policy Committee. SUMMARY... of the Interior is renewing the Royalty Policy Committee. The Royalty Policy Committee provides...

Characterization of BEGe detectors in the HADES underground laboratory

NASA Astrophysics Data System (ADS)

Andreotti, Erica; Gerda Collaboration

2013-08-01

This paper describes the characterization of newly produced Broad Energy Germanium (BEGe) detectors, enriched in the isotope 76Ge. These detectors have been produced in the frame of the GERDA experiment. The aim of the characterization campaign consists in the determination of all the important operational parameters (active volume, dead layer thickness and uniformity, energy resolution, detector stability in time, quality of pulse shape discrimination). A protocol test procedure and devoted set-ups, partially automated, have been developed in view of the large number (∼ 25) of BEGe's detectors to be tested. The characterization is carried out in the HADES underground laboratory, located 225 m below ground (∼ 500 m water equivalent) in Mol, Belgium.

75 FR 16499 - Royalty Policy Committee (RPC) Notice of Renewal

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-01

..., Minerals Management Service; Denver, Colorado 80225-0165; telephone number (303) 231-3392. Certification I... DEPARTMENT OF THE INTERIOR Royalty Policy Committee (RPC) Notice of Renewal AGENCY: Minerals... Secretary of the Interior on the management of Federal and Indian mineral leases and revenues under the laws...

Study of Plasma Waves Observed onboard Rosetta in the 67P/ChuryumovGerasimenko Comet Environment Using High Time Resolution Density Data Inferred from RPC-MIP and RPC-LAP Cross-calibration

NASA Astrophysics Data System (ADS)

Breuillard, H.; Henri, P.; Vallières, X.; Eriksson, A. I.; Odelstad, E.; Johansson, F. L.; Richter, I.; Goetz, C.; Wattieaux, G.; Tsurutani, B.; Hajra, R.; Le Contel, O.

2017-12-01

During two years, the groundbreaking ESA/Rosetta mission was able to escort comet 67P where previous cometary missions were only limited to flybys. This enabled for the first time to make in-situ measurements of the evolution of a comet's plasma environment. The density and temperature measured by Rosetta are derived from RPC-Mutual Impedance Probe (MIP) and RPC-Langmuir Probe (LAP). On one hand, low time resolution electron density are calculated using the plasma frequency extracted from the MIP mutual impedance spectra. On the other hand, high time resolution density fluctuations are estimated from the spacecraft potential measured by LAP. In this study, using a simple spacecraft charging model, we perform a cross-calibration of MIP plasma density and LAP spacecraft potential variations to obtain high time resolution measurements of the electron density. These results are also used to constrain the electron temperature. Then we make use of these new dataset, together with RPC-MAG magnetic field measurements, to investigate for the first time the compressibility and the correlations between plasma and magnetic field variations, for both singing comet waves and steepened waves observed, respectively during low and high cometary outgassing activity, in the plasma environment of comet 67P.

Early Evolution of Comet 67P Studied with the RPC-LAP onboard Rosetta

NASA Astrophysics Data System (ADS)

Miloch, W. J.; Yang, L.; Paulsson, J. J.; Wedlund, C. S.; Odelstad, E.; Edberg, N. J. T.; Koenders, C.; Eriksson, A.

2016-12-01

In-situ measurements within the Rosetta mission allow for studies of the cometary environment at different stages of cometary evolution. The Rosetta Plasma Consortium (RPC) is a set of five instruments on board the spacecraft that specialise in the measurements of plasma environment of comet 67P. One of the instruments is RPC-LAP, which consists of two Langmuir Probes and can measure the density, temperature, and flow speed of the plasma in the vicinity of the comet. At the early stage of the Rosetta mission, when the spacecraft is far from the nucleus of comet 67P, the ion part of the current-voltage characteristics of RPC-LAP1 is dominated by the photoemission current, which surpasses the currents from the dilute solar wind plasma. As Rosetta starts orbiting around the nucleus in September 2014, LAP1 picks up signatures of local plasma density enhancements corresponding to variations of water-group ions observed in the vicinity of the comet. With the help of current-voltage characteristics and the spacecraft potential, we identify and characterise in space and time the entering of this coma-dominated, high-density plasma region. This high-density region is observed at the northern hemisphere of the comet during early activity. The transition manifests as a steep gradient in the density with respect to the distance to the comet nucleus. We discuss these RPC-LAP results together with the corresponding measurements by other instruments to provide a comprehensive picture of the transition. We show that the early cometary plasma can be seen as composed of two distinct regions: an outer region characterised by solar wind plasma and small quantities of pickup ions, and an inner region with enhanced plasma densities.

Oxygen ion implantation induced microstructural changes and electrical conductivity in Bakelite RPC detector material

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kumar, K. V. Aneesh, E-mail: aneesh1098@gmail.com; Ravikumar, H. B., E-mail: hbr@physics.uni-mysore.ac.in; Ranganathaiah, C., E-mail: cr@physics.uni-mysore.ac.in

2016-05-06

In order to explore the structural modification induced electrical conductivity, samples of Bakelite Resistive Plate Chamber (RPC) detector materials were exposed to 100 keV Oxygen ion in the fluences of 10{sup 12}, 10{sup 13}, 10{sup 14} and 10{sup 15} ions/cm{sup 2}. Ion implantation induced microstructural changes have been studied using Positron Annihilation Lifetime Spectroscopy (PALS) and X-Ray Diffraction (XRD) techniques. Positron lifetime parameters viz., o-Ps lifetime and its intensity shows the deposition of high energy interior track and chain scission leads to the formation of radicals, secondary ions and electrons at lower ion implantation fluences (10{sup 12} to10{sup 14} ions/cm{supmore » 2}) followed by cross-linking at 10{sup 15} ions/cm{sup 2} fluence due to the radical reactions. The reduction in electrical conductivity of Bakelite detector material is correlated to the conducting pathways and cross-links in the polymer matrix. The appropriate implantation energy and fluence of Oxygen ion on polymer based Bakelite RPC detector material may reduce the leakage current, improves the efficiency, time resolution and thereby rectify the aging crisis of the RPC detectors.« less

Operation of low-noise single-gap RPC modules exposed to ionisation rates up to 1 kHz /cm2

NASA Astrophysics Data System (ADS)

Ćwiok, M.; Dominik, W.; Górski, M.; Królikowski, J.

2004-11-01

Two single gap medium-size RPC modules, made of bakelite plates of very good mechanical quality of the surface and having initial volume resistivity of 1 ×1010 Ω cm, were tested in the Gamma Irradiation Facility at CERN at ionisation rates up to 1 kHz /cm2. The internal surfaces facing the gas volume of one RPC module were cladded with a thin layer of linseed oil varnish for comparison of oiled and non-oiled RPC operation. The results refer to the gas mixture of C2H2F4/isobutane (97:3) with SF6 addition below 1%. The single gap modules exhibited full detection efficiency plateau for the high voltage range of about 1 kV at full intensity of gamma rays. Good timing characteristics allowed to reach 95% efficiency at fully opened irradiation source with time window of 20 ns. The intrinsic noise rate for a non-oiled and an oiled RPC gap was, respectively, below 5 and 1 Hz /cm2 at full efficiency over 1 kV voltage range.

Dose Optimization in TOF-PET/MR Compared to TOF-PET/CT

PubMed Central

Queiroz, Marcelo A.; Delso, Gaspar; Wollenweber, Scott; Deller, Timothy; Zeimpekis, Konstantinos; Huellner, Martin; de Galiza Barbosa, Felipe; von Schulthess, Gustav; Veit-Haibach, Patrick

2015-01-01

Purpose To evaluate the possible activity reduction in FDG-imaging in a Time-of-Flight (TOF) PET/MR, based on cross-evaluation of patient-based NECR (noise equivalent count rate) measurements in PET/CT, cross referencing with phantom-based NECR curves as well as initial evaluation of TOF-PET/MR with reduced activity. Materials and Methods A total of 75 consecutive patients were evaluated in this study. PET/CT imaging was performed on a PET/CT (time-of-flight (TOF) Discovery D 690 PET/CT). Initial PET/MR imaging was performed on a newly available simultaneous TOF-PET/MR (Signa PET/MR). An optimal NECR for diagnostic purposes was defined in clinical patients (NECRP) in PET/CT. Subsequent optimal activity concentration at the acquisition time ([A]0) and target NECR (NECRT) were obtained. These data were used to predict the theoretical FDG activity requirement of the new TOF-PET/MR system. Twenty-five initial patients were acquired with (retrospectively reconstructed) different imaging times equivalent for different activities on the simultaneous PET/MR for the evaluation of clinically realistic FDG-activities. Results The obtained values for NECRP, [A]0 and NECRT were 114.6 (± 14.2) kcps (Kilocounts per second), 4.0 (± 0.7) kBq/mL and 45 kcps, respectively. Evaluating the NECRT together with the phantom curve of the TOF-PET/MR device, the theoretical optimal activity concentration was found to be approximately 1.3 kBq/mL, which represents 35% of the activity concentration required by the TOF-PET/CT. Initial evaluation on patients in the simultaneous TOF-PET/MR shows clinically realistic activities of 1.8 kBq/mL, which represent 44% of the required activity. Conclusion The new TOF-PET/MR device requires significantly less activity to generate PET-images with good-to-excellent image quality, due to improvements in detector geometry and detector technologies. The theoretically achievable dose reduction accounts for up to 65% but cannot be fully translated into clinical

[Molecular cloning and characterization of cDNA of the rpc10+ gene encoding the smallest subunit of nuclear RNA polymerases of Schizosaccharomyces pombe].

PubMed

Shpakovskiĭ, G V; Lebedenko, E N

1997-05-01

The full-length cDNA of the rpc10+ gene encoding mini-subunit Rpc10, which is common for all three nuclear RNA polymerases of the fission yeast Schizosaccharomyces pombe, was cloned and sequenced. The Rpc10 subunit of Sz. pombe and its homologs from S. cerevisiae and H. sapiens are positively charged proteins with a highly conserved C-terminal region and an invariant zinc-binding domain (Zn-finger) of a typical amino acid composition: YxCx2Cx12RCx2CGxR. Functional tests of heterospecific complementation, using tetrad analysis or plasmid shuffling, showed that the Rpc10 subunit of Sz. pombe can successfully replace the homologous ABC10 alpha subunit in nuclear RNA polymerases I-III of S. cerevisiae.

Online gas analysis and diagnosis for RPC detectors in the ATLAS experiment

NASA Astrophysics Data System (ADS)

de Asmundis, Riccardo

2007-03-01

Resistive Plate Counters (RPC) detectors need a very strict control of gas parameters: motivations for this statement come from both the request of stability in the detector working point, and chemical consideration concerning potentially aggressive materials generated during the ionization processes into the sensitive gap; the latter point can be relevant because of a possible damage to the internal surface of the detector that has to be avoided in order to ensure an high detection efficiency of the RPC during their ten years or more of operation in ATLAS. In order to understand these aspects, detailed studies on gas behavior have been carried on at the GIF-X5 at CERN (2002-2005), based on Gas Chromatographic and spectroscopy techniques. Main results of these analysis are presented here, together with the design of the online analyzer to be installed on ATLAS conceived to keep control of gas quality and to trigger maintenance interventions on the gas system, in particular on the purification subsystem.

Functional requirements for an intelligent RPC. [remote power controller for spaceborne electrical distribution system

NASA Technical Reports Server (NTRS)

Aucoin, B. M.; Heller, R. P.

1990-01-01

An intelligent remote power controller (RPC) based on microcomputer technology can implement advanced functions for the accurate and secure detection of all types of faults on a spaceborne electrical distribution system. The intelligent RPC will implement conventional protection functions such as overcurrent, under-voltage, and ground fault protection. Advanced functions for the detection of soft faults, which cannot presently be detected, can also be implemented. Adaptive overcurrent protection changes overcurrent settings based on connected load. Incipient and high-impedance fault detection provides early detection of arcing conditions to prevent fires, and to clear and reconfigure circuits before soft faults progress to a hard-fault condition. Power electronics techniques can be used to implement fault current limiting to prevent voltage dips during hard faults. It is concluded that these techniques will enhance the overall safety and reliability of the distribution system.

Determination of the glycation sites of Bacillus anthracis neoglycoconjugate vaccine by MALDI-TOF/TOF-CID-MS/MS and LC-ESI-QqTOF-tandem mass spectrometry

PubMed Central

Jahouh, Farid; Hou, Shu-jie; Kováč, Pavol; Banoub, Joseph H.

2012-01-01

We present herein an efficient mass spectrometric method for the localization of the glycation sites of a model neoglycoconjugate vaccine formed by a construct of the tetrasaccharide side chain of the Bacillus anthracis exosporium and the protein carrier bovine serum albumin. The glycoconjugate was digested with both trypsin and GluC V8 endoproteinases, and the digests were then analyzed by MALDI-TOF/TOF-CID-MS/MS and nano-LC-ESI-QqTOF-CID-MS/MS. The sequences of the unknown peptides analyzed by MALDI-TOF/TOF-CID-MS/MS, following digestion with the GluC V8 endoproteinase, allowed us to recognize three glycopeptides whose glycation occupancies were, respectively, on Lys 235, Lys 420, and Lys 498. Similarly, the same analysis was performed on the tryptic digests, which permitted us to recognize two glycation sites on Lys 100 and Lys 374. In addition, we have also used LC-ESI-QqTOF-CID-MS/MS analysis for the identification of the tryptic digests. However, this analysis identified a higher number of glycopeptides than would be expected from a glycoconjugate composed of a carbohydrate–protein ratio of 5.4:1, which would have resulted in glycation occupancies of 18 specific sites. This discrepancy was due to the large number of glycoforms formed during the synthetic carbohydrate–spacer–carrier protein conjugation. Likewise, the LC-ESI-QqTOF-MS/MS analysis of the GluC V8 digest also identified 17 different glycation sites on the synthetic glycoconjugate. PMID:22012665

Top-down proteomic identification of bacterial protein biomarkers and toxins using MALDI-TOF-TOF-MS/MS and post-source decay

USDA-ARS?s Scientific Manuscript database

Matrix-assisted laser desorption/ionization time-of-flight-time-of-flight mass spectrometry(MALDI-TOF-TOF-MS)has provided new capabilities for the rapid identification of digested and non-digested proteins. The tandem (MS/MS) capability of TOF-TOF instruments allows precursor ion selection/isolation...

High-energy Collision-induced Dissociation by MALDI TOF/TOF Causes Charge-Remote Fragmentation of Steroid Sulfates

PubMed Central

Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B.; Holy, Timothy E.; Gross, Michael L.

2014-01-01

A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote-fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers. PMID:24781458

High-energy collision-induced dissociation by MALDI TOF/TOF causes charge-remote fragmentation of steroid sulfates.

PubMed

Yan, Yuetian; Ubukata, Masaaki; Cody, Robert B; Holy, Timothy E; Gross, Michael L

2014-08-01

A method for structural elucidation of biomolecules dating to the 1980s utilized high-energy collisions (~10 keV, laboratory frame) that induced charge-remote fragmentations (CRF), a class of fragmentations particularly informative for lipids, steroids, surfactants, and peptides. Unfortunately, the capability for high-energy activation has largely disappeared with the demise of magnetic sector instruments. With the latest designs of tandem time-of-flight mass spectrometers (TOF/TOF), however, this capability is now being restored to coincide with the renewed interest in metabolites and lipids, including steroid-sulfates and other steroid metabolites. For these metabolites, structure determinations are required at concentration levels below that appropriate for NMR. To meet this need, we explored CRF with TOF/TOF mass spectrometry for two groups of steroid sulfates, 3-sulfates and 21-sulfates. We demonstrated that the current generation of MALDI TOF/TOF instruments can generate charge-remote fragmentations for these materials. The resulting collision-induced dissociation (CID) spectra are useful for positional isomer differentiation and very often allow the complete structure determination of the steroid. We also propose a new nomenclature that directly indicates the cleavage sites on the steroid ring with carbon numbers.

MAP Reconstruction for Fourier Rebinned TOF-PET Data

PubMed Central

Bai, Bing; Lin, Yanguang; Zhu, Wentao; Ren, Ran; Li, Quanzheng; Dahlbom, Magnus; DiFilippo, Frank; Leahy, Richard M.

2014-01-01

Time-of-flight (TOF) information improves signal to noise ratio in Positron Emission Tomography (PET). Computation cost in processing TOF-PET sinograms is substantially higher than for nonTOF data because the data in each line of response is divided among multiple time of flight bins. This additional cost has motivated research into methods for rebinning TOF data into lower dimensional representations that exploit redundancies inherent in TOF data. We have previously developed approximate Fourier methods that rebin TOF data into either 3D nonTOF or 2D nonTOF formats. We refer to these methods respectively as FORET-3D and FORET-2D. Here we describe maximum a posteriori (MAP) estimators for use with FORET rebinned data. We first derive approximate expressions for the variance of the rebinned data. We then use these results to rescale the data so that the variance and mean are approximately equal allowing us to use the Poisson likelihood model for MAP reconstruction. MAP reconstruction from these rebinned data uses a system matrix in which the detector response model accounts for the effects of rebinning. Using these methods we compare performance of FORET-2D and 3D with TOF and nonTOF reconstructions using phantom and clinical data. Our phantom results show a small loss in contrast recovery at matched noise levels using FORET compared to reconstruction from the original TOF data. Clinical examples show FORET images that are qualitatively similar to those obtained from the original TOF-PET data but a small increase in variance at matched resolution. Reconstruction time is reduced by a factor of 5 and 30 using FORET3D+MAP and FORET2D+MAP respectively compared to 3D TOF MAP, which makes these methods attractive for clinical applications. PMID:24504374

Inclusive reconstruction of hadron resonances in elementary and heavy-ion collisions with HADES

NASA Astrophysics Data System (ADS)

Kornakov, Georgy

2016-11-01

The unambiguous identification of hadron modifications in hot and dense QCD matter is one of the important goals in nuclear physics. In the regime of 1 - 2 GeV kinetic energy per nucleon, HADES has measured rare and penetrating probes in elementary and heavy-ion collisions. The main creation mechanism of mesons is the excitation and decay of baryonic resonances throughout the fireball evolution. The reconstruction of shortlived (≈ 1 fm/c) resonance states through their decay products is notoriously difficult. We have developed a new iterative algorithm, which builds the best hypothesis of signal and background by distortion of individual particle properties. This allows to extract signals with signal-to-background ratios of <1%.

Ozanimod (RPC1063) is a potent sphingosine-1-phosphate receptor-1 (S1P1 ) and receptor-5 (S1P5 ) agonist with autoimmune disease-modifying activity.

PubMed

Scott, F L; Clemons, B; Brooks, J; Brahmachary, E; Powell, R; Dedman, H; Desale, H G; Timony, G A; Martinborough, E; Rosen, H; Roberts, E; Boehm, M F; Peach, R J

2016-06-01

Sphingosine1-phosphate (S1P) receptors mediate multiple events including lymphocyte trafficking, cardiac function, and endothelial barrier integrity. Stimulation of S1P1 receptors sequesters lymphocyte subsets in peripheral lymphoid organs, preventing their trafficking to inflamed tissue sites, modulating immunity. Targeting S1P receptors for treating autoimmune disease has been established in clinical studies with the non-selective S1P modulator, FTY720 (fingolimod, Gilenya™). The purpose of this study was to assess RPC1063 for its therapeutic utility in autoimmune diseases. The specificity and potency of RPC1063 (ozanimod) was evaluated for all five S1P receptors, and its effect on cell surface S1P1 receptor expression, was characterized in vitro. The oral pharmacokinetic (PK) parameters and pharmacodynamic effects were established in rodents, and its activity in three models of autoimmune disease (experimental autoimmune encephalitis, 2,4,6-trinitrobenzenesulfonic acid colitis and CD4(+) CD45RB(hi) T cell adoptive transfer colitis) was assessed. RPC1063 was specific for S1P1 and S1P5 receptors, induced S1P1 receptor internalization and induced a reversible reduction in circulating B and CCR7(+) T lymphocytes in vivo. RPC1063 showed high oral bioavailability and volume of distribution, and a circulatory half-life that supports once daily dosing. Oral RPC1063 reduced inflammation and disease parameters in all three autoimmune disease models. S1P receptor selectivity, favourable PK properties and efficacy in three distinct disease models supports the clinical development of RPC1063 for the treatment of relapsing multiple sclerosis and inflammatory bowel disease, differentiates RPC1063 from other S1P receptor agonists, and could result in improved safety outcomes in the clinic. © 2016 The British Pharmacological Society.

High sensitive and throughput screening of Aflatoxin using MALDI-TOF-TOF-PSD-MS/MS

USDA-ARS?s Scientific Manuscript database

We have achieved sensitive and efficient detection of aflatoxin B1(AFB1) through matrix-assisted laser desorption/ionization time-of-flight-time-of-flight mass spectrometry (MALDI-TOF-TOF) and post-source decay (PSD) tandem mass spectrometry (MS/MS) using an acetic acid – a-cyano-4-hydroxycinnamic a...

Characterization of Long-Chain Fatty Acid as N-(4-Aminomethylphenyl) Pyridinium Derivative by MALDI LIFT-TOF/TOF Mass Spectrometry

NASA Astrophysics Data System (ADS)

Frankfater, Cheryl; Jiang, Xuntian; Hsu, Fong-Fu

2018-05-01

Charge remote fragmentation (CRF) elimination of CnH2n+2 residues along the aliphatic tail of long chain fatty acid is hall mark of keV high-energy CID fragmentation process. It is an important fragmentation pathway leading to structural characterization of biomolecules by CID tandem mass spectrometry. In this report, we describe MALDI LIFT TOF-TOF mass spectrometric approach to study a wide variety of fatty acids (FAs), which were derivatized to N-(4-aminomethylphenyl) pyridinium (AMPP) derivative, and desorbed as M+ ions by laser with or without matrix. The high-energy MALDI LIFT TOF-TOF mass spectra of FA-AMPP contain fragment ions mainly deriving from CRF cleavages of CnH2n+2 residues, as expected. These ions together with ions from specific cleavages of the bond(s) involving the functional group within the molecule provide more complete structural identification than those produced by low-energy CID/HCD using a linear ion-trap instrument. However, this LIFT TOF-TOF mass spectrometric approach inherits low sensitivity, a typical feature of high-energy CID tandem mass spectrometry. Because of the lack of unit mass precursor ion selection with sufficient sensitivity of the current LIFT TOF-TOF technology, product ion spectra from same chain length fatty acids with difference in one or two double bonds in a mixture are not distinguishable.

REST, regulated by RA through miR-29a and the proteasome pathway, plays a crucial role in RPC proliferation and differentiation.

PubMed

Wang, Yuyao; Zhang, Dandan; Tang, Zhimin; Zhang, Yi; Gao, Huiqin; Ni, Ni; Shen, Bingqiao; Sun, Hao; Gu, Ping

2018-04-18

One of the primary obstacles in the application of retinal progenitor cells (RPCs) to the treatment of retinal degenerative diseases, such as age-related macular degeneration (AMD) and retinitis pigmentosa (RP), is their limited ability to proliferate and differentiate into specific retinal neurons. In this study, we revealed that repressor element-1-silencing transcription factor (REST), whose expression could be transcriptionally and post-transcriptionally mediated by retinoic acid (RA, one isomeride of a vitamin A derivative used as a differentiation-inducing agent in many disease treatments), plays a pivotal role in the regulation of proliferation and differentiation of RPCs. Our results show that direct knockdown of endogenous REST reduced RPC proliferation but accelerated RPC differentiation toward retinal neurons, which phenocopied the observed effects of RA on RPCs. Further studies disclosed that the expression level of REST could be downregulated by RA not only through upregulating microRNA (miR)-29a, which directly interacted with the 3'-untranslated region (3'-UTR) of the REST mRNA, but also through promoting REST proteasomal degradation. These results show us a novel functional protein, REST, which regulates RPC proliferation and differentiation, can be mediated by RA. Understanding the mechanisms of REST and RA in RPC fate determination enlightens a promising future for the application of REST and RA in the treatment of retinal degeneration diseases.

Ozanimod (RPC1063) is a potent sphingosine‐1‐phosphate receptor‐1 (S1P1) and receptor‐5 (S1P5) agonist with autoimmune disease‐modifying activity

PubMed Central

Clemons, B; Brooks, J; Brahmachary, E; Powell, R; Dedman, H; Desale, H G; Timony, G A; Martinborough, E; Rosen, H; Roberts, E; Boehm, M F; Peach, R J

2016-01-01

Background and Purpose Sphingosine1‐phosphate (S1P) receptors mediate multiple events including lymphocyte trafficking, cardiac function, and endothelial barrier integrity. Stimulation of S1P1 receptors sequesters lymphocyte subsets in peripheral lymphoid organs, preventing their trafficking to inflamed tissue sites, modulating immunity. Targeting S1P receptors for treating autoimmune disease has been established in clinical studies with the non‐selective S1P modulator, FTY720 (fingolimod, Gilenya™). The purpose of this study was to assess RPC1063 for its therapeutic utility in autoimmune diseases. Experimental Approach The specificity and potency of RPC1063 (ozanimod) was evaluated for all five S1P receptors, and its effect on cell surface S1P1 receptor expression, was characterized in vitro. The oral pharmacokinetic (PK) parameters and pharmacodynamic effects were established in rodents, and its activity in three models of autoimmune disease (experimental autoimmune encephalitis, 2,4,6‐trinitrobenzenesulfonic acid colitis and CD4+CD45RBhi T cell adoptive transfer colitis) was assessed. Key Results RPC1063 was specific for S1P1 and S1P5 receptors, induced S1P1 receptor internalization and induced a reversible reduction in circulating B and CCR7+ T lymphocytes in vivo. RPC1063 showed high oral bioavailability and volume of distribution, and a circulatory half‐life that supports once daily dosing. Oral RPC1063 reduced inflammation and disease parameters in all three autoimmune disease models. Conclusions and Implications S1P receptor selectivity, favourable PK properties and efficacy in three distinct disease models supports the clinical development of RPC1063 for the treatment of relapsing multiple sclerosis and inflammatory bowel disease, differentiates RPC1063 from other S1P receptor agonists, and could result in improved safety outcomes in the clinic. PMID:26990079

[MALDI-TOF and SELDI-TOF analysis: "tandem" techniques to identify potential biomarker in fibromyalgia].

PubMed

Giacomelli, C; Bazzichi, L; Giusti, L; Ciregia, F; Baldini, C; Da Valle, Y; De Feo, F; Sernissi, F; Rossi, A; Bombardieri, S; Lucacchini, A

2011-11-09

Fibromyalgia (FM) is characterized by the presence of chronic widespread pain throughout the musculoskeletal system and diffuse tenderness. Unfortunately, no laboratory tests have been appropriately validated for FM and correlated with the subsets and activity. The aim of this study was to apply a proteomic technique in saliva of FM patients: the Surface Enhance Laser Desorption/Ionization Time-of-Flight (SELDI-TOF). For this study, 57 FM patients and 35 HC patients were enrolled. The proteomic analysis of saliva was carried out using SELDI-TOF. The analysis was performed using different chip arrays with different characteristics of binding. The statistical analysis was performed using cluster analysis and the difference between two groups was underlined using Student’s t-test. Spectra analysis highlighted the presence of several peaks differently expressed in FM patients compared with controls. The preliminary results obtained by SELDI-TOF analysis were compared with those obtained in our previous study performed on whole saliva of FM patients by using electrophoresis. The m/z of two peaks, increased in FM patients, seem to overlap well with the molecular weight of calgranulin A and C and Rho GDP-dissociation inhibitor 2, which we had found up-regulated in our previous study. These preliminary results showed the possibility of identifying potential salivary biomarker through salivary proteomic analysis with MALDI-TOF and SELDI-TOF in FM patients. The peaks observed allow us to focus on some of the particular pathogenic aspects of FM, the oxidative stress which contradistinguishes this condition, the involvement of proteins related to the cytoskeletal arrangements, and central sensibilization.

Investigating the microstructure of keratin extracted from wool: peptide sequence (MALDI-TOF/TOF) and protein conformation (FTIR)

USDA-ARS?s Scientific Manuscript database

Keratin was extracted from wool by reduction with 2-mercaptoethanol. It was isolated as intact keratin and characterized by its similar molecular weight, protein composition, and secondary structure to native keratin. Gel electrophoresis patterns and MALDI-TOF/TOF peptide sequences provided the ide...

Characterization of RPC operation with new environmental friendly mixtures for LHC application and beyond

NASA Astrophysics Data System (ADS)

Guida, R.; Capeans, M.; Mandelli, B.

2016-07-01

The large muon trigger systems based on Resistive Plate Chambers (RPC) at the LHC experiments are currently operated with R134a based mixture. Unfortunately R134a is considered a greenhouse gas with high impact on the enviroment and therefore will be subject to regulations aiming in strongly reducing the available quantity on the market. The immediat effects might be instability on the price and incertitude in the product availability. Alternative gases (HFO-1234yf and HFO-1234ze) have been already identified by industry for specific applications as replacement of R134a. Moreover, HFCs similar to the R134a but with lower global warming potential (GWP) are already available (HFC-245fa, HFC-32, HFC-152a). The present contribution describes the results obtained with RPCs operated with new enviromemtal friendly gases. A particular attention has been addressed to the possibility of maintening the current operation conditions (i.e. currently used applied voltage and front-end electronics) in order to be able to use a new mixture for RPC systems even where the common infrastructure (i.e. high voltage and detector components) cannot be replaced for operation at higher applied voltages.

Topochemical Analysis of Cell Wall Components by TOF-SIMS.

PubMed

Aoki, Dan; Fukushima, Kazuhiko

2017-01-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a recently developing analytical tool and a type of imaging mass spectrometry. TOF-SIMS provides mass spectral information with a lateral resolution on the order of submicrons, with widespread applicability. Sometimes, it is described as a surface analysis method without the requirement for sample pretreatment; however, several points need to be taken into account for the complete utilization of the capabilities of TOF-SIMS. In this chapter, we introduce methods for TOF-SIMS sample treatments, as well as basic knowledge of wood samples TOF-SIMS spectral and image data analysis.

Differentiation of isomeric N-glycan structures by normal-phase liquid chromatography-MALDI-TOF/TOF tandem mass spectrometry.

PubMed

Maslen, Sarah; Sadowski, Pawel; Adam, Alex; Lilley, Kathryn; Stephens, Elaine

2006-12-15

The detailed characterization of protein N-glycosylation is very demanding given the many different glycoforms and structural isomers that can exist on glycoproteins. Here we report a fast and sensitive method for the extensive structure elucidation of reducing-end labeled N-glycan mixtures using a combination of capillary normal-phase HPLC coupled off-line to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and TOF/TOF-MS/MS. Using this method, isobaric N-glycans released from honey bee phospholipase A2 and Arabidopsis thaliana glycoproteins were separated by normal-phase chromatography and subsequently identified by key fragment ions in the MALDI-TOF/TOF tandem mass spectra. In addition, linkage and branching information were provided by abundant cross-ring and "elimination" fragment ions in the MALDI-CID spectra that gave extensive structural information. Furthermore, the fragmentation characteristics of N-glycans reductively aminated with 2-aminobenzoic acid and 2-aminobenzamide were compared. The identification of N-glycans containing 3-linked core fucose was facilitated by distinctive ions present only in the MALDI-CID spectra of 2-aminobenzoic acid-labeled oligosaccharides. To our knowledge, this is the first MS/MS-based technique that allows confident identification of N-glycans containing 3-linked core fucose, which is a major allergenic determinant on insect and plant glycoproteins.

Ambient VOC-Measurements by GC-PTR-TOF

NASA Astrophysics Data System (ADS)

Langebner, S.; Schnitzhofer, R.; Hasler, C.; Jocher, M.; Hansel, A.; Brilli, F.

2011-12-01

Authors: Stephan LANGEBNER, Federico BRILLI, Ralf SCHNITZHOFER, Christoph HASLER, Markus JOCHER, Armin HANSEL; During the past 16 years PTR MS (Proton Transfer Reaction Mass Spectrometry) became a well established technique for real time measurements of environmentally important volatile organic compounds (VOCs) [HANSEL 1995]. The recent development of PTR ToF [GRAUS 2010] increased the VOC separation capability by strongly improving the mass separation capability and the duty cycle. Now isobaric compounds can be separated and whole mass spectra are recorded within a fraction of a second. Isomeric VOCs, however, remain undistinguishable with this technique. Therefore a Thermo-Desorption-System-Gas-Chromatograph (TDS GC) with isomeric separation capabilities was coupled with a PTR ToF. The performance of this new GC PTR TOF instrument was evaluated analysing ambient air for several days. The measurement cycle started with simultaneous GC-sampling and direct PTR ToF measurements of ambient air. After the fifteen minute TDS cycle, the output of the GC column was directed to the PTR ToF and the timely separated VOC peaks were recorded for 40 minutes. We will present first results which look very promising e.g. different monoterpene isomers can be clearly distinguished at ambient levels.

Archaeal TFEα/β is a hybrid of TFIIE and the RNA polymerase III subcomplex hRPC62/39

PubMed Central

Blombach, Fabian; Salvadori, Enrico; Fouqueau, Thomas; Yan, Jun; Reimann, Julia; Sheppard, Carol; Smollett, Katherine L; Albers, Sonja V; Kay, Christopher WM; Thalassinos, Konstantinos; Werner, Finn

2015-01-01

Transcription initiation of archaeal RNA polymerase (RNAP) and eukaryotic RNAPII is assisted by conserved basal transcription factors. The eukaryotic transcription factor TFIIE consists of α and β subunits. Here we have identified and characterised the function of the TFIIEβ homologue in archaea that on the primary sequence level is related to the RNAPIII subunit hRPC39. Both archaeal TFEβ and hRPC39 harbour a cubane 4Fe-4S cluster, which is crucial for heterodimerization of TFEα/β and its engagement with the RNAP clamp. TFEα/β stabilises the preinitiation complex, enhances DNA melting, and stimulates abortive and productive transcription. These activities are strictly dependent on the β subunit and the promoter sequence. Our results suggest that archaeal TFEα/β is likely to represent the evolutionary ancestor of TFIIE-like factors in extant eukaryotes. DOI: http://dx.doi.org/10.7554/eLife.08378.001 PMID:26067235

MALDI-TOF and cluster-TOF-SIMS imaging of Fabry disease biomarkers

NASA Astrophysics Data System (ADS)

Touboul, David; Roy, Sandrine; Germain, Dominique P.; Chaminade, Pierre; Brunelle, Alain; Laprevote, Olivier

2007-02-01

Fabry disease is an X-linked disorder of glycosphingolipid metabolism, in which a partial or total deficiency of [alpha]-galactosidase A, a lysosomal enzyme, results in the progressive accumulation of neutral glycosphingolipids (globotriaosylceramide and digalactosylceramide) in most fluids and tissues of the body. Few information is available about the composition and distribution in tissues of the accumulated glycosphingolipids species. Mass spectrometry imaging is an innovative technique, which can provide pieces of information about the distribution of numerous biological compounds, such as lipids, directly on the tissue sections. MALDI-TOF and cluster-TOF-SIMS imaging approaches were used to study the localization of lipids (cholesterol, cholesterol sulfate, vitamin E, glycosphingolipids ...) on skin and kidney sections of patients affected by the Fabry disease. Numerous information on pathophysiology were enlightened by both techniques.

Pharmaceutical identifier confirmation via DART-TOF.

PubMed

Easter, Jacob L; Steiner, Robert R

2014-07-01

Pharmaceutical analysis comprises a large amount of the casework in forensic controlled substances laboratories. In order to reduce the time of analysis for pharmaceuticals, a Direct Analysis in Real Time ion source coupled with an accurate mass time-of-flight (DART-TOF) mass spectrometer was used to confirm identity. DART-TOF spectral data for pharmaceutical samples were analyzed and evaluated by comparison to standard spectra. Identical mass pharmaceuticals were differentiated using collision induced dissociation fragmentation, present/absent ions, and abundance comparison box plots; principal component analysis (PCA) and linear discriminant analysis (LDA) were used for differentiation of identical mass mixed drug spectra. Mass assignment reproducibility and robustness tests were performed on the DART-TOF spectra. Impacts on the forensic science community include a decrease in analysis time over the traditional gas chromatograph/mass spectrometry (GC/MS) confirmations, better laboratory efficiency, and simpler sample preparation. Using physical identifiers and the DART-TOF to confirm pharmaceutical identity will eliminate the use of GC/MS and effectively reduce analysis time while still complying with accepted analysis protocols. This will prove helpful in laboratories with large backlogs and will simplify the confirmation process. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

A new calibrant for MALDI-TOF-TOF-PSD-MS/MS of non-digested proteins for top-down proteomic analysis

USDA-ARS?s Scientific Manuscript database

RATIONALE: Matrix-assisted laser desorption/ionization (MALDI) time-of-flight-time-of-flight (TOF-TOF) tandem mass spectrometry (MS/MS) has seen increasing use for post-source decay (PSD)-MS/MS analysis of non-digested protein ions for top-down proteomic identification. However, there is no commonl...

Sodiation as a tool for enhancing the diagnostic value of MALDI-TOF/TOF-MS spectra of complex astaxanthin ester mixtures from Haematococcus pluvialis.

PubMed

Weesepoel, Yannick; Vincken, Jean-Paul; Pop, Raluca Maria; Liu, Kun; Gruppen, Harry

2013-07-01

The microalga Haematococcus pluvialis produces the pigment astaxanthin mainly in esterified form with a multitude of fatty acids, which results in a complex mixture of carotenol mono- and diesters. For rapid fingerprinting of these esters, matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF/TOF-MS) might be an alternative to traditional chromatographic separation combined with MS. Investigation of ionization and fragmentation of astaxanthin mono- and diester palmitate standards in MALDI-TOF/TOF-MS showed that sodium adduct parent masses [M + Na](+) gave much simpler MS(2) spectra than radical / protonated [M](+●) / [M + H](+) parents. [M + Na](+) fragments yielded diagnostic polyene-specific eliminations and fatty acid neutral losses, whereas [M](+●) / [M + H](+) fragmentation resulted in a multitude of non-diagnostic daughters. For diesters, a benzonium fragment, formed by polyene elimination, was required for identification of the second fatty acid attached to the astaxanthin backbone. Parents were forced into [M + Na](+) ionization by addition of sodium acetate, and best signal-to-noise ratios were obtained in the 0.1 to 1.0 mM range. This method was applied to fingerprinting astaxanthin esters in a crude H. pluvialis extract. Prior to MALDI-TOF/TOF-MS, the extract was fractionated by normal phase Flash chromatography to obtain fractions enriched in mono- and diesters and to remove pheophytin a, which compromised monoester signals. All 12 types of all-trans esterified esters found in LC were identified with MALDI-TOF/TOF-MS, with the exception of two minor monoesters. Copyright © 2013 John Wiley & Sons, Ltd.

Analytic TOF PET reconstruction algorithm within DIRECT data partitioning framework

PubMed Central

Matej, Samuel; Daube-Witherspoon, Margaret E.; Karp, Joel S.

2016-01-01

Iterative reconstruction algorithms are routinely used for clinical practice; however, analytic algorithms are relevant candidates for quantitative research studies due to their linear behavior. While iterative algorithms also benefit from the inclusion of accurate data and noise models the widespread use of TOF scanners with less sensitivity to noise and data imperfections make analytic algorithms even more promising. In our previous work we have developed a novel iterative reconstruction approach (Direct Image Reconstruction for TOF) providing convenient TOF data partitioning framework and leading to very efficient reconstructions. In this work we have expanded DIRECT to include an analytic TOF algorithm with confidence weighting incorporating models of both TOF and spatial resolution kernels. Feasibility studies using simulated and measured data demonstrate that analytic-DIRECT with appropriate resolution and regularization filters is able to provide matched bias vs. variance performance to iterative TOF reconstruction with a matched resolution model. PMID:27032968

Analytic TOF PET reconstruction algorithm within DIRECT data partitioning framework

NASA Astrophysics Data System (ADS)

Matej, Samuel; Daube-Witherspoon, Margaret E.; Karp, Joel S.

2016-05-01

Iterative reconstruction algorithms are routinely used for clinical practice; however, analytic algorithms are relevant candidates for quantitative research studies due to their linear behavior. While iterative algorithms also benefit from the inclusion of accurate data and noise models the widespread use of time-of-flight (TOF) scanners with less sensitivity to noise and data imperfections make analytic algorithms even more promising. In our previous work we have developed a novel iterative reconstruction approach (DIRECT: direct image reconstruction for TOF) providing convenient TOF data partitioning framework and leading to very efficient reconstructions. In this work we have expanded DIRECT to include an analytic TOF algorithm with confidence weighting incorporating models of both TOF and spatial resolution kernels. Feasibility studies using simulated and measured data demonstrate that analytic-DIRECT with appropriate resolution and regularization filters is able to provide matched bias versus variance performance to iterative TOF reconstruction with a matched resolution model.

Proteome analysis of excretory-secretory proteins of Entamoeba histolytica HM1:IMSS via LC-ESI-MS/MS and LC-MALDI-TOF/TOF.

PubMed

Ujang, Jorim Anak; Kwan, Soon Hong; Ismail, Mohd Nazri; Lim, Boon Huat; Noordin, Rahmah; Othman, Nurulhasanah

2016-01-01

Excretory-secretory (ES) proteins of E. histolytica are thought to play important roles in the host invasion, metabolism, and defence. Elucidation of the types and functions of E. histolytica ES proteins can further our understanding of the disease pathogenesis. Thus, the aim of this study is to use proteomics approach to better understand the complex ES proteins of the protozoa. E. histolytica ES proteins were prepared by culturing the trophozoites in protein-free medium. The ES proteins were identified using two mass spectrometry tools, namely, LC-ESI-MS/MS and LC-MALDI-TOF/TOF. The identified proteins were then classified according to their biological processes, molecular functions, and cellular components using the Panther classification system (PantherDB). A complementary list of 219 proteins was identified; this comprised 201 proteins detected by LC-ESI-MS/MS and 107 proteins by LC-MALDI-TOF/TOF. Of the 219 proteins, 89 were identified by both mass-spectrometry systems, while 112 and 18 proteins were detected exclusively by LC-ESI-MS/MS and LC-MALDI-TOF/TOF respectively. Biological protein functional analysis using PantherDB showed that 27% of the proteins were involved in metabolic processes. Using molecular functional and cellular component analyses, 35% of the proteins were found to be involved in catalytic activity, and 21% were associated with the cell parts. This study showed that complementary use of LC-ESI-MS/MS and LC-MALDI-TOF/TOF has improved the identification of ES proteins. The results have increased our understanding of the types of proteins excreted/secreted by the amoeba and provided further evidence of the involvement of ES proteins in intestinal colonisation and evasion of the host immune system, as well as in encystation and excystation of the parasite.

Highly accurate adaptive TOF determination method for ultrasonic thickness measurement

NASA Astrophysics Data System (ADS)

Zhou, Lianjie; Liu, Haibo; Lian, Meng; Ying, Yangwei; Li, Te; Wang, Yongqing

2018-04-01

Determining the time of flight (TOF) is very critical for precise ultrasonic thickness measurement. However, the relatively low signal-to-noise ratio (SNR) of the received signals would induce significant TOF determination errors. In this paper, an adaptive time delay estimation method has been developed to improve the TOF determination’s accuracy. An improved variable step size adaptive algorithm with comprehensive step size control function is proposed. Meanwhile, a cubic spline fitting approach is also employed to alleviate the restriction of finite sampling interval. Simulation experiments under different SNR conditions were conducted for performance analysis. Simulation results manifested the performance advantage of proposed TOF determination method over existing TOF determination methods. When comparing with the conventional fixed step size, and Kwong and Aboulnasr algorithms, the steady state mean square deviation of the proposed algorithm was generally lower, which makes the proposed algorithm more suitable for TOF determination. Further, ultrasonic thickness measurement experiments were performed on aluminum alloy plates with various thicknesses. They indicated that the proposed TOF determination method was more robust even under low SNR conditions, and the ultrasonic thickness measurement accuracy could be significantly improved.

Collective flow measurements with HADES in Au+Au collisions at 1.23A GeV

NASA Astrophysics Data System (ADS)

Kardan, Behruz; Hades Collaboration

2017-11-01

HADES has a large acceptance combined with a good mass-resolution and therefore allows the study of dielectron and hadron production in heavy-ion collisions with unprecedented precision. With the statistics of seven billion Au-Au collisions at 1.23A GeV recorded in 2012, the investigation of higher-order flow harmonics is possible. At the BEVALAC and SIS18 directed and elliptic flow has been measured for pions, charged kaons, protons, neutrons and fragments, but higher-order harmonics have not yet been studied. They provide additional important information on the properties of the dense hadronic medium produced in heavy-ion collisions. We present here a high-statistics, multidifferential measurement of v1 and v2 for protons in Au+Au collisions at 1.23A GeV.

Characterization of 3 mm glass electrodes and development of RPC detectors for INO-ICAL experiment

NASA Astrophysics Data System (ADS)

Kaur, Daljeet; Kumar, Ashok; Gaur, Ankit; Kumar, Purnendu; Hasbuddin, Md.; Mishra, Swati; Kumar, Praveen; Naimuddin, Md.

2015-02-01

India-based Neutrino Observatory (INO) is a multi-institutional facility, planned to be built up in South India. The INO facility will host a 51 kton magnetized Iron CALorimeter (ICAL) detector to study atmospheric muon neutrinos. Iron plates have been chosen as the target material whereas Resistive Plate Chambers (RPCs) have been chosen as the active detector element for the ICAL experiment. Due to the large number of RPCs needed ( 28,000 of 2 m×2 m in size) for ICAL experiment and for the long lifetime of the experiment, it is necessary to perform a detailed R&D such that each and every parameter of the detector performance can be optimized to improve the physics output. In this paper, we report on the detailed material and electrical properties studies for various types of glass electrodes available locally. We also report on the performance studies carried out on the RPCs made with these electrodes as well as the effect of gas composition and environmental temperature on the detector performance. We also lay emphasis on the usage of materials for RPC electrodes and the suitable environmental conditions applicable for operating the RPC detector for optimal physics output at INO-ICAL experiment.

A new strategy for faster urinary biomarkers identification by Nano-LC-MALDI-TOF/TOF mass spectrometry

PubMed Central

Benkali, K; Marquet, P; Rérolle, JP; Le Meur, Y; Gastinel, LN

2008-01-01

Background LC-MALDI-TOF/TOF analysis is a potent tool in biomarkers discovery characterized by its high sensitivity and high throughput capacity. However, methods based on MALDI-TOF/TOF for biomarkers discovery still need optimization, in particular to reduce analysis time and to evaluate their reproducibility for peak intensities measurement. The aims of this methodological study were: (i) to optimize and critically evaluate each step of urine biomarker discovery method based on Nano-LC coupled off-line to MALDI-TOF/TOF, taking full advantage of the dual decoupling between Nano-LC, MS and MS/MS to reduce the overall analysis time; (ii) to evaluate the quantitative performance and reproducibility of nano-LC-MALDI analysis in biomarker discovery; and (iii) to evaluate the robustness of biomarkers selection. Results A pool of urine sample spiked at increasing concentrations with a mixture of standard peptides was used as a specimen for biological samples with or without biomarkers. Extraction and nano-LC-MS variabilities were estimated by analyzing in triplicates and hexaplicates, respectively. The stability of chromatographic fractions immobilised with MALDI matrix on MALDI plates was evaluated by successive MS acquisitions after different storage times at different temperatures. Low coefficient of variation (CV%: 10–22%) and high correlation (R2 > 0.96) values were obtained for the quantification of the spiked peptides, allowing quantification of these peptides in the low fentomole range, correct group discrimination and selection of "specific" markers using principal component analysis. Excellent peptide integrity and stable signal intensity were found when MALDI plates were stored for periods of up to 2 months at +4°C. This allowed storage of MALDI plates between LC separation and MS acquisition (first decoupling), and between MS and MSMS acquisitions while the selection of inter-group discriminative ions is done (second decoupling). Finally the recording of

Dissemination of data measured at the CERN n_TOF facility

NASA Astrophysics Data System (ADS)

Dupont, E.; Otuka, N.; Cabellos, O.; Aberle, O.; Aerts, G.; Altstadt, S.; Alvarez, H.; Alvarez-Velarde, F.; Andriamonje, S.; Andrzejewski, J.; Audouin, L.; Bacak, M.; Badurek, G.; Balibrea, J.; Barbagallo, M.; Barros, S.; Baumann, P.; Bécares, V.; Bečvář, F.; Beinrucker, C.; Belloni, F.; Berthier, B.; Berthoumieux, E.; Billowes, J.; Boccone, V.; Bosnar, D.; Brown, A.; Brugger, M.; Caamaño, M.; Calviani, M.; Calviño, F.; Cano-Ott, D.; Capote, R.; Cardella, R.; Carrapiço, C.; Casanovas, A.; Castelluccio, D. M.; Cennini, P.; Cerutti, F.; Chen, Y. H.; Chiaveri, E.; Chin, M.; Colonna, N.; Cortés, G.; Cortés-Giraldo, M. A.; Cosentino, L.; Couture, A.; Cox, J.; Damone, L. A.; David, S.; Deo, K.; Diakaki, M.; Dillmann, I.; Domingo-Pardo, C.; Dressler, R.; Dridi, W.; Duran, I.; Eleftheriadis, C.; Embid-Segura, M.; Fernández-Domínguez, B.; Ferrant, L.; Ferrari, A.; Ferreira, P.; Finocchiaro, P.; Fraval, K.; Frost, R. J. W.; Fujii, K.; Furman, W.; Ganesan, S.; Garcia, A. R.; Gawlik, A.; Gheorghe, I.; Gilardoni, S.; Giubrone, G.; Glodariu, T.; Göbel, K.; Gomez-Hornillos, M. B.; Goncalves, I. F.; Gonzalez-Romero, E.; Goverdovski, A.; Gramegna, F.; Griesmayer, E.; Guerrero, C.; Gunsing, F.; Gurusamy, P.; Haight, R.; Harada, H.; Heftrich, T.; Heil, M.; Heinitz, S.; Hernández-Prieto, A.; Heyse, J.; Igashira, M.; Isaev, S.; Jenkins, D. G.; Jericha, E.; Kadi, Y.; Kaeppeler, F.; Kalamara, A.; Karadimos, D.; Karamanis, D.; Katabuchi, T.; Kavrigin, P.; Kerveno, M.; Ketlerov, V.; Khryachkov, V.; Kimura, A.; Kivel, N.; Kokkoris, M.; Konovalov, V.; Krtička, M.; Kroll, J.; Kurtulgil, D.; Lampoudis, C.; Langer, C.; Leal-Cidoncha, E.; Lederer, C.; Leeb, H.; Naour, C. Le; Lerendegui-Marco, J.; Leong, L. S.; Licata, M.; Meo, S. Lo; Lonsdale, S. J.; Losito, R.; Lozano, M.; Macina, D.; Manousos, A.; Marganiec, J.; Martinez, T.; Marrone, S.; Masi, A.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Matteucci, F.; Maugeri, E. A.; Mazzone, A.; Mendoza, E.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Mirea, M.; Mondelaers, W.; Montesano, S.; Moreau, C.; Mosconi, M.; Musumarra, A.; Negret, A.; Nolte, R.; O'Brien, S.; Oprea, A.; Palomo-Pinto, F. R.; Pancin, J.; Paradela, C.; Patronis, N.; Pavlik, A.; Pavlopoulos, P.; Perkowski, J.; Perrot, L.; Pigni, M. T.; Plag, R.; Plompen, A.; Plukis, L.; Poch, A.; Porras, I.; Praena, J.; Pretel, C.; Quesada, J. M.; Radeck, D.; Rajeev, K.; Rauscher, T.; Reifarth, R.; Riego, A.; Robles, M.; Roman, F.; Rout, P. C.; Rudolf, G.; Rubbia, C.; Rullhusen, P.; Ryan, J. A.; Sabaté-Gilarte, M.; Salgado, J.; Santos, C.; Sarchiapone, L.; Sarmento, R.; Saxena, A.; Schillebeeckx, P.; Schmidt, S.; Schumann, D.; Sedyshev, P.; Smith, A. G.; Sosnin, N. V.; Stamatopoulos, A.; Stephan, C.; Suryanarayana, S. V.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tarrío, D.; Tassan-Got, L.; Tavora, L.; Terlizzi, R.; Tsinganis, A.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Versaci, R.; Vermeulen, M. J.; Villamarin, D.; Vicente, M. C.; Vlachoudis, V.; Vlastou, R.; Voss, F.; Wallner, A.; Walter, S.; Ware, T.; Warren, S.; Weigand, M.; Weiß, C.; Wolf, C.; Wiesher, M.; Wisshak, K.; Woods, P. J.; Wright, T.; Žugec, P.

2017-09-01

The n_TOF neutron time-of-flight facility at CERN is used for high quality nuclear data measurements from thermal energy up to hundreds of MeV. In line with the CERN open data policy, the n_TOF Collaboration takes actions to preserve its unique data, facilitate access to them in standardised format, and allow their re-use by a wide community in the fields of nuclear physics, nuclear astrophysics and various nuclear technologies. The present contribution briefly describes the n_TOF outcomes, as well as the status of dissemination and preservation of n_TOF final data in the international EXFOR library.

TOF-SIMS imaging technique with information entropy

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Kawashima, Y.; Kudo, Masahiro

2005-05-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is capable of chemical imaging of proteins on insulated samples in principal. However, selection of specific peaks related to a particular protein, which are necessary for chemical imaging, out of numerous candidates had been difficult without an appropriate spectrum analysis technique. Therefore multivariate analysis techniques, such as principal component analysis (PCA), and analysis with mutual information defined by information theory, have been applied to interpret SIMS spectra of protein samples. In this study mutual information was applied to select specific peaks related to proteins in order to obtain chemical images. Proteins on insulated materials were measured with TOF-SIMS and then SIMS spectra were analyzed by means of the analysis method based on the comparison using mutual information. Chemical mapping of each protein was obtained using specific peaks related to each protein selected based on values of mutual information. The results of TOF-SIMS images of proteins on the materials provide some useful information on properties of protein adsorption, optimality of immobilization processes and reaction between proteins. Thus chemical images of proteins by TOF-SIMS contribute to understand interactions between material surfaces and proteins and to develop sophisticated biomaterials.

Towards Spectral Library-free MALDI-TOF MS Bacterial Identification.

PubMed

Cheng, Ding; Qiao, Liang; Horvatovich, Péter

2018-05-11

Bacterial identification is of great importance in clinical diagnosis, environmental monitoring and food safety control. Among various strategies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has drawn significant interests, and has been clinically used. Nevertheless, current bioinformatics solutions use spectral libraries for the identification of bacterial strains. Spectral library generation requires acquisition of MALDI-TOF spectra from monoculture bacterial colonies, which is time-consuming and not possible for many species and strains. We propose a strategy for bacterial typing by MALDI-TOF using protein sequences from public database, i.e. UniProt. Ten genes were identified to encode proteins most often observed by MALD-TOF from bacteria through 500 times repeated a 10-fold double cross-validation procedure, using 403 MALDI-TOF spectra corresponding to 14 genera, 81 species and 403 strains, and the protein sequences of 1276 species in UniProt. The 10 genes were then used to annotate peaks on MALDI-TOF spectra of bacteria for bacterial identification. With the approach, bacteria can be identified at the genus level by searching against a database containing the protein sequences of 42 genera of bacteria from UniProt. Our approach identified 84.1% of the 403 spectra correctly at the genus level. Source code of the algorithm is available at https://github.com/dipcarbon/BacteriaMSLF.

Testing of multigap Resistive Plate Chambers for Electron Ion Collider Detector Development

NASA Astrophysics Data System (ADS)

Hamilton, Hannah; Phenix Collaboration

2015-10-01

Despite decades of research on the subject, some details of the spin structure of the nucleon continues to be unknown. To improve our knowledge of the nucleon spin structure, the construction of a new collider is needed. This is one of the primary goals of the proposed Electron Ion Collider (EIC). Planned EIC spectrometers will require good particle identification. This can be provided by time of flight (TOF) detectors with excellent timing resolutions of 10 ps. A potential TOF detector that could meet this requirement is a glass multigap resistive plate chamber (mRPC). These mRPCs can provide excellent timing resolution at a low cost. The current glass mRPC prototypes have a total of twenty 0.1 mm thick gas gaps. In order to test the feasibility of this design, a cosmic test stand was assembled. This stand used the coincidence of scintillators as a trigger, and contains fast electronics. The construction, the method of testing, and the test results of the mRPCs will be presented.

The upgraded HADES trigger and data acquisition system

NASA Astrophysics Data System (ADS)

Michel, J.; Böhmer, M.; Kajetanowicz, M.; Korcyl, G.; Maier, L.; Palka, M.; Stroth, J.; Tarantola, A.; Traxler, M.; Ugur, C.; Yurevich, S.

2011-12-01

The HADES experiment is a High Acceptance Di-Electron Spectrometer located at GSI in Darmstadt, Germany. Recently, its trigger and data acquisition system was upgraded. The main goal was to substantially increase the event rate capability by a factor of up to 20 to reach 100 kHz in light and 20 kHz in heavy ion reaction systems. The total data rate written to storage is about 400 MByte/s in peak. In this context, the complete read-out system was exchanged to FPGA-based platforms using optical communication. For data transport a general-purpose real-time network protocol was developed to meet the strong requirements of the system. In particular, trigger information has to reach all front-end modules with latencies of less than 5 μs through up to 10 intermediate hubs in a star-like network setup. Monitoring and slow control features as well as readout and trigger distribution were joined in a single network protocol made up by three virtual channels with inherent arbitration by priority and a typical switching time of 100 ns. The full DAQ system includes about 550 FPGAs distributed over the complete detector system. For control and monitoring a virtual address space spanning the whole network is provided. Data are merged by the network hubs into data streams and passed on to a server farm using an Ethernet infrastructure. Due to the electromagnetic noise environment, several transmission error detection and correction features were included. In collaboration with groups from experiments of the FAIR accelerator complex, further developments based on the versatile hardware and communication protocol are being pursued.

Evaluation of ice-tea quality by DART-TOF/MS.

PubMed

Rajchl, Aleš; Prchalová, Jana; Kružík, Vojtěch; Ševčík, Rudolf; Čížková, Helena

2015-11-01

DART (Direct Analysis in Real Time) coupled with Time-of-Flight Mass Spectrometry (TOF/MS) has been used for analyses of ice-teas. The article focuses on quality and authenticity of ice-teas as one of the most important tea-based products on the market. Twenty-one samples of ice-teas (black and green) were analysed. Selected compounds of ice-teas were determined: theobromine, caffeine, total phenolic compounds, total soluble solids, total amino acid concentration, preservatives and saccharides were determined. Fingerprints of DART-TOF/MS spectra were used for comprehensive assessment of the ice-tea samples. The DART-TOF/MS method was used for monitoring the following compounds: citric acid, caffeine, saccharides, artificial sweeteners (saccharin, acesulphame K), and preservatives (sorbic and benzoic acid), phosphoric acid and phenolic compounds. The measured data were subjected to a principal components analysis. The HPLC and DART-TOF/MS methods were compared in terms of determination of selected compounds (caffeine, benzoic acid, sorbic acid and saccharides) in the ice-teas. The DART-TOF/MS technique seems to be a suitable method for fast screening, testing quality and authenticity of tea-based products. Copyright © 2015 John Wiley & Sons, Ltd.

Complementation of UPLC-Q-TOF-MS and CESI-Q-TOF-MS on identification and determination of peptides from bovine lactoferrin.

PubMed

Chen, Hui; Shi, Pujie; Fan, Fengjiao; Tu, Maolin; Xu, Zhe; Xu, Xianbing; Du, Ming

2018-05-01

Digested peptides of bovine lactoferrin as the functional hydrolysates were identified by the Q-TOF tandem mass spectrometry (Q-TOF-MS) coupled with ultra performance liquid chromatograph (UPLC) and capillary electrophoresis (CE). The former (UPLC-Q-TOF-MS) identified 106 peptides while the latter (CE-Q-TOF-MS) characterized 102 peptides after comparison of peptides in terms of their molecular weight (MW), mass-to-charge ratio (m/z), and isoelectric point (pI). In addition, the hydrophilic value, net charge (q), and molecular radius (r) of the peptides were calculated, and a correlation analysis of the two methods was conducted between the retention time (RT) and r/q ratio of the peptides in order to elucidate the different separation principles of the unique peptides. It was shown that the peptides with larger hydrophilic value were beneficial to be separated by UPLC, while the peptides with larger r/q ratio were beneficial to be separated by CE. Combination of the above mentioned two complementary techniques have confidently improved the sequence coverage of lactoferrin and enhanced the identification of peptides, which makes it up to 65.8% in this study. Copyright © 2018. Published by Elsevier B.V.

MALDI-TOF-mass spectrometry applications in clinical microbiology.

PubMed

Seng, Piseth; Rolain, Jean-Marc; Fournier, Pierre Edouard; La Scola, Bernard; Drancourt, Michel; Raoult, Didier

2010-11-01

MALDI-TOF-mass spectrometry (MS) has been successfully adapted for the routine identification of microorganisms in clinical microbiology laboratories in the past 10 years. This revolutionary technique allows for easier and faster diagnosis of human pathogens than conventional phenotypic and molecular identification methods, with unquestionable reliability and cost-effectiveness. This article will review the application of MALDI-TOF-MS tools in routine clinical diagnosis, including the identification of bacteria at the species, subspecies, strain and lineage levels, and the identification of bacterial toxins and antibiotic-resistance type. We will also discuss the application of MALDI-TOF-MS tools in the identification of Archaea, eukaryotes and viruses. Pathogenic identification from colony-cultured, blood-cultured, urine and environmental samples is also reviewed.

Detection of Protein Modifications and Counterfeit Protein Pharmaceuticals Using iTRAQ and MALDI TOF/TOF Mass Spectrometry: Studies with Insulins

PubMed Central

Ye, Hongping; Hill, John; Kauffman, John; Gryniewicz, Connie; Han, Xianlin

2013-01-01

iTRAQ (isotope tags for relative and absolute quantification) reagent coupled with MALDI TOF/TOF mass spectrometric analysis has been evaluated as both a qualitative and quantitative method for the detection of modifications to active pharmaceutical ingredients derived from recombinant DNA technologies, and as a method to detect counterfeit drug products. Five types of insulin (human, bovine, porcine, Lispro, Lantus®) were used as model products in the study because of their minor variations in amino acid sequence. Several experiments were conducted in which each insulin variant was separately digested with Glu-C, and the digestate was labeled with one of four different iTRAQ reagents. All digestates were then combined for desalting and MALDI TOF/TOF mass spectrometric analysis. When the digestion procedure was optimized, the insulin sequence coverage was 100%. Five different types of insulin were readily differentiated, including Human insulin (P28K29) and Lispro (K28P29), which only differ by the interchange of two contiguous residues. Moreover, quantitative analyses show that the results obtained from the iTRAQ method agree well with those determined by other conventional methods. Collectively, the iTRAQ method can be used as a qualitative and quantitative technique for the detection of protein modification and counterfeiting. PMID:18489896

Complementary b/y fragment ion pairs from post-source decay of metastable YahO for calibration of MALDI-TOF-TOF-MS/MS

USDA-ARS?s Scientific Manuscript database

Complementary b/y fragment ion pairs from post-source decay (PSD) of metastable YahO protein ion were evaluated for use in the calibration of MALDI-TOF-TOF for tandem mass spectrometry (MS/MS). The yahO gene from pathogenic Escherichia coli O157:H7 strain EDL933 was cloned into a pBAD18 plasmid vect...

From HADES to PARADISE—atomistic simulation of defects in minerals

NASA Astrophysics Data System (ADS)

Parker, Stephen C.; Cooke, David J.; Kerisit, Sebastien; Marmier, Arnaud S.; Taylor, Sarah L.; Taylor, Stuart N.

2004-07-01

The development of the HADES code by Michael Norgett in the 1970s enabled, for the first time, the routine simulation of point defects in inorganic solids at the atomic scale. Using examples from current research we illustrate how the scope and applications of atomistic simulations have widened with time and yet still follow an approach readily identifiable with this early work. Firstly we discuss the use of the Mott-Littleton methodology to study the segregation of various isovalent cations to the (00.1) and (01.2) surfaces of haematite (agr-Fe2O3). The results show that the size of the impurities has a considerable effect on the magnitude of the segregation energy. We then extend these simulations to investigate the effect of the concentration of the impurities at the surface on the segregation process using a supercell approach. We consider next the effect of segregation to stepped surfaces illustrating this with recent work on segregation of La3+ to CaF2 surfaces, which show enhanced segregation to step edges. We discuss next the application of lattice dynamics to modelling point defects in complex oxide materials by applying this to the study of hydrogen incorporation into bgr-Mg2SiO4. Finally our attention is turned to a method for considering the surface energy of physically defective surfaces and we illustrate its approach by considering the low index surfaces of agr-Al2O3.

Quantified, Interactive Simulation of AMCW ToF Camera Including Multipath Effects

PubMed Central

Lambers, Martin; Kolb, Andreas

2017-01-01

In the last decade, Time-of-Flight (ToF) range cameras have gained increasing popularity in robotics, automotive industry, and home entertainment. Despite technological developments, ToF cameras still suffer from error sources such as multipath interference or motion artifacts. Thus, simulation of ToF cameras, including these artifacts, is important to improve camera and algorithm development. This paper presents a physically-based, interactive simulation technique for amplitude modulated continuous wave (AMCW) ToF cameras, which, among other error sources, includes single bounce indirect multipath interference based on an enhanced image-space approach. The simulation accounts for physical units down to the charge level accumulated in sensor pixels. Furthermore, we present the first quantified comparison for ToF camera simulators. We present bidirectional reference distribution function (BRDF) measurements for selected, purchasable materials in the near-infrared (NIR) range, craft real and synthetic scenes out of these materials and quantitatively compare the range sensor data. PMID:29271888

Quantified, Interactive Simulation of AMCW ToF Camera Including Multipath Effects.

PubMed

Bulczak, David; Lambers, Martin; Kolb, Andreas

2017-12-22

In the last decade, Time-of-Flight (ToF) range cameras have gained increasing popularity in robotics, automotive industry, and home entertainment. Despite technological developments, ToF cameras still suffer from error sources such as multipath interference or motion artifacts. Thus, simulation of ToF cameras, including these artifacts, is important to improve camera and algorithm development. This paper presents a physically-based, interactive simulation technique for amplitude modulated continuous wave (AMCW) ToF cameras, which, among other error sources, includes single bounce indirect multipath interference based on an enhanced image-space approach. The simulation accounts for physical units down to the charge level accumulated in sensor pixels. Furthermore, we present the first quantified comparison for ToF camera simulators. We present bidirectional reference distribution function (BRDF) measurements for selected, purchasable materials in the near-infrared (NIR) range, craft real and synthetic scenes out of these materials and quantitatively compare the range sensor data.

YahO protein as a calibrant for top-down proteomic identification of Shiga toxin using MALDI-TOF-TOF-MS/MS and post-source decay

USDA-ARS?s Scientific Manuscript database

Matrix-assisted laser desorption/ionization tandem time-of-flight (MALDI-TOF-TOF) mass spectrometry is increasingly utilized for rapid top-down proteomic identification of proteins. This identification may involve analysis of either a pure protein or a protein mixture. For analysis of a pure protein...

CE-TOF/MS: fundamental concepts, instrumental considerations and applications.

PubMed

Staub, Aline; Schappler, Julie; Rudaz, Serge; Veuthey, Jean-Luc

2009-05-01

This review discusses the fundamental principles of TOF analyzers and covers the great progress that has been made in this area in recent years (i.e. orthogonal acceleration, reflectron). This paper also gives an overview of applications performed by CE coupled to TOF/MS detection. The main domains of interest include the analysis of biomolecules and natural compounds.

APD Response Time Measurements for Future TOF-E Systems

NASA Astrophysics Data System (ADS)

Starkey, M. J.; Ogasawara, K.; Dayeh, M. A.; Desai, M. I.

2017-12-01

In space physics, the ability to detect ions is crucial to understanding plasma distributions in the solar wind. This usually typically requires the determination of the particle's mass, charge, and total energy. Current ion detection schemes are implemented in three sequential parts; an electrostatic analyzer for energy per charge (E/Q) measurements, a time-of-flight (TOF) for mass per charge (M/Q) measurements, and a solid-state detector (SSD) for total energy (E) measurements. Recent work has suggested the use of avalanche photodiode detectors (APD) for a simultaneous TOF and total energy (TOF-E) measurement system, which would replace traditional SSDs, simplify design, and reduce costs. Although TOF based ion spectrometry typically requires timing resolution of <1ns, the timing profile for ion detection by APDs is not well understood. In this study we examine the timing profile of 3 different APDs for ion measurements over a suprathermal energy range of 50-300 keV. The three APDs differ by their doping type (N or P) and their detector thickness (30 μm or 150 μm). We find that APD P30, which is P doped and 30μm thick, provides the fastest rise times of the three APDs. Furthermore, these rise times are species independent and less than 1 ns. Our study shows that APDs are capable of sub-nanosecond response times for low energy ions and thus supports the future use of APDs in replacing SSDs in some TOF-E systems.

MALDI-TOF typing highlights geographical and fluconazole resistance clusters in Candida glabrata.

PubMed

Dhieb, C; Normand, A C; Al-Yasiri, M; Chaker, E; El Euch, D; Vranckx, K; Hendrickx, M; Sadfi, N; Piarroux, R; Ranque, S

2015-06-01

Utilizing matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra for Candida glabrata typing would be a cost-effective and easy-to-use alternative to classical DNA-based typing methods. This study aimed to use MALDI-TOF for the typing of C. glabrata clinical isolates from various geographical origins and test its capacity to differentiate between fluconazole-sensitive and -resistant strains.Both microsatellite length polymorphism (MLP) and MALDI-TOF mass spectra of 58 C. glabrata isolates originating from Marseilles (France) and Tunis (Tunisia) as well as collection strains from diverse geographic origins were analyzed. The same analysis was conducted on a subset of C. glabrata isolates that were either susceptible (MIC ≤ 8 mg/l) or resistant (MIC ≥ 64 mg/l) to fluconazole.According to the seminal results, both MALDI-TOF and MLP classifications could highlight C. glabrata population structures associated with either geographical dispersal barriers (p < 10(-5)) or the selection of antifungal drug resistance traits (<10(-5)).In conclusion, MALDI-TOF geographical clustering was congruent with MPL genotyping and highlighted a significant population genetic structure according to fluconazole susceptibility in C. glabrata. Furthermore, although MALDI-TOF and MLP resulted in distinct classifications, MALDI-TOF also classified the isolates with respect to their fluconazole susceptibility profile. Further prospective studies are required to evaluate the capacity of MALDI-TOF typing to investigate C. glabrata infection outbreaks and predict the antifungal susceptibility profile of clinical laboratory isolates. © The Author 2015. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Applications of MALDI-TOF technology in clinical microbiology].

PubMed

Suarez, S; Nassif, X; Ferroni, A

2015-02-01

Until now, the identification of micro-organisms has been based on the cultural and biochemical characteristics of bacterial and fungal species. Recently, Mass Spectrometry type Matrix-Assisted Laser Desorption Ionization-Time of Flight (MALDI-TOF MS) was developed in clinical microbiology laboratories. This new technology allows identification of micro-organisms directly from colonies of bacteria and fungi within few minutes. In addition, it can be used to identify germs directly from positive blood culture bottles or directly from urine samples. Other ways are being explored to expand the use of MALDI-TOF in clinical microbiology laboratories. Indeed, some studies propose to detect bacterial antibiotic resistance while others compare strains within species for faster strain typing. The main objective of this review is to update data from the recent literature for different applications of MALDI-TOF technique in microbiological diagnostic routine. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Graphene Oxide as a Novel Evenly Continuous Phase Matrix for TOF-SIMS

NASA Astrophysics Data System (ADS)

Cai, Lesi; Sheng, Linfeng; Xia, Mengchan; Li, Zhanping; Zhang, Sichun; Zhang, Xinrong; Chen, Hongyuan

2017-03-01

Using matrix to enhance the molecular ion signals for biomolecule identification without loss of spatial resolution caused by matrix crystallization is a great challenge for the application of TOF-SIMS in real-world biological research. In this report, graphene oxide (GO) was used as a matrix for TOF-SIMS to improve the secondary ion yields of intact molecular ions ([M + H]+). Identifying and distinguishing the molecular ions of lipids ( m/z >700) therefore became straightforward. The spatial resolution of TOF-SIMS imaging could also be improved as GO can form a homogeneous layer of matrix instead of crystalline domain, which prevents high spatial resolution in TOF-SIMS imaging. Lipid mapping in presence of GO revealed the delicate morphology and distribution of single vesicles with a diameter of 800 nm. On GO matrix, the vesicles with similar shape but different chemical composition could be distinguished using molecular ions. This novel matrix holds potentials in such applications as the analysis and imaging of complex biological samples by TOF-SIMS.

MALDI-TOF MS in the Microbiology Laboratory: Current Trends.

PubMed

Schubert, Sören; Kostrzewa, Markus

2017-01-01

Within less than a decade matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has become a gold standard for microbial identification in clinical microbiology laboratories. Besides identification of microorganisms the typing of single strains as well as the antibiotic and antimycotic resistance testing has come into focus in order to speed up the microbiological diagnostic. However, the full potential of MALDI-TOF MS has not been tapped yet and future technological advancements will certainly expedite this method towards novel applications and enhancement of current practice. So, the following chapter shall be rather a brainstorming and forecast of how MALDI-TOF MS will develop to influence clinical diagnostics and microbial research in the future. It shall open up the stage for further discussions and does not claim for overall validity.

Spontaneous-Desorption Ionizer for a TOF-MS

NASA Technical Reports Server (NTRS)

Schultz, J. Albert

2006-01-01

A time-of-flight mass spectrometer (TOF-MS) like the one mentioned in the immediately preceding article has been retrofitted with an ionizer based on a surface spontaneous-desorption process. This ionizer includes an electron multiplier in the form of a microchannel plate (MCP). Relative to an ionizer based on a hot-filament electron source, this ionizer offers advantages of less power consumption and greater mechanical ruggedness. The current density and stability characteristics of the electron emission of this ionizer are similar to those of a filament-based ionizer. In tests of various versions of this ionizer in the TOF-MS, electron currents up to 100 nA were registered. Currents of microamperes or more - great enough to satisfy requirements in most TOFMS applications - could be obtained by use of MCPs different from those used in the tests, albeit at the cost of greater bulk. One drawback of this ionizer is that the gain of the MCP decreases as a function of the charge extracted thus far; the total charge that can be extracted over the operational lifetime is about 1 coulomb. An MCP in the ion-detector portion of the TOF-MS is subject to the same limitation.

Secondary metabolite profiling of Curcuma species grown at different locations using GC/TOF and UPLC/Q-TOF MS.

PubMed

Lee, Jueun; Jung, Youngae; Shin, Jeoung-Hwa; Kim, Ho Kyoung; Moon, Byeong Cheol; Ryu, Do Hyun; Hwang, Geum-Sook

2014-07-04

Curcuma, a genus of rhizomatous herbaceous species, has been used as a spice, traditional medicine, and natural dye. In this study, the metabolite profile of Curcuma extracts was determined using gas chromatography-time of flight mass spectrometry (GC/TOF MS) and ultrahigh-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS) to characterize differences between Curcuma aromatica and Curcuma longa grown on the Jeju-do or Jin-do islands, South Korea. Previous studies have performed primary metabolite profiling of Curcuma species grown in different regions using NMR-based metabolomics. This study focused on profiling of secondary metabolites from the hexane extract of Curcuma species. Principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) plots showed significant differences between the C. aromatica and C. longa metabolite profiles, whereas geographical location had little effect. A t-test was performed to identify statistically significant metabolites, such as terpenoids. Additionally, targeted profiling using UPLC/Q-TOF MS showed that the concentration of curcuminoids differed depending on the plant origin. Based on these results, a combination of GC- and LC-MS allowed us to analyze curcuminoids and terpenoids, the typical bioactive compounds of Curcuma, which can be used to discriminate Curcuma samples according to species or geographical origin.

Graphene Oxide as a Novel Evenly Continuous Phase Matrix for TOF-SIMS.

PubMed

Cai, Lesi; Sheng, Linfeng; Xia, Mengchan; Li, Zhanping; Zhang, Sichun; Zhang, Xinrong; Chen, Hongyuan

2017-03-01

Using matrix to enhance the molecular ion signals for biomolecule identification without loss of spatial resolution caused by matrix crystallization is a great challenge for the application of TOF-SIMS in real-world biological research. In this report, graphene oxide (GO) was used as a matrix for TOF-SIMS to improve the secondary ion yields of intact molecular ions ([M + H] + ). Identifying and distinguishing the molecular ions of lipids (m/z >700) therefore became straightforward. The spatial resolution of TOF-SIMS imaging could also be improved as GO can form a homogeneous layer of matrix instead of crystalline domain, which prevents high spatial resolution in TOF-SIMS imaging. Lipid mapping in presence of GO revealed the delicate morphology and distribution of single vesicles with a diameter of 800 nm. On GO matrix, the vesicles with similar shape but different chemical composition could be distinguished using molecular ions. This novel matrix holds potentials in such applications as the analysis and imaging of complex biological samples by TOF-SIMS. Graphical Abstract ᅟ.

A flexible FPGA based QDC and TDC for the HADES and the CBM calorimeters

NASA Astrophysics Data System (ADS)

Rost, A.; Galatyuk, T.; Koenig, W.; Michel, J.; Pietraszko, J.; Skott, P.; Traxler, M.

2017-02-01

A Charge-to-Digital-Converter (QDC) and Time-to-Digital-Converter (TDC) based on a commercial FPGA (Field Programmable Gate Array) was developed to read out PMT signals of the planned HADES electromagnetic calorimeter (ECAL) at GSI Helmholtzzentrum für Schwerionenforschung GmbH (Darmstadt, Germany). The main idea is to convert the charge measurement of a detector signal into a time measurement, where the charge is encoded in the width of a digital pulse, while the arrival time information is encoded in the leading edge time of the pulse. The PaDiWa-AMPS prototype front-end board for the TRB3 (General Purpose Trigger and Readout Board—version 3) which implements this conversion method was developed and qualified. The already well established TRB3 platform provides the needed precise time measurements and serves as a data acquisition system. We present the read-out concept and the performance of the prototype boards in laboratory and also under beam conditions. First steps have been completed in order to adapt this concept to SiPM signals of the hadron calorimeter in the CBM experiment at the planned FAIR facility (Darmstadt).

[Utility of MALDI-TOF MS for the identification of anaerobic bacteria].

PubMed

Zárate, Mariela S; Romano, Vanesa; Nievas, Jimena; Smayevsky, Jorgelina

2014-01-01

The analysis by MALDI-TOF MS (Matrix-assited laser desorption/ionization time-of-flight mass spectrometry) has become a reference method for the identification of microorganisms in Clinical Microbiology. However, data on some groups of microorganisms are still controversial. The aim of this study is to determine the utility of MALDI-TOF MS for the identification of clinical isolates of anaerobic bacteria. One-hundred and six anaerobic bacteria isolates were analyzed by MALDI-TOF MS and by conventional biochemical tests. In those cases where identification by conventional methodology was not applicable or in the face of discordance between sequencing methodologies, 16 S rRNA gene sequence analysis was performed. The conventional method and MALDI-TOF MS agreed at genus and species level by 95.3 %. Concordance in gram-negative bacilli was 91.4% and 100% among gram-positive bacilli; there was also concordance both in the 8 isolates studied in gram-positive cocci and in the single gram-negative cocci included. The data obtained in this study demonstrate that MALDI-TOF MS offers the possibility of adequate identification of anaerobic bacteria. Copyright © 2014 Asociación Colombiana de Psiquiatría. Publicado por Elsevier España. All rights reserved.

Flavonoids as matrices for MALDI-TOF mass spectrometric analysis of transition metal complexes

NASA Astrophysics Data System (ADS)

Petkovic, Marijana; Petrovic, Biljana; Savic, Jasmina; Bugarcic, Zivadin D.; Dimitric-Markovic, Jasmina; Momic, Tatjana; Vasic, Vesna

2010-02-01

Matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a suitable method for the analysis of inorganic and organic compounds and biomolecules. This makes MALDI-TOF MS convenient for monitoring the interaction of metallo-drugs with biomolecules. Results presented in this manuscript demonstrate that flavonoids such as apigenin, kaempferol and luteolin are suitable for MALDI-TOF MS analysis of Pt(II), Pd(II), Pt(IV) and Ru(III) complexes, giving different signal-to-noise ratios of the analyte peak. The MALDI-TOF mass spectra of inorganic complexes acquired with these flavonoid matrices are easy to interpret and have some advantages over the application of other commonly used matrices: a low number of matrix peaks are detectable and the coordinative metal-ligand bond is, in most cases, preserved. On the other hand, flavonoids do not act as typical matrices, as their excess is not required for the acquisition of MALDI-TOF mass spectra of inorganic complexes.

Effect of Local TOF Kernel Miscalibrations on Contrast-Noise in TOF PET

NASA Astrophysics Data System (ADS)

Clementel, Enrico; Mollet, Pieter; Vandenberghe, Stefaan

2013-06-01

TOF PET imaging requires specific calibrations: accurate characterization of the system timing resolution and timing offset is required to achieve the full potential image quality. Current system models used in image reconstruction assume a spatially uniform timing resolution kernel. Furthermore, although the timing offset errors are often pre-corrected, this correction becomes less accurate with the time since, especially in older scanners, the timing offsets are often calibrated only during the installation, as the procedure is time-consuming. In this study, we investigate and compare the effects of local mismatch of timing resolution when a uniform kernel is applied to systems with local variations in timing resolution and the effects of uncorrected time offset errors on image quality. A ring-like phantom was acquired on a Philips Gemini TF scanner and timing histograms were obtained from coincidence events to measure timing resolution along all sets of LORs crossing the scanner center. In addition, multiple acquisitions of a cylindrical phantom, 20 cm in diameter with spherical inserts, and a point source were simulated. A location-dependent timing resolution was simulated, with a median value of 500 ps and increasingly large local variations, and timing offset errors ranging from 0 to 350 ps were also simulated. Images were reconstructed with TOF MLEM with a uniform kernel corresponding to the effective timing resolution of the data, as well as with purposefully mismatched kernels. To CRC vs noise curves were measured over the simulated cylinder realizations, while the simulated point source was processed to generate timing histograms of the data. Results show that timing resolution is not uniform over the FOV of the considered scanner. The simulated phantom data indicate that CRC is moderately reduced in data sets with locally varying timing resolution reconstructed with a uniform kernel, while still performing better than non-TOF reconstruction. On the other

Shiga toxin 2 subtypes of enterohemorrhagic E. coli O157:H- E32511 analyzed by RT-qPCR and top-down proteomics using MALDI-TOF-TOF-MS

USDA-ARS?s Scientific Manuscript database

We have measured the relative abundance of the B-subunits and mRNA transcripts of two Stx2 subtypes present in Shiga toxin-producing Escherichia coli (STEC) O157:H- strain E32511 using matrix-assisted laser desorption/ionization time-of-flight-time-of-flight tandem mass spectrometry (MALDI-TOF-TOF-M...

Retrofitting of Reinforced Concrete Beams using Reactive Powder Concrete (RPC)

NASA Astrophysics Data System (ADS)

Karthik, S.; Sundaravadivelu, Karthik

2017-07-01

Strengthening of existing damaged structures is one of the leading studies in civil engineering. The purpose of retrofitting is to structurally treat the member with an aim to restore the structure to its original strength. The focus of this project is to study the behaviour of damaged Reinforced Concrete beam retrofitted with Reactive Powder Concrete (RPC) Overlay. Reinforced concrete beams of length 1200 mm, width 100 mm and depth 200 mm were casted with M30 grade of concrete in the laboratory and cured for 28 days. One beam is taken as control and are tested under two point loading to find out ultimate load. Remaining beams are subjected to 90 % ultimate load of control beams. The partially damaged beams are retrofitted with Reactive Powder Concrete Overlay at the full tension face of the beam and side overlay depends upon the respectable retrofitting techniques with 10 mm and 20 mm thick layer to find optimum. Materials like steel fibres are added to enhance the ductility by eliminating coarse particle for homogeneity of the structure. Finally, the modes of failure for retrofitted beams are analysed experimentally under two point loading & compared the results with Control beam.

Compton scatter tomography in TOF-PET

NASA Astrophysics Data System (ADS)

Hemmati, Hamidreza; Kamali-Asl, Alireza; Ay, Mohammadreza; Ghafarian, Pardis

2017-10-01

Scatter coincidences contain hidden information about the activity distribution on the positron emission tomography (PET) imaging system. However, in conventional reconstruction, the scattered data cause the blurring of images and thus are estimated and subtracted from detected coincidences. List mode format provides a new aspect to use time of flight (TOF) and energy information of each coincidence in the reconstruction process. In this study, a novel approach is proposed to reconstruct activity distribution using the scattered data in the PET system. For each single scattering coincidence, a scattering angle can be determined by the recorded energy of the detected photons, and then possible locations of scattering can be calculated based on the scattering angle. Geometry equations show that these sites lie on two arcs in 2D mode or the surface of a prolate spheroid in 3D mode, passing through the pair of detector elements. The proposed method uses a novel and flexible technique to estimate source origin locations from the possible scattering locations, using the TOF information. Evaluations were based on a Monte-Carlo simulation of uniform and non-uniform phantoms at different resolutions of time and detector energy. The results show that although the energy uncertainties deteriorate the image spatial resolution in the proposed method, the time resolution has more impact on image quality than the energy resolution. With progress of the TOF system, the reconstruction using the scattered data can be used in a complementary manner, or to improve image quality in the next generation of PET systems.

Testing Mylar Multi-Gap Resistive Plate Chambers

NASA Astrophysics Data System (ADS)

Towell, Cecily; EIC PID Consortium Collaboration

2016-09-01

Quantum Chromodynamics (QCD) is the fundamental theory that successfully explains strong force interactions. To continue the effective study of QCD in nuclear structure, plans are being made to construct an Electron Ion Collider (EIC). Part of the preparation for the EIC includes continued detector development to push beyond their current capabilities. This includes Time of Flight (TOF) detectors, which are used for particle identification. Multi-Gap Resistive Plate Chambers (mRPCs) are a type of TOF detector that typically use glass to make small gas gaps within the detector to produce fast signals when a high energy particle goes through the detector. These extremely thin gaps of 0.2mm are key in achieving the excellent timing resolution capability of these detectors. A new mRPC design is being tested with the goal of reaching a timing resolution of 10ps. This design uses sheets of mylar in place of the glass so that the width of the dividers is smaller, thus vastly increasing the number of gas gaps. Multiple versions of this mylar mRPC have been made and tested. The methods for producing these mRPCs and their performance will be discussed. This research was supported by US DOE MENP Grant DE-FG02-03ER41243.

TOF-SIMS Analysis of Red Color Inks of Writing and Printing Tools on Questioned Documents.

PubMed

Lee, Jihye; Nam, Yun Sik; Min, Jisook; Lee, Kang-Bong; Lee, Yeonhee

2016-05-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a well-established surface technique that provides both elemental and molecular information from several monolayers of a sample surface while also allowing depth profiling or image mapping to be performed. Static TOF-SIMS with improved performances has expanded the application of TOF-SIMS to the study of a variety of organic, polymeric, biological, archaeological, and forensic materials. In forensic investigation, the use of a minimal sample for the analysis is preferable. Although the TOF-SIMS technique is destructive, the probing beams have microsized diameters so that only small portion of the questioned sample is necessary for the analysis, leaving the rest available for other analyses. In this study, TOF-SIMS and attenuated total reflectance Fourier transform infrared (ATR-FTIR) were applied to the analysis of several different pen inks, red sealing inks, and printed patterns on paper. The overlapping areas of ballpoint pen writing, red seal stamping, and laser printing in a document were investigated to identify the sequence of recording. The sequence relations for various cases were determined from the TOF-SIMS mapping image and the depth profile. TOF-SIMS images were also used to investigate numbers or characters altered with two different red pens. TOF-SIMS was successfully used to determine the sequence of intersecting lines and the forged numbers on the paper. © 2016 American Academy of Forensic Sciences.

Analysis of human serum lipoprotein lipid composition using MALDI-TOF mass spectrometry.

PubMed

Hidaka, Hiroya; Hanyu, Noboru; Sugano, Mitsutoshi; Kawasaki, Kenji; Yamauchi, Kazuyoshi; Katsuyama, Tsutomu

2007-01-01

This study used matrix-assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify all lipid classes in human serum lipoproteins. After the major lipoproteins classes were isolated from serum by ultracentrifugation, the lipids were extracted and mixed with 2,5-dihydroxybenzoic acid (2,5-DHB) dissolved in Folch's solution (chloroform/methanol 2:1, v/v). MALDI-TOF MS analysis of the samples identified phospholipids (PLs), lysophospholipids (lysoPLs), sphingolipids (SLs), triglycerides (TGs), cholesteryl esters (CEs), and free cholesterol; it also showed the characteristics of individual fatty acid chains in serum lipids. MALDI-TOF MS allowed analysis of strongly hydrophobic and non-polar molecules such as CEs and TGs as well as hydrophilic molecules such as phospholipids. Direct analysis of fatty acids was not possible. The concentrations of lipids were not consistent with the ion peak intensities, since the extent of polarity affected the ionization characteristics of the molecules. However, lipid molecules with similar molecular structures but various fatty acid chains, such as phosphatidylcholine (PCs), were analyzed quantitatively by MALDI-TOF MS. Quantitative measurement of cholesterol was possible with the use of an internal standard. This study shows that MALDI-TOF MS can be used for direct investigation and quantitative analysis of the phospholipid composition of serum lipoproteins.

Identification of bacteria isolated from veterinary clinical specimens using MALDI-TOF MS.

PubMed

Pavlovic, Melanie; Wudy, Corinna; Zeller-Peronnet, Veronique; Maggipinto, Marzena; Zimmermann, Pia; Straubinger, Alix; Iwobi, Azuka; Märtlbauer, Erwin; Busch, Ulrich; Huber, Ingrid

2015-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has recently emerged as a rapid and accurate identification method for bacterial species. Although it has been successfully applied for the identification of human pathogens, it has so far not been well evaluated for routine identification of veterinary bacterial isolates. This study was performed to compare and evaluate the performance of MALDI-TOF MS based identification of veterinary bacterial isolates with commercially available conventional test systems. Discrepancies of both methods were resolved by sequencing 16S rDNA and, if necessary, the infB gene for Actinobacillus isolates. A total of 375 consecutively isolated veterinary samples were collected. Among the 357 isolates (95.2%) correctly identified at the genus level by MALDI-TOF MS, 338 of them (90.1% of the total isolates) were also correctly identified at the species level. Conventional methods offered correct species identification for 319 isolates (85.1%). MALDI-TOF identification therefore offered more accurate identification of veterinary bacterial isolates. An update of the in-house mass spectra database with additional reference spectra clearly improved the identification results. In conclusion, the presented data suggest that MALDI-TOF MS is an appropriate platform for classification and identification of veterinary bacterial isolates.

Rapid detection of AAC(6')-Ib-cr production using a MALDI-TOF MS strategy.

PubMed

Pardo, C-A; Tan, R N; Hennequin, C; Beyrouthy, R; Bonnet, R; Robin, F

2016-12-01

Plasmid-mediated quinolone resistance mechanisms have become increasingly prevalent among Enterobacteriaceae strains since the 1990s. Among these mechanisms, AAC(6')-Ib-cr is the most difficult to detect. Different detection methods have been developed, but they require expensive procedures such as Sanger sequencing, pyrosequencing, polymerase chain reaction (PCR) restriction, or the time-consuming phenotypic method of Wachino. In this study, we describe a simple matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) method which can be easily implemented in clinical laboratories that use the MALDI-TOF technique for bacterial identification. We tested 113 strains of Enterobacteriaceae, of which 64 harbored the aac(6')-Ib-cr gene. We compared two MALDI-TOF strategies, which differed by their norfloxacin concentration (0.03 vs. 0.5 g/L), and the method of Wachino with the PCR and sequencing strategy used as the reference. The MALDI-TOF strategy, performed with 0.03 g/L norfloxacin, and the method of Wachino yielded the same high performances (Se = 98 %, Sp = 100 %), but the turnaround time of the MALDI-TOF strategy was faster (<5 h), simpler, and inexpensive (<1 Euro). Our study shows that the MALDI-TOF strategy has the potential to become a major method for the detection of many different enzymatic resistance mechanisms.

TOF-SIMS investigation of metallic material surface after culturing cells

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Hiromoto, Sachiko; Hanawa, Takao; Kudo, Masahiro

2004-06-01

Biomolecules such as extracellular matrix and adhesive proteins generated by adhered cells on metallic specimens were characterized by means of time-of-flight secondary ion mass spectrometry (TOF-SIMS) in order to clarify the interaction between cells and metal surfaces. Since composition and structure of the extracellular matrix depends on conditions of cells, characterization of the interaction between cells and metallic specimens is important in order to evaluate the biocompatibility and the degradation behavior of metallic biomaterials and artificial organs. Moreover, the obtained data can contribute to the development of new metallic biomaterials. TOF-SIMS spectra were analyzed by means of mutual information described by information theory and principal components analysis (PCA). The results show that cells have great influence on adsorption of biomolecules on metallic materials because they change surface conditions of the materials. Thus TOF-SIMS is a useful technique to investigate the interaction between metallic biomaterials and cells.

TOF-SIMS imaging of protein adsorption on dialysis membrane

NASA Astrophysics Data System (ADS)

Aoyagi, Satoka; Hayama, Msayo; Hasegawa, Urara; Sakai, Kiyotaka; Hoshi, Takahiro; Kudo, Masahiro

2004-06-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is capable of chemical imaging of proteins on insulated samples such as hollow-fiber dialysis membranes. Albumin loss and a lowering of diffusive permeability caused by protein adsorption on dialysis membranes should be reduced in order to enhance dialysis adequacy of the patients. Bovine serum albumin (BSA)-adsorbed hollow-fiber dialysis membranes were tested in the present study. TOF-SIMS images and spectra of both native membranes and BSA-adsorbed membranes were compared in order to identify secondary ions related to BSA and membranes. Peaks of secondary ions related to BSA and each membrane were selected by means of information theory, and they are characterized by principal component analysis (PCA). Chemical images of BSA adsorption on both native and treated membranes were obtained to find that BSA permeability and interaction between the membranes and BSA definitely depend on the properties of a membrane. TOF-SIMS imaging obtained with information theory is a powerful tool to estimate protein adsorption on the dialysis membranes.

Exploratory analysis of TOF-SIMS data from biological surfaces

NASA Astrophysics Data System (ADS)

Vaidyanathan, Seetharaman; Fletcher, John S.; Henderson, Alex; Lockyer, Nicholas P.; Vickerman, John C.

2008-12-01

The application of multivariate analytical tools enables simplification of TOF-SIMS datasets so that useful information can be extracted from complex spectra and images, especially those that do not give readily interpretable results. There is however a challenge in understanding the outputs from such analyses. The problem is complicated when analysing images, given the additional dimensions in the dataset. Here we demonstrate how the application of simple pre-processing routines can enable the interpretation of TOF-SIMS spectra and images. For the spectral data, TOF-SIMS spectra used to discriminate bacterial isolates associated with urinary tract infection were studied. Using different criteria for picking peaks before carrying out PC-DFA enabled identification of the discriminatory information with greater certainty. For the image data, an air-dried salt stressed bacterial sample, discussed in another paper by us in this issue, was studied. Exploration of the image datasets with and without normalisation prior to multivariate analysis by PCA or MAF resulted in different regions of the image being highlighted by the techniques.

Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garabedian, Alyssa; Benigni, Paolo; Ramirez, Cesar E.

Abstract. In the present work, the potential of trapped ion mobility spectrometry coupled to TOF mass spectrometry (TIMS-TOF MS) for discovery and targeted monitoring of peptide biomarkers from human-in-mouse xenograft tumor tissue was evaluated. In particular, a TIMS-MS workflow was developed for the detection and quantification of peptide biomarkers using internal heavy analogs, taking advantage of the high mobility resolution (R = 150–250) prior to mass analysis. Five peptide biomarkers were separated, identified, and quantified using offline nanoESI-TIMSCID- TOF MS; the results were in good agreement with measurements using a traditional LC-ESI-MS/MS proteomics workflow. The TIMS-TOF MS analysis permitted peptidemore » biomarker detection based on accurate mobility, mass measurements, and high sequence coverage for concentrations in the 10–200 nM range, while simultaneously achieving discovery measurements« less

How to: identify non-tuberculous Mycobacterium species using MALDI-TOF mass spectrometry.

PubMed

Alcaide, F; Amlerová, J; Bou, G; Ceyssens, P J; Coll, P; Corcoran, D; Fangous, M-S; González-Álvarez, I; Gorton, R; Greub, G; Hery-Arnaud, G; Hrábak, J; Ingebretsen, A; Lucey, B; Marekoviċ, I; Mediavilla-Gradolph, C; Monté, M R; O'Connor, J; O'Mahony, J; Opota, O; O'Reilly, B; Orth-Höller, D; Oviaño, M; Palacios, J J; Palop, B; Pranada, A B; Quiroga, L; Rodríguez-Temporal, D; Ruiz-Serrano, M J; Tudó, G; Van den Bossche, A; van Ingen, J; Rodriguez-Sanchez, B

2018-06-01

The implementation of MALDI-TOF MS for microorganism identification has changed the routine of the microbiology laboratories as we knew it. Most microorganisms can now be reliably identified within minutes using this inexpensive, user-friendly methodology. However, its application in the identification of mycobacteria isolates has been hampered by the structure of their cell wall. Improvements in the sample processing method and in the available database have proved key factors for the rapid and reliable identification of non-tuberculous mycobacteria isolates using MALDI-TOF MS. The main objective is to provide information about the proceedings for the identification of non-tuberculous isolates using MALDI-TOF MS and to review different sample processing methods, available databases, and the interpretation of the results. Results from relevant studies on the use of the available MALDI-TOF MS instruments, the implementation of innovative sample processing methods, or the implementation of improved databases are discussed. Insight about the methodology required for reliable identification of non-tuberculous mycobacteria and its implementation in the microbiology laboratory routine is provided. Microbiology laboratories where MALDI-TOF MS is available can benefit from its capacity to identify most clinically interesting non-tuberculous mycobacteria in a rapid, reliable, and inexpensive manner. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Rocuronium: automatic infusion versus manual administration with TOF monitorisation.

PubMed

Ozturk Arikan, Fatma Gulcin; Turan, Guldem; Ozgultekin, Asu; Sivrikaya, Zubeyir; Cosar, Bekir Cem; Onder, Dondu Nisa

2016-10-01

TOF (train-of-four) monitoring provides objective data in application of neuromuscular blocking agent. Thus, applicator-based differences are eliminated and optimum muscle relaxation is maintained during operation. In the present study, we aimed to compare the effects of target-controlled infusion system and standard TOF monitoring, on use of rocuronium. ASA I-II patients, who were aged between 18 and 75 years and scheduled for elective abdominal surgery at Haydarpaşa Numune Training and Research Hospital, were enrolled in the study. In order to evaluate neuromuscular blockade, the patients in Group 1 were connected to the acceleromyography device of the target-controlled infusion pump (Veryark-CLMRIS-I-China) while the ones in Group 2 were connected to the routinely used acceleromyography device (TOF Watch SX). There was no significant difference between groups regarding patient characteristics, the durations of anaesthesia and surgery, quality of intubation, time to extubation and time to recovery (TOF ratio of 0.9). Intubation time was significantly longer in Group 1 (Automated group) as compared to Group 2 (Control group) (p < 0.05). The total rocuronium amount used in Group 1 was found to be significantly higher than the amount used in Group 2 (p < 0.05). There was no clinical evidence of residual neuromuscular blockage or reoccurrence of neuromuscular blockage in any patient in either group. Both methods can be used for administration of neuromuscular blocker agent during moderate time anesthesia. No advantage was noted when rocuronium was administered via automatical infusion pump during anaesthesia.

Strangeness at high μB: Recent data from FOPI and HADES

NASA Astrophysics Data System (ADS)

Leifels, Yvonne

2018-02-01

Strangeness production in heavy-ion reactions at incident energies at or below the threshold in NN collisions gives access to the characteristics of bulk nuclear matter and the properties of strange particles inside the hot and dense nuclear medium, like potentials and interaction cross sections. At these energies strangeness is produced in multi-step processes potentially via excitation of intermediate heavy resonances. The amount of experimental data on strangeness production at these energies has increased substantially during the last years due to the FOPI and the HADES experiments at SIS18 at GSI. Experimental data on K+ and K0 production support the assumption that particles with an s quark feel a moderate repulsive potential in the nuclear medium. The situation is not that clear in the case of K-. Here, spectra and flow of K- mesons is influenced by the contribution of ø mesons which are decaying into K+K- pairs with a branching ratio of 48.9 %. Depending on incident energy upto 30 % of all K- mesons measured in heavyion collisions are originating from ø-decays. Strangeness production yields - except the yield of Ξ- are described by thermal hadronisation models. Experimental data not only measured for heavy-ion collisions but also in proton induced reactions are described with sets of temperature T and baryon chemical potential μb which are close to a universal freeze-out curve which is fitting also experimental data obtained at lower baryon chemical potential. Despite the good description of most particle production yields, the question how this is achieved is still not settled and should be the focus of further investigations.

Screening of 439 Pesticide Residues in Fruits and Vegetables by Gas Chromatography-Quadrupole-Time-of-Flight Mass Spectrometry Based on TOF Accurate Mass Database and Q-TOF Spectrum Library.

PubMed

Li, Jian-Xun; Li, Xiao-Ying; Chang, Qiao-Ying; Li, Yan; Jin, Ling-He; Pang, Guo-Fang; Fan, Chun-Lin

2018-05-03

Because of its unique characteristics of accurate mass full-spectrum acquisition, high resolution, and fast acquisition rates, GC-quadrupole-time-of-flight MS (GC-Q-TOF/MS) has become a powerful tool for pesticide residue analysis. In this study, a TOF accurate mass database and Q-TOF spectrum library of 439 pesticides were established, and the parameters of the TOF database were optimized. Through solid-phase extraction (SPE), whereby pesticides are extracted from fruit and vegetable substrates by using 40 mL 1% acetic acid in acetonitrile (v/v), purified by the Carbon/NH₂ SPE cartridge, and finally detected by GC-Q-TOF/MS, the rapid analysis of 439 pesticides in fruits and vegetables can be achieved. The methodology verification results show that more than 70 and 91% of pesticides, spiked in fruits and vegetables with concentrations of 10 and 100 μg/kg, respectively, saw recoveries that conform to the European Commission's criterion of between 70 and 120% with RSD ≤20%. Eighty-one percent of pesticides have screening detection limits lower than 10 μg/kg, which makes this a reliable analysis technology for the monitoring of pesticide residues in fruits and vegetables. This technology was further validated for its characteristics of high precision, high speed, and high throughput through successful detection of 9817 samples during 2013-2015.

Quantitative detection of RO2 radicals and other products from cyclohexene ozonolysis with ammonium-CI3-TOF and acetate-CI-API-TOF

NASA Astrophysics Data System (ADS)

Hansel, A.; Scholz, W.; Mentler, B.; Fischer, L.; Berndt, T.

2017-12-01

The performance of the novel ammonium-CI3-TOF utilizing NH4+ adduct ion chemistry to measure quantitatively first generation oxidized product molecules (OMs) as well as highly oxidized organic molecules (HOMs) was investigated for the first time. The gas-phase ozonolysis of cyclohexene served as a test system in order to evaluate the capability of the detection systems. Experiments have been carried out in the TROPOS free-jet flow system at close to atmospheric conditions. Product ion signals were simultaneously observed by the ammonium-CI3-TOF and the acetate-CI-API-TOF. Both instruments are in remarkable good agreement within a factor of two for HOMs. For OMs not containing an OOH group the acetate technique can considerably underestimate OM concentrations by 2-3 orders of magnitude. First steps of cyclohexene ozonolysis generate ten different (m/z product peaks) main products comprising 92% of observed OMs. The remaining 8% are distributed over several (m/z peaks) minor products that can be attributed to HOMs, predominately to highly oxidized RO2 radicals. Summing up, observed ammonium-CI3-TOF products yield 4.9 x 109 molecules cm-³ in excellent agreement with the amount of reacted cyclohexene of 5.0 x 109 molecules cm-³ for reactant concentrations of [O3] = 2.25 x 1012 molecules cm-³ and [cyclohexene] = 2.0 x 1012 molecules cm-³ and a reaction time of 7.9 s. NH4+ adduct ion chemistry based CIMS techniques offer a unique opportunity for complete detection of the whole product distribution, and consequently, for a much better understanding of atmospheric oxidation processes.

Unlocking the proteomic information encoded in MALDI-TOF-MS data used for microbial identification and characterization.

PubMed

Fagerquist, Clifton K

2017-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is increasingly utilized as a rapid technique to identify microorganisms including pathogenic bacteria. However, little attention has been paid to the significant proteomic information encoded in the MS peaks that collectively constitute the MS 'fingerprint'. This review/perspective is intended to explore this topic in greater detail in the hopes that it may spur interest and further research in this area. Areas covered: This paper examines the recent literature on utilizing MALDI-TOF for bacterial identification. Critical works highlighting protein biomarker identification of bacteria, arguments for and against protein biomarker identification, proteomic approaches to biomarker identification, emergence of MALDI-TOF-TOF platforms and their use for top-down proteomic identification of bacterial proteins, protein denaturation and its effect on protein ion fragmentation, collision cross-sections and energy deposition during desorption/ionization are also explored. Expert commentary: MALDI-TOF and TOF-TOF mass spectrometry platforms will continue to provide chemical analyses that are rapid, cost-effective and high throughput. These instruments have proven their utility in the taxonomic identification of pathogenic bacteria at the genus and species level and are poised to more fully characterize these microorganisms to the benefit of clinical microbiology, food safety and other fields.

Application of MALDI-TOF MS for the Identification of Food Borne Bacteria

PubMed Central

Pavlovic, Melanie; Huber, Ingrid; Konrad, Regina; Busch, Ulrich

2013-01-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently emerged as a powerful tool for the routine identification of clinical isolates. MALDI-TOF MS based identification of bacteria has been shown to be more rapid, accurate and cost-efficient than conventional phenotypic techniques or molecular methods. Rapid and reliable identification of food-associated bacteria is also of crucial importance for food processing and product quality. This review is concerned with the applicability of MALDI-TOF MS for routine identification of foodborne bacteria taking the specific requirements of food microbiological laboratories and the food industry into account. The current state of knowledge including recent findings and new approaches are discussed. PMID:24358065

Identification of clinically relevant Corynebacterium strains by Api Coryne, MALDI-TOF-mass spectrometry and molecular approaches.

PubMed

Alibi, S; Ferjani, A; Gaillot, O; Marzouk, M; Courcol, R; Boukadida, J

2015-09-01

We evaluated the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) for the identification of 97 Corynebacterium clinical in comparison to identification strains by Api Coryne and MALDI-TOF-MS using 16S rRNA gene and hypervariable region of rpoB genes sequencing as a reference method. C. striatum was the predominant species isolated followed by C. amycolatum. There was an agreement between Api Coryne strips and MALDI-TOF-MS identification in 88.65% of cases. MALDI-TOF-MS was unable to differentiate C. aurimucosum from C. minutissimum and C. minutissimum from C. singulare but reliably identify 92 of 97 (94.84%) strains. Two strains remained incompletely identified to the species level by MALDI-TOF-MS and molecular approaches. They belonged to Cellulomonas and Pseudoclavibacter genus. In conclusion, MALDI-TOF-MS is a rapid and reliable method for the identification of Corynebacterium species. However, some limits have been noted and have to be resolved by the application of molecular methods. Copyright © 2015. Published by Elsevier SAS.

Radiation-hard ceramic Resistive Plate Chambers for forward TOF and T0 systems

NASA Astrophysics Data System (ADS)

Akindinov, A.; Dreyer, J.; Fan, X.; Kämpfer, B.; Kiselev, S.; Kotte, R.; Garcia, A. Laso; Malkevich, D.; Naumann, L.; Nedosekin, A.; Plotnikov, V.; Stach, D.; Sultanov, R.; Voloshin, K.

2017-02-01

Resistive Plate Chambers with ceramic electrodes are the main candidates for a use in precise multi-channel timing systems operating in high-radiation conditions. We report the latest R&D results on these detectors aimed to meet the requirements of the forward T0 counter at the CBM experiment. RPC design, gas mixture, limits on the bulk resistivity of ceramic electrodes, efficiency, time resolution, counting rate capabilities and ageing test results are presented.

MALDI-TOF MS of Trichoderma: A model system for the identification of microfungi

USDA-ARS?s Scientific Manuscript database

This investigation aimed to assess whether MALDI-TOF MS analysis of proteomics could be applied to the study of Trichoderma, a fungal genus selected because it includes many species and is phylogenetically well defined. We also investigated whether MALDI-TOF MS analysis of proteomics would reveal ap...

What Is New in Clinical Microbiology—Microbial Identification by MALDI-TOF Mass Spectrometry

PubMed Central

Murray, Patrick R.

2012-01-01

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) offers the possibility of accurate, rapid, inexpensive identification of bacteria, fungi, and mycobacteria isolated in clinical microbiology laboratories. The procedures for preanalytic processing of organisms and analysis by MALDI-TOF MS are technically simple and reproducible, and commercial databases and interpretive algorithms are available for the identification of a wide spectrum of clinically significant organisms. Although only limited work has been reported on the use of this technique to identify molds, perform strain typing, or determine antibiotic susceptibility results, these are fruitful areas of promising research. As experience is gained with MALDI-TOF MS, it is expected that the databases will be expanded to resolve many of the current inadequate identifications (eg, no identification, genus-level identification) and algorithms for potential misidentification will be developed. The current lack of Food and Drug Administration approval of any MALDI-TOF MS system for organism identification limits widespread use in the United States. PMID:22795961

Towards Discovery and Targeted Peptide Biomarker Detection Using nanoESI-TIMS-TOF MS

NASA Astrophysics Data System (ADS)

Garabedian, Alyssa; Benigni, Paolo; Ramirez, Cesar E.; Baker, Erin S.; Liu, Tao; Smith, Richard D.; Fernandez-Lima, Francisco

2018-05-01

In the present work, the potential of trapped ion mobility spectrometry coupled to TOF mass spectrometry (TIMS-TOF MS) for discovery and targeted monitoring of peptide biomarkers from human-in-mouse xenograft tumor tissue was evaluated. In particular, a TIMS-MS workflow was developed for the detection and quantification of peptide biomarkers using internal heavy analogs, taking advantage of the high mobility resolution (R = 150-250) prior to mass analysis. Five peptide biomarkers were separated, identified, and quantified using offline nanoESI-TIMS-CID-TOF MS; the results were in good agreement with measurements using a traditional LC-ESI-MS/MS proteomics workflow. The TIMS-TOF MS analysis permitted peptide biomarker detection based on accurate mobility, mass measurements, and high sequence coverage for concentrations in the 10-200 nM range, while simultaneously achieving discovery measurements of not initially targeted peptides as markers from the same proteins and, eventually, other proteins. [Figure not available: see fulltext.

Identification of fungal microorganisms by MALDI-TOF mass spectrometry.

PubMed

Chalupová, Jana; Raus, Martin; Sedlářová, Michaela; Sebela, Marek

2014-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as a reliable tool for fast identification and classification of microorganisms. In this regard, it represents a strong challenge to microscopic and molecular biology methods. Nowadays, commercial MALDI systems are accessible for biological research work as well as for diagnostic applications in clinical medicine, biotechnology and industry. They are employed namely in bacterial biotyping but numerous experimental strategies have also been developed for the analysis of fungi, which is the topic of the present review. Members of many fungal genera such as Aspergillus, Fusarium, Penicillium or Trichoderma and also various yeasts from clinical samples (e.g. Candida albicans) have been successfully identified by MALDI-TOF MS. However, there is no versatile method for fungi currently available even though the use of only a limited number of matrix compounds has been reported. Either intact cell/spore MALDI-TOF MS is chosen or an extraction of surface proteins is performed and then the resulting extract is measured. Biotrophic fungal phytopathogens can be identified via a direct acquisition of MALDI-TOF mass spectra e.g. from infected plant organs contaminated by fungal spores. Mass spectrometric peptide/protein profiles of fungi display peaks in the m/z region of 1000-20000, where a unique set of biomarker ions may appear facilitating a differentiation of samples at the level of genus, species or strain. This is done with the help of a processing software and spectral database of reference strains, which should preferably be constructed under the same standardized experimental conditions. Copyright © 2013 Elsevier Inc. All rights reserved.

Analysis of protein glycation products by MALDI-TOF/MS.

PubMed

Kislinger, Thomas; Humeny, Andreas; Peich, Carlo C; Becker, Cord-Michael; Pischetsrieder, Monika

2005-06-01

Matrix-assisted laser desorption ionization-mass spectrometry with time-of-flight detection (MALDI-TOF/MS) is a promising tool to analyze advanced glycation end product (AGE)-modified proteins. The combination of soft ionization (MALDI) with time-of-flight mass detection allows analysis of peptides and proteins of a molecular mass up to 300 kDa with minimal sample workup. Because the direct structural analysis of intact AGE proteins is not possible due to the formation of broad and poorly resolved peaks, peptide mapping was introduced into the analysis of AGE proteins by MALDI-TOF/MS, allowing site-specific analysis of defined AGEs. When methylglyoxal-modified lysozyme was subjected to MALDI-TOF/MS peptide mapping, methylimidazolone and argpyrimidine attached to the arginine residue and carboxyethyl (CEL) bound to the lysine were detected on peptide(aa1-7) (KVFGRCE). In contrast, only one methylimidazolone was found on peptide(aa8-35) (LAAAMKRHGLDNYRGYSLGNWVCAAKFE) and peptide(aa120-129) (VQAWIRGCRL), respectively. The analysis of AGE protein, which had been incubated with glucose, revealed the presence of an Amadori product and a carboxymethyl residue (CML) on peptide(aa1-7) and peptide(aa8-35), as well as an imidazolone A on peptide(aa120-129). Furthermore, the early Maillard reaction of lysozyme, which had been glycated by seven different sugars, was monitored by MALDI-TOF/MS peptide mapping. Finally, this approach was successfully applied for site- and product-specific relative quantification of AGEs. For example, kinetics of CML and Amadori product formation on peptide(aa1-7), as well as imidazolone A formation on peptide(aa120-129), were determined.

Detection of Rickettsia spp in Ticks by MALDI-TOF MS

PubMed Central

Yssouf, Amina; Almeras, Lionel; Terras, Jérôme; Socolovschi, Cristina; Raoult, Didier; Parola, Philippe

2015-01-01

Background Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has been shown to be an effective tool for the rapid identification of arthropods, including tick vectors of human diseases. Methodology/Principal Findings The objective of the present study was to evaluate the use of MALDI-TOF MS to identify tick species, and to determine the presence of rickettsia pathogens in the infected Ticks. Rhipicephalus sanguineus and Dermacentor marginatus Ticks infected or not by R. conorii conorii or R. slovaca, respectively, were used as experimental models. The MS profiles generated from protein extracts prepared from tick legs exhibited mass peaks that distinguished the infected and uninfected Ticks, and successfully discriminated the Rickettsia spp. A blind test was performed using Ticks that were laboratory-reared, collected in the field or removed from patients and infected or not by Rickettsia spp. A query against our in-lab arthropod MS reference database revealed that the species and infection status of all Ticks were correctly identified at the species and infection status levels. Conclusions/Significance Taken together, the present work demonstrates the utility of MALDI-TOF MS for a dual identification of tick species and intracellular bacteria. Therefore, MALDI-TOF MS is a relevant tool for the accurate detection of Rickettsia spp in Ticks for both field monitoring and entomological diagnosis. The present work offers new perspectives for the monitoring of other vector borne diseases that present public health concerns. PMID:25659152

Electronics design of the RPC system for the OPERA muon spectrometer

NASA Astrophysics Data System (ADS)

Acquafredda, R.; Ambrosio, M.; Balsamo, E.; Barichello, G.; Bergnoli, A.; Consiglio, L.; Corradi, G.; dal Corso, F.; Felici, G.; Manea, C.; Masone, V.; Parascandolo, P.; Sorrentino, G.

2004-09-01

The present document describes the front-end electronics of the RPC system that instruments the magnet muon spectrometer of the OPERA experiment. The main task of the OPERA spectrometer is to provide particle tracking information for muon identification and simplify the matching between the Precision Trackers. As no trigger has been foreseen for the experiment, the spectrometer electronics must be self-triggered with single-plane readout capability. Moreover, precision time information must be added within each event frame for off-line reconstruction. The read-out electronics is made of three different stages: the Front-End Boards (FEBs) system, the Controller Boards (CBs) system and the Trigger Boards (TBs) system. The FEB system provides discrimination of the strip incoming signals; a FAST-OR output of the input signals is also available for trigger plane signal generation. FEB signals are acquired by the CB system that provides the zero suppression and manages the communication to the DAQ and Slow Control. A Trigger Board allows to operate in both self-trigger mode (the FEB's FAST-OR signal starts the plane acquisition) or in external-trigger mode (different conditions can be set on the FAST-OR signals generated from different planes).

TOFSIMS-P: a web-based platform for analysis of large-scale TOF-SIMS data.

PubMed

Yun, So Jeong; Park, Ji-Won; Choi, Il Ju; Kang, Byeongsoo; Kim, Hark Kyun; Moon, Dae Won; Lee, Tae Geol; Hwang, Daehee

2011-12-15

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) has been a useful tool to profile secondary ions from the near surface region of specimens with its high molecular specificity and submicrometer spatial resolution. However, the TOF-SIMS analysis of even a moderately large size of samples has been hampered due to the lack of tools for automatically analyzing the huge amount of TOF-SIMS data. Here, we present a computational platform to automatically identify and align peaks, find discriminatory ions, build a classifier, and construct networks describing differential metabolic pathways. To demonstrate the utility of the platform, we analyzed 43 data sets generated from seven gastric cancer and eight normal tissues using TOF-SIMS. A total of 87 138 ions were detected from the 43 data sets by TOF-SIMS. We selected and then aligned 1286 ions. Among them, we found the 66 ions discriminating gastric cancer tissues from normal ones. Using these 66 ions, we then built a partial least square-discriminant analysis (PLS-DA) model resulting in a misclassification error rate of 0.024. Finally, network analysis of the 66 ions showed disregulation of amino acid metabolism in the gastric cancer tissues. The results show that the proposed framework was effective in analyzing TOF-SIMS data from a moderately large size of samples, resulting in discrimination of gastric cancer tissues from normal tissues and identification of biomarker candidates associated with the amino acid metabolism.

LC-IM-TOF Instrument Control & Data Visualization Software

DOE Office of Scientific and Technical Information (OSTI.GOV)

2011-05-12

Liquid Chromatography-Ion Mobility-time of Flight Instrument Control and Data Visualization software is designed to control instrument voltages for the Ion Mobility drift tube. It collects and stores information collected from the Agilent TOF instrument and analyses/displays the ion intensity information acquired. The software interface can be split into 3 categories -- Instrument Settings/Controls, Data Acquisition, and Viewer. The Instrument Settings/Controls prepares the instrument for Data Acquisition. The Viewer contains common objects that are used by Instrument Settings/Controls and Data Acquisition. Intensity information is collected in 1 nanosec bins and separated by TOF pulses called scans. A collection of scans aremore » stored side by side making up an accumulation. In order for the computer to keep up with the stream of data, 30-50 accumulations are commonly summed into a single frame. A collection of frames makes up an experiment. The Viewer software then takes the experiment and presents the data in several possible ways, each frame can be viewed in TOF bins or m/z (mass to charge ratio). The experiment can be viewed frame by frame, merging several frames, or by viewing the peak chromatogram. The user can zoom into the data, export data, and/or animate frames. Additional features include calibration of the data and even post-processing multiplexed data.« less

Cocoa content influences chocolate molecular profile investigated by MALDI-TOF mass spectrometry.

PubMed

Bonatto, Cínthia C; Silva, Luciano P

2015-06-01

Chocolate authentication is a key aspect of quality control and safety. Matrix-assisted laser desorption ionization time-of flight (MALDI-TOF) mass spectrometry (MS) has been demonstrated to be useful for molecular profiling of cells, tissues, and even food. The present study evaluated if MALDI-TOF MS analysis on low molecular mass profile may classify chocolate samples according to the cocoa content. The molecular profiles of seven processed commercial chocolate samples were compared by using MALDI-TOF MS. Some ions detected exclusively in chocolate samples corresponded to the metabolites of cocoa or other constituents. This method showed the presence of three distinct clusters according to confectionery and sensorial features of the chocolates and was used to establish a mass spectra database. Also, novel chocolate samples were evaluated in order to check the validity of the method and to challenge the database created with the mass spectra of the primary samples. Thus, the method was shown to be reliable for clustering unknown samples into the main chocolate categories. Simple sample preparation of the MALDI-TOF MS approach described will allow the surveillance and monitoring of constituents during the molecular profiling of chocolates. © 2014 Society of Chemical Industry.

The MR-TOF-MS isobar separator for the TITAN facility at TRIUMF

NASA Astrophysics Data System (ADS)

Jesch, Christian; Dickel, Timo; Plaß, Wolfgang R.; Short, Devin; Ayet San Andres, Samuel; Dilling, Jens; Geissel, Hans; Greiner, Florian; Lang, Johannes; Leach, Kyle G.; Lippert, Wayne; Scheidenberger, Christoph; Yavor, Mikhail I.

2015-11-01

At TRIUMF's Ion Trap for Atomic and Nuclear Science (TITAN) a multiple-reflection time-of-flight mass spectrometer (MR-TOF-MS) will extend TITAN's capabilities and facilitate mass measurements and in-trap decay spectroscopy of exotic nuclei that so far have not been possible due to strong isobaric contamination. This MR-TOF-MS will also enable mass measurements of very short-lived nuclides (half-life > 1 ms) that are produced in very low quantities (a few detected ions overall). In order to allow the installation of an MR-TOF-MS in the restricted space on the platform, on which the TITAN facility is located, novel mass spectrometric methods have been developed. Transport, cooling and distribution of the ions inside the device is done using a buffer gas-filled RFQ-based ion beam switchyard. Mass selection is achieved using a dynamic retrapping technique after time-of-flight analysis in an electrostatic isochronous reflector system. Only due to the combination of these novel methods the realization of an MR-TOF-MS based isobar separator at TITAN has become possible. The device has been built, commissioned off-line and is currently under installation at TITAN.

Accurate differentiation of Mycobacterium chimaera from Mycobacterium intracellulare by MALDI-TOF MS analysis.

PubMed

Pranada, Arthur B; Witt, Ellen; Bienia, Michael; Kostrzewa, Markus; Timke, Markus

2017-05-01

The increasing number of infections caused by nontuberculous mycobacteria (NTM) has prompted the need for rapid and precise identification methods of these pathogens. Several studies report the applicability of MALDI-TOF mass spectrometry (MS) for identification of NTM. However, some closely related species have very similar spectral mass fingerprints, and until recently, Mycobacterium chimaera and M. intracellulare could not be separated from each other by MALDI-TOF MS. The conventional identification methods used in routine diagnostics have similar limitations. Recently, the differentiation of these two species within the Mycobacterium avium complex has become increasingly important due to reports of M. chimaera infections related to open heart surgery in Europe and in the USA. In this report, a method for the distinct differentiation of M. chimaera and M. intracellulare using a more detailed analysis of MALDI-TOF mass spectra is presented. Species-specific peaks could be identified and it was possible to assign all isolates (100 %) from reference strain collections as well as clinical isolates to the correct species. We have developed a model for the accurate identification of M. chimaera and M. intracellulare by MALDI-TOF MS. This approach has the potential for routine use in microbiology laboratories, as the model itself can be easily implemented into the software of the currently available systems by MALDI-TOF MS manufacturers.

The n_TOF facility: Neutron beams for challenging future measurements at CERN

NASA Astrophysics Data System (ADS)

Chiaveri, E.; Aberle, O.; Andrzejewski, J.; Audouin, L.; Bacak, M.; Balibrea, J.; Barbagallo, M.; Bečvář, F.; Berthoumieux, E.; Billowes, J.; Bosnar, D.; Brown, A.; Caamaño, M.; Calviño, F.; Calviani, M.; Cano-Ott, D.; Cardella, R.; Casanovas, A.; Cerutti, F.; Chen, Y. H.; Colonna, N.; Cortés, G.; Cortés-Giraldo, M. A.; Cosentino, L.; Damone, L. A.; Diakaki, M.; Domingo-Pardo, C.; Dressler, R.; Dupont, E.; Durán, I.; Fernández-Domínguez, B.; Ferrari, A.; Ferreira, P.; Finocchiaro, P.; Göbel, K.; García, A. R.; Gawlik, A.; Gilardoni, S.; Glodariu, T.; Gonçalves, I. F.; González, E.; Griesmayer, E.; Guerrero, C.; Gunsing, F.; Harada, H.; Heinitz, S.; Heyse, J.; Jenkins, D. G.; Jericha, E.; Käppeler, F.; Kadi, Y.; Kalamara, A.; Kavrigin, P.; Kimura, A.; Kivel, N.; Kokkoris, M.; Krtička, M.; Kurtulgil, D.; Leal-Cidoncha, E.; Lederer, C.; Leeb, H.; Lerendegui-Marco, J.; Meo, S. Lo; Lonsdale, S. J.; Macina, D.; Marganiec, J.; Martínez, T.; Masi, A.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Maugeri, E. A.; Mazzone, A.; Mendoza, E.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Musumarra, A.; Negret, A.; Nolte, R.; Oprea, A.; Patronis, N.; Pavlik, A.; Perkowski, J.; Porras, I.; Praena, J.; Quesada, J. M.; Radeck, D.; Rauscher, T.; Reifarth, R.; Rubbia, C.; Ryan, J. A.; Sabaté-Gilarte, M.; Saxena, A.; Schillebeeckx, P.; Schumann, D.; Smith, A. G.; Sosnin, N. V.; Stamatopoulos, A.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tassan-Got, L.; Tsinganis, A.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vlachoudis, V.; Vlastou, R.; Wallner, A.; Warren, S.; Woods, P. J.; Wright, T.; Žugec, P.

2017-09-01

The CERN n_TOF neutron beam facility is characterized by a very high instantaneous neutron flux, excellent TOF resolution at the 185 m long flight path (EAR-1), low intrinsic background and coverage of a wide range of neutron energies, from thermal to a few GeV. These characteristics provide a unique possibility to perform high-accuracy measurements of neutron-induced reaction cross-sections and angular distributions of interest for fundamental and applied Nuclear Physics. Since 2001, the n_TOF Collaboration has collected a wealth of high quality nuclear data relevant for nuclear astrophysics, nuclear reactor technology, nuclear medicine, etc. The overall efficiency of the experimental program and the range of possible measurements has been expanded with the construction of a second experimental area (EAR-2), located 20 m on the vertical of the n_TOF spallation target. This upgrade, which benefits from a neutron flux 30 times higher than in EAR-1, provides a substantial extension in measurement capabilities, opening the possibility to collect data on neutron cross-section of isotopes with short half-lives or available in very small amounts. This contribution will outline the main characteristics of the n_TOF facility, with special emphasis on the new experimental area. In particular, we will discuss the innovative features of the EAR-2 neutron beam that make possible to perform very challenging measurements on short-lived radioisotopes or sub-mg samples, out of reach up to now at other neutron facilities around the world. Finally, the future perspectives of the facility will be presented.

MALDI-TOF mass spectrometry in the clinical mycology laboratory: identification of fungi and beyond.

PubMed

Posteraro, Brunella; De Carolis, Elena; Vella, Antonietta; Sanguinetti, Maurizio

2013-04-01

MALDI-TOF mass spectrometry (MS) is becoming essential in most clinical microbiology laboratories throughout the world. Its successful use is mainly attributable to the low operational costs, the universality and flexibility of detection, as well as the specificity and speed of analysis. Based on characteristic protein spectra obtained from intact cells - by means of simple, rapid and reproducible preanalytical and analytical protocols - MALDI-TOF MS allows a highly discriminatory identification of yeasts and filamentous fungi starting from colonies. Whenever used early, direct identification of yeasts from positive blood cultures has the potential to greatly shorten turnaround times and to improve laboratory diagnosis of fungemia. More recently, but still at an infancy stage, MALDI-TOF MS is used to perform strain typing and to determine antifungal drug susceptibility. In this article, the authors discuss how the MALDI-TOF MS technology is destined to become a powerful tool for routine mycological diagnostics.

Phosphorylation of CMG helicase and Tof1 is required for programmed fork arrest

PubMed Central

Bastia, Deepak; Srivastava, Pankaj; Zaman, Shamsu; Choudhury, Malay; Mohanty, Bidyut K.; Bacal, Julien; Langston, Lance D.; Pasero, Philippe; O’Donnell, Michael E.

2016-01-01

Several important physiological transactions, including control of replicative life span (RLS), prevention of collision between replication and transcription, and cellular differentiation, require programmed replication fork arrest (PFA). However, a general mechanism of PFA has remained elusive. We previously showed that the Tof1–Csm3 fork protection complex is essential for PFA by antagonizing the Rrm3 helicase that displaces nonhistone protein barriers that impede fork progression. Here we show that mutations of Dbf4-dependent kinase (DDK) of Saccharomyces cerevisiae, but not other DNA replication factors, greatly reduced PFA at replication fork barriers in the spacer regions of the ribosomal DNA array. A key target of DDK is the mini chromosome maintenance (Mcm) 2–7 complex, which is known to require phosphorylation by DDK to form an active CMG [Cdc45 (cell division cycle gene 45), Mcm2–7, GINS (Go, Ichi, Ni, and San)] helicase. In vivo experiments showed that mutational inactivation of DDK caused release of Tof1 from the chromatin fractions. In vitro binding experiments confirmed that CMG and/or Mcm2–7 had to be phosphorylated for binding to phospho-Tof1–Csm3 but not to its dephosphorylated form. Suppressor mutations that bypass the requirement for Mcm2–7 phosphorylation by DDK restored PFA in the absence of the kinase. Retention of Tof1 in the chromatin fraction and PFA in vivo was promoted by the suppressor mcm5-bob1, which bypassed DDK requirement, indicating that under this condition a kinase other than DDK catalyzed the phosphorylation of Tof1. We propose that phosphorylation regulates the recruitment and retention of Tof1–Csm3 by the replisome and that this complex antagonizes the Rrm3 helicase, thereby promoting PFA, by preserving the integrity of the Fob1–Ter complex. PMID:27298353

The Ongoing Revolution of MALDI-TOF Mass Spectrometry for Microbiology Reaches Tropical Africa

PubMed Central

Fall, Bécaye; Lo, Cheikh Ibrahima; Samb-Ba, Bissoume; Perrot, Nadine; Diawara, Silman; Gueye, Mamadou Wague; Sow, Kowry; Aubadie-Ladrix, Maxence; Mediannikov, Oleg; Sokhna, Cheikh; Diemé, Yaya; Chatellier, Sonia; Wade, Boubacar; Raoult, Didier; Fenollar, Florence

2015-01-01

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) represents a revolution in routine pathogen identification in clinical microbiology laboratories. A MALDI-TOF MS was introduced to tropical Africa in the clinical microbiology laboratory of the Hôpital Principal de Dakar (Senegal) and used for routine pathogen identification. Using MS, 2,429 bacteria and fungi isolated from patients were directly assayed, leading to the identification of 2,082 bacteria (85.7%) and 206 fungi (8.5%) at the species level, 109 bacteria (4.5%) at the genus level, and 16 bacteria (0.75%) at the family level. Sixteen isolates remained unidentified (0.75%). Escherichia coli was the most prevalent species (25.8%) followed by Klebsiella pneumoniae (14.8%), Streptococcus agalactiae (6.2%), Acinetobacter baumannii (6.1%), Pseudomonas aeruginosa (5.9%), and Staphylococcus aureus (5.9%). MALDI-TOF MS has also enabled the detection of rare bacteria and fungi. MALDI-TOF MS is a powerful tool for the identification of bacterial and fungal species involved in infectious diseases in tropical Africa. PMID:25601995

Enhanced MALDI-TOF MS Analysis of Phosphopeptides Using an Optimized DHAP/DAHC Matrix

PubMed Central

Hou, Junjie; Xie, Zhensheng; Xue, Peng; Cui, Ziyou; Chen, Xiulan; Li, Jing; Cai, Tanxi; Wu, Peng; Yang, Fuquan

2010-01-01

Selecting an appropriate matrix solution is one of the most effective means of increasing the ionization efficiency of phosphopeptides in matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). In this study, we systematically assessed matrix combinations of 2, 6-dihydroxyacetophenone (DHAP) and diammonium hydrogen citrate (DAHC), and demonstrated that the low ratio DHAP/DAHC matrix was more effective in enhancing the ionization of phosphopeptides. Low femtomole level of phosphopeptides from the tryptic digests of α-casein and β-casein was readily detected by MALDI-TOF-MS in both positive and negative ion mode without desalination or phosphopeptide enrichment. Compared with the DHB/PA matrix, the optimized DHAP/DAHC matrix yielded superior sample homogeneity and higher phosphopeptide measurement sensitivity, particularly when multiple phosphorylated peptides were assessed. Finally, the DHAP/DAHC matrix was applied to identify phosphorylation sites from α-casein and β-casein and to characterize two phosphorylation sites from the human histone H1 treated with Cyclin-Dependent Kinase-1 (CDK1) by MALDI-TOF/TOF MS. PMID:20339515

Bacterial flora analysis of coliforms in sewage, river water, and ground water using MALDI-TOF mass spectrometry.

PubMed

Suzuki, Yoshihiro; Niina, Kouki; Matsuwaki, Tomonori; Nukazawa, Kei; Iguchi, Atsushi

2018-01-28

The aim of this study was to rapidly and effectively analyze coliforms, which are the most fundamental indicators of water quality for fecal pollution, using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Coliform bacteria were isolated from municipal sewage, river water, and groundwater. For each sample, 100 isolates were determined by MALDI-TOF MS. In addition, these same 100 isolates were also identified via 16S rRNA gene sequence analysis. Obtained MALDI-TOF MS data were compared with the 16S rRNA sequencing analysis, and the validity of MALDI-TOF MS for classification of coliform bacteria was examined. The concordance rate of bacterial identification for the 100 isolates obtained by MALDI-TOF MS analysis and 16S rRNA gene sequence analysis for sewage, river water, and ground water were 96%, 74%, and 62% at the genus level, respectively. Among the sewage, river water, and ground water samples, the coliform bacterial flora were distinct. The dominant genus of coliforms in sewage, river water, and groundwater were Klebsiella spp., Enterobacter spp., and Serratia spp., respectively. We determined that MALDI-TOF MS is a rapid and accurate tool that can be used to identify coliforms. Therefore, without using conventional 16S rRNA sequencing, it is possible to rapidly and effectively classify coliforms in water using MALDI-TOF MS.

Integrated quantitative and qualitative workflow for in vivo bioanalytical support in drug discovery using hybrid Q-TOF-MS.

PubMed

Ranasinghe, Asoka; Ramanathan, Ragu; Jemal, Mohammed; D'Arienzo, Celia J; Humphreys, W Griffith; Olah, Timothy V

2012-03-01

UHPLC coupled with orthogonal acceleration hybrid quadrupole-TOF (Q-TOF)-MS is an emerging technique offering new strategies for the efficient screening of new chemical entities and related molecules at the early discovery stage within the pharmaceutical industry. In the first part of this article, we examine the main instrumental parameters that are critical for the integration of UHPLC-Q-TOF technology to existing bioanalytical workflows, in order to provide simultaneous quantitative and qualitative bioanalysis of samples generated following in vivo studies. Three modern Q-TOF mass spectrometers, including Bruker maXis™, Agilent 6540 and Sciex TripleTOF™ 5600, all interfaced with UHPLC systems, are evaluated in the second part of the article. The scope of this work is to demonstrate the potential of Q-TOF for the analysis of typical small molecules, therapeutic peptides (molecular weight <6000 Da), and enzymatically (i.e., trypsin, chymotrypsin and pepsin) cleaved peptides from larger proteins. This work focuses mainly on full-scan TOF data obtained under ESI conditions, the major mode of TOF operation in discovery bioanalytical research, where the compounds are selected based on their pharmacokinetic/pharmacodynamic behaviors using animal models prior to selecting a few desirable candidates for further development. Finally, important emerging TOF technologies that could potentially benefit bioanalytical research in the semi-quantification of metabolites without synthesized standards are discussed. Particularly, the utility of captive spray ionization coupled with TripleTOF 5600 was evaluated for improving sensitivity and providing normalized MS response for drugs and their metabolites. The workflow proposed compromises neither the efficiency, nor the quality of pharmacokinetic data in support of early drug discovery programs.

MALDI-TOF for the rapid detection of carbapenemase-producing Enterobacteriaceae: comparison of the commercialized MBT STAR®-Carba IVD Kit with two in-house MALDI-TOF techniques and the RAPIDEC® CARBA NP.

PubMed

Dortet, Laurent; Tandé, Didier; de Briel, Dominique; Bernabeu, Sandrine; Lasserre, Camille; Gregorowicz, Guillaume; Jousset, Agnès B; Naas, Thierry

2018-06-11

There is an urgent need for accurate and fast diagnostic tests to identify carbapenemase-producing bacteria. Here, we have evaluated three MALDI-TOF-based techniques to detect carbapenemase-producing Enterobacteriaceae (CPE) from cultured colonies. The performance of three MALDI-TOF-based techniques, including the commercialized MBT STAR®-Carba IVD Kit (Bruker Daltonics) and two in-house protocols performed on the Microflex LT Biotyper (Bruker Daltonics) and the VITEK® MS Plus (bioMérieux), were compared with those of the RAPIDEC® CARBA NP (bioMérieux). A collection of 175 isolates including 120 carbapenemase producers and 55 non-carbapenemase producers was tested. Samples were tested blind in the three participating centres. The repeatability of the MBT STAR®-Carba IVD Kit was also evaluated. The three MALDI-TOF techniques possess sensitivities ranging from 95% to 100% and specificities from 98.2% to 100% compared with 99.2% and 100%, respectively, for the RAPIDEC® CARBA NP. The MBT STAR®-Carba IVD Kit gave highly reproducible results and is the only technique able to provide a concomitant identification of the bacterial isolate. The three MALDI-TOF techniques possess a fast turnaround time (less than 1.5 h). Overall, MALDI-TOF is a reliable technique for the rapid detection of CPE from cultured colonies. MBT STAR®-Carba IVD Kit, the only commercially available assay, could easily be implemented in a clinical microbiology laboratory if it is already equipped with a Microflex LT Biotyper mass spectrometer.

Identification of urinary tract pathogens after 3-hours urine culture by MALDI-TOF mass spectrometry.

PubMed

Haiko, Johanna; Savolainen, Laura E; Hilla, Risto; Pätäri-Sampo, Anu

2016-10-01

Complicated urinary tract infections, such as pyelonephritis, may lead to sepsis. Rapid diagnosis is needed to identify the causative urinary pathogen and to verify the appropriate empirical antimicrobial therapy. We describe here a rapid identification method for urinary pathogens: urine is incubated on chocolate agar for 3h at 35°C with 5% CO2 and subjected to MALDI-TOF MS analysis by VITEK MS. Overall 207 screened clinical urine samples were tested in parallel with conventional urine culture. The method, called U-si-MALDI-TOF (urine short incubation MALDI-TOF), showed correct identification for 86% of Gram-negative urinary tract pathogens (Escherichia coli, Klebsiella pneumoniae, and other Enterobacteriaceae), when present at >10(5)cfu/ml in culture (n=107), compared with conventional culture method. However, Gram-positive bacteria (n=28) were not successfully identified by U-si-MALDI-TOF. This method is especially suitable for rapid identification of E. coli, the most common cause of urinary tract infections and urosepsis. Turnaround time for identification using U-si-MALDI-TOF compared with conventional urine culture was improved from 24h to 4-6h. Copyright © 2016 Elsevier B.V. All rights reserved.

The Effect of Susceptibility Artifacts Related to Metallic Implants on Adjacent-Lesion Assessment in Simultaneous TOF PET/MR.

PubMed

Svirydenka, Hanna; Delso, Gaspar; De Galiza Barbosa, Felipe; Huellner, Martin; Davison, Helen; Fanti, Stefano; Veit-Haibach, Patrick; Ter Voert, Edwin E G W

2017-07-01

Metalic implants may affect attenuation correction (AC) in PET/MR imaging. The purpose of this study was to evaluate the effect of susceptibility artifacts related to metallic implants on adjacent metabolically active lesions in clinical simultaneous PET/MR scanning for both time-of-flight (TOF) and non-TOF reconstructed PET images. Methods: We included 27 patients without implants but with confirmed 18 F-FDG-avid lesions adjacent to common implant locations. In all patients, a clinically indicated whole-body 18 F-FDG PET/MR scan was acquired. Baseline non-TOF and TOF PET images were reconstructed. Reconstruction was repeated after the introduction of artificial signal voids in the AC map to simulate metallic implants in standard anatomic areas. All reconstructed images were qualitatively and quantitatively assessed and compared with the baseline images. Results: In total, 51 lesions were assessed. In 40 and 50 of these cases (non-TOF and TOF, respectively), the detectability of the lesions did not change; in 9 and 1 cases, the detectability changed; and in 2 non-TOF cases, the lesions were no longer visible after the introduction of metallic artifacts. The inclusion of TOF information significantly reduced artifacts due to simulated implants in the femoral head, sternum, and spine ( P = 0.01, 0.01, and 0.03, respectively). It also improved image quality in these locations ( P = 0.02, 0.01, and 0.01, respectively). The mean percentage error was -3.5% for TOF and -4.8% for non-TOF reconstructions, meaning that the inclusion of TOF information reduced the percentage error in SUV max by 28.5% ( P < 0.01). Conclusion: Qualitatively, there was a significant reduction of artifacts in the femoral head, sternum, and spine. There was also a significant qualitative improvement in image quality in these locations. Furthermore, our study indicated that simulated susceptibility artifacts related to metallic implants have a significant effect on small, moderately 18 F

MALDI-TOF MS Distinctly Differentiates Nontypable Haemophilus influenzae from Haemophilus haemolyticus

PubMed Central

Zhang, Huifang; Zhang, Yongchan; Gao, Yuan; Xu, Li; Lv, Jing; Wang, Yingtong; Zhang, Jianzhong; Shao, Zhujun

2013-01-01

Nontypable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus exhibit different pathogenicities, but to date, there remains no definitive and reliable strategy for differentiating these strains. In this study, we evaluated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a potential method for differentiating NTHi and H. haemolyticus. The phylogenetic analysis of concatenated 16S rRNA and recombinase A (recA) gene sequences, outer membrane protein P6 gene sequencing and single-gene PCR were used as reference methods. The original reference database (ORD, provided with the Biotyper software) and new reference database (NRD, extended with Chinese strains) were compared for the evaluation of MALDI-TOF MS. Through a search of the ORD, 76.9% of the NTHi (40/52) and none of the H. haemolyticus (0/20) strains were identified at the species level. However, all NTHi and H. haemolyticus strains used for identification were accurately recognized at the species level when searching the NRD. From the dendrogram clustering of the main spectra projections, the Chinese and foreign H. influenzae reference strains were categorized into two distinct groups, and H. influenzae and H. haemolyticus were also separated into two categories. Compared to the existing methods, MALDI-TOF MS has the advantage of integrating high throughput, accuracy and speed. In conclusion, MALDI-TOF MS is an excellent method for differentiating NTHi and H. haemolyticus. This method can be recommended for use in appropriately equipped laboratories. PMID:23457514

Security Implications of OPC, OLE, DCOM, and RPC in Control Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

2006-01-01

OPC is a collection of software programming standards and interfaces used in the process control industry. It is intended to provide open connectivity and vendor equipment interoperability. The use of OPC technology simplifies the development of control systems that integrate components from multiple vendors and support multiple control protocols. OPC-compliant products are available from most control system vendors, and are widely used in the process control industry. OPC was originally known as OLE for Process Control; the first standards for OPC were based on underlying services in the Microsoft Windows computing environment. These underlying services (OLE [Object Linking and Embedding],more » DCOM [Distributed Component Object Model], and RPC [Remote Procedure Call]) have been the source of many severe security vulnerabilities. It is not feasible to automatically apply vendor patches and service packs to mitigate these vulnerabilities in a control systems environment. Control systems using the original OPC data access technology can thus inherit the vulnerabilities associated with these services. Current OPC standardization efforts are moving away from the original focus on Microsoft protocols, with a distinct trend toward web-based protocols that are independent of any particular operating system. However, the installed base of OPC equipment consists mainly of legacy implementations of the OLE for Process Control protocols.« less

Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface.

PubMed

Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

2015-06-05

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states.

Multi-dimensional TOF-SIMS analysis for effective profiling of disease-related ions from the tissue surface

PubMed Central

Park, Ji-Won; Jeong, Hyobin; Kang, Byeongsoo; Kim, Su Jin; Park, Sang Yoon; Kang, Sokbom; Kim, Hark Kyun; Choi, Joon Sig; Hwang, Daehee; Lee, Tae Geol

2015-01-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) emerges as a promising tool to identify the ions (small molecules) indicative of disease states from the surface of patient tissues. In TOF-SIMS analysis, an enhanced ionization of surface molecules is critical to increase the number of detected ions. Several methods have been developed to enhance ionization capability. However, how these methods improve identification of disease-related ions has not been systematically explored. Here, we present a multi-dimensional SIMS (MD-SIMS) that combines conventional TOF-SIMS and metal-assisted SIMS (MetA-SIMS). Using this approach, we analyzed cancer and adjacent normal tissues first by TOF-SIMS and subsequently by MetA-SIMS. In total, TOF- and MetA-SIMS detected 632 and 959 ions, respectively. Among them, 426 were commonly detected by both methods, while 206 and 533 were detected uniquely by TOF- and MetA-SIMS, respectively. Of the 426 commonly detected ions, 250 increased in their intensities by MetA-SIMS, whereas 176 decreased. The integrated analysis of the ions detected by the two methods resulted in an increased number of discriminatory ions leading to an enhanced separation between cancer and normal tissues. Therefore, the results show that MD-SIMS can be a useful approach to provide a comprehensive list of discriminatory ions indicative of disease states. PMID:26046669

Effect of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Alone versus MALDI-TOF MS Combined with Real-Time Antimicrobial Stewardship Interventions on Time to Optimal Antimicrobial Therapy in Patients with Positive Blood Cultures.

PubMed

Beganovic, Maya; Costello, Michael; Wieczorkiewicz, Sarah M

2017-05-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) decreases the time to organism identification and improves clinical and financial outcomes. The purpose of this study was to evaluate the impact of MALDI-TOF MS alone versus MALDI-TOF MS combined with real-time, pharmacist-driven, antimicrobial stewardship (AMS) intervention on patient outcomes. This single-center, pre-post, quasiexperimental study evaluated hospitalized patients with positive blood cultures identified via MALDI-TOF MS combined with prospective AMS intervention compared to a control cohort with MALDI-TOF MS identification without AMS intervention. AMS intervention included: real-time MALDI-TOF MS pharmacist notification and prospective AMS provider feedback. The primary outcome was the time to optimal therapy (TTOT). A total of 252 blood cultures, 126 in each group, were included in the final analysis. MALDI-TOF MS plus AMS intervention significantly reduced the overall TTOT (75.17 versus 43.06 h; P < 0.001), the Gram-positive contaminant TTOT (48.21 versus 11.75 h; P < 0.001), the Gram-negative infection (GNI) TTOT (71.83 versus 35.98 h; P < 0.001), and the overall hospital length of stay (LOS; 15.03 versus 9.02 days; P = 0.021). The TTOT for Gram-positive infection (GPI) was improved (64.04 versus 41.61 h; P = 0.082). For GPI, the hospital LOS (14.64 versus 10.31 days; P = 0.002) and length of antimicrobial therapy 24.30 versus 18.97 days; P = 0.018) were reduced. For GNI, the time to microbiologic clearance (51.13 versus 34.51 h; P < 0.001), the hospital LOS (15.40 versus 7.90 days; P = 0.027), and the intensive care unit LOS (5.55 versus 1.19 days; P = 0.035) were reduced. To achieve optimal outcomes, rapid identification with MALDI-TOF MS combined with real-time AMS intervention is more impactful than MALDI-TOF MS alone. Copyright © 2017 American Society for Microbiology.

No scanning depth imaging system based on TOF

NASA Astrophysics Data System (ADS)

Sun, Rongchun; Piao, Yan; Wang, Yu; Liu, Shuo

2016-03-01

To quickly obtain a 3D model of real world objects, multi-point ranging is very important. However, the traditional measuring method usually adopts the principle of point by point or line by line measurement, which is too slow and of poor efficiency. In the paper, a no scanning depth imaging system based on TOF (time of flight) was proposed. The system is composed of light source circuit, special infrared image sensor module, processor and controller of image data, data cache circuit, communication circuit, and so on. According to the working principle of the TOF measurement, image sequence was collected by the high-speed CMOS sensor, and the distance information was obtained by identifying phase difference, and the amplitude image was also calculated. Experiments were conducted and the experimental results show that the depth imaging system can achieve no scanning depth imaging function with good performance.

A multi-center ring trial for the identification of anaerobic bacteria using MALDI-TOF MS.

PubMed

Veloo, A C M; Jean-Pierre, H; Justesen, U S; Morris, T; Urban, E; Wybo, I; Shah, H N; Friedrich, A W; Morris, T; Shah, H N; Jean-Pierre, H; Justesen, U S; Nagy, E; Urban, E; Kostrzewa, M; Veloo, A; Friedrich, A W

2017-12-01

Inter-laboratory reproducibility of Matrix Assisted Laser Desorption Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of anaerobic bacteria has not been shown before. Therefore, ten anonymized anaerobic strains were sent to seven participating laboratories, an initiative of the European Network for the Rapid Identification of Anaerobes (ENRIA). On arrival the strains were cultured and identified using MALDI-TOF MS. The spectra derived were compared with two different Biotyper MALDI-TOF MS databases, the db5627 and the db6903. The results obtained using the db5627 shows a reasonable variation between the different laboratories. However, when a more optimized database is used, the variation is less pronounced. In this study we show that an optimized database not only results in a higher number of strains which can be identified using MALDI-TOF MS, but also corrects for differences in performance between laboratories. Copyright © 2017 Elsevier Ltd. All rights reserved.

Rapid identification and source-tracking of Listeria monocytogenes using MALDI-TOF mass spectrometry.

PubMed

Jadhav, Snehal; Gulati, Vandana; Fox, Edward M; Karpe, Avinash; Beale, David J; Sevior, Danielle; Bhave, Mrinal; Palombo, Enzo A

2015-06-02

Listeria monocytogenes is an important foodborne pathogen responsible for the sometimes fatal disease listeriosis. Public health concerns and stringent regulations associated with the presence of this pathogen in food and food processing environments underline the need for rapid and reliable detection and subtyping techniques. In the current study, the application of matrix assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF MS) as a single identification and source-tracking tool for a collection of L. monocytogenes isolates, obtained predominantly from dairy sources within Australia, was explored. The isolates were cultured on different growth media and analysed using MALDI-TOF MS at two incubation times (24 and 48 h). Whilst reliable genus-level identification was achieved from most media, identification at the species level was found to be dependent on culture conditions. Successful speciation was highest for isolates cultured on the chromogenic Agar Listeria Ottaviani Agosti agar (ALOA, 91% of isolates) and non-selective horse blood agar (HBA, 89%) for 24h. Chemometric statistical analysis of the MALDI-TOF MS data enabled source-tracking of L. monocytogenes isolates obtained from four different dairy sources. Strain-level discrimination was also observed to be influenced by culture conditions. In addition, t-test/analysis of variance (ANOVA) was used to identify potential biomarker peaks that differentiated the isolates according to their source of isolation. Source-tracking using MALDI-TOF MS was compared and correlated with the gold standard pulsed-field gel electrophoresis (PFGE) technique. The discriminatory index and the congruence between both techniques were compared using the Simpsons Diversity Index and adjusted Rand and Wallace coefficients. Overall, MALDI-TOF MS based source-tracking (using data obtained by culturing the isolates on HBA) and PFGE demonstrated good congruence with a Wallace coefficient of 0.71 and

Identification of Algerian Field-Caught Phlebotomine Sand Fly Vectors by MALDI-TOF MS

PubMed Central

Lafri, Ismail; Almeras, Lionel; Bitam, Idir; Caputo, Aurelia; Yssouf, Amina; Forestier, Claire-Lise; Izri, Arezki; Raoult, Didier; Parola, Philippe

2016-01-01

Background Phlebotomine sand flies are known to transmit Leishmania parasites, bacteria and viruses that affect humans and animals in many countries worldwide. Precise sand fly identification is essential to prevent phlebotomine-borne diseases. Over the past two decades, progress in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as an accurate tool for arthropod identification. The objective of the present study was to investigate the usefulness of MALDI-TOF MS as a tool for identifying field-caught phlebotomine. Methodology/Principal Findings Sand flies were captured in four sites in north Algeria. A subset was morphologically and genetically identified. Six species were found in these areas and a total of 28 stored frozen specimens were used for the creation of the reference spectrum database. The relevance of this original method for sand fly identification was validated by two successive blind tests including the morphological identification of 80 new specimens which were stored at -80°C, and 292 unknown specimens, including engorged specimens, which were preserved under different conditions. Intra-species reproducibility and inter-species specificity of the protein profiles were obtained, allowing us to distinguish specimens at the gender level. Querying of the sand fly database using the MS spectra from the blind test groups revealed concordant results between morphological and MALDI-TOF MS identification. However, MS identification results were less efficient for specimens which were engorged or stored in alcohol. Identification of 362 phlebotomine sand flies, captured at four Algerian sites, by MALDI-TOF MS, revealed that the subgenus Larroussius was predominant at all the study sites, except for in M’sila where P. (Phlebotomus) papatasi was the only sand fly species detected. Conclusion The present study highlights the application of MALDI-TOF MS for monitoring sand fly fauna captured in the field

[Application of MALDI-TOF-MS in gene testing for non-syndromic hearing loss].

PubMed

Zeng, Yun; Jiang, Dan; Feng, Da-fei; Jin, Dong-dong; Wu, Xiao-hui; Ding, Yan-li; Zou, Jing

2013-12-01

To investigate the feasibility of Matrix-Assisted Laser Desorption-Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) , according to the genetic test of non-syndromic hearing loss (NSHL), and check using the direct sequencing. Peripheral blood was collected from 454 NSHL patients. DNA samples were extracted and 20 loci of the four common disease-causing genes were analysed by MALDI-TOF-MS, including GJB2 (35delG, 167delT, 176_191del16, 235delC, 299_300delAT ), GJB3 (538C→T, 547G→A), SLC26A4 (281C→T, 589G→A, IVS7-2A→G, 1174A→T, 1226G→A, 1229C→T, IVS15+5G→A, 1975G→C, 2027T→A, 2162C→T, 2168A→G), and mitochondrial 12S rRNA (1494C→T, 1555A→G). Direct sequencing was also used to analyse the aforementioned 20 loci in order to validate the accuracy of MALDI-TOF-MS. Among the 454 patients, 166 cases (36.56%) of disease-causing mutations were detected, which included 69 cases (21.15%) of GJB2 gene mutation, four cases (0.88%) of GJB3 gene mutation, 64 cases (14.10%) of SLC26A4 gene mutation, and three cases (0.66%) of mitochondrial 12S rRNA gene mutation. Moreover, the results obtained from direct sequencing and MALDI-TOF-MS were consistent, and the results showed that the two methods were consistent. The MALDI-TOF-MS detection method was designed based on the hearing loss-related mutation hotspots seen in the Chinese population, and it has a high detection rate for NSHL related mutations. In comparison to the conventional detection methods, MALDI-TOF-MS has the following advantages: more detection sites, greater coverage, accurate, high throughput and low cost. Therefore, this method is capable of satisfying the needs of clinical detection for hearing impairment and it is suitable for large-scale implementation.

Identification of Algerian Field-Caught Phlebotomine Sand Fly Vectors by MALDI-TOF MS.

PubMed

Lafri, Ismail; Almeras, Lionel; Bitam, Idir; Caputo, Aurelia; Yssouf, Amina; Forestier, Claire-Lise; Izri, Arezki; Raoult, Didier; Parola, Philippe

2016-01-01

Phlebotomine sand flies are known to transmit Leishmania parasites, bacteria and viruses that affect humans and animals in many countries worldwide. Precise sand fly identification is essential to prevent phlebotomine-borne diseases. Over the past two decades, progress in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has emerged as an accurate tool for arthropod identification. The objective of the present study was to investigate the usefulness of MALDI-TOF MS as a tool for identifying field-caught phlebotomine. Sand flies were captured in four sites in north Algeria. A subset was morphologically and genetically identified. Six species were found in these areas and a total of 28 stored frozen specimens were used for the creation of the reference spectrum database. The relevance of this original method for sand fly identification was validated by two successive blind tests including the morphological identification of 80 new specimens which were stored at -80°C, and 292 unknown specimens, including engorged specimens, which were preserved under different conditions. Intra-species reproducibility and inter-species specificity of the protein profiles were obtained, allowing us to distinguish specimens at the gender level. Querying of the sand fly database using the MS spectra from the blind test groups revealed concordant results between morphological and MALDI-TOF MS identification. However, MS identification results were less efficient for specimens which were engorged or stored in alcohol. Identification of 362 phlebotomine sand flies, captured at four Algerian sites, by MALDI-TOF MS, revealed that the subgenus Larroussius was predominant at all the study sites, except for in M'sila where P. (Phlebotomus) papatasi was the only sand fly species detected. The present study highlights the application of MALDI-TOF MS for monitoring sand fly fauna captured in the field. The low cost, reliability and rapidity of MALDI-TOF

Characterizing Neutron Diagnostics on the nTOF Line at SUNY Geneseo

NASA Astrophysics Data System (ADS)

Harrison, Hannah; Seppala, Hannah; Visca, Hannah; Wakwella, Praveen; Fletcher, Kurt; Padalino, Stephen; Forrest, Chad; Regan, Sean; Sangster, Craig

2016-10-01

Charged particle beams from SUNY Geneseo's 1.7 MV Tandem Pelletron Accelerator induce nuclear reactions that emit neutrons ranging from 0.5 to 17.9 MeV via 2H(d,n)3He and 11B(d,n)12C. This adjustable neutron source can be used to calibrate ICF and HEDP neutron scintillators for ICF diagnostics. However, gamma rays and muons, which are often present during an accelerator-based calibration, are difficult to differentiate from neutron signals in scintillators. To mitigate this problem, a new neutron time-of-flight (nTOF) line has been constructed. The nTOF timing is measured using the associated particle technique. A charged particle produced by the nuclear reaction serves as a start signal, while its associated neutron is the stop signal. Each reaction is analyzed event-by-event to determine whether the scintillator signal was generated by a neutron, gamma or muon. Using this nTOF technique, the neutron response for different scintillation detectors can be determined. Funded in part by a LLE contract through the DOE.

Assessment of heat treatment of dairy products by MALDI-TOF-MS.

PubMed

Meltretter, Jasmin; Birlouez-Aragon, Inès; Becker, Cord-Michael; Pischetsrieder, Monika

2009-12-01

The formation of the Amadori product from lactose (protein lactosylation) is a major parameter to evaluate the quality of processed milk. Here, MALDI-TOF-MS was used for the relative quantification of lactose-adducts in heated milk. Milk was heated at a temperature of 70, 80, and 100 degrees C between 0 and 300 min, diluted, and subjected directly to MALDI-TOF-MS. The lactosylation rate of alpha-lactalbumin increased with increasing reaction temperature and time. The results correlated well with established markers for heat treatment of milk (concentration of total soluble protein, soluble alpha-lactalbumin and beta-lactoglobulin at pH 4.6, and fluorescence of advanced Maillard products and soluble tryptophan index; r=0.969-0.997). The method was also applied to examine commercially available dairy products. In severely heated products, protein pre-purification by immobilized metal affinity chromatography improved spectra quality. Relative quantification of protein lactosylation by MALDI-TOF-MS proved to be a very fast and reliable method to monitor early Maillard reaction during milk processing.

Rapid typing of Mannheimia haemolytica major genotypes 1 and 2 using MALDI-TOF mass spectrometry

USDA-ARS?s Scientific Manuscript database

Genotype 2 M. haemolytica predominantly associate over genotype 1 with the lungs of cattle with respiratory disease and ICEs containing antimicrobial resistance genes. Distinct protein masses were detected by MALDI-TOF MS between genotype 1 and 2 strains. MALDI-TOF MS could rapidly differentiate ge...

New Insights for Diagnosis of Pineapple Fusariosis by MALDI-TOF MS Technique.

PubMed

Santos, Cledir; Ventura, José Aires; Lima, Nelson

2016-08-01

Fusarium is one of the most economically important fungal genus, since it includes many pathogenic species which cause a wide range of plant diseases. Morphological or molecular biology identification of Fusarium species is a limiting step in the fast diagnosis and treatment of plant disease caused by these fungi. Mass spectrometry by matrix-assisted laser/desorption ionisation-time-of-flight (MALDI-TOF)-based fingerprinting approach was applied to the fungal growth monitoring and direct detection of strain Fusarium guttiforme E-480 inoculated in both pineapple cultivars Pérola and Imperial side shoots, that are susceptible and resistant, respectively, to this fungal strain. MALDI-TOF MS technique was capable to detect fungal molecular mass peaks in the susceptible pineapple stem side shoot tissue. It is assumed that these molecular masses are mainly constituted by ribosomal proteins. MALDI-TOF-based fingerprinting approach has herein been demonstrated to be sensitive and accurate for the direct detection of F. guttiforme E-480 molecular masses on both susceptible and resistant pineapple side stem free of any pre-treatment. According to the results obtained, the changing on molecular mass peaks of infected susceptible pineapple tissue together with the possibility of fungal molecular masses analysis into this pineapple tissue can be a good indication for an early diagnosis by MALDI-TOF MS of pineapple fusariosis.

High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS.

PubMed

Miescher Schwenninger, S; Freimüller Leischtfeld, S; Gantenbein-Demarchi, C

2016-11-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful biotyping tool increasingly used for high-throughput identification of clinical microbial isolates, however, in food fermentation research this approach is still not well established. This study examines the microbial biodiversity of cocoa bean fermentation based on the isolation of micro-organisms in cocoa-producing regions, followed by MALDI-TOF MS in Switzerland. A preceding 6-week storage test to mimic lengthy transport of microbial samples from cocoa-producing regions to Switzerland was performed with strains of Lactobacillus plantarum, Acetobacter pasteurianus and Saccharomyces cerevisiae. Weekly MALDI-TOF MS analysis was able to successfully identify microbiota to the species level after storing live cultures on slant agar at mild temperatures (7°C) and/or in 75% aqueous ethanol at differing temperatures (-20, 7 and 30°C). The efficacy of this method was confirmed by on-site recording of the microbial biodiversity in cocoa bean fermentation in Bolivia and Brazil, with a total of 1126 randomly selected isolates. MALDI-TOF MS analyses revealed known dominant cocoa bean fermentation species with Lact. plantarum and Lactobacillus fermentum in the lactic acid bacteria taxon, Hanseniaspora opuntiae and S. cerevisiae in the yeast taxon, and Acet. pasteurianus, Acetobacter fabarum, Acetobacter ghanensis and Acetobacter senegalensis in the acetic acid bacteria taxon. Microbial identification with MALDI-TOF MS has increased the number of samples that can be analysed in a given time, a prerequisite for high-throughput methods. This method is already widely used for the identification of clinical microbial isolates, whereas in food fermentation research, including cocoa bean fermentation, microbiota is mostly identified by time-consuming, biochemical-based phenotyping and molecular approaches. This study presents the use of MALDI-TOF MS for characterizing the

MALDI-TOF MS identification of Anopheles gambiae Giles blood meal crushed on Whatman filter papers.

PubMed

Niare, Sirama; Almeras, Lionel; Tandina, Fatalmoudou; Yssouf, Amina; Bacar, Affane; Toilibou, Ali; Doumbo, Ogobara; Raoult, Didier; Parola, Philippe

2017-01-01

Identification of the source of mosquito blood meals is an important component for disease control and surveillance. Recently, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling has emerged as an effective tool for mosquito blood meal identification, using the abdomens of freshly engorged mosquitoes. In the field, mosquito abdomens are crushed on Whatman filter papers to determine the host feeding patterns by identifying the origin of their blood meals. The aim of this study was to test whether crushing engorged mosquito abdomens on Whatman filter papers was compatible with MALDI-TOF MS for mosquito blood meal identification. Both laboratory reared and field collected mosquitoes were tested. Sixty Anopheles gambiae Giles were experimentally engorged on the blood of six distinct vertebrate hosts (human, sheep, rabbit, dog, chicken and rat). The engorged mosquito abdomens were crushed on Whatman filter papers for MALDI-TOF MS analysis. 150 Whatman filter papers, with mosquitoes engorged on cow and goat blood, were preserved. A total of 77 engorged mosquito abdomens collected in the Comoros Islands and crushed on Whatman filter papers were tested with MALDI-TOF MS. The MS profiles generated from mosquito engorged abdomens crushed on Whatman filter papers exhibited high reproducibility according to the original host blood. The blood meal host was correctly identified from mosquito abdomens crushed on Whatman filter papers by MALDI-TOF MS. The MS spectra obtained after storage were stable regardless of the room temperature and whether or not they were frozen. The MS profiles were reproducible for up to three months. For the Comoros samples, 70/77 quality MS spectra were obtained and matched with human blood spectra. This was confirmed by molecular tools. The results demonstrated that MALDI-TOF MS could identify mosquito blood meals from Whatman filter papers collected in the field during entomological surveys. The

Rapid identification of acetic acid bacteria using MALDI-TOF mass spectrometry fingerprinting.

PubMed

Andrés-Barrao, Cristina; Benagli, Cinzia; Chappuis, Malou; Ortega Pérez, Ruben; Tonolla, Mauro; Barja, François

2013-03-01

Acetic acid bacteria (AAB) are widespread microorganisms characterized by their ability to transform alcohols and sugar-alcohols into their corresponding organic acids. The suitability of matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) for the identification of cultured AAB involved in the industrial production of vinegar was evaluated on 64 reference strains from the genera Acetobacter, Gluconacetobacter and Gluconobacter. Analysis of MS spectra obtained from single colonies of these strains confirmed their basic classification based on comparative 16S rRNA gene sequence analysis. MALDI-TOF analyses of isolates from vinegar cross-checked by comparative sequence analysis of 16S rRNA gene fragments allowed AAB to be identified, and it was possible to differentiate them from mixed cultures and non-AAB. The results showed that MALDI-TOF MS analysis was a rapid and reliable method for the clustering and identification of AAB species. Copyright © 2012 Elsevier GmbH. All rights reserved.

Molecular and MALDI-TOF identification of ticks and tick-associated bacteria in Mali

PubMed Central

Diarra, Adama Zan; Almeras, Lionel; Berenger, Jean-Michel; Koné, Abdoulaye K.; Bocoum, Zakaria; Dabo, Abdoulaye; Doumbo, Ogobara; Raoult, Didier; Parola, Philippe

2017-01-01

Ticks are considered the second vector of human and animal diseases after mosquitoes. Therefore, identification of ticks and associated pathogens is an important step in the management of these vectors. In recent years, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been reported as a promising method for the identification of arthropods including ticks. The objective of this study was to improve the conditions for the preparation of tick samples for their identification by MALDI-TOF MS from field-collected ethanol-stored Malian samples and to evaluate the capacity of this technology to distinguish infected and uninfected ticks. A total of 1,333 ticks were collected from mammals in three distinct sites from Mali. Morphological identification allowed classification of ticks into 6 species including Amblyomma variegatum, Hyalomma truncatum, Hyalomma marginatum rufipes, Rhipicephalus (Boophilus) microplus, Rhipicephalus evertsi evertsi and Rhipicephalus sanguineus sl. Among those, 471 ticks were randomly selected for molecular and proteomic analyses. Tick legs submitted to MALDI-TOF MS revealed a concordant morpho/molecular identification of 99.6%. The inclusion in our MALDI-TOF MS arthropod database of MS reference spectra from ethanol-preserved tick leg specimens was required to obtain reliable identification. When tested by molecular tools, 76.6%, 37.6%, 20.8% and 1.1% of the specimens tested were positive for Rickettsia spp., Coxiella burnetii, Anaplasmataceae and Borrelia spp., respectively. These results support the fact that MALDI-TOF is a reliable tool for the identification of ticks conserved in alcohol and enhances knowledge about the diversity of tick species and pathogens transmitted by ticks circulating in Mali. PMID:28742123

Molecular and MALDI-TOF identification of ticks and tick-associated bacteria in Mali.

PubMed

Diarra, Adama Zan; Almeras, Lionel; Laroche, Maureen; Berenger, Jean-Michel; Koné, Abdoulaye K; Bocoum, Zakaria; Dabo, Abdoulaye; Doumbo, Ogobara; Raoult, Didier; Parola, Philippe

2017-07-01

Ticks are considered the second vector of human and animal diseases after mosquitoes. Therefore, identification of ticks and associated pathogens is an important step in the management of these vectors. In recent years, Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been reported as a promising method for the identification of arthropods including ticks. The objective of this study was to improve the conditions for the preparation of tick samples for their identification by MALDI-TOF MS from field-collected ethanol-stored Malian samples and to evaluate the capacity of this technology to distinguish infected and uninfected ticks. A total of 1,333 ticks were collected from mammals in three distinct sites from Mali. Morphological identification allowed classification of ticks into 6 species including Amblyomma variegatum, Hyalomma truncatum, Hyalomma marginatum rufipes, Rhipicephalus (Boophilus) microplus, Rhipicephalus evertsi evertsi and Rhipicephalus sanguineus sl. Among those, 471 ticks were randomly selected for molecular and proteomic analyses. Tick legs submitted to MALDI-TOF MS revealed a concordant morpho/molecular identification of 99.6%. The inclusion in our MALDI-TOF MS arthropod database of MS reference spectra from ethanol-preserved tick leg specimens was required to obtain reliable identification. When tested by molecular tools, 76.6%, 37.6%, 20.8% and 1.1% of the specimens tested were positive for Rickettsia spp., Coxiella burnetii, Anaplasmataceae and Borrelia spp., respectively. These results support the fact that MALDI-TOF is a reliable tool for the identification of ticks conserved in alcohol and enhances knowledge about the diversity of tick species and pathogens transmitted by ticks circulating in Mali.

Technologies in the Whole-Genome Age: MALDI-TOF-Based Genotyping.

PubMed

Vogel, Nicolas; Schiebel, Katrin; Humeny, Andreas

2009-01-01

With the decipherment of the human genome, new questions have moved into the focus of today's research. One key aspect represents the discovery of DNA variations capable to influence gene transcription, RNA splicing, or regulating processes, and their link to pathology. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS) is a powerful tool for the qualitative investigation and relative quantification of variations like single nucleotide polymorphisms, DNA methylation, microsatellite instability, or loss of heterozygosity. After its introduction into proteomics, efforts were made to adopt this technique to DNA analysis. Initially intended for peptide/protein analysis, it held several difficulties for application to nucleic acids. Today, MALDI-TOF-MS has reached worldwide acceptance and application in nucleic acid research, with a wide spectrum of methods being available. One of the most versatile approaches relies on primer extension to genotype single alleles, microsatellite repeat lengths or the methylation status of a given cytosine. Optimized methods comprising intelligent primer design and proper nucleotide selection for primer extension enabled multiplexing of reactions, rendering the analysis more economic due to parallel genotyping of several alleles in a single experiment. Laboratories equipped with MALDI-TOF-MS possess a universal technical platform for the analysis of a large variety of different molecules.

Plasma-laser ion discrimination by TOF technique applied to coupled SiC detectors.

NASA Astrophysics Data System (ADS)

Cavallaro, Salvatore

2018-01-01

The rate estimation of nuclear reactions induced in high intensity laser-target interaction (≥1016 W/cm2), is strongly depending on the neutron detection efficiency and ion charge discrimination, according to particles involved in exit open-channels. Ion discrimination is basically performed by means of analysis of pits observed on track detector, which is critically dependent on calibration and/or fast TOF devices based on SiC and diamond detectors. Last setup is used to determine the ion energy and to obtain a rough estimation of yields. However, for each TOF interval, the dependence of yield from the energy deposited in the detector sensitive region, introduces a distortion in the ion spectra. Moreover, if two ion species are present in the same spectrum, the discrimination of their contribution is not attainable. In this paper a new method is described which allows to discriminate the contribution of two ion species in the wide energy range of nuclear reactions induced in laser-target interactions. The method is based on charge response of two TOF-SiC detectors, of suitable thicknesses, placed in adjacent positions. In presence of two ion species, the response of the detectors, associated with different energy losses, can determine the ion specific contribution to each TOF interval.

Pushing the Limits of MALDI-TOF Mass Spectrometry: Beyond Fungal Species Identification

PubMed Central

Rizzato, Cosmeri; Lombardi, Lisa; Zoppo, Marina; Lupetti, Antonella; Tavanti, Arianna

2015-01-01

Matrix assisted laser desorption ionization time of flight (MALDI-TOF) is a powerful analytical tool that has revolutionized microbial identification. Routinely used for bacterial identification, MALDI-TOF has recently been applied to both yeast and filamentous fungi, confirming its pivotal role in the rapid and reliable diagnosis of infections. Subspecies-level identification holds an important role in epidemiological investigations aimed at tracing virulent or drug resistant clones. This review focuses on present and future applications of this versatile tool in the clinical mycology laboratory. PMID:29376916

Improved mass resolution and mass accuracy in TOF-SIMS spectra and images using argon gas cluster ion beams.

PubMed

Shon, Hyun Kyong; Yoon, Sohee; Moon, Jeong Hee; Lee, Tae Geol

2016-06-09

The popularity of argon gas cluster ion beams (Ar-GCIB) as primary ion beams in time-of-flight secondary ion mass spectrometry (TOF-SIMS) has increased because the molecular ions of large organic- and biomolecules can be detected with less damage to the sample surfaces. However, Ar-GCIB is limited by poor mass resolution as well as poor mass accuracy. The inferior quality of the mass resolution in a TOF-SIMS spectrum obtained by using Ar-GCIB compared to the one obtained by a bismuth liquid metal cluster ion beam and others makes it difficult to identify unknown peaks because of the mass interference from the neighboring peaks. However, in this study, the authors demonstrate improved mass resolution in TOF-SIMS using Ar-GCIB through the delayed extraction of secondary ions, a method typically used in TOF mass spectrometry to increase mass resolution. As for poor mass accuracy, although mass calibration using internal peaks with low mass such as hydrogen and carbon is a common approach in TOF-SIMS, it is unsuited to the present study because of the disappearance of the low-mass peaks in the delayed extraction mode. To resolve this issue, external mass calibration, another regularly used method in TOF-MS, was adapted to enhance mass accuracy in the spectrum and image generated by TOF-SIMS using Ar-GCIB in the delayed extraction mode. By producing spectra analyses of a peptide mixture and bovine serum albumin protein digested with trypsin, along with image analyses of rat brain samples, the authors demonstrate for the first time the enhancement of mass resolution and mass accuracy for the purpose of analyzing large biomolecules in TOF-SIMS using Ar-GCIB through the use of delayed extraction and external mass calibration.

Real-time motion artifacts compensation of ToF sensors data on GPU

NASA Astrophysics Data System (ADS)

Lefloch, Damien; Hoegg, Thomas; Kolb, Andreas

2013-05-01

Over the last decade, ToF sensors attracted many computer vision and graphics researchers. Nevertheless, ToF devices suffer from severe motion artifacts for dynamic scenes as well as low-resolution depth data which strongly justifies the importance of a valid correction. To counterbalance this effect, a pre-processing approach is introduced to greatly improve range image data on dynamic scenes. We first demonstrate the robustness of our approach using simulated data to finally validate our method using sensor range data. Our GPU-based processing pipeline enhances range data reliability in real-time.

Application of MALDI-TOF mass spectrometry in clinical diagnostic microbiology.

PubMed

De Carolis, Elena; Vella, Antonietta; Vaccaro, Luisa; Torelli, Riccardo; Spanu, Teresa; Fiori, Barbara; Posteraro, Brunella; Sanguinetti, Maurizio

2014-09-12

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently emerged as a powerful technique for identification of microorganisms, changing the workflow of well-established laboratories so that its impact on microbiological diagnostics has been unparalleled. In comparison with conventional identification methods that rely on biochemical tests and require long incubation procedures, MALDI-TOF MS has the advantage of identifying bacteria and fungi directly from colonies grown on culture plates in a few minutes and with simple procedures. Numerous studies on different systems available demonstrate the reliability and accuracy of the method, and new frontiers have been explored besides microbial species level identification, such as direct identification of pathogens from positive blood cultures, subtyping, and drug susceptibility detection.

TOF-SIMS imaging of chlorhexidine-digluconate transport in frozen hydrated biofilms of the fungus Candida albicans

NASA Astrophysics Data System (ADS)

Tyler, Bonnie J.; Rangaranjan, Srinath; Möller, Jörg; Beumer, Andre'; Arlinghaus, Heinrich F.

2006-07-01

The diffusion of the anti-microbial chlorhexidine digluconate (CHG) has been studied in C. albicans biofilms by time-of-flight secondary-ion mass spectrometry (TOF-SIMS). C. albicans has been shown to become resistant to common anti-microbial agents, including CHG, when growing as a biofilm. Mass transport resistance within biofilms has commonly been suggested as a resistance mechanism, but measurement of transport for most anti-microbial agents in biofilms has proven extremely difficult because of the heterogeneity of the biofilms and the difficulty in detecting these agents within an intact biofilm. In this study, TOF-SIMS has been used to study the transport of CHG and glucose in a frozen hydrated biofilm. The TOF-SIMS images reveal a progression of CHG from the top of the biofilm to its base with time. Images suggest that there are channels within the biofilm and show preferential binding of CHG to cellular components of the biofilm. Additionally, both living and dead cells can be identified in the TOF-SIMS images by the sequestration of K + and the presence of cell markers. This study demonstrates that TOF-SIMS has the unique potential to simultaneously observe the presence of an antimicrobial agent, concentration of nutrients, and the viability of the cell population.

Chemical Visualization of Sweat Pores in Fingerprints Using GO-Enhanced TOF-SIMS.

PubMed

Cai, Lesi; Xia, Meng-Chan; Wang, Zhaoying; Zhao, Ya-Bin; Li, Zhanping; Zhang, Sichun; Zhang, Xinrong

2017-08-15

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) has been used in imaging of small molecules (<500 Da) in fingerprints, such as gunshot residues and illicit drugs. However, identifying and mapping relatively high mass molecules are quite difficult owing to insufficient ion yield of their molecular ions. In this report, graphene oxide (GO)-enhanced TOF-SIMS was used to detect and image relatively high mass molecules such as poison, alkaloids (>600 Da) and controlled drugs, and antibiotics (>700 Da) in fingerprints. Detail features of fingerprints such as the number and distribution of sweat pores in a ridge and even the delicate morphology of one pore were clearly revealed in SIMS images of relatively high mass molecules. The detail features combining with identified chemical composition were sufficient to establish a human identity and link the suspect to a crime scene. The wide detectable mass range and high spatial resolution make GO-enhanced TOF-SIMS a promising tool in accurate and fast analysis of fingerprints, especially in fragmental fingerprint analysis.

[3D-TOF MR-angiography with high spatial resolution for surgical planning in insular lobe gliomas].

PubMed

Bykanov, A E; Pitskhelauri, D I; Pronin, I N; Tonoyan, A S; Kornienko, V N; Zakharova, N E; Turkin, A M; Sanikidze, A Z; Shkarubo, M A; Shkatova, A M; Shults, E I

2015-01-01

Despite the obvious progress in modern neurosurgery, surgery for glial tumors of the insular lobe is often associated with a high risk of postoperative neurological deficit, which is primarily caused by damage to perforating arteries of the M1 segment of the middle cerebral artery. The work is aimed at evaluating the effectiveness of high resolution time-of-flight (3D-TOF) MR angiography in imaging of medial and lateral lenticulostriate arteries and determining their relationship to tumor edge in patients with gliomas of the insula. 3D-TOF MR angiography data were analyzed in 20 patients with primarily diagnosed cerebral gliomas involving the insula. All patients underwent non-contrast enhanced 3D-TOF MR angiography. In 6 cases, 3D-TOF MRA was performed before and after contrast enhancement. 3D-TOF angiography before intravenous contrast injection was capable of visualizing the medial lenticulostriate arteries in 19 patients (95% of all cases) and lateral lenticulostriate arteries in 18 patients (90% of all cases). Contrast-enhanced 3D-TOF angiography allows for better visualization of both the proximal and distal segments of lenticulostriate arteries. Three variants of relationship between the tumor and lenticulostriate arteries were identified. Variant I: the tumor grew over the arteries without their displacement in 2 cases (10% of the total number of observations); variant II: the tumor caused medial displacement of arteries without growing over them in 11 cases (55% of the total number of observations); variant III: the tumor partially grew over and displaced arteries in 2 cases (10%). In 25% of cases (5 patients), tumor was poorly visualized on 3D-TOF MR angiograms because their signal characteristics did not differ from those of the medulla (tumor tissue was T1 isointense). As a result, it was impossible to determine the relationship between the tumor and lenticulostriate arteries. High spatial resolution time-of-flight MR angiography can be recommended for

Time-of-flight scattering and recoiling spectrometer (TOF-SARS) for surface analysis

NASA Astrophysics Data System (ADS)

Grizzi, O.; Shi, M.; Bu, H.; Rabalais, J. W.

1990-02-01

A UHV spectrometer system has been designed and constructed for time-of-flight scattering and recoiling spectrometry (TOF-SARS). The technique uses a pulsed primary ion beam and TOF methods for analysis of both scattered and recoiled neutrals (N) and ions (I) simultaneously with continuous scattering angle variation over a flight path of ≊1 m. The pulsed ion beam line uses an electron impact ionization source with acceleration up to 5 keV; pulse widths down to 20 ns with average current densities of 0.05-5.0 nA/mm2 have been obtained. Typical current densities used herein are ≊0.1 nA/mm2 and TOF spectra can be collected with a total ion dose of <10-3 ions/surface atom. A channel electron multiplier detector, which is sensitive to both ions and fast neutrals, is mounted on a long tube connected to a precision rotary motion feedthru, allowing continuous rotation over a scattering angular range 0°<θ<165°. The sample is mounted on a precision manipulator, allowing azimuthal δ and incident α angle rotation, as well as translation along three orthogonal axes. The system also accommodates standard surface analysis instrumentation for LEED, AES, XPS, and UPS. The capabilities of the system are demonstrated by the following examples: (A) TOF spectra versus scattering angle θ; (B) comparison to LEED and AES; (C) surface and adsorbate structure determinations; (D) monitoring surface roughness; (E) surface semichanneling measurements; (F) measurements of scattered ion fractions; and (G) ion induced Auger electron emission.

MALDI-TOF MS as a tool to identify foodborne yeasts and yeast-like fungi.

PubMed

Quintilla, Raquel; Kolecka, Anna; Casaregola, Serge; Daniel, Heide M; Houbraken, Jos; Kostrzewa, Markus; Boekhout, Teun; Groenewald, Marizeth

2018-02-02

Since food spoilage by yeasts causes high economic losses, fast and accurate identifications of yeasts associated with food and food-related products are important for the food industry. In this study the efficiency of the matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify food related yeasts was evaluated. A CBS in-house MALDI-TOF MS database was created and later challenged with a blinded test set of 146 yeast strains obtained from food and food related products. Ninety eight percent of the strains were correctly identified with log score values>1.7. One strain, Mrakia frigida, gained a correct identification with a score value<1.7. Two strains could not be identified at first as they represented a mix of two different species. These mixes were Rhodotorula babjevae with Meyerozyma caribbica and Clavispora lusitaniae with Debaryomyces hansenii. After separation, all four species could be correctly identified with scores>1.7. Ambiguous identifications were observed due to two incorrect reference mass spectra's found in the commercial database BDAL v.4.0, namely Candida sake DSM 70763 which was re-identified as Candida oleophila, and Candida inconspicua DSM 70631 which was re-identified as Pichia membranifaciens. MALDI-TOF MS can distinguish between most of the species, but for some species complexes, such as the Kazachstania telluris and Mrakia frigida complexes, MALDI-TOF MS showed limited resolution and identification of sibling species was sometimes problematic. Despite this, we showed that the MALDI-TOF MS is applicable for routine identification and validation of foodborne yeasts, but a further update of the commercial reference databases is needed. Copyright © 2017 Elsevier B.V. All rights reserved.

Bayesian Peptide Peak Detection for High Resolution TOF Mass Spectrometry.

PubMed

Zhang, Jianqiu; Zhou, Xiaobo; Wang, Honghui; Suffredini, Anthony; Zhang, Lin; Huang, Yufei; Wong, Stephen

2010-11-01

In this paper, we address the issue of peptide ion peak detection for high resolution time-of-flight (TOF) mass spectrometry (MS) data. A novel Bayesian peptide ion peak detection method is proposed for TOF data with resolution of 10 000-15 000 full width at half-maximum (FWHW). MS spectra exhibit distinct characteristics at this resolution, which are captured in a novel parametric model. Based on the proposed parametric model, a Bayesian peak detection algorithm based on Markov chain Monte Carlo (MCMC) sampling is developed. The proposed algorithm is tested on both simulated and real datasets. The results show a significant improvement in detection performance over a commonly employed method. The results also agree with expert's visual inspection. Moreover, better detection consistency is achieved across MS datasets from patients with identical pathological condition.

Quantification issues of trace metal contaminants on silicon wafers by means of TOF-SIMS, ICP-MS, and TXRF

NASA Astrophysics Data System (ADS)

Rostam-Khani, P.; Hopstaken, M. J. P.; Vullings, P.; Noij, G.; O'Halloran, O.; Claassen, W.

2004-06-01

Measurement of surface metal contamination on silicon wafers is essential for yield enhancement in IC manufacturing. Vapor phase decomposition coupled with either inductively coupled plasma mass spectrometry (VPD-ICP-MS), or total reflection X-ray fluorescence (VPD-TXRF), TXRF and more recently time of flight secondary ion mass spectrometry (TOF-SIMS) are used to monitor surface metal contamination. These techniques complement each other in their respective strengths and weaknesses. For reliable and accurate quantification, so-called relative sensitivity factors (RSF) are required for TOF-SIMS analysis. For quantification purposes in VPD, the collection efficiency (CE) is important to ensure complete collection of contamination. A standard procedure has been developed that combines the determination of these RSFs as well as the collection efficiency using all the analytical techniques mentioned above. Therefore, sample wafers were intentionally contaminated and analyzed (by TOF-SIMS) directly after preparation. After VPD-ICP-MS, several scanned surfaces were analyzed again by TOF-SIMS. Comparing the intensities of the specific metals before and after the VPD-DC procedure on the scanned surface allows the determination of so-called removing efficiency (RE). In general, very good agreement was obtained comparing the four analytical techniques after updating the RSFs for TOF-SIMS. Progress has been achieved concerning the CE evaluation as well as determining the RSFs more precisely for TOF-SIMS.

Establishing MALDI-TOF as Versatile Drug Discovery Readout to Dissect the PTP1B Enzymatic Reaction.

PubMed

Winter, Martin; Bretschneider, Tom; Kleiner, Carola; Ries, Robert; Hehn, Jörg P; Redemann, Norbert; Luippold, Andreas H; Bischoff, Daniel; Büttner, Frank H

2018-07-01

Label-free, mass spectrometric (MS) detection is an emerging technology in the field of drug discovery. Unbiased deciphering of enzymatic reactions is a proficient advantage over conventional label-based readouts suffering from compound interference and intricate generation of tailored signal mediators. Significant evolvements of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS, as well as associated liquid handling instrumentation, triggered extensive efforts in the drug discovery community to integrate the comprehensive MS readout into the high-throughput screening (HTS) portfolio. Providing speed, sensitivity, and accuracy comparable to those of conventional, label-based readouts, combined with merits of MS-based technologies, such as label-free parallelized measurement of multiple physiological components, emphasizes the advantages of MALDI-TOF for HTS approaches. Here we describe the assay development for the identification of protein tyrosine phosphatase 1B (PTP1B) inhibitors. In the context of this precious drug target, MALDI-TOF was integrated into the HTS environment and cross-compared with the well-established AlphaScreen technology. We demonstrate robust and accurate IC 50 determination with high accordance to data generated by AlphaScreen. Additionally, a tailored MALDI-TOF assay was developed to monitor compound-dependent, irreversible modification of the active cysteine of PTP1B. Overall, the presented data proves the promising perspective for the integration of MALDI-TOF into drug discovery campaigns.

A computational platform for MALDI-TOF mass spectrometry data: application to serum and plasma samples.

PubMed

Mantini, Dante; Petrucci, Francesca; Pieragostino, Damiana; Del Boccio, Piero; Sacchetta, Paolo; Candiano, Giovanni; Ghiggeri, Gian Marco; Lugaresi, Alessandra; Federici, Giorgio; Di Ilio, Carmine; Urbani, Andrea

2010-01-03

Mass spectrometry (MS) is becoming the gold standard for biomarker discovery. Several MS-based bioinformatics methods have been proposed for this application, but the divergence of the findings by different research groups on the same MS data suggests that the definition of a reliable method has not been achieved yet. In this work, we propose an integrated software platform, MASCAP, intended for comparative biomarker detection from MALDI-TOF MS data. MASCAP integrates denoising and feature extraction algorithms, which have already shown to provide consistent peaks across mass spectra; furthermore, it relies on statistical analysis and graphical tools to compare the results between groups. The effectiveness in mass spectrum processing is demonstrated using MALDI-TOF data, as well as SELDI-TOF data. The usefulness in detecting potential protein biomarkers is shown comparing MALDI-TOF mass spectra collected from serum and plasma samples belonging to the same clinical population. The analysis approach implemented in MASCAP may simplify biomarker detection, by assisting the recognition of proteomic expression signatures of the disease. A MATLAB implementation of the software and the data used for its validation are available at http://www.unich.it/proteomica/bioinf. (c) 2009 Elsevier B.V. All rights reserved.

[Applications of MALDI-TOF-MS in clinical microbiology laboratory].

PubMed

Carbonnelle, Etienne; Nassif, Xavier

2011-10-01

For twenty years, mass spectrometry (MS) has emerged as a particularly powerful tool for analysis and characterization of proteins in research. It is only recently that this technology, especially MALDI-TOF-MS (Matrix Assisted Laser Desorption Ionization Time-Of-Flight) has entered the field of routine microbiology. This method has proven to be reliable and safe for the identification of bacteria, yeasts, filamentous fungi and dermatophytes. MALDI-TOF-MS is a rapid, precise and cost-effective method for identification, compared to conventional phenotypic techniques or molecular biology. Its ability to analyse whole microorganisms with few sample preparation has greatly reduced the time to identification (1-2 min). Furthermore, this technology can be used to identify bacteria directly from clinical samples as blood culture bottles or urines. Future applications will be developed in order to provide direct information concerning virulence or resistance protein markers. © 2011 médecine/sciences – Inserm / SRMS.

Trends and new developments in gaseous detectors

NASA Astrophysics Data System (ADS)

Hoch, M.

Almost one century ago the method of particle detection with gaseous detectors was invented. Since then they have been exploited successfully in many experiments using a wide variety of different applications. The development is still going on today. The underlying working principles are today well understood and with the help of modern simulation techniques, new configurations can be easily examined and optimized before a first experimental test. Traditional wire chamber ensembles demonstrate that they are still up to date and are well prepared to meet also the challenges of LHC. Applications will be discussed using TPCs in high multiplicity environments with standard Multi-Wire Proportional Chamber (MWPC) as readout as well as drift tubes in a muon spectrometer for a Large Hardron Collider (LHC) experiment. Triggered by the evolving printed circuit technology, a new generation of gaseous detectors with very high position resolution and rate capability has emerged. Two representatives (MICROMEGAS, GEM) have proved their reliability in various experiments and are promising candidates for future projects. Performance and results will be discussed for these detectors. Furthermore, achievements in RPC-based detectors will be discussed. The standard Trigger RPC is a reliable low-cost semi-industrial manufactured device with good time resolution. Thin gap RPCs (Multigap-, and High Rate Timing RPC) show very fast signal response at high efficiency and significantly increased rate capability and will be applied in TOF detectors.

Rapid and reliable MALDI-TOF mass spectrometry identification of Candida non-albicans isolates from bloodstream infections.

PubMed

Pulcrano, Giovanna; Iula, Dora Vita; Vollaro, Antonio; Tucci, Alessandra; Cerullo, Monica; Esposito, Matilde; Rossano, Fabio; Catania, Maria Rosaria

2013-09-01

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) fingerprinting has recently become an effective instrument for rapid microbiological diagnostics and in particular for identification of micro-organisms directly in a positive blood culture. The aim of the study was to evaluate a collection of 82 stored yeast isolates from bloodstream infection, by MALDI-TOF MS; 21 isolates were identified also directly from positive blood cultures and in the presence of other co-infecting micro-organisms. Of the 82 isolates grown on plates, 64 (76%) were correctly identified by the Vitek II system and 82 (100%) by MALDI-TOF MS; when the two methods gave different results, the isolate was identified by PCR. MALDI-TOF MS was unreliable in identifying two isolates (Candida glabrata and Candida parapsilosis) directly from blood culture; however, direct analysis from positive blood culture samples was fast and effective for the identification of yeast, which is of great importance for early and adequate treatment. © 2013. Published by Elsevier B.V. All rights reserved.

Development of capacitive multiplexing circuit for SiPM-based time-of-flight (TOF) PET detector

NASA Astrophysics Data System (ADS)

Choe, Hyeok-Jun; Choi, Yong; Hu, Wei; Yan, Jianhua; Jung, Jin Ho

2017-04-01

There has been great interest in developing a time-of-flight (TOF) PET to improve the signal-to-noise ratio of PET image relative to that of non-TOF PET. Silicon photomultiplier (SiPM) arrays have attracted attention for use as a fast TOF PET photosensor. Since numerous SiPM arrays are needed to construct a modern human PET, a multiplexing method providing both good timing performance and high channel reduction capability is required to develop a SiPM-based TOF PET. The purpose of this study was to develop a capacitive multiplexing circuit for the SiPM-based TOF PET. The proposed multiplexing circuit was evaluated by measuring the coincidence resolving time (CRT) and the energy resolution as a function of the overvoltage using three different capacitor values of 15, 30, and 51 pF. A flood histogram was also obtained and quantitatively assessed. Experiments were performed using a 4× 4 array of 3× 3 mm2 SiPMs. Regarding the capacitor values, the multiplexing circuit using a smaller capacitor value showed the best timing performance. On the other hand, the energy resolution and flood histogram quality of the multiplexing circuit deteriorated as the capacitor value became smaller. The proposed circuit was able to achieve a CRT of 260+/- 4 ps FWHM and an energy resolution of 17.1 % with a pair of 2× 2× 20 mm3 LYSO crystals using a capacitor value of 30 pF at an overvoltage of 3.0 V. It was also possible to clearly resolve a 6× 6 array of LYSO crystals in the flood histogram using the multiplexing circuit. The experiment results indicate that the proposed capacitive multiplexing circuit is useful to obtain an excellent timing performance and a crystal-resolving capability in the flood histogram with a minimal degradation of the energy resolution, as well as to reduce the number of the readout channels of the SiPM-based TOF PET detector.

[EXPRESS IDENTIFICATION OF POSITIVE BLOOD CULTURES USING DIRECT MALDI-TOF MASS SPECTROMETRY].

PubMed

Popov, D A; Ovseenko, S T; Vostrikova, T Yu

2015-01-01

To evaluate the effectiveness of direct identification of pathogens of bacteremia by direct matrix assisted laser desorption ionization time-flight mass spectrometry (mALDI-TOF) compared to routine method. A prospective study included 211 positive blood cultures obtained from 116 patients (106 adults and 10 children, aged from 2 weeks to 77 years old in the ICU after open heart surgery. Incubation was carried out under aerobic vials with a sorbent for antibiotics Analyzer BacT/ALERT 3D 120 (bioMerieux, France) in parallel with the primary sieving blood cultures on solid nutrient media with subsequent identification of pure cultures using MALDI-TOF mass spectrometry analyzer Vitek MS, bioMerieux, France routine method), after appropriate sample preparation we carried out a direct (without screening) MALDI-TOF mass spectrometric study of monocomponental blood cultures (n = 201). using a routine method in 211 positive blood cultures we identified 23 types of microorganisms (Staphylococcus (n = 87), Enterobacteria- ceae (n = 71), Enterococci (n = 20), non-fermentative Gram-negative bacteria (n = 18), others (n = 5). The average time of incubation of samples to obtain a signal of a blood culture growth was 16.2 ± 7.4 h (from 3.75 to 51 hours.) During the first 12 hours of incubation, growth was obtained in 32.4% of the samples, and on the first day in 92.2%. In the direct mass spectrometric analysis mnonocomponental blood cultures (n = 201) is well defined up to 153 species of the sample (76.1%), while the share of successful identification of Gram-negative bacteria was higher than that of Gram-positive (85.4 and 69, 1%, respectively p = 0.01). The high degree of consistency in the results of standard and direct method of identifying blood cultures using MALDI-TOF mass spectrometry (κ = 0.96, p < 0.001; the samples included in the calculation for which both option given result). Duration of the direct mass spectrometric analysis, including sample preparation, was no

MALDI-TOF mass spectrometry as a potential tool for Trichomonas vaginalis identification.

PubMed

Calderaro, Adriana; Piergianni, Maddalena; Montecchini, Sara; Buttrini, Mirko; Piccolo, Giovanna; Rossi, Sabina; Arcangeletti, Maria Cristina; Medici, Maria Cristina; Chezzi, Carlo; De Conto, Flora

2016-06-10

Trichomonas vaginalis is a flagellated protozoan causing trichomoniasis, a sexually transmitted human infection, with around 276.4 million new cases estimated by World Health Organization. Culture is the gold standard method for the diagnosis of T. vaginalis infection. Recently, immunochromatographic assays as well as PCR assays for the detection of T. vaginalis antigen or DNA, respectively, have been also available. Although the well-known genome sequence of T. vaginalis has made possible the application of proteomic studies, few data are available about the overall proteomic expression profiling of T. vaginalis. The aim of this study was to investigate the potential application of MALDI-TOF MS as a new tool for the identification of T. vaginalis. Twenty-one isolates were analysed by MALDI-TOF MS after the creation of a Main Spectrum Profile (MSP) from a T. vaginalis reference strain (G3) and its subsequent supplementation in the Bruker Daltonics database, not including any profile of protozoa. This was achieved after the development of a new identification method created by modifying the range setting (6-10 kDa) for the MALDI-TOF MS analysis in order to exclude the overlapping of peaks derived from the culture media used in this study. Two MSP reference spectra were created in 2 different range: 3-15 kDa (standard range setting) and 6-10 kDa (new range setting). Both MSP spectra were deposited in the MALDI BioTyper database for further identification of additional T. vaginalis strains. All the 21 strains analysed in this study were correctly identified by using the new identification method. In this study it was demonstrated that changes in the MALDI-TOF MS standard parameters usually used to identify bacteria and fungi allowed the identification of the protozoan T. vaginalis. This study shows the usefulness of MALDI-TOF MS in the reliable identification of microorganism grown on complex liquid media such as the protozoan T. vaginalis, on the basis of the

Sequencing RNA by a combination of exonuclease digestion and uridine specific chemical cleavage using MALDI-TOF.

PubMed Central

Tolson, D A; Nicholson, N H

1998-01-01

The determination of DNA sequences by partial exonuclease digestion followed by Matrix-Assisted Laser Desorption Time of Flight Mass Spectrometry (MALDI-TOF) is a well established method. When the same procedure is applied to RNA, difficulties arise due to the small (1 Da) mass difference between the nucleotides U and C, which makes unambiguous assignment difficult using a MALDI-TOF instrument. Here we report our experiences with sequence specific endonucleases and chemical methods followed by MALDI-TOF to resolve these sequence ambiguities. We have found chemical methods superior to endonucleases both in terms of correct specificity and extent of sequence coverage. This methodology can be used in combination with exonuclease digestion to rapidly assign RNA sequences. PMID:9421498

Rapid and accurate bacterial identification in probiotics and yoghurts by MALDI-TOF mass spectrometry.

PubMed

Angelakis, Emmanouil; Million, Matthieu; Henry, Mireille; Raoult, Didier

2011-10-01

Probiotic food is manufactured by adding probiotic strains simultaneously with starter cultures in fermentation tanks. Here, we investigate the accuracy and feasibility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for bacterial identification at the species level in probiotic food and yoghurts. Probiotic food and yoghurts were cultured in Columbia and Lactobacillus specific agar and tested by quantitative real-time PCR (qPCR) for the detection and quantification of Lactobacillus sp. Bacterial identification was performed by MALDI-TOF analysis and by amplification and sequencing of tuf and 16S rDNA genes. We tested 13 probiotic food and yoghurts and we identified by qPCR that they presented 10(6) to 10(7) copies of Lactobacillus spp. DNA/g. All products contained very large numbers of living bacteria varying from 10(6) to 10(9) colony forming units/g. These bacteria were identified as Lactobacillus casei, Lactococcus lactis, Bifidobacterium animalis, Lactobacillus delbrueckii, and Streptococcus thermophilus. MALDI-TOF MS presented 92% specificity compared to the molecular assays. In one product we found L. lactis, instead of Bifidus spp. which was mentioned on the label and for another L. delbrueckii and S. thermophilus instead of Bifidus spp. MALDI-TOF MS allows a rapid and accurate bacterial identification at the species level in probiotic food and yoghurts. Although the safety and functionality of probiotics are species and strain dependent, we found a discrepancy between the bacterial strain announced on the label and the strain identified. Practical Application:  MALDI-TOF MS is rapid and specific for the identification of bacteria in probiotic food and yoghurts. Although the safety and functionality of probiotics are species and strain dependent, we found a discrepancy between the bacterial strain announced on the label and the strain identified. © 2011 Institute of Food Technologists®

Drug screening in medical examiner casework by high-resolution mass spectrometry (UPLC-MSE-TOF).

PubMed

Rosano, Thomas G; Wood, Michelle; Ihenetu, Kenneth; Swift, Thomas A

2013-10-01

Postmortem drug findings yield important analytical evidence in medical examiner casework, and chromatography coupled with nominal mass spectrometry (MS) serves as the predominant general unknown screening approach. We report screening by ultra performance liquid chromatography (UPLC) coupled with hybrid quadrupole time-of-flight mass spectrometer (MS(E)-TOF), with comparison to previously validated nominal mass UPLC-MS and UPLC-MS-MS methods. UPLC-MS(E)-TOF screening for over 950 toxicologically relevant drugs and metabolites was performed in a full-spectrum (m/z 50-1,000) mode using an MS(E) acquisition of both molecular and fragment ion data at low (6 eV) and ramped (10-40 eV) collision energies. Mass error averaged 1.27 ppm for a large panel of reference drugs and metabolites. The limit of detection by UPLC-MS(E)-TOF ranges from 0.5 to 100 ng/mL and compares closely with UPLC-MS-MS. The influence of column recovery and matrix effect on the limit of detection was demonstrated with ion suppression by matrix components correlating closely with early and late eluting reference analytes. Drug and metabolite findings by UPLC-MS(E)-TOF were compared with UPLC-MS and UPLC-MS-MS analyses of postmortem blood in 300 medical examiner cases. Positive findings by all methods totaled 1,528, with a detection rate of 57% by UPLC-MS, 72% by UPLC-MS-MS and 80% by combined UPLC-MS and UPLC-MS-MS screening. Compared with nominal mass screening methods, UPLC-MS(E)-TOF screening resulted in a 99% detection rate and, in addition, offered the potential for the detection of nontargeted analytes via high-resolution acquisition of molecular and fragment ion data.

Visualization of water transport into soybean nodules by Tof-SIMS cryo system.

PubMed

Iijima, Morio; Watanabe, Toshimasa; Yoshida, Tomoharu; Kawasaki, Michio; Kato, Toshiyuki; Yamane, Koji

2015-04-15

This paper examined the route of water supply into soybean nodules through the new visualization technique of time of flight secondary ion mass spectrometry (Tof-SIMS) cryo system, and obtained circumstantial evidence for the water inflow route. The maximum resolution of the Tof-SIMS imaging used by this study was 1.8 μm (defined as the three pixel step length), which allowed us to detect water movement at the cellular level. Deuterium-labeled water was supplied to soybean plants for 4h and the presence of deuterium in soybean nodules was analyzed by the Tof-SIMS cryo system. Deuterium ions were found only in the endodermis tissue surrounding the central cylinder in soybean nodules. Neither xylem vessels nor phloem complex itself did not indicate any deuterium accumulation. Deuterium-ion counts in the endodermis tissue were not changed by girdling treatment, which restricted water movement through the phloem complex. The results strongly indicated that nodule tissues did not receive water directly from the phloem complex, but received water through root cortex apoplastic pathway from the root axis. Copyright © 2015 Elsevier GmbH. All rights reserved.

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis.

PubMed

Singhal, Neelja; Kumar, Manish; Kanaujia, Pawan K; Virdi, Jugsharan S

2015-01-01

Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi.

Bayesian Peptide Peak Detection for High Resolution TOF Mass Spectrometry

PubMed Central

Zhang, Jianqiu; Zhou, Xiaobo; Wang, Honghui; Suffredini, Anthony; Zhang, Lin; Huang, Yufei; Wong, Stephen

2011-01-01

In this paper, we address the issue of peptide ion peak detection for high resolution time-of-flight (TOF) mass spectrometry (MS) data. A novel Bayesian peptide ion peak detection method is proposed for TOF data with resolution of 10 000–15 000 full width at half-maximum (FWHW). MS spectra exhibit distinct characteristics at this resolution, which are captured in a novel parametric model. Based on the proposed parametric model, a Bayesian peak detection algorithm based on Markov chain Monte Carlo (MCMC) sampling is developed. The proposed algorithm is tested on both simulated and real datasets. The results show a significant improvement in detection performance over a commonly employed method. The results also agree with expert’s visual inspection. Moreover, better detection consistency is achieved across MS datasets from patients with identical pathological condition. PMID:21544266

Application of targeted quantitative proteomics analysis in human cerebrospinal fluid using a liquid chromatography matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (LC MALDI TOF/TOF) platform.

PubMed

Pan, Sheng; Rush, John; Peskind, Elaine R; Galasko, Douglas; Chung, Kathryn; Quinn, Joseph; Jankovic, Joseph; Leverenz, James B; Zabetian, Cyrus; Pan, Catherine; Wang, Yan; Oh, Jung Hun; Gao, Jean; Zhang, Jianpeng; Montine, Thomas; Zhang, Jing

2008-02-01

Targeted quantitative proteomics by mass spectrometry aims to selectively detect one or a panel of peptides/proteins in a complex sample and is particularly appealing for novel biomarker verification/validation because it does not require specific antibodies. Here, we demonstrated the application of targeted quantitative proteomics in searching, identifying, and quantifying selected peptides in human cerebrospinal spinal fluid (CSF) using a matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometer (MALDI TOF/TOF)-based platform. The approach involved two major components: the use of isotopic-labeled synthetic peptides as references for targeted identification and quantification and a highly selective mass spectrometric analysis based on the unique characteristics of the MALDI instrument. The platform provides high confidence for targeted peptide detection in a complex system and can potentially be developed into a high-throughput system. Using the liquid chromatography (LC) MALDI TOF/TOF platform and the complementary identification strategy, we were able to selectively identify and quantify a panel of targeted peptides in the whole proteome of CSF without prior depletion of abundant proteins. The effectiveness and robustness of the approach associated with different sample complexity, sample preparation strategies, as well as mass spectrometric quantification were evaluated. Other issues related to chromatography separation and the feasibility for high-throughput analysis were also discussed. Finally, we applied targeted quantitative proteomics to analyze a subset of previously identified candidate markers in CSF samples of patients with Parkinson's disease (PD) at different stages and Alzheimer's disease (AD) along with normal controls.

MALDI-TOF mass spectrometry for differentiation between Streptococcus pneumoniae and Streptococcus pseudopneumoniae.

PubMed

van Prehn, Joffrey; van Veen, Suzanne Q; Schelfaut, Jacqueline J G; Wessels, Els

2016-05-01

We compared the Vitek MS and Microflex MALDI-TOF mass spectrometry platform for species differentiation within the Streptococcus mitis group with PCR assays targeted at lytA, Spn9802, and recA as reference standard. The Vitek MS correctly identified 10/11 Streptococcus pneumoniae, 13/13 Streptococcus pseudopneumoniae, and 12/13 S. mitis/oralis. The Microflex correctly identified 9/11 S. pneumoniae, 0/13 S. pseudopneumoniae, and 13/13 S. mitis/oralis. MALDI-TOF is a powerful tool for species determination within the mitis group. Diagnostic accuracy varies depending on platform and database used. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for qualitative analysis of drugs.

PubMed

Pavlic, Marion; Libiseller, Kathrin; Oberacher, Herbert

2006-09-01

The potential of the combined use of ESI-QqTOF-MS and ESI-QqTOF-MS/MS with mass-spectral library search for the identification of therapeutic and illicit drugs has been evaluated. Reserpine was used for standardizing experimental conditions and for characterization of the performance of the applied mass spectrometric system. Experiments revealed that because of the mass accuracy, the stability of calibration, and the reproducibility of fragmentation, the QqTOF mass spectrometer is an appropriate platform for establishment of a tandem-mass-spectral library. Three-hundred and nineteen substances were used as reference samples to build the spectral library. For each reference compound, product-ion spectra were acquired at ten different collision-energy values between 5 eV and 50 eV. For identification of unknown compounds, a library search algorithm was developed. The closeness of matching between a measured product-ion spectrum and a spectrum stored in the library was characterized by a value called "match probability", which took into account the number of matched fragment ions, the number of fragment ions observed in the two spectra, and the sum of the intensity differences calculated for matching fragments. A large value for the match probability indicated a close match between the measured and the reference spectrum. A unique feature of the library search algorithm-an implemented spectral purification option-enables characterization of multi-contributor fragment-ion spectra. With the aid of this software feature, substances comprising only 1.0% of the total amount of binary mixtures were unequivocally assigned, in addition to the isobaric main contributors. The spectral library was successfully applied to the characterization of 39 forensic casework samples.

Identification and differentiation of food-related bacteria: A comparison of FTIR spectroscopy and MALDI-TOF mass spectrometry.

PubMed

Wenning, Mareike; Breitenwieser, Franziska; Konrad, Regina; Huber, Ingrid; Busch, Ulrich; Scherer, Siegfried

2014-08-01

The food industry requires easy, accurate, and cost-effective techniques for microbial identification to ensure safe products and identify microbial contaminations. In this work, FTIR spectroscopy and MALDI-TOF mass spectrometry were assessed for their suitability and applicability for routine microbial diagnostics of food-related microorganisms by analyzing their robustness according to changes in incubation time and medium, identification accuracy and their ability to differentiate isolates down to the strain level. Changes in the protocol lead to a significantly impaired performance of FTIR spectroscopy, whereas they had only little effects on MALDI-TOF MS. Identification accuracy was tested using 174 food-related bacteria (93 species) from an in-house strain collection and 40 fresh isolates from routine food analyses. For MALDI-TOF MS, weaknesses in the identification of bacilli and pseudomonads were observed; FTIR spectroscopy had most difficulties in identifying pseudomonads and enterobacteria. In general, MALDI-TOF MS obtained better results (52-85% correct at species level), since the analysis of mainly ribosomal proteins is more robust and seems to be more reliable. FTIR spectroscopy suffers from the fact that it generates a whole-cell fingerprint and intraspecies diversity may lead to overlapping species borders which complicates identification. In the present study values between 56% and 67% correct species identification were obtained. On the opposite, this high sensitivity offers the opportunity of typing below the species level which was not possible using MALDI-TOF MS. Using fresh isolates from routine diagnostics, both techniques performed well with 88% (MALDI-TOF) and 75% (FTIR) correct identifications at species level, respectively. Copyright © 2014 Elsevier B.V. All rights reserved.

Screening natural antioxidants in peanut shell using DPPH-HPLC-DAD-TOF/MS methods.

PubMed

Qiu, Jiying; Chen, Leilei; Zhu, Qingjun; Wang, Daijie; Wang, Wenliang; Sun, Xin; Liu, Xiaoyong; Du, Fangling

2012-12-15

Peanut shell, a byproduct in oil production, is rich in natural antioxidants. Here, a rapid and efficient method using DPPH-HPLC-DAD-TOF/MS was used for the first time to screen antioxidants in peanut shell. The method is based on the hypothesis that upon reaction with 1, 1-diphenyl-2-picrylhydrazyl (DPPH), the peak areas of compounds with potential antioxidant activities in the HPLC chromatogram will be significantly reduced or disappeared, and the identity confirmation could be achieved by HPLC-DAD-TOF/MS technique. With this method, three compounds possessing potential antioxidant activities were found abundantly in the methanolic extract of peanut shell. They were identified as 5,7-dihydroxychromone, eriodictyol, and luteolin. The contents of these compounds were 0.59, 0.92, and 2.36 mg/g, respectively, and luteolin possessed the strongest radical scavenging capacity. DPPH-HPLC-DAD-TOF/MS assay facilitated rapid identification and determination of natural antioxidants in peanut shell, which may be helpful for value-added utilization of peanut processing byproducts. Copyright © 2012 Elsevier Ltd. All rights reserved.

[Evaluation of mass spectrometry: MALDI-TOF MS for fast and reliable yeast identification].

PubMed

Relloso, María S; Nievas, Jimena; Fares Taie, Santiago; Farquharson, Victoria; Mujica, María T; Romano, Vanesa; Zarate, Mariela S; Smayevsky, Jorgelina

2015-01-01

The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technique known as MALDI-TOF MS is a tool used for the identification of clinical pathogens by generating a protein spectrum that is unique for a given species. In this study we assessed the identification of clinical yeast isolates by MALDI-TOF MS in a university hospital from Argentina and compared two procedures for protein extraction: a rapid method and a procedure based on the manufacturer's recommendations. A short protein extraction procedure was applied in 100 isolates and the rate of correct identification at genus and species level was 98.0%. In addition, we analyzed 201 isolates, previously identified by conventional methods, using the methodology recommended by the manufacturer and there was 95.38% coincidence in the identification at species level. MALDI TOF MS showed to be a fast, simple and reliable tool for yeast identification. Copyright © 2014 Asociación Argentina de Microbiología. Publicado por Elsevier España, S.L.U. All rights reserved.

MALDI-TOF Mass Spectrometry: A Powerful Tool for Clinical Microbiology at Hôpital Principal de Dakar, Senegal (West Africa)

PubMed Central

Lo, Cheikh I.; Fall, Bécaye; Sambe-Ba, Bissoume; Diawara, Silman; Gueye, Mamadou W.; Mediannikov, Oleg; Sokhna, Cheikh; Faye, Ngor; Diemé, Yaya; Wade, Boubacar; Raoult, Didier; Fenollar, Florence

2015-01-01

Our team in Europe has developed the routine clinical laboratory identification of microorganisms by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS). To evaluate the utility of MALDI-TOF MS in tropical Africa in collaboration with local teams, we installed an apparatus in the Hôpital Principal de Dakar (Senegal), performed routine identification of isolates, and confirmed or completed their identification in France. In the case of discordance or a lack of identification, molecular biology was performed. Overall, 153/191 (80.1%) and 174/191 (91.1%) isolates yielded an accurate and concordant identification for the species and genus, respectively, with the 2 different MALDI-TOF MSs in Dakar and Marseille. The 10 most common bacteria, representing 94.2% of all bacteria routinely identified in the laboratory in Dakar (Escherichia coli, Klebsiella pneumoniae, Streptococcus agalactiae, Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus haemolyticus, Enterobacter cloacae, Enterococcus faecalis, and Staphylococcus epidermidis) were accurately identified with the MALDI-TOF MS in Dakar. The most frequent misidentification in Dakar was at the species level for Achromobacter xylosoxidans, which was inaccurately identified as Achromobacter denitrificans, and the bacteria absent from the database, such as Exiguobacterium aurientacum or Kytococcus schroeteri, could not be identified. A few difficulties were observed with MALDI-TOF MS for Bacillus sp. or oral streptococci. 16S rRNA sequencing identified a novel bacterium, “Necropsobacter massiliensis.” The robust identification of microorganisms by MALDI-TOF MS in Dakar and Marseille demonstrates that MALDI-TOF MS can be used as a first-line tool in clinical microbiology laboratories in tropical countries. PMID:26716681

The origin and reduction of spurious extrahepatic counts observed in 90Y non-TOF PET imaging post radioembolization

NASA Astrophysics Data System (ADS)

Walrand, Stephan; Hesse, Michel; Jamar, François; Lhommel, Renaud

2018-04-01

Our literature survey revealed a physical effect unknown to the nuclear medicine community, i.e. internal bremsstrahlung emission, and also the existence of long energy resolution tails in crystal scintillation. None of these effects has ever been modelled in PET Monte Carlo (MC) simulations. This study investigates whether these two effects could be at the origin of two unexplained observations in 90Y imaging by PET: the increasing tails in the radial profile of true coincidences, and the presence of spurious extrahepatic counts post radioembolization in non-TOF PET and their absence in TOF PET. These spurious extrahepatic counts hamper the microsphere delivery check in liver radioembolization. An acquisition of a 32P vial was performed on a GSO PET system. This is the ideal setup to study the impact of bremsstrahlung x-rays on the true coincidence rate when no positron emission and no crystal radioactivity are present. A MC simulation of the acquisition was performed using Gate-Geant4. MC simulations of non-TOF PET and TOF-PET imaging of a synthetic 90Y human liver radioembolization phantom were also performed. Internal bremsstrahlung and long energy resolution tails inclusion in MC simulations quantitatively predict the increasing tails in the radial profile. In addition, internal bremsstrahlung explains the discrepancy previously observed in bremsstrahlung SPECT between the measure of the 90Y bremsstrahlung spectrum and its simulation with Gate-Geant4. However the spurious extrahepatic counts in non-TOF PET mainly result from the failure of conventional random correction methods in such low count rate studies and poor robustness versus emission-transmission inconsistency. A novel proposed random correction method succeeds in cleaning the spurious extrahepatic counts in non-TOF PET. Two physical effects not considered up to now in nuclear medicine were identified to be at the origin of the unusual 90Y true coincidences radial profile. TOF reconstruction removing

Characterization of Novel Fusaricidins Produced by Paenibacillus polymyxa-M1 Using MALDI-TOF Mass Spectrometry

NASA Astrophysics Data System (ADS)

Vater, Joachim; Niu, Ben; Dietel, Kristin; Borriss, Rainer

2015-09-01

Paenibacillus polymyxa-M1 is a potent producer of bioactive compounds, such as lipopeptides, polyketides, and lantibiotics of biotechnological and medical interest. Genome sequencing revealed nine gene clusters for nonribosomal biosynthesis of such agents. Here we report on the investigation of the fusaricidins, a complex of cyclic lipopeptides containing 15-guanidino-3-hydroxypentadecanoic acid (GHPD) as fatty acid component by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). More than 20 variants of these compounds were detected and characterized in detail. Mass spectrometric sequence analysis was performed by MALDI-LIFT-TOF/TOF fragment analysis. The obtained product ion spectra show a specific processing in the fatty acid part. GHPD is cleaved between the α- and ß-position yielding two fragments a and b, one bearing the end-standing guanidine group and another one comprising the residual two C-atoms of GHPD with the attached peptide moiety. The complete sequence of all fusaricidins was derived from sets of bn- and yn-ions. The fusaricidin complex can be divided into four lipopeptide families, three of them showing variations of the amino acid in position 3, Val or Ile for the first and Tyr or Phe for families 2 and 3, respectively. A collection of novel fusaricidins was detected differing from those of families 1-3 by an additional residue of 71 Da (family 4). LIFT-TOF/TOF fragment spectra of these species imply that in their peptide moiety, an Ala-residue is attached by an ester bond to the free hydroxyl group of Thr4. More than 10 novel fusaricidins were characterized mass spectrometrically.

Whole-cell MALDI-TOF MS: a new tool to assess the multifaceted activation of macrophages.

PubMed

Ouedraogo, Richard; Daumas, Aurélie; Ghigo, Eric; Capo, Christian; Mege, Jean-Louis; Textoris, Julien

2012-10-22

Whole-cell MALDI-TOF MS is routinely used to identify bacterial species in clinical samples. This technique has also proven to allow identification of intact mammalian cells, including macrophages. Here, we wondered whether this approach enabled the assessment human macrophages plasticity. The whole-cell MALDI-TOF spectra of macrophages stimulated with IFN-γ and IL-4, two inducers of M1 and M2 macrophage polarisation, consisted of peaks ranging from 2 to 12 kDa. The spectra of unstimulated and stimulated macrophages were clearly different. The fingerprints induced by the M1 agonists, IFN-γ, TNF, LPS and LPS+IFN-γ, and the M2 agonists, IL-4, TGF-β1 and IL-10, were specific and readily identifiable. Thus, whole-cell MALDI-TOF MS was able to characterise M1 and M2 macrophage subtypes. In addition, the fingerprints induced by extracellular (group B Streptococcus, Staphylococcus aureus) or intracellular (BCG, Orientia tsutsugamushi, Coxiella burnetii) bacteria were bacterium-specific. The whole-cell MALDI-TOF MS fingerprints therefore revealed the multifaceted activation of human macrophages. This approach opened a new avenue of studies to assess the immune response in the clinical setting, by monitoring the various activation patterns of immune cells in pathological conditions. Copyright © 2012 Elsevier B.V. All rights reserved.

Cerebral TOF Angiography at 7T: Impact of B1+ Shimming with a 16-Channel Transceiver Array

PubMed Central

Schmitter, Sebastian; Wu, Xiaoping; Adriany, Gregor; Auerbach, Edward J.; Uğurbil, Kâmil; Van de Moortele, Pierre-François

2014-01-01

Purpose Time-of-flight (TOF) MR imaging is clinically among the most common cerebral non-contrast enhanced MR angiography techniques allowing for high spatial resolution. As shown by several groups TOF contrast significantly improves at ultra-high field (UHF) of B0=7T, however, spatially varying transmit B1 (B1+) fields at 7T reduce TOF contrast uniformity, typically resulting in sub-optimal contrast and reduced vessel conspicuity in the brain periphery. Methods Using a 16-channel B1+ shimming system we compare different dynamically applied B1+ phase shimming approaches on the RF excitation to improve contrast homogeneity for a (0.5 mm)3 resolution multi-slab TOF acquisition. In addition, B1+ shimming applied on the venous saturation pulse was investigated to improve venous suppression, subcutaneous fat signal reduction and enhanced background suppression originating from MT effect. Results B1+ excitation homogeneity was improved by a factor 2.2 to 2.6 on average depending on the shimming approach, compared to a standard CP-like phase setting, leading to improved vessel conspicuity particularly in the periphery. Stronger saturation, higher fat suppression and improved background suppression were observed when dynamically applying B1+ shimming on the venous saturation pulse. Conclusion B1+ shimming can significantly improve high resolution TOF vascular investigations at UHF, holding strong promise for non contrast-enhanced clinical applications. PMID:23640915

Validation of MALDI-TOF MS for rapid classification and identification of lactic acid bacteria, with a focus on isolates from traditional fermented foods in Northern Vietnam.

PubMed

Doan, N T L; Van Hoorde, K; Cnockaert, M; De Brandt, E; Aerts, M; Le Thanh, B; Vandamme, P

2012-10-01

To evaluate the potential use of MALDI-TOF MS for fast and reliable classification and identification of lactic acid bacteria (LAB) from traditional fermented foods. A total of 119 strains of LAB from fermented meat (nem chua) were analysed with both (GTG)(5)-PCR fingerprinting and MALDI-TOF MS. Cluster analysis of the profiles revealed five species represented by a single isolate both in (GTG)(5)-PCR and in MALDI-TOF MS; five species grouped alike for (GTG)(5)-PCR and for MALDI-TOF MS; however, differences in minimal similarity between the delineated (GTG)(5)-PCR and MALDI-TOF MS clusters could be observed; three species showed more heterogeneity in their MALDI-TOF MS profiles compared to their (GTG)(5)-PCR profiles; two species, each represented by a single MALDI-TOF cluster, were subdivided in the corresponding (GTG)(5)-PCR dendrogram. As proof of the identification potential of MALDI-TOF MS, LAB diversity from one fermented mustard sample was analysed using MALDI-TOF MS. PheS gene sequencing was used for validation. MALDI-TOF MS is a powerful, fast, reliable and cost-effective technique for the identification of LAB associated with the production of fermented foods. Food LAB can be identified using MALDI-TOF MS, and its application could possibly be extended to other food matrices and/or other food-derived micro-organisms. © 2012 The Authors. Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

A simple and effective method for detecting precipitated proteins in MALDI-TOF MS.

PubMed

Oshikane, Hiroyuki; Watabe, Masahiko; Nakaki, Toshio

2018-04-01

MALDI-TOF MS has developed rapidly into an essential analytical tool for the life sciences. Cinnamic acid derivatives are generally employed in routine molecular weight determinations of intact proteins using MALDI-TOF MS. However, a protein of interest may precipitate when mixed with matrix solution, perhaps preventing MS detection. We herein provide a simple approach to enable the MS detection of such precipitated protein species by means of a "direct deposition method" -- loading the precipitant directly onto the sample plate. It is thus expected to improve routine MS analysis of intact proteins. Copyright © 2018. Published by Elsevier Inc.

PTR-QMS versus PTR-TOF comparison in a region with oil and natural gas extraction industry in the Uintah Basin in 2013

NASA Astrophysics Data System (ADS)

Warneke, C.; Veres, P.; Murphy, S. M.; Soltis, J.; Field, R. A.; Graus, M. G.; Koss, A.; Li, S.-M.; Li, R.; Yuan, B.; Roberts, J. M.; de Gouw, J. A.

2015-01-01

Here we compare volatile organic compound (VOC) measurements using a standard proton-transfer-reaction quadrupole mass spectrometer (PTR-QMS) with a new proton-transfer-reaction time of flight mass spectrometer (PTR-TOF) during the Uintah Basin Winter Ozone Study 2013 (UBWOS2013) field experiment in an oil and gas field in the Uintah Basin, Utah. The PTR-QMS uses a quadrupole, which is a mass filter that lets one mass to charge ratio pass at a time, whereas the PTR-TOF uses a time of flight mass spectrometer, which takes full mass spectra with typical 0.1 s-1 min integrated acquisition times. The sensitivity of the PTR-QMS in units of counts per ppbv (parts per billion by volume) is about a factor of 10-35 times larger than the PTR-TOF, when only one VOC is measured. The sensitivity of the PTR-TOF is mass dependent because of the mass discrimination caused by the sampling duty cycle in the orthogonal-acceleration region of the TOF. For example, the PTR-QMS on mass 33 (methanol) is 35 times more sensitive than the PTR-TOF and for masses above 120 amu less than 10 times more. If more than 10-35 compounds are measured with PTR-QMS, the sampling time per ion decreases and the PTR-TOF has higher signals per unit measuring time for most masses. For UBWOS2013 the PTR-QMS measured 34 masses in 37 s and on that timescale the PTR-TOF is more sensitive for all masses. The high mass resolution of the TOF allows for the measurements of compounds that cannot be separately detected with the PTR-QMS, such as oxidation products from alkanes and cycloalkanes emitted by oil and gas extraction. PTR-TOF masses do not have to be preselected, allowing for identification of unanticipated compounds. The measured mixing ratios of the two instruments agreed very well (R2 ≥ 0.92 and within 20%) for all compounds and masses monitored with the PTR-QMS.

PTR-QMS vs. PTR-TOF comparison in a region with oil and natural gas extraction industry in the Uintah Basin in 2013

NASA Astrophysics Data System (ADS)

Warneke, C.; Veres, P. R.; Murphy, S. M.; Soltis, J.; Field, R. A.; Graus, M. G.; Koss, A.; Li, S.-M.; Li, R.; Yuan, B.; Roberts, J. M.; de Gouw, J. A.

2014-07-01

Here we compare volatile organic compound (VOC) measurements using a standard Proton-Transfer-Reaction Quadrupole Mass Spectrometer (PTR-QMS) with a new Proton-Transfer-Reaction Time Of Flight Mass Spectrometer (PTR-TOF) during the Uintah Basin Winter Ozone Study 2013 (UBWOS2013) field experiment in an oil and gas field in the Uintah Basin, Utah. The PTR-QMS uses a quadrupole, which is a mass filter that lets one mass pass at a time, whereas the PTR-TOF uses a Time Of Flight mass spectrometer, which takes full mass spectra with typical 0.1 s to 1 min integrated acquisition times. The sensitivity of the PTR-QMS in units of counts per ppbv is about a factor of 10-35 times larger than the PTR-TOF, when only one VOC is measured. The sensitivity of the PTR-TOF is mass dependent because of the mass discrimination caused by the sampling duty cycle in the orthogonal-acceleration region of the TOF. For example, the PTR-QMS on mass 33 (methanol) is 35 times more sensitive than the PTR-TOF and for masses above 120 amu less than 10 times more. If more than 10-35 compounds are measured with PTR-QMS, the sampling time per ion decreases and the PTR-TOF has higher signals per unit measuring time for most masses. For UBWOS2013 the PTR-QMS measured 34 masses in 37 s and on that time-scale the PTR-TOF is more sensitive for all masses. The high mass resolution of the TOF allows for the measurements of compounds that cannot be separately detected with the PTR-QMS, such as oxidation products from alkanes and cycloalkanes emitted by oil and gas extraction. PTR-TOF masses do not have to be pre-selected allowing for identification of unanticipated compounds. The measured mixing ratios of the two instruments agreed very well (R2 ≥ 0.92 and within 20%) for all compounds and masses monitored with the PTR-QMS.

The use of MALDI-TOF ICMS as an alternative tool for Trichophyton rubrum identification and typing.

PubMed

Pereira, Leonel; Dias, Nicolina; Santos, Cledir; Lima, Nelson

2014-01-01

In this study, the potential of matrix-assisted laser desorption/ionization time-of-flight intact cell mass spectrometry (MALDI-TOF ICMS) was investigated for the identification of clinical isolates. The isolates were analyzed at the species and strain level. Spectral identification by MALDI-TOF ICMS was performed for all strains, and compared with the results of sequencing of the internal transcribed spacers (ITS1 and ITS2), and the 5.8S rDNA region. PCR fingerprinting analysis using primers M13, (GACA)4, and (AC)10 was performed in order to assess the intra-specific variability of Trichophyton rubrum strains. The identification of strains at species level by MALDI-TOF ICMS was in agreement with the previously performed morphological and biochemical analysis. Sequence data confirmed spectral mass identification at species level. Intra-specific variability was assessed. Within the T. rubrum cluster, strains were distributed into smaller highly related sub-groups with a similarity values above 85%. MALDI-TOF ICMS was shown to be a rapid, low-cost and accurate alternative tool for the identification and strain typing of T. rubrum. Copyright © 2012 Elsevier España, S.L. All rights reserved.

MALDI-TOF MS identification of anaerobic bacteria: assessment of pre-analytical variables and specimen preparation techniques.

PubMed

Hsu, Yen-Michael S; Burnham, Carey-Ann D

2014-06-01

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a tool for identifying clinically relevant anaerobes. We evaluated the analytical performance characteristics of the Bruker Microflex with Biotyper 3.0 software system for identification of anaerobes and examined the impact of direct formic acid (FA) treatment and other pre-analytical factors on MALDI-TOF MS performance. A collection of 101 anaerobic bacteria were evaluated, including Clostridium spp., Propionibacterium spp., Fusobacterium spp., Bacteroides spp., and other anaerobic bacterial of clinical relevance. The results of our study indicate that an on-target extraction with 100% FA improves the rate of accurate identification without introducing misidentification (P<0.05). In addition, we modify the reporting cutoffs for the Biotyper "score" yielding acceptable identification. We found that a score of ≥1.700 can maximize the rate of identification. Of interest, MALDI-TOF MS can correctly identify anaerobes grown in suboptimal conditions, such as on selective culture media and following oxygen exposure. In conclusion, we report on a number of simple and cost-effective pre- and post-analytical modifications could enhance MALDI-TOF MS identification for anaerobic bacteria. Copyright © 2014 Elsevier Inc. All rights reserved.

Neutron cross-sections for next generation reactors: new data from n_TOF.

PubMed

Colonna, N; Abbondanno, U; Aerts, G; Alvarez, H; Alvarez-Velarde, F; Andriamonje, S; Andrzejewski, J; Assimakopoulos, P; Audouin, L; Badurek, G; Baumann, P; Becvar, F; Berthoumieux, E; Calviani, M; Calviño, F; Cano-Ott, D; Capote, R; de Albornoz, A Carrillo; Cennini, P; Chepel, V; Chiaveri, E; Cortes, G; Couture, A; Cox, J; Dahlfors, M; David, S; Dillman, I; Dolfini, R; Domingo-Pardo, C; Dridi, W; Duran, I; Eleftheriadis, C; Ferrant, L; Ferrari, A; Ferreira-Marques, R; Frais-Koelbl, H; Fujii, K; Furman, W; Goncalves, I; González-Romero, E; Goverdovski, A; Gramegna, F; Griesmayer, E; Guerrero, C; Gunsing, F; Haas, B; Haight, R; Heil, M; Herrera-Martinez, A; Igashira, M; Isaev, S; Jericha, E; Käppeler, F; Kadi, Y; Karadimos, D; Karamanis, D; Kerveno, M; Ketlerov, V; Koehler, P; Konovalov, V; Kossionides, E; Krticka, M; Lampoudis, C; Leeb, H; Lindote, A; Lopes, I; Lozano, M; Lukic, S; Marganiec, J; Marques, L; Marrone, S; Martínez, T; Massimi, C; Mastinu, P; Mengoni, A; Milazzo, P M; Moreau, C; Mosconi, M; Neves, F; Oberhummer, H; O'Brien, S; Oshima, M; Pancin, J; Papachristodoulou, C; Papadopoulos, C; Paradela, C; Patronis, N; Pavlik, A; Pavlopoulos, P; Perrot, L; Pigni, M T; Plag, R; Plompen, A; Plukis, A; Poch, A; Pretel, C; Quesada, J; Rauscher, T; Reifarth, R; Rosetti, M; Rubbia, C; Rudolf, G; Rullhusen, P; Salgado, J; Sarchiapone, L; Savvidis, I; Stephan, C; Tagliente, G; Tain, J L; Tassan-Got, L; Tavora, L; Terlizzi, R; Vannini, G; Vaz, P; Ventura, A; Villamarin, D; Vicente, M C; Vlachoudis, V; Vlastou, R; Voss, F; Walter, S; Wendler, H; Wiescher, M; Wisshak, K

2010-01-01

In 2002, an innovative neutron time-of-flight facility started operation at CERN: n_TOF. The main characteristics that make the new facility unique are the high instantaneous neutron flux, high resolution and wide energy range. Combined with state-of-the-art detectors and data acquisition system, these features have allowed to collect high accuracy neutron cross-section data on a variety of isotopes, many of which radioactive, of interest for Nuclear Astrophysics and for applications to advanced reactor technologies. A review of the most important results on capture and fission reactions obtained so far at n_TOF is presented, together with plans for new measurements related to nuclear industry. Copyright 2010 Elsevier Ltd. All rights reserved.

Bactec™ blood culture bottles allied to MALDI-TOF mass spectrometry: rapid etiologic diagnosis of bacterial endophthalmitis.

PubMed

Tanaka, Tatiana; Oliveira, Luiza Manhezi de Freitas; Ferreira, Bruno Fortaleza de Aquino; Kato, Juliana Mika; Rossi, Flavia; Correa, Karoline de Lemes Giuntini; Pimentel, Sergio Luis Gianotti; Yamamoto, Joyce Hisae; Almeida Junior, João Nóbrega

2017-07-01

Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has been used for direct identification of pathogens from blood-inoculated blood culture bottles (BCBs). We showed that MALDI-TOF MS is an useful technique for rapid identification of the causative agents of endophthalmitis from vitreous humor-inoculated BCBs with a simple protocol. Copyright © 2017 Elsevier Inc. All rights reserved.

Comparative analysis of Campylobacter isolates from wild birds and chickens using MALDI-TOF MS, biochemical testing, and DNA sequencing.

PubMed

Lawton, Samantha J; Weis, Allison M; Byrne, Barbara A; Fritz, Heather; Taff, Conor C; Townsend, Andrea K; Weimer, Bart C; Mete, Aslı; Wheeler, Sarah; Boyce, Walter M

2018-05-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) was compared to conventional biochemical testing methods and nucleic acid analyses (16S rDNA sequencing, hippurate hydrolysis gene testing, whole genome sequencing [WGS]) for species identification of Campylobacter isolates obtained from chickens ( Gallus gallus domesticus, n = 8), American crows ( Corvus brachyrhynchos, n = 17), a mallard duck ( Anas platyrhynchos, n = 1), and a western scrub-jay ( Aphelocoma californica, n = 1). The test results for all 27 isolates were in 100% agreement between MALDI-TOF MS, the combined results of 16S rDNA sequencing, and the hippurate hydrolysis gene PCR ( p = 0.0027, kappa = 1). Likewise, the identifications derived from WGS from a subset of 14 isolates were in 100% agreement with the MALDI-TOF MS identification. In contrast, biochemical testing misclassified 5 isolates of C. jejuni as C. coli, and 16S rDNA sequencing alone was not able to differentiate between C. coli and C. jejuni for 11 sequences ( p = 0.1573, kappa = 0.0857) when compared to MALDI-TOF MS and WGS. No agreement was observed between MALDI-TOF MS dendrograms and the phylogenetic relationships revealed by rDNA sequencing or WGS. Our results confirm that MALDI-TOF MS is a fast and reliable method for identifying Campylobacter isolates to the species level from wild birds and chickens, but not for elucidating phylogenetic relationships among Campylobacter isolates.

A multiplexed TOF and DOI capable PET detector using a binary position sensitive network.

PubMed

Bieniosek, M F; Cates, J W; Levin, C S

2016-11-07

Time of flight (TOF) and depth of interaction (DOI) capabilities can significantly enhance the quality and uniformity of positron emission tomography (PET) images. Many proposed TOF/DOI PET detectors require complex readout systems using additional photosensors, active cooling, or waveform sampling. This work describes a high performance, low complexity, room temperature TOF/DOI PET module. The module uses multiplexed timing channels to significantly reduce the electronic readout complexity of the PET detector while maintaining excellent timing, energy, and position resolution. DOI was determined using a two layer light sharing scintillation crystal array with a novel binary position sensitive network. A 20 mm effective thickness LYSO crystal array with four 3 mm  ×  3 mm silicon photomultipliers (SiPM) read out by a single timing channel, one energy channel and two position channels achieved a full width half maximum (FWHM) coincidence time resolution of 180  ±  2 ps with 10 mm of DOI resolution and 11% energy resolution. With sixteen 3 mm  ×  3 mm SiPMs read out by a single timing channel, one energy channel and four position channels a coincidence time resolution 204  ±  1 ps was achieved with 10 mm of DOI resolution and 15% energy resolution. The methods presented here could significantly simplify the construction of high performance TOF/DOI PET detectors.

MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis

PubMed Central

Singhal, Neelja; Kumar, Manish; Kanaujia, Pawan K.; Virdi, Jugsharan S.

2015-01-01

Currently microorganisms are best identified using 16S rRNA and 18S rRNA gene sequencing. However, in recent years matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a potential tool for microbial identification and diagnosis. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. The technology has been readily imbibed by microbiologists who have reported usage of MALDI-TOF MS for a number of purposes like, microbial identification and strain typing, epidemiological studies, detection of biological warfare agents, detection of water- and food-borne pathogens, detection of antibiotic resistance and detection of blood and urinary tract pathogens etc. The limitation of the technology is that identification of new isolates is possible only if the spectral database contains peptide mass fingerprints of the type strains of specific genera/species/subspecies/strains. This review provides an overview of the status and recent applications of mass spectrometry for microbial identification. It also explores the usefulness of this exciting new technology for diagnosis of diseases caused by bacteria, viruses, and fungi. PMID:26300860

A CD45-based barcoding approach to multiplex mass-cytometry (CyTOF).

PubMed

Lai, Liyun; Ong, Raymond; Li, Juntao; Albani, Salvatore

2015-04-01

CyTOF enables the study of the immune system with a complexity, depth, and multidimensionality never achieved before. However, the full potential of using CyTOF can be limited by scarce cell samples. Barcoding strategies developed based on direct labeling of cells using maleimido-monoamide-DOTA (m-DOTA) provide a very useful tool. However, using m-DOTA has some inherent problems, mainly associated with signal intensity. This may be a source of uncertainty when samples are multiplexed. As an alternative or complementary approach to m-DOTA, conjugating an antibody, specific for a membrane protein present on most immune cells, with different isotopes could address the issues of stability and signal intensity needed for effective barcoding. We chose for this purpose CD45, and designed experiments to address different types of cultures and the ability to detect extra- and intra-cellular targets. We show here that our approach provides an useful alternative to m-DOTA in terms of sensitivity, specificity, flexibility, and user-friendliness. Our manuscript provides details to effectively barcode immune cells, overcoming limitations in current technology and enabling the use of CyTOF with scarce samples (for instance precious clinical samples). © 2015 The Authors. Published by Wiley Periodicals, Inc.

Implant-specific follow-up imaging of treated intracranial aneurysms: TOF-MRA vs. metal artifact reduced intravenous flat panel computed tomography angiography (FPCTA).

PubMed

Hänsel, N H; Schubert, G A; Scholz, B; Nikoubashman, O; Othman, A E; Wiesmann, M; Pjontek, R; Brockmann, M A

2018-02-01

To compare the diagnostic quality of time-of-flight magnetic resonance angiography (TOF-MRA) and metal-artefact-reduction (MAR) flat-panel-detector computed tomography angiography (FPCTA) and to determine the imaging technique best suited for evaluation endovascular and surgically treated aneurysms. The image quality of TOF-MRA and MAR-FPCTA of 44 intracranial implants (coiling: n=20; clipping: n=15; coiling + stenting: n=9) in a patient cohort of 25 was evaluated by two independent readers. Images obtained using MAR-FPCTA (20 second scan time, 496 projections, intravenous contrast medium administration; Artis Zee, Siemens Healthcare, Forchheim) were compared with TOF-MRA-images (1.5 or 3 T). Nominal data were analysed using McNemar's chi-square test and ordinal variables using the Wilcoxon rank test. Compared to TOF-MRA, MAR-FPCTA was significantly better suited to detect aneurysm remnants and to evaluate parent vessels after clipping (p<0.01). For coil packages >160 mm 3 , TOF-MRA provided significantly better assessment than MAR-FPCTA (p<0.01). For small coil packages (<160 mm 3 ), no significant difference between TOF-MRA and MAR-FPCTA (p=0.232) was observed. For different clip sizes (cut-off 492 mm 3 ) likewise no significant differences were found. The interobserver comparison showed high interrater agreement. MAR-FPCTA is significantly better suited for follow-up examinations of clipped aneurysms, whereas for larger coil packages TOF-MRA is preferable. Smaller coil packages can be analysed using MAR-FPCTA or TOF-MRA. Copyright © 2017 The Royal College of Radiologists. Published by Elsevier Ltd. All rights reserved.

Composition and structure of surfaces by time-of-flight scattering and recoiling spectrometry (TOF-SARS)

NASA Astrophysics Data System (ADS)

Ahn, Jeongheon

1997-10-01

Time-of-flight scattering and recoiling spectrometry (TOF-SARS) was applied to characterize surface structures in order to understand the chemical and physical phenomena on various surfaces. The combination of TOF-SARS, LEED, and classical ion trajectory simulations has allowed characterization of the elemental composition in the outermost atomic layers, surface symmetry, and possible reconstruction or relaxation. The composition and structure of the CdS\\{0001\\}-(1 x 1) and CdS\\{000bar1\\}-(1 x 1) surfaces were investigated. The termination layer of each surface was determined by grazing incidence TOF-SARS. Both (1 x 1) surfaces are bulk-terminated without any reconstruction or relaxation detected by TOF-SARS. Each surface has two domains which are rotated by 60sp° from each other and there exist steps on both surfaces. The CdS\\{0001\\}-(1 x 1) surface is stabilized by O and H covering half a monolayer which are structurally ordered on the surface, while the O and H on the CdS\\{000bar1\\}-(1 x 1) stabilize the surface without ordering. The study of GaN\\{000bar1\\}-(1 x 1) shows the bulk-termination of the surface with no detectable reconstruction or relaxation. The surface is terminated in a N layer with Ga in the 2sp{nd}-layer. H atoms are bound to the outermost N atoms with a coverage of ˜3/4 monolayer and protrude outward from the surface. The surface termination, composition and structure of the Alsb2Osb3 (sapphire) were examined. The surface relaxation was studied quantitatively using classical ion trajectory simulations along with TOF-SARS. The surface undergoes 1sp{st}{-}2sp{nd}-layer relaxation as large as 0.5 A from the bulk value resulting in near coplanarity of Al and O atoms. The reconstruction of the Ni\\{100\\}-(2 x 2)-C surface was studied by TOF-SARS. The surface contained 80% of the (2 x 2)p4g phase and 20% of the unreconstructed (2 x 2) phase. The displacement of Ni atoms was determined by comparing the experimental and simulated results.

MALDI-TOF mass spectrometry and high-consequence bacteria: safety and stability of biothreat bacterial sample testing in clinical diagnostic laboratories.

PubMed

Tracz, Dobryan M; Tober, Ashley D; Antonation, Kym S; Corbett, Cindi R

2018-03-01

We considered the application of MALDI-TOF mass spectrometry for BSL-3 bacterial diagnostics, with a focus on the biosafety of live-culture direct-colony testing and the stability of stored extracts. Biosafety level 2 (BSL-2) bacterial species were used as surrogates for BSL-3 high-consequence pathogens in all live-culture MALDI-TOF experiments. Viable BSL-2 bacteria were isolated from MALDI-TOF mass spectrometry target plates after 'direct-colony' and 'on-plate' extraction testing, suggesting that the matrix chemicals alone cannot be considered sufficient to inactivate bacterial culture and spores in all samples. Sampling of the instrument interior after direct-colony analysis did not recover viable organisms, suggesting that any potential risks to the laboratory technician are associated with preparation of the MALDI-TOF target plate before or after testing. Secondly, a long-term stability study (3 years) of stored MALDI-TOF extracts showed that match scores can decrease below the threshold for reliable species identification (<1.7), which has implications for proficiency test panel item storage and distribution.

Identification of prohibitin 1 as a potential prognostic biomarker in human pancreatic carcinoma using modified aqueous two-phase partition system combined with 2D-MALDI-TOF-TOF-MS/MS.

PubMed

Zhong, Ning; Cui, Yazhou; Zhou, Xiaoyan; Li, Tianliang; Han, Jinxiang

2015-02-01

Membrane proteins are an important source of potential targets for anticancer drugs or biomarkers for early diagnosis. In this study, we used a modified aqueous two-phase partition system combined with two-dimensional (2D) matrix-assisted laser desorption ionization (MALDI) time of flight (TOF) mass spectrometry (MS, 2D-MALDI-TOF-TOF-MS/MS) analysis to isolate and identify membrane proteins in PANC-1 pancreatic cancer cells. Using this method, we identified 55 proteins, of which 31 (56.4 %) were membrane proteins, which, according to gene ontology annotation, are associated with various cellular processes including cell signal transduction, differentiation, and apoptosis. Immunohistochemical analysis showed that the expression level of one of the identified mitochondria membrane proteins, prohibitin 1 (PHB1), is correlated with pancreatic carcinoma differentiation; PHB1 is expressed at a higher level in normal pancreatic tissue than in well-differentiated carcinoma tissue. Further studies showed that PHB1 plays a proapoptotic role in human pancreatic cancer cells, which suggests that PHB1 has antitumorigenic properties. In conclusion, we have provided a modified method for isolating and identifying membrane proteins and demonstrated that PHB1 may be a promising biomarker for early diagnosis and therapy of pancreatic (and potentially other) cancers.

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists

PubMed Central

Rahi, Praveen; Prakash, Om; Shouche, Yogesh S.

2016-01-01

Matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry (MALDI-TOF MS) based biotyping is an emerging technique for high-throughput and rapid microbial identification. Due to its relatively higher accuracy, comprehensive database of clinically important microorganisms and low-cost compared to other microbial identification methods, MALDI-TOF MS has started replacing existing practices prevalent in clinical diagnosis. However, applicability of MALDI-TOF MS in the area of microbial ecology research is still limited mainly due to the lack of data on non-clinical microorganisms. Intense research activities on cultivation of microbial diversity by conventional as well as by innovative and high-throughput methods has substantially increased the number of microbial species known today. This important area of research is in urgent need of rapid and reliable method(s) for characterization and de-replication of microorganisms from various ecosystems. MALDI-TOF MS based characterization, in our opinion, appears to be the most suitable technique for such studies. Reliability of MALDI-TOF MS based identification method depends mainly on accuracy and width of reference databases, which need continuous expansion and improvement. In this review, we propose a common strategy to generate MALDI-TOF MS spectral database and advocated its sharing, and also discuss the role of MALDI-TOF MS based high-throughput microbial identification in microbial ecology studies. PMID:27625644

Rapid identification of oral Actinomyces species cultivated from subgingival biofilm by MALDI-TOF-MS

PubMed Central

Stingu, Catalina S.; Borgmann, Toralf; Rodloff, Arne C.; Vielkind, Paul; Jentsch, Holger; Schellenberger, Wolfgang; Eschrich, Klaus

2015-01-01

Background Actinomyces are a common part of the residential flora of the human intestinal tract, genitourinary system and skin. Isolation and identification of Actinomyces by conventional methods is often difficult and time consuming. In recent years, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has become a rapid and simple method to identify bacteria. Objective The present study evaluated a new in-house algorithm using MALDI-TOF-MS for rapid identification of different species of oral Actinomyces cultivated from subgingival biofilm. Design Eleven reference strains and 674 clinical strains were used in this study. All the strains were preliminarily identified using biochemical methods and then subjected to MALDI-TOF-MS analysis using both similarity-based analysis and classification methods (support vector machine [SVM]). The genotype of the reference strains and of 232 clinical strains was identified by sequence analysis of the 16S ribosomal RNA (rRNA). Results The sequence analysis of the 16S rRNA gene of all references strains confirmed their previous identification. The MALDI-TOF-MS spectra obtained from the reference strains and the other clinical strains undoubtedly identified as Actinomyces by 16S rRNA sequencing were used to create the mass spectra reference database. Already a visual inspection of the mass spectra of different species reveals both similarities and differences. However, the differences between them are not large enough to allow a reliable differentiation by similarity analysis. Therefore, classification methods were applied as an alternative approach for differentiation and identification of Actinomyces at the species level. A cross-validation of the reference database representing 14 Actinomyces species yielded correct results for all species which were represented by more than two strains in the database. Conclusions Our results suggest that a combination of MALDI-TOF-MS with powerful

MALDI-TOF MS typing of a nosocomial methicillin-resistant Staphylococcus aureus outbreak in a neonatal intensive care unit.

PubMed

Steensels, Deborah; Deplano, Ariane; Denis, Olivier; Simon, Anne; Verroken, Alexia

2017-08-01

The early detection of a methicillin-resistant Staphylococcus aureus (MRSA) outbreak is decisive to control its spread and rapidly initiate adequate infection control measures. Therefore, prompt determination of epidemiologic relatedness of clinical MRSA isolates is essential. Genetic typing methods have a high discriminatory power but their availability remains restricted. In this study, we aimed to challenge matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a typing tool of a nosocomial MRSA outbreak in a neonatal intensive care unit. Over a 2-year period, 15 MRSA isolates were recovered from patients (n = 14) and health care workers (n = 1) at the neonatal intensive care unit. Five reference strains were included for comparison. Identification was performed by MALDI-TOF MS and susceptibility profiles determined by automated broth microdilution. Typing analysis by MALDI-TOF MS included mean spectrum profiles and subsequent dendrogram creation using BioNumerics software. Results were compared with spa typing and pulsed-field gel electrophoresis (PFGE). Our study showed good concordance (93%) between PFGE, spa typing, and MALDI-TOF MS for the outbreak-related MRSA strains. MALDI-TOF MS typing showed excellent typeability and discriminatory power but showed poor reproducibility. This study is one of the first to document the potential usefulness of MALDI-TOF MS with standardized data analysis as a typing tool for investigating a nosocomial MRSA outbreak. A concordance of 93% compared to reference typing techniques was observed. However, because of poor reproducibility, long-term follow-up of prospective isolated strains is not practical for routine use. Further studies are needed to confirm our observations.

Chemometric classification of morphologically similar Umbelliferae medicinal herbs by DART-TOF-MS fingerprint.

PubMed

Lee, Sang Min; Kim, Hye-Jin; Jang, Young Pyo

2012-01-01

It needs many years of special training to gain expertise on the organoleptic classification of botanical raw materials and, even for those experts, discrimination among Umbelliferae medicinal herbs remains an intricate challenge due to their morphological similarity. To develop a new chemometric classification method using a direct analysis in real time-time of flight-mass spectrometry (DART-TOF-MS) fingerprinting for Umbelliferae medicinal herbs and to provide a platform for its application to the discrimination of other herbal medicines. Angelica tenuissima, Angelica gigas, Angelica dahurica and Cnidium officinale were chosen for this study and ten samples of each species were purchased from various Korean markets. DART-TOF-MS was employed on powdered raw materials to obtain a chemical fingerprint of each sample and the orthogonal partial-least squares method in discriminant analysis (OPLS-DA) was used for multivariate analysis. All samples of collected species were successfully discriminated from each other according to their characteristic DART-TOF-MS fingerprint. Decursin (or decursinol angelate) and byakangelicol were identified as marker molecules for Angelica gigas and A. dahurica, respectively. Using the OPLS method for discriminant analysis, Angelica tenuissima and Cnidium officinale were clearly separated into two groups. Angelica tenuissima was characterised by the presence of ligustilide and unidentified molecular ions of m/z 239 and 283, while senkyunolide A together with signals with m/z 387 and 389 were the marker compounds for Cnidium officinale. Elaborating with chemoinformatics, DART-TOF-MS fingerprinting with chemoinformatic tools results in a powerful method for the classification of morphologically similar Umbelliferae medicinal herbs and quality control of medicinal herbal products, including the extracts of these crude drugs. Copyright © 2012 John Wiley & Sons, Ltd.

Evaluation of capacity to detect ability to form biofilm in Candida parapsilosis sensu stricto strains by MALDI-TOF MS.

PubMed

Mlynáriková, Katarína; Šedo, Ondrej; Růžička, Filip; Zdráhal, Zbyněk; Holá, Veronika; Mahelová, Martina

2016-11-01

Matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is, currently, used as a rapid and reliable tool in microbial diagnostics. The discriminatory power of the method extends its applicability also beyond species level. This study examined the possibility to use MALDI-TOF MS to differentiate between Candida parapsilosis sensu stricto biofilm-positive (n = 12) and biofilm-negative (n = 9) strains. The results indicated a grouping trend within MALDI-TOF mass spectra belonging to each of the tested groups. However, these trends were eclipsed by mass spectral variations resulting from limited repeatability of the method, making its application for the selected purpose impossible. Improvement in the discriminatory power of the method was not obtained neither by using different matrices (α-cyano-4-hydroxycinnamic acid, ferulic acid, 5-chloro-2-mercaptobenzothionazole) for MALDI-TOF MS analysis nor by testing different culture conditions (cultivation length, culture media).

Neutron cross section measurements at n-TOF for ADS related studies

NASA Astrophysics Data System (ADS)

Mastinu, P. F.; Abbondanno, U.; Aerts, G.; Álvarez, H.; Alvarez-Velarde, F.; Andriamonje, S.; Andrzejewski, J.; Assimakopoulos, P.; Audouin, L.; Badurek, G.; Bustreo, N.; aumann, P.; vá, F. Be; Berthoumieux, E.; Calviño, F.; Cano-Ott, D.; Capote, R.; Carrillo de Albornoz, A.; Cennini, P.; Chepel, V.; Chiaveri, E.; Colonna, N.; Cortes, G.; Couture, A.; Cox, J.; Dahlfors, M.; David, S.; Dillmann, I.; Dolfini, R.; Domingo-Pardo, C.; Dridi, W.; Duran, I.; Eleftheriadis, C.; Embid-Segura, M.; Ferrant, L.; Ferrari, A.; Ferreira-Marques, R.; itzpatrick, L.; Frais-Kölbl, H.; Fujii, K.; Furman, W.; Guerrero, C.; Goncalves, I.; Gallino, R.; Gonzalez-Romero, E.; Goverdovski, A.; Gramegna, F.; Griesmayer, E.; Gunsing, F.; Haas, B.; Haight, R.; Heil, M.; Herrera-Martinez, A.; Igashira, M.; Isaev, S.; Jericha, E.; Kadi, Y.; Käppeler, F.; Karamanis, D.; Karadimos, D.; Kerveno, M.; Ketlerov, V.; Koehler, P.; Konovalov, V.; Kossionides, E.; Krti ka, M.; Lamboudis, C.; Leeb, H.; Lindote, A.; Lopes, I.; Lozano, M.; Lukic, S.; Marganiec, J.; Marques, L.; Marrone, S.; Massimi, C.; Mengoni, A.; Milazzo, P. M.; Moreau, C.; Mosconi, M.; Neves, F.; Oberhummer, H.; O'Brien, S.; Oshima, M.; Pancin, J.; Papachristodoulou, C.; Papadopoulos, C.; Paradela, C.; Patronis, N.; Pavlik, A.; Pavlopoulos, P.; Perrot, L.; Plag, R.; Plompen, A.; Plukis, A.; Poch, A.; Pretel, C.; Quesada, J.; Rauscher, T.; Reifarth, R.; Rosetti, M.; Rubbia, C.; Rudolf, G.; Rullhusen, P.; Salgado, J.; Sarchiapone, L.; Savvidis, I.; Stephan, C.; Tagliente, G.; Tain, J. L.; Tassan-Got, L.; Tavora, L.; Terlizzi, R.; Vannini, G.; Vaz, P.; Ventura, A.; Villamarin, D.; Vincente, M. C.; Vlachoudis, V.; Vlastou, R.; Voss, F.; Walter, S.; Wendler, H.; Wiescherand, M.; Wisshak, K.

2006-05-01

A neutron Time-of-Flight facility (n_TOF) is available at CERN since 2001. The innovative features of the neutron beam, in particular the high instantaneous flux, the wide energy range, the high resolution and the low background, make this facility unique for measurements of neutron induced reactions relevant to the field of Emerging Nuclear Technologies, as well as to Nuclear Astrophysics and Fundamental Nuclear Physics. The scientific motivations that have led to the construction of this new facility are here presented. The main characteristics of the n_TOF neutron beam are described, together with the features of the experimental apparata used for cross-section measurements. The main results of the first measurement campaigns are presented. Preliminary results of capture cross-section measurements of minor actinides, important to ADS project for nuclear waste transmutation, are finally discussed.

Obstacle Classification and 3D Measurement in Unstructured Environments Based on ToF Cameras

PubMed Central

Yu, Hongshan; Zhu, Jiang; Wang, Yaonan; Jia, Wenyan; Sun, Mingui; Tang, Yandong

2014-01-01

Inspired by the human 3D visual perception system, we present an obstacle detection and classification method based on the use of Time-of-Flight (ToF) cameras for robotic navigation in unstructured environments. The ToF camera provides 3D sensing by capturing an image along with per-pixel 3D space information. Based on this valuable feature and human knowledge of navigation, the proposed method first removes irrelevant regions which do not affect robot's movement from the scene. In the second step, regions of interest are detected and clustered as possible obstacles using both 3D information and intensity image obtained by the ToF camera. Consequently, a multiple relevance vector machine (RVM) classifier is designed to classify obstacles into four possible classes based on the terrain traversability and geometrical features of the obstacles. Finally, experimental results in various unstructured environments are presented to verify the robustness and performance of the proposed approach. We have found that, compared with the existing obstacle recognition methods, the new approach is more accurate and efficient. PMID:24945679

Exploring MALDI-TOF MS approach for a rapid identification of Mycobacterium avium ssp. paratuberculosis field isolates.

PubMed

Ricchi, M; Mazzarelli, A; Piscini, A; Di Caro, A; Cannas, A; Leo, S; Russo, S; Arrigoni, N

2017-03-01

The aim of the study was to explore the suitability of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) for a rapid and correct identification of Mycobacterium avium ssp. paratuberculosis (MAP) field isolates. MALDI-TOF MS approach is becoming one of the most popular tests for the identification of intact bacterial cells which has been shown to be fast and reliable. For this purpose, 36 MAP field isolates were analysed through MALDI-TOF MS and the spectra compared with two different databases: one provided by the vendor of the system employed (Biotyper ver. 3·0; Bruker Daltonics) and a homemade database containing spectra from both tuberculous and nontuberculous Mycobacteria. Moreover, principal component analysis procedure was employed to confirm the ability of MALDI-TOF MS to discriminate between very closely related subspecies. Our results suggest MAP can be differentiated from other Mycobacterium species, both when the species are very close (M. intracellulare) and when belonging to different subspecies (M. avium ssp. avium and M. avium ssp. silvaticum). The procedure applied is fast, easy to perform, and achieves an earlier accurate species identification of MAP and nontuberculous Mycobacteria in comparison to other procedures. The gold standard test for the diagnosis of paratuberculosis is still isolation of MAP by cultural methods, but additional assays, such as qPCR and subculturing for determination of mycobactin dependency are required to confirm its identification. We have provided here evidence pertaining to the usefulness of MALDI-TOF MS approach for a rapid identification of this mycobacterium among other members of M. avium complex. © 2016 The Society for Applied Microbiology.

[Rapid identification of two new isomers in bear bile powder by LC-Q-TOF-MS combined with PCC oxidation].

PubMed

Jian, Long-Hai; Hu, Chun; Yu, Hong; Wang, Ke; Ji, Shen

2013-07-01

A rapid method of Liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-Q-TOF-MS) combined with pyridinium chlorochromate (PCC) oxidation has been developed to determine chemical structures of two novel isomers in bear bile powder. Derivatives of ursodeoxycholic acid (UDCA) and chenodeoxycholic acid (CDCA) were semi-synthesized by PCC oxidation, then were analyzed by LC-Q-TOF-MS. Separation was carried out on a reverse column with the mobile phase of acetonitrile-0.1% formic acid (45:55). The data of Q-TOF-MS was acquired by MS, MS/MS, positive and negative modes. Since UDCA and CDCA were stereochemical isomeric at an alcohol position, two oxidation products were same and have been confirmed by LC-Q-TOF-MS. Other two products were also determined based on the PCC oxidation theory. Samples of bear bile powder were dissolved by methanol and measured by LC-Q-TOF-MS. Two unknown peaks were found and identified by matching their retention times and accurate mass spectra ions with PCC oxidation productS. Finally, the structures of two new bile acids in bear bile powder were confirmed as 3alpha-hydroxy-7-oxo-5beta-cholanic acid, 7alpha-hydroxy-3-oxo-5beta-cholanic acid, respectively.

Advantages of TOF-SIMS analysis of hydroxyapatite and fluorapatite in comparison with XRD, HR-TEM and FT-IR.

PubMed

Okazaki, Masayuki; Hirata, Isao; Matsumoto, Takuya; Takahashi, Junzo

2005-12-01

The chemical analysis of hydroxyapatite and fluorapatite was carried out using time-of-flight secondary ion mass spectrometry (TOF-SIMS). Hydroxyapatite and fluorapatite were synthesized at 80 +/- 1 degrees C and pH 7.4 +/- 0.2. Fluorapatite was better crystallized, with its (300) reflection shifted to a slightly higher angle. High-resolution transmission electron microscopy clearly revealed a typical, regular hexagonal cross section perpendicular to the c-axis for fluorapatite and a flattened hexagonal cross section for hydroxyapatite. FT-IR spectra of fluorapatite confirmed the absence of OH absorption peak--which was seen in hydroxyapatite at about 3570 cm(-1). TOF-SIMS mass spectra showed a peak at 40 amu due to calcium. In addition, a peak at 19 amu due to fluorine could be clearly seen, although the intensities of PO, PO2, and PO3 were very low. It was confirmed that TOF-SIMS clearly showed the differences between positive and negative mass spectra of hydroxyapatite and fluorapatite, especially for F-. We concluded that TOF-SIMS exhibited distinct advantages compared with other methods of analysis.

Evaluation of MALDI-TOF MS (Matrix-Assisted Laser Desorption-Ionization Time-of-Flight Mass Spectrometry) for routine identification of anaerobic bacteria.

PubMed

Rodríguez-Sánchez, Belén; Alcalá, Luis; Marín, Mercedes; Ruiz, Adrián; Alonso, Elena; Bouza, Emilio

2016-12-01

Information regarding the use of MALDI-TOF MS as an alternative to conventional laboratory methods for the rapid and reliable identification of bacterial isolates is still limited. In this study, MALDI-TOF MS was evaluated on 295 anaerobic isolates previously identified by 16S rRNA gene sequencing and with biochemical tests (Rapid ID 32A system, BioMérieux). In total, 85.8% of the isolates were identified by MALDI-TOF MS at the species level vs 49.8% using the Rapid ID 32A system (p < 0.0001). None of the isolates was discordantly identified at the genus level using MALDI-TOF MS and only 9 of them could not be identified using the method. Thus, our results show that MALDI-TOF MS is a robust and reliable tool for the identification of anaerobic isolates in the microbiology laboratory. Its implementation will reduce the turnaround time for a final identification and the number of isolates that require 16S rRNA sequencing. Copyright © 2016 Elsevier Ltd. All rights reserved.

The subunits of the S-phase checkpoint complex Mrc1/Tof1/Csm3: dynamics and interdependence

PubMed Central

2014-01-01

Background The S-phase checkpoint aims to prevent cells from generation of extensive single-stranded DNA that predisposes to genome instability. The S. cerevisiae complex Tof1/Csm3/Mrc1 acts to restrain the replicative MCM helicase when DNA synthesis is prohibited. Keeping the replication machinery intact allows restart of the replication fork when the block is relieved. Although the subunits of the Tof1/Csm3/Mrc1 complex are well studied, the impact of every single subunit on the triple complex formation and function needs to be established. Findings This work studies the cellular localization and the chromatin binding of GFP-tagged subunits when the complex is intact and when a subunit is missing. We demonstrate that the complex is formed in cell nucleus, not the cytoplasm, as Tof1, Csm3 and Mrc1 enter the nucleus independently from one another. Via in situ chromatin binding assay we show that a Tof1-Csm3 dimer formation and chromatin binding is required to ensure the attachment of Mrc1 to chromatin. Our study indicates that the translocation into the nucleus is not the process to regulate the timing of chromatin association of Mrc1. We also studied the nuclear behavior of Mrc1 subunit in the process of adaptation to the presence hydroxyurea. Our results indicate that after prolonged HU incubation, cells bypass the S-phase checkpoint and proceed throughout the cell cycle. This process is accompanied by Mrc1 chromatin detachment and Rad53 dephosphorylation. Conclusions In S. cerevisiae the subunits of the S-phase checkpoint complex Mrc1/Tof1/Csm3 independently enter the cell nucleus, where a Tof1-Csm3 dimer is formed to ensure the chromatin binding of Mrc1 and favor DNA replication and S-phase checkpoint fork arrest. In the process of adaptation to the presence of hydroxyurea Mrc1 is detached from chromatin and Rad53 checkpoint activity is diminished in order to allow S-phase checkpoint escape and completion of the cell cycle. PMID:25379053

The subunits of the S-phase checkpoint complex Mrc1/Tof1/Csm3: dynamics and interdependence.

PubMed

Uzunova, Sonya Dimitrova; Zarkov, Alexander Stefanov; Ivanova, Anna Marianova; Stoynov, Stoyno Stefanov; Nedelcheva-Veleva, Marina Nedelcheva

2014-01-01

The S-phase checkpoint aims to prevent cells from generation of extensive single-stranded DNA that predisposes to genome instability. The S. cerevisiae complex Tof1/Csm3/Mrc1 acts to restrain the replicative MCM helicase when DNA synthesis is prohibited. Keeping the replication machinery intact allows restart of the replication fork when the block is relieved. Although the subunits of the Tof1/Csm3/Mrc1 complex are well studied, the impact of every single subunit on the triple complex formation and function needs to be established. This work studies the cellular localization and the chromatin binding of GFP-tagged subunits when the complex is intact and when a subunit is missing. We demonstrate that the complex is formed in cell nucleus, not the cytoplasm, as Tof1, Csm3 and Mrc1 enter the nucleus independently from one another. Via in situ chromatin binding assay we show that a Tof1-Csm3 dimer formation and chromatin binding is required to ensure the attachment of Mrc1 to chromatin. Our study indicates that the translocation into the nucleus is not the process to regulate the timing of chromatin association of Mrc1. We also studied the nuclear behavior of Mrc1 subunit in the process of adaptation to the presence hydroxyurea. Our results indicate that after prolonged HU incubation, cells bypass the S-phase checkpoint and proceed throughout the cell cycle. This process is accompanied by Mrc1 chromatin detachment and Rad53 dephosphorylation. In S. cerevisiae the subunits of the S-phase checkpoint complex Mrc1/Tof1/Csm3 independently enter the cell nucleus, where a Tof1-Csm3 dimer is formed to ensure the chromatin binding of Mrc1 and favor DNA replication and S-phase checkpoint fork arrest. In the process of adaptation to the presence of hydroxyurea Mrc1 is detached from chromatin and Rad53 checkpoint activity is diminished in order to allow S-phase checkpoint escape and completion of the cell cycle.

Cosensitized Porphyrin System for High-Performance Solar Cells with TOF-SIMS Analysis.

PubMed

Wu, Wenjun; Xiang, Huaide; Fan, Wei; Wang, Jinglin; Wang, Haifeng; Hua, Xin; Wang, Zhaohui; Long, Yitao; Tian, He; Zhu, Wei-Hong

2017-05-17

To date, development of organic sensitizers has been predominately focused on light harvesting, highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels, and the electron transferring process. In contrast, their adsorption mode as well as the dynamic loading behavior onto nanoporous TiO 2 is rarely considered. Herein, we have employed the time-of-flight secondary ion mass spectrometry (TOF-SIMS) to gain insight into the competitive dye adsorption mode and kinetics in the cosensitized porphyrin system. Using novel porphyrin dye FW-1 and D-A-π-A featured dye WS-5, the different bond-breaking mode in TOF-SIMS and dynamic dye-loading amount during the coadsorption process are well-compared with two different anchoring groups, such as benzoic acid and cyanoacrylic acid. With the bombardment mode in TOF-SIMS spectra, we have speculated that the cyano group grafts onto nanoporous TiO 2 as tridentate binding for the common anchoring unit of cyanoacrylic acid and confirmed it through extensive first-principles density functional theory calculation by anchoring either the carboxyl or cyano group, which shows that the cyano group can efficiently participate in the adsorption of the WS-5 molecule onto the TiO 2 nanocrystal. The grafting reinforcement interaction between the cyano group and TiO 2 in WS-5 can well-explain the rapid adsorption characteristics. A strong coordinate bond between the lone pair of electrons on the nitrogen or oxygen atom and the Lewis acid sites of TiO 2 can increase electron injection efficiencies with respect to those from the bond between the benzoic acid group and the Brønsted acid sites of the TiO 2 surface. Upon optimization of the coadsorption process with dye WS-5, the photoelectric conversion efficiency based on porphyrin dye FW-1 is increased from 6.14 to 9.72%. The study on the adsorption dynamics of organic sensitizers with TOF-SIMS analysis might provide a new venue for improvement of cosensitized solar

Development of a TOF SIMS setup at the Zagreb heavy ion microbeam facility

NASA Astrophysics Data System (ADS)

Tadić, Tonči; Bogdanović Radović, Iva; Siketić, Zdravko; Cosic, Donny Domagoj; Skukan, Natko; Jakšić, Milko; Matsuo, Jiro

2014-08-01

We describe a new Time-of-flight Secondary Ion Mass Spectrometry (TOF SIMS) setup for MeV SIMS application, which is constructed and installed at the heavy ion microbeam facility at the Ruđer Bošković Institute in Zagreb. The TOF-SIMS setup is developed for high sensitivity molecular imaging using a heavy ion microbeam that focuses ion beams (from C to I) with sub-micron resolution. Dedicated pulse processing electronics for MeV SIMS application have been developed, enabling microbeam-scanning control, incoming ion microbeam pulsing and molecular mapping. The first results showing measured MeV SIMS spectra as well as molecular maps for samples of interest are presented and discussed.

[MALDI-TOF mass spectrometry in the investigation of large high-molecular biological compounds].

PubMed

Porubl'ova, L V; Rebriiev, A V; Hromovyĭ, T Iu; Minia, I I; Obolens'ka, M Iu

2009-01-01

MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight) mass spectrometry has become, in the recent years, a tool of choice for analyses of biological polymers. The wide mass range, high accuracy, informativity and sensitivity make it a superior method for analysis of all kinds of high-molecular biological compounds including proteins, nucleic acids and lipids. MALDI-TOF-MS is particularly suitable for the identification of proteins by mass fingerprint or microsequencing. Therefore it has become an important technique of proteomics. Furthermore, the method allows making a detailed analysis of post-translational protein modifications, protein-protein and protein-nucleic acid interactions. Recently, the method was also successfully applied to nucleic acid sequencing as well as screening for mutations.

Comparison of 3D TOF-MRA and 3D CE-MRA at 3T for imaging of intracranial aneurysms.

PubMed

Cirillo, Mario; Scomazzoni, Francesco; Cirillo, Luigi; Cadioli, Marcello; Simionato, Franco; Iadanza, Antonella; Kirchin, Miles; Righi, Claudio; Anzalone, Nicoletta

2013-12-01

To compare 3T elliptical-centric CE MRA with 3T TOF MRA for the detection and characterization of unruptured intracranial aneurysms (UIAs), by using digital subtracted angiography (DSA) as reference. Twenty-nine patients (12 male, 17 female; mean age: 62 years) with 41 aneurysms (34 saccular, 7 fusiform; mean diameter: 8.85 mm [range 2.0-26.4mm]) were evaluated with MRA at 3T each underwent 3D TOF-MRA examination without contrast and then a 3D contrast-enhanced (CE-MRA) examination with 0.1mmol/kg bodyweight gadobenate dimeglumine and k-space elliptic mapping (Contrast ENhanced Timing Robust Angiography [CENTRA]). Both TOF and CE-MRA images were used to evaluate morphologic features that impact the risk of rupture and the selection of a treatment. Almost half (20/41) of UIAs were located in the internal carotid artery, 7 in the anterior communicating artery, 9 in the middle cerebral artery and 4 in the vertebro-basilar arterial system. All patients also underwent DSA before or after the MR examination. The CE-MRA results were in all cases consistent with the DSA dataset. No differences were noted between 3D TOF-MRA and CE-MRA concerning the detection and location of the 41 aneurysms or visualization of the parental artery. Differences were apparent concerning the visualization of morphologic features, especially for large aneurysms (>13 mm). An irregular sac shape was demonstrated for 21 aneurysms on CE-MRA but only 13/21 aneurysms on 3D TOF-MRA. Likewise, CE-MRA permitted visualization of an aneurismal neck and calculation of the sac/neck ratio for all 34 aneurysms with a neck demonstrated at DSA. Conversely, a neck was visible for only 24/34 aneurysms at 3D TOF-MRA. 3D CE-MRA detected 15 aneurysms with branches originating from the sac and/or neck, whereas branches were recognized in only 12/15 aneurysms at 3D TOF-MRA. For evaluation of intracranial aneurysms at 3T, 3D CE-MRA is superior to 3D TOF-MRA for assessment of sac shape, detection of aneurysmal neck, and

2D-DIGE and MALDI TOF/TOF MS analysis reveal that small GTPase signaling pathways may play an important role in cadmium-induced colon cell malignant transformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Jian, E-mail: lujian@ujs.edu.cn; Institute of Life Sciences, Jiangsu University, Zhenjiang 212013; Zhou, Zhongping

Cadmium is a toxic heavy metal present in the environment and in industrial materials. Cadmium has demonstrated carcinogenic activity that induces cell transformation, but how this occurs is unclear. We used 2D-DIGE and MALDI TOF/TOF MS combined with bioinformatics and immunoblotting to investigate the molecular mechanism of cadmium transformation. We found that small GTPases were critical for transformation. Additionally, proteins involved in mitochondrial transcription, DNA repair, and translation also had altered expression patterns in cadmium treated cells. Collectively, our results suggest that activation of small GTPases contributes to cadmium-induced transformation of colon cells. - Highlights: • Colon epithelial cell linemore » is firstly successfully transformed by cadmium. • 2D-DIGE is applied to visualize the differentially expressed proteins. • RhoA plays an important role in cadmium induced malignant transformation. • Bioinformatic and experimental methods are combined to explore new mechanisms.« less

Application of MALDI-TOF MS Systems in the Rapid Identification of Campylobacter spp. of Public Health Importance.

PubMed

Hsieh, Ying-Hsin; Wang, Yun F; Moura, Hercules; Miranda, Nancy; Simpson, Steven; Gowrishankar, Ramnath; Barr, John; Kerdahi, Khalil; Sulaiman, Irshad M

2018-05-01

Campylobacteriosis is an infectious gastrointestinal disease caused by Campylobacter spp. In most cases, it is either underdiagnosed or underreported due to poor diagnostics and limited databases. Several DNA-based molecular diagnostic techniques, including 16S ribosomal RNA (rRNA) sequence typing, have been widely used in the species identification of Campylobacter. Nevertheless, these assays are time-consuming and require a high quality of bacterial DNA. Matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) MS is an emerging diagnostic technology that can provide the rapid identification of microorganisms by using their intact cells without extraction or purification. In this study, we analyzed 24 American Type Culture Collection reference isolates of 16 Campylobacter spp. and five unknown clinical bacterial isolates for rapid identification utilizing two commercially available MADI-TOF MS platforms, namely the bioMérieux VITEK® MS and Bruker Biotyper systems. In addition, 16S rRNA sequencing was performed to confirm the species-level identification of the unknown clinical isolates. Both MALDI-TOF MS systems identified the isolates of C. jejuni, C. coli, C. lari, and C. fetus. The results of this study suggest that the MALDI-TOF MS technique can be used in the identification of Campylobacter spp. of public health importance.

Follow-up assessment of coiled intracranial aneurysms using zTE MRA as compared with TOF MRA: a preliminary image quality study.

PubMed

Shang, Song'an; Ye, Jing; Luo, Xianfu; Qu, Jianxun; Zhen, Yong; Wu, Jingtao

2017-10-01

To prospectively assess coiled intracranial aneurysms using a novel non-contrast enhanced zero echo time (zTE) MR angiography (MRA) method, and compare its image quality with time-of-flight (TOF) MRA, using digital subtraction angiography (DSA) as reference. Twenty-five patients (10 males and 15 females; age 53.96 ± 12.46 years) were enrolled in this monocentric study. MRA sequences were performed 24 h before DSA. Susceptibility artefact intensity and flow signal within the parent artery were carried out using a 4-point scale. Occlusion status was assessed using the 3-grade Montreal scale. Scores of zTE were higher than TOF for both susceptibility artefact intensity (3.42 ± 0.64, 2.92 ± 0.63, P = 0.01) and flow signal (3.66 ± 0.95, 3.24 ± 1.24, P = 0.01). DSA revealed 17 complete occlusions, five residual neck aneurysms and two residual aneurysms. Inter-observer agreement was excellent (weighted κ: 0.89) for zTE and good (weighted κ: 0.68) for TOF. Intermodality agreement was excellent for zTE (weighted κ: 0.95) and good for TOF (weighted κ: 0.80). Correlations of both MRA sequences with DSA were high (zTE, Spearman's ρ: 0.91; TOF, Spearman's ρ: 0.81). zTE MRA showed promising results for follow-up assessment of coiled intracranial aneurysms and was superior to TOF MRA for visualizing the parent artery and evaluating occlusion status. • Various MRA sequences were applied for follow-up assessment of coiled intracranial aneurysms. • zTE MRA was less sensitive to susceptibility artefacts and haemodynamics. • In this monocentric study, zTE MRA was equivalent to DSA. • zTE MRA maybe an alternative to TOF MRA for follow-up assessment.

Rapid Classification and Identification of Microcystis aeruginosa Strains Using MALDI-TOF MS and Polygenetic Analysis.

PubMed

Sun, Li-Wei; Jiang, Wen-Jing; Sato, Hiroaki; Kawachi, Masanobu; Lu, Xi-Wu

2016-01-01

Matrix-assisted laser desorption-ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was used to establish a rapid, simple, and accurate method to differentiate among strains of Microcystis aeruginosa, one of the most prevalent types of bloom-forming cyanobacteria. M. aeruginosa NIES-843, for which a complete genome has been sequenced, was used to characterize ribosomal proteins as biomarkers and to optimize conditions for observing ribosomal proteins as major peaks in a given mass spectrum. Thirty-one of 52 ribosomal subunit proteins were detected and identified along the mass spectrum. Fifty-five strains of M. aeruginosa from different habitats were analyzed using MALDI-TOF MS; among these samples, different ribosomal protein types were observed. A polygenetic analysis was performed using an unweighted pair-group method with arithmetic means and different ribosomal protein types to classify the strains into five major clades. Two clades primarily contained toxic strains, and the other three clades contained exclusively non-toxic strains. This is the first study to differentiate cyanobacterial strains using MALDI-TOF MS.

Contaminant screening of wastewater with HPLC-IM-qTOF-MS and LC+LC-IM-qTOF-MS using a CCS database.

PubMed

Stephan, Susanne; Hippler, Joerg; Köhler, Timo; Deeb, Ahmad A; Schmidt, Torsten C; Schmitz, Oliver J

2016-09-01

Non-target analysis has become an important tool in the field of water analysis since a broad variety of pollutants from different sources are released to the water cycle. For identification of compounds in such complex samples, liquid chromatography coupled to high resolution mass spectrometry are often used. The introduction of ion mobility spectrometry provides an additional separation dimension and allows determining collision cross sections (CCS) of the analytes as a further physicochemical constant supporting the identification. A CCS database with more than 500 standard substances including drug-like compounds and pesticides was used for CCS data base search in this work. A non-target analysis of a wastewater sample was initially performed with high performance liquid chromatography (HPLC) coupled to an ion mobility-quadrupole-time of flight mass spectrometer (IM-qTOF-MS). A database search including exact mass (±5 ppm) and CCS (±1 %) delivered 22 different compounds. Furthermore, the same sample was analyzed with a two-dimensional LC method, called LC+LC, developed in our group for the coupling to IM-qTOF-MS. This four dimensional separation platform revealed 53 different compounds, identified over exact mass and CCS, in the examined wastewater sample. It is demonstrated that the CCS database can also help to distinguish between isobaric structures exemplified for cyclophosphamide and ifosfamide. Graphical Abstract Scheme of sample analysis and database screening.

Evaluation of three sample preparation methods for the direct identification of bacteria in positive blood cultures by MALDI-TOF.

PubMed

Tanner, Hannah; Evans, Jason T; Gossain, Savita; Hussain, Abid

2017-01-18

Patient mortality is significantly reduced by rapid identification of bacteria from sterile sites. MALDI-TOF can identify bacteria directly from positive blood cultures and multiple sample preparation methods are available. We evaluated three sample preparation methods and two MALDI-TOF score cut-off values. Positive blood culture bottles with organisms present in Gram stains were prospectively analysed by MALDI-TOF. Three lysis reagents (Saponin, SDS, and SepsiTyper lysis bufer) were applied to each positive culture followed by centrifugation, washing and protein extraction steps. Methods were compared using the McNemar test and 16S rDNA sequencing was used to assess discordant results. In 144 monomicrobial cultures, using ≥2.000 as the cut-off value, species level identifications were obtained from 69/144 (48%) samples using Saponin, 86/144 (60%) using SDS, and 91/144 (63%) using SepsiTyper. The difference between SDS and SepsiTyper was not statistically significant (P = 0.228). Differences between Saponin and the other two reagents were significant (P < 0.01). Using ≥1.700 plus top three results matching as the cut-off value, species level identifications were obtained from 100/144 (69%) samples using Saponin, 103/144 (72%) using SDS, and 106/144 (74%) using SepsiTyper and there was no statistical difference between the methods. No true discordances between culture and direct MALDI-TOF identification were observed in monomicrobial cultures. In 32 polymicrobial cultures, MALDI-TOF identified one organism in 34-75% of samples depending on the method. This study demonstrates two inexpensive in-house detergent lysis methods are non-inferior to a commercial kit for analysis of positive blood cultures by direct MALDI-TOF in a clinical diagnostic microbiology laboratory.

Characterization of Enterococcus species isolated from marine recreational waters by MALDI-TOF MS and Rapid ID API® 20 Strep system.

PubMed

Christ, Ana Paula Guarnieri; Ramos, Solange Rodrigues; Cayô, Rodrigo; Gales, Ana Cristina; Hachich, Elayse Maria; Sato, Maria Inês Zanoli

2017-05-15

MALDI-TOF Mass Spectrometry Biotyping has proven to be a reliable method for identifying bacteria at the species level based on the analysis of the ribosomal proteins mass fingerprint. We evaluate the usefulness of this method to identify Enterococcus species isolated from marine recreational water at Brazilian beaches. A total of 127 Enterococcus spp. isolates were identified to species level by bioMérieux's API® 20 Strep and MALDI-TOF systems. The biochemical test identified 117/127 isolates (92%), whereas MALDI identified 100% of the isolates, with an agreement of 63% between the methods. The 16S rRNA gene sequencing of isolates with discrepant results showed that MALDI-TOF and API® correctly identified 74% and 11% of these isolates, respectively. This discrepancy probably relies on the bias of the API® has to identify clinical isolates. MALDI-TOF proved to be a feasible approach for identifying Enterococcus from environmental matrices increasing the rapidness and accuracy of results. Copyright © 2017 Elsevier Ltd. All rights reserved.

16S-ARDRA and MALDI-TOF mass spectrometry as tools for identification of Lactobacillus bacteria isolated from poultry.

PubMed

Dec, Marta; Puchalski, Andrzej; Urban-Chmiel, Renata; Wernicki, Andrzej

2016-06-13

The objective of our study is to evaluate the potential use of Amplified 16S Ribosomal DNA Restriction Analysis (16S-ARDRA) and MALDI-TOF mass spectrometry (MS) as methods for species identification of Lactobacillus strains in poultry. A total of 80 Lactobacillus strains isolated from the cloaca of chicken, geese and turkeys were identified to the species level by MALDI-TOF MS (on-plate extraction method) and 16S-ARDRA. The two techniques produced comparable classification results, some of which were additionally confirmed by sequencing of 16S rDNA. MALDI-TOF MS enabled rapid species identification but produced more than one reliable identification result for 16.25 % of examined strains (mainly of the species L. johnsonii). For 30 % of isolates intermediate log(scores) of 1.70-1.99 were obtained, indicating correct genus identification but only presumptive species identification. The 16S-ARDRA protocol was based on digestion of 16S rDNA with the restriction enzymes MseI, HinfI, MboI and AluI. This technique was able to distinguish 17 of the 19 Lactobacillus reference species tested and enabled identification of all 80 wild isolates. L. salivarius dominated among the 15 recognized species, followed by L. johnsonii and L. ingluviei. The MALDI-TOF MS and 16S-ARDRA assays are valuable tools for the identification of avian lactobacilli to the species level. MALDI-TOF MS is a fast, simple and cost-effective technique, and despite generating a high percentage of results with a log(score) <2.00, the on-plate extraction method is characterized by high-performance. For samples for which Biotyper produces more than one reliable result, MALDI-TOF MS must be used in combination with genotypic techniques to achieve unambiguous results. 16S-ARDRA is simple, repetitive method with high power of discrimination, whose sole limitation is its inability to discriminate between species with very high 16S rDNA sequence homology, such as L. casei and L. zeae. The assays can be used for

Measurement of cosmic muon angular distribution and vertical integrated flux by 2 m × 2 m RPC stack at IICHEP-Madurai

NASA Astrophysics Data System (ADS)

Pethuraj, S.; Datar, V. M.; Majumder, G.; Mondal, N. K.; Ravindran, K. C.; Satyanarayana, B.

2017-09-01

The 50 kton INO-ICAL is a proposed underground high energy physics experiment at Theni, India (9o57'N, 77o16'E) to study the neutrino oscillation parameters using atmospheric neutrinos. The Resistive Plate Chamber (RPC) has been chosen as the active detector element for the ICAL detector. An experimental setup consisting of 12 layers of glass RPCs of size 2 m × 2 m has been built at IICHEP, Madurai to study the long term stability and performance of RPCs which are produced on a large scale in Indian industry. In this paper, the studies on the performance of RPCs are presented along with the angular distribution of muons at Madurai (9o56'N,78o00'E and Altitude ≈ 160 m from sea level).

Database and interactive monitoring system for the photonics and electronics of RPC Muon Trigger in CMS experiment

NASA Astrophysics Data System (ADS)

Wiacek, Daniel; Kudla, Ignacy M.; Pozniak, Krzysztof T.; Bunkowski, Karol

2005-02-01

The main task of the RPC (Resistive Plate Chamber) Muon Trigger monitoring system design for the CMS (Compact Muon Solenoid) experiment (at LHC in CERN Geneva) is the visualization of data that includes the structure of electronic trigger system (e.g. geometry and imagery), the way of its processes and to generate automatically files with VHDL source code used for programming of the FPGA matrix. In the near future, the system will enable the analysis of condition, operation and efficiency of individual Muon Trigger elements, registration of information about some Muon Trigger devices and present previously obtained results in interactive presentation layer. A broad variety of different database and programming concepts for design of Muon Trigger monitoring system was presented in this article. The structure and architecture of the system and its principle of operation were described. One of ideas for building this system is use object-oriented programming and design techniques to describe real electronics systems through abstract object models stored in database and implement these models in Java language.

Dehydrogenation and dehalogenation of amines in MALDI-TOF MS investigated by isotopic labeling.

PubMed

Kang, Chuanqing; Zhou, Yihan; Du, Zhijun; Bian, Zheng; Wang, Jianwei; Qiu, Xuepeng; Gao, Lianxun; Sun, Yuequan

2013-12-01

Secondary and tertiary amines have been reported to form [M-H](+) that correspond to dehydrogenation in matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS). In this investigation, we studied the dehydrogenation of amines in MALDI-TOF MS by isotopic labeling. Aliphatic amines were labeled with deuterium on the methylene of an N-benzyl group, which resulted in the formation of [M-D](+) and [M-H](+) ions by dedeuteration and dehydrogenation, respectively. This method revealed the proton that was removed. The spectra of most tertiary amines with an N-benzyl group showed high-intensity [M-D](+) and [M-H](+) ion peaks, whereas those of secondary amines showed low-intensity ion peaks. Ratios between the peak intensities of [M-D](+) and [M-H](+) greater than 1 suggested chemoselective dehydrogenation at the N-benzyl groups. The presence of an electron donor group on the N-benzyl groups enhanced the selectivity. The dehalogenation of amines with an N-(4-halobenzyl) group was also observed alongside dehydrogenation. The amino ions from dehalogenation can undergo second dehydrogenation. These results provide the first direct evidence about the position at which dehydrogenation of an amine occurs and the first example of dehalogenation of haloaromatic compounds in MALDI-TOF MS. These results should be helpful in the structural identification and elucidation of synthetic and natural molecules. Copyright © 2013 John Wiley & Sons, Ltd.

Intact Cell MALDI-TOF MS on Sperm: A Molecular Test For Male Fertility Diagnosis.

PubMed

Soler, Laura; Labas, Valérie; Thélie, Aurore; Grasseau, Isabelle; Teixeira-Gomes, Ana-Paula; Blesbois, Elisabeth

2016-06-01

Currently, evaluation of sperm quality is primarily based on in vitro measures of sperm function such as motility, viability and/or acrosome reaction. However, results are often poorly correlated with fertility, and alternative diagnostic tools are therefore needed both in veterinary and human medicine. In a recent pilot study, we demonstrated that MS profiles from intact chicken sperm using MALDI-TOF profiles could detect significant differences between fertile/subfertile spermatozoa showing that such profiles could be useful for in vitro male fertility testing. In the present study, we performed larger standardized experimental procedures designed for the development of fertility- predictive mathematical models based on sperm cell MALDI-TOF MS profiles acquired through a fast, automated method. This intact cell MALDI-TOF MS-based method showed high diagnostic accuracy in identifying fertile/subfertile males in a large male population of known fertility from two distinct genetic lineages (meat and egg laying lines). We additionally identified 40% of the m/z peaks observed in sperm MS profiles through a top-down high-resolution protein identification analysis. This revealed that the MALDI-TOF MS spectra obtained from intact sperm cells contained a large proportion of protein degradation products, many implicated in important functional pathways in sperm such as energy metabolism, structure and movement. Proteins identified by our predictive model included diverse and important functional classes providing new insights into sperm function as it relates to fertility differences in this experimental system. Thus, in addition to the chicken model system developed here, with the use of appropriate models these methods should effectively translate to other animal taxa where similar tests for fertility are warranted. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

A designed experiments approach to optimizing MALDI-TOF MS spectrum processing parameters enhances detection of antibiotic resistance in Campylobacter jejuni

USDA-ARS?s Scientific Manuscript database

MALDI-TOF MS has been utilized as a reliable and rapid tool for microbial fingerprinting at the genus and species levels. Recently, there has been keen interest in using MALDI-TOF MS beyond the genus and species levels to rapidly identify antibiotic resistant strains of bacteria. The purpose of this...

MALDI-TOF mass spectrometry for rapid diagnosis of postoperative endophthalmitis.

PubMed

Mailhac, Adriane; Durand, Harmonie; Boisset, Sandrine; Maubon, Danièle; Berger, Francois; Maurin, Max; Chiquet, Christophe; Bidart, Marie

2017-01-30

This study describes an innovative strategy for rapid detection and identification of bacteria causing endophthalmitis, combining the use of an automated blood culture system with MALDI-TOF mass spectrometry methodology. Using this protocol, we could identify 96% of 45 bacterial strains isolated from vitreous samples collected in acute post-operative endophthalmitis patients. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessment of various parameters to improve MALDI-TOF MS reference spectra libraries constructed for the routine identification of filamentous fungi.

PubMed

Normand, Anne-Cécile; Cassagne, Carole; Ranque, Stéphane; L'ollivier, Coralie; Fourquet, Patrick; Roesems, Sam; Hendrickx, Marijke; Piarroux, Renaud

2013-04-08

The poor reproducibility of matrix-assisted desorption/ionization time-of-flight (MALDI-TOF) spectra limits the effectiveness of the MALDI-TOF MS-based identification of filamentous fungi with highly heterogeneous phenotypes in routine clinical laboratories. This study aimed to enhance the MALDI-TOF MS-based identification of filamentous fungi by assessing several architectures of reference spectrum libraries. We established reference spectrum libraries that included 30 filamentous fungus species with various architectures characterized by distinct combinations of the following: i) technical replicates, i.e., the number of analyzed deposits for each culture used to build a reference meta-spectrum (RMS); ii) biological replicates, i.e., the number of RMS derived from the distinct subculture of each strain; and iii) the number of distinct strains of a given species. We then compared the effectiveness of each library in the identification of 200 prospectively collected clinical isolates, including 38 species in 28 genera.Identification effectiveness was improved by increasing the number of both RMS per strain (p<10-4) and strains for a given species (p<10-4) in a multivariate analysis. Addressing the heterogeneity of MALDI-TOF spectra derived from filamentous fungi by increasing the number of RMS obtained from distinct subcultures of strains included in the reference spectra library markedly improved the effectiveness of the MALDI-TOF MS-based identification of clinical filamentous fungi.

Assessment of various parameters to improve MALDI-TOF MS reference spectra libraries constructed for the routine identification of filamentous fungi

PubMed Central

2013-01-01

Background The poor reproducibility of matrix-assisted desorption/ionization time-of-flight (MALDI-TOF) spectra limits the effectiveness of the MALDI-TOF MS-based identification of filamentous fungi with highly heterogeneous phenotypes in routine clinical laboratories. This study aimed to enhance the MALDI-TOF MS-based identification of filamentous fungi by assessing several architectures of reference spectrum libraries. Results We established reference spectrum libraries that included 30 filamentous fungus species with various architectures characterized by distinct combinations of the following: i) technical replicates, i.e., the number of analyzed deposits for each culture used to build a reference meta-spectrum (RMS); ii) biological replicates, i.e., the number of RMS derived from the distinct subculture of each strain; and iii) the number of distinct strains of a given species. We then compared the effectiveness of each library in the identification of 200 prospectively collected clinical isolates, including 38 species in 28 genera. Identification effectiveness was improved by increasing the number of both RMS per strain (p<10-4) and strains for a given species (p<10-4) in a multivariate analysis. Conclusion Addressing the heterogeneity of MALDI-TOF spectra derived from filamentous fungi by increasing the number of RMS obtained from distinct subcultures of strains included in the reference spectra library markedly improved the effectiveness of the MALDI-TOF MS-based identification of clinical filamentous fungi. PMID:23565856

Visualization of lenticulostriate arteries at 3T: Optimization of slice-selective off-resonance sinc pulse-prepared TOF-MRA and its comparison with flow-sensitive black-blood MRA.

PubMed

Okuchi, Sachi; Okada, Tomohisa; Fujimoto, Koji; Fushimi, Yasutaka; Kido, Aki; Yamamoto, Akira; Kanagaki, Mitsunori; Dodo, Toshiki; Mehemed, Taha M; Miyazaki, Mitsue; Zhou, Xiangzhi; Togashi, Kaori

2014-06-01

To optimize visualization of lenticulostriate artery (LSA) by time-of-flight (TOF) magnetic resonance angiography (MRA) with slice-selective off-resonance sinc (SORS) saturation transfer contrast pulses and to compare capability of optimal TOF-MRA and flow-sensitive black-blood (FSBB) MRA to visualize the LSA at 3T. This study was approved by the local ethics committee, and written informed consent was obtained from all the subjects. TOF-MRA was optimized in 20 subjects by comparing SORS pulses of different flip angles: 0, 400°, and 750°. Numbers of LSAs were counted. The optimal TOF-MRA was compared to FSBB-MRA in 21 subjects. Images were evaluated by the numbers and length of visualized LSAs. LSAs were significantly more visualized in TOF-MRA with SORS pulses of 400° than others (P < .003). When the optimal TOF-MRA was compared to FSBB-MRA, the visualization of LSA using FSBB (mean branch numbers 11.1, 95% confidence interval (CI) 10.0-12.1; mean total length 236 mm, 95% CI 210-263 mm) was significantly better than using TOF (4.7, 95% CI 4.1-5.3; 78 mm, 95% CI 67-89 mm) for both numbers and length of the LSA (P < .0001). LSA visualization was best with 400° SORS pulses for TOF-MRA but FSBB-MRA was better than TOF-MRA, which indicates its clinical potential to investigate the LSA on a 3T magnetic resonance imaging. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

Readout electronics for CBM-TOF super module quality evaluation based on 10 Gbps ethernet

NASA Astrophysics Data System (ADS)

Jiang, D.; Cao, P.; Huang, X.; Zheng, J.; Wang, Q.; Li, B.; Li, J.; Liu, S.; An, Q.

2017-07-01

The Compressed Baryonic Matter-Time of Flight (CBM-TOF) wall uses high performance of Multi-gap Resistive Plate Chambers (MRPC) assembled in super modules to identify charged particles with high channel density and high measurement precision at high event rate. Electronics meet the challenge for reading data out from a super module at high speed of about 6 Gbps in real time. In this paper, the readout electronics for CBM-TOF super module quality evaluation is proposed based on 10 Gigabit Ethernet. The digitized TOF data from one super module will be concentrated at the front-end electronics residing on the side of the super module and transmitted to an extreme speed readout module (XSRM) housed in the backend crate through the PCI Express (PCIe) protocol via optic channels. Eventually, the XSRM transmits data to the data acquisition (DAQ) system through four 10 Gbps Ethernet ports in real time. This readout structure has advantages of high performance and expansibility. Furthermore, it is easy to operate. Test results on the prototype show that the overall data readout performance for each XSRM can reach up to 28.8 Gbps, which means XSRM can meet the requirement of reading data out from 4 super modules with 1280 channels in real time.

MALDI-TOF MS is more accurate than VITEK II ANC card and API Rapid ID 32 A system for the identification of Clostridium species.

PubMed

Kim, Young Jin; Kim, Si Hyun; Park, Hyun-Jung; Park, Hae-Geun; Park, Dongchul; Song, Sae Am; Lee, Hee Joo; Yong, Dongeun; Choi, Jun Yong; Kook, Joong-Ki; Kim, Hye Ran; Shin, Jeong Hwan

2016-08-01

All 50 Clostridium difficile strains were definitely identified by Vitek2 system, Rapid ID 32A system, and MALDI-TOF. For 18 non-difficile Clostridium strains, the identification results were correct in 0, 2, and 17 strains by Vitek2, Rapid ID 32A, and MALDI-TOF, respectively. MALDI-TOF could be used as the primary tool for identification of Clostridium species. Copyright © 2016 Elsevier Ltd. All rights reserved.

MALDI-TOF Mass Spectrometry for the Detection and Differentiation of Entamoeba histolytica and Entamoeba dispar

PubMed Central

Calderaro, Adriana; Piergianni, Maddalena; Buttrini, Mirko; Montecchini, Sara; Piccolo, Giovanna; Gorrini, Chiara; Rossi, Sabina; Chezzi, Carlo; Arcangeletti, Maria Cristina; Medici, Maria Cristina; De Conto, Flora

2015-01-01

Detection of Entamoeba histolytica and its differentiation from Entamoeba dispar is an important goal of the clinical parasitology laboratory. The aim of this study was the identification and differentiation of E. histolytica and E. dispar by MALDI-TOF MS, in order to evaluate the application of this technique in routine diagnostic practice. MALDI-TOF MS was applied to 3 amebic reference strains and to 14 strains isolated from feces that had been differentiated by molecular methods in our laboratory. Protein extracts from cultures of these strains (axenic cultures for the 3 reference strains and monoxenic cultures for the 14 field isolates) were analyzed by MALDI-TOF MS and the spectra obtained were analyzed by statistical software. Five peaks discriminating between E. histolytica and E. dispar reference strains were found by protein profile analysis: 2 peaks (8,246 and 8,303 Da) specific for E. histolytica and 3 (4,714; 5,541; 8,207 Da) for E. dispar. All clinical isolates except one showed the discriminating peaks expected for the appropriate species. For 2 fecal samples from which 2 strains (1 E. histolytica and 1 E. dispar) out of the 14 included in this study were isolated, the same discriminating peaks found in the corresponding isolated amebic strains were detected after only 12h (E. histolytica) and 24h (E. dispar) of incubation of the fecal samples in Robinson’s medium without serum. Our study shows that MALDI-TOF MS can be used to discriminate between E. histolytica and E. dispar using in vitro xenic cultures and it also could have potential for the detection of these species in clinical samples. PMID:25874612

Rapid and reliable discrimination between Shigella species and Escherichia coli using MALDI-TOF mass spectrometry.

PubMed

Paauw, Armand; Jonker, Debby; Roeselers, Guus; Heng, Jonathan M E; Mars-Groenendijk, Roos H; Trip, Hein; Molhoek, E Margo; Jansen, Hugo-Jan; van der Plas, Jan; de Jong, Ad L; Majchrzykiewicz-Koehorst, Joanna A; Speksnijder, Arjen G C L

2015-01-01

E. coli-Shigella species are a cryptic group of bacteria in which the Shigella species are distributed within the phylogenetic tree of E. coli. The nomenclature is historically based and the discrimination of these genera developed as a result of the epidemiological need to identify the cause of shigellosis, a severe disease caused by Shigella species. For these reasons, this incorrect classification of shigellae persists to date, and the ability to rapidly characterize E. coli and Shigella species remains highly desirable. Until recently, existing matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) assays used to identify bacteria could not discriminate between E. coli and Shigella species. Here we present a rapid classification method for the E. coli-Shigella phylogroup based on MALDI-TOF MS which is supported by genetic analysis. E. coli and Shigella isolates were collected and genetically characterized by MLVA. A custom reference library for MALDI-TOF MS that represents the genetic diversity of E. coli and Shigella strains was developed. Characterization of E. coli and Shigella species is based on an approach with Biotyper software. Using this reference library it was possible to distinguish between Shigella species and E. coli. Of the 180 isolates tested, 94.4% were correctly classified as E. coli or shigellae. The results of four (2.2%) isolates could not be interpreted and six (3.3%) isolates were classified incorrectly. The custom library extends the existing MALDI-TOF MS method for species determination by enabling rapid and accurate discrimination between Shigella species and E. coli. Copyright © 2015 Elsevier GmbH. All rights reserved.

Hybrid Ion-Detector/Data-Acquisition System for a TOF-MS

NASA Technical Reports Server (NTRS)

Burton, William D., Jr.; Schultz, J. Albert; Vaughn, Valentine; McCully, Michael; Ulrich, Steven; Egan, Thomas F.

2006-01-01

A modified ion-detector/data-acquisition system has been devised to increase the dynamic range of a time-of-flight mass spectrometer (TOF-MS) that, previously, included a microchannel-plate detector and a data-acquisition system based on counting pulses and time-tagging them by use of a time-to-digital converter (TDC). The dynamic range of the TOF-MS was limited by saturation of the microchannel plate detector, which can handle no more than a few million counts per second. The modified system includes (1) a combined microchannel plate/discrete ion multiplier and (2) a hybrid data-acquisition system that simultaneously performs analog current or voltage measurements and multianode single-ion-pulse-counting time-of-flight measurements to extend the dynamic range of a TDC into the regime in which a mass peak comprises multiple ions arriving simultaneously at the detector. The multianode data are used to determine, in real time, whether the detector is saturated. When saturation is detected, the data-acquisition system selectively enables circuitry that simultaneously determines the ion-peak intensity by measuring the time profile of the analog current or voltage detector-output signal.

Rapid Identification of Microorganisms from Positive Blood Culture by MALDI-TOF MS After Short-Term Incubation on Solid Medium.

PubMed

Curtoni, Antonio; Cipriani, Raffaella; Marra, Elisa Simona; Barbui, Anna Maria; Cavallo, Rossana; Costa, Cristina

2017-01-01

Matrix-assisted laser-desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a useful tool for rapid identification of microorganisms. Unfortunately, its direct application to positive blood culture is still lacking standardized procedures. In this study, we evaluated an easy- and rapid-to-perform protocol for MALDI-TOF MS direct identification of microorganisms from positive blood culture after a short-term incubation on solid medium. This protocol was used to evaluate direct identification of microorganisms from 162 positive monomicrobial blood cultures; at different incubation times (3, 5, 24 h), MALDI-TOF MS assay was performed from the growing microorganism patina. Overall, MALDI-TOF MS concordance with conventional methods at species level was 60.5, 80.2, and 93.8% at 3, 5, and 24 h, respectively. Considering only bacteria, the identification performances at species level were 64.1, 85.0, and 94.1% at 3, 5, and 24 h, respectively. This protocol applied to a commercially available MS typing system may represent, a fast and powerful diagnostic tool for pathogen direct identification and for a promptly and pathogen-driven antimicrobial therapy in selected cases.

[Studies of bacterial typing with MALDI-TOF].

PubMed

Culebras, Esther; Alvarez-Buylla, Adela; Jose Artacho Reinoso, M; Antonio Lepe, Jose

2016-06-01

MALDI-TOF (matrix-assisted laser desorption ionization time-of-flight) mass spectrometry has emerged as a potential tool for microbial characterization and identification in many microbiology departments. The technology is rapid, sensitive, and relatively inexpensive in terms of both the labour and costs involved. This review provides an overview on its utility for strain typing and epidemiological studies and explains the methodological approaches that can be used both for the performance of the technique and for the analysis of results. Finally, the review summarizes studies on the characterization of distinct bacterial species. Copyright © 2016 Elsevier España, S.L.U. All rights reserved.

Profiling LC-DAD-ESI-TOF MS method for the determination of phenolic metabolites from avocado (Persea americana).

PubMed

Hurtado-Fernández, Elena; Carrasco-Pancorbo, Alegría; Fernández-Gutiérrez, Alberto

2011-03-23

A powerful HPLC-DAD-ESI-TOF MS method was established for the efficient identification of the chemical constituents in the methanolic extracts of avocado (Persea americana). Separation and detection conditions were optimized by using a standard mix containing 39 compounds belonging to phenolic acids and different categories of flavonoids, analytes that could be potentially present in the avocado extracts. Optimum LC separation was achieved on a Zorbax Eclipse Plus C18 analytical column (4.6×150 mm, 1.8 μm particle size) by gradient elution with water+acetic acid (0.5%) and acetonitrile as mobile phases, at a flow rate of 1.6 mL/min. The detection was carried out by ultraviolet-visible absorption and ESI-TOF MS. The developed method was applied to the study of 3 different varieties of avocado, and 17 compounds were unequivocally identified with standards. Moreover, around 25 analytes were tentatively identified by taking into account the accuracy and isotopic information provided by TOF MS.

Independent component analysis for the extraction of reliable protein signal profiles from MALDI-TOF mass spectra.

PubMed

Mantini, Dante; Petrucci, Francesca; Del Boccio, Piero; Pieragostino, Damiana; Di Nicola, Marta; Lugaresi, Alessandra; Federici, Giorgio; Sacchetta, Paolo; Di Ilio, Carmine; Urbani, Andrea

2008-01-01

Independent component analysis (ICA) is a signal processing technique that can be utilized to recover independent signals from a set of their linear mixtures. We propose ICA for the analysis of signals obtained from large proteomics investigations such as clinical multi-subject studies based on MALDI-TOF MS profiling. The method is validated on simulated and experimental data for demonstrating its capability of correctly extracting protein profiles from MALDI-TOF mass spectra. The comparison on peak detection with an open-source and two commercial methods shows its superior reliability in reducing the false discovery rate of protein peak masses. Moreover, the integration of ICA and statistical tests for detecting the differences in peak intensities between experimental groups allows to identify protein peaks that could be indicators of a diseased state. This data-driven approach demonstrates to be a promising tool for biomarker-discovery studies based on MALDI-TOF MS technology. The MATLAB implementation of the method described in the article and both simulated and experimental data are freely available at http://www.unich.it/proteomica/bioinf/.

Ga + TOF-SIMS lineshape analysis for resolution enhancement of MALDI MS spectra of a peptide mixture

NASA Astrophysics Data System (ADS)

Malyarenko, D. I.; Chen, H.; Wilkerson, A. L.; Tracy, E. R.; Cooke, W. E.; Manos, D. M.; Sasinowski, M.; Semmes, O. J.

2004-06-01

The use of mass spectrometry to obtain molecular profiles indicative of alteration of concentrations of peptides in body fluids is currently the subject of intense investigation. For surface-based time-of-flight mass spectrometry the reliability and specificity of such profiling methods depend both on the resolution of the measuring instrument and on the preparation of samples. The present work is a part of a program to use Ga + beam TOF-SIMS alone, and as an adjunct to MALDI, in the development of reliable protein and peptide markers for diseases. Here, we describe techniques to prepare samples of relatively high-mass peptides, which serve as calibration standards and proxies for biomarkers. These are: Arg8-vasopressin, human angiotensin II, and somatostatin. Their TOF-SIMS spectra show repeatable characteristic features, with mass resolution exceeding 2000, including parent peaks and chemical adducts. The lineshape analysis for high-resolution parent peaks is shown to be useful for filter construction and deconvolution of inferior resolution SELDI-TOF spectra of calibration peptide mixture.

Multiplex detection of protein toxins using MALDI-TOF-TOF tandem mass spectrometry: application in unambiguous toxin detection from bioaerosol.

PubMed

Alam, Syed Imteyaz; Kumar, Bhoj; Kamboj, Dev Vrat

2012-12-04

Protein toxins, such as botulinum neurotoxins (BoNTs), Clostridium perfringens epsilon toxin (ETX), staphylococcal enterotoxin B (SEB), shiga toxin (STX), and plant toxin ricin, are involved in a number of diseases and are considered as potential agents for bioterrorism and warfare. From a bioterrorism and warfare perspective, these agents are likely to cause maximum damage to a civilian or military population through an inhalational route of exposure and aerosol is considered the envisaged mode of delivery. Unambiguous detection of toxin from aerosol is of paramount importance, both for bringing mitigation protocols into operation and for implementation of effective medical countermeasures, in case a "biological cloud" is seen over a population. A multiplex, unambiguous, and qualitative detection of protein toxins is reported here using tandem mass spectrometry with MALDI-TOF-TOF. The methodology involving simple sample processing steps was demonstrated to identify toxins (ETX, Clostridium perfringes phospholipase C, and SEB) from blind spiked samples. The novel directed search approach using a list of unique peptides was used to identify toxins from a complex protein mixture. The bioinformatic analysis of seven protein toxins for elucidation of unique peptides with conservation status across all known sequences provides a high confidence for detecting toxins originating from any geographical location and source organism. Use of tandem MS data with peptide sequence information increases the specificity of the method. A prototype for generation of aerosol using a nebulizer and collection using a cyclone collector was used to provide a proof of concept for unambiguous detection of toxin from aerosol using precursor directed tandem mass spectrometry combined with protein database searching. ETX prototoxin could be detected from aerosol at 0.2 ppb concentration in aerosol.

Absolute Quantification of Rifampicin by MALDI Imaging Mass Spectrometry Using Multiple TOF/TOF Events in a Single Laser Shot

NASA Astrophysics Data System (ADS)

Prentice, Boone M.; Chumbley, Chad W.; Caprioli, Richard M.

2017-01-01

Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) allows for the visualization of molecular distributions within tissue sections. While providing excellent molecular specificity and spatial information, absolute quantification by MALDI IMS remains challenging. Especially in the low molecular weight region of the spectrum, analysis is complicated by matrix interferences and ionization suppression. Though tandem mass spectrometry (MS/MS) can be used to ensure chemical specificity and improve sensitivity by eliminating chemical noise, typical MALDI MS/MS modalities only scan for a single MS/MS event per laser shot. Herein, we describe TOF/TOF instrumentation that enables multiple fragmentation events to be performed in a single laser shot, allowing the intensity of the analyte to be referenced to the intensity of the internal standard in each laser shot while maintaining the benefits of MS/MS. This approach is illustrated by the quantitative analyses of rifampicin (RIF), an antibiotic used to treat tuberculosis, in pooled human plasma using rifapentine (RPT) as an internal standard. The results show greater than 4-fold improvements in relative standard deviation as well as improved coefficients of determination (R2) and accuracy (>93% quality controls, <9% relative errors). This technology is used as an imaging modality to measure absolute RIF concentrations in liver tissue from an animal dosed in vivo. Each microspot in the quantitative image measures the local RIF concentration in the tissue section, providing absolute pixel-to-pixel quantification from different tissue microenvironments. The average concentration determined by IMS is in agreement with the concentration determined by HPLC-MS/MS, showing a percent difference of 10.6%.

Efficient identification of Malassezia yeasts by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

PubMed

Kolecka, A; Khayhan, K; Arabatzis, M; Velegraki, A; Kostrzewa, M; Andersson, A; Scheynius, A; Cafarchia, C; Iatta, R; Montagna, M T; Youngchim, S; Cabañes, F J; Hoopman, P; Kraak, B; Groenewald, M; Boekhout, T

2014-02-01

Infections caused by Malassezia yeasts are most likely underdiagnosed, because fatty acid supplementation is needed for growth. Rapid identification of Malassezia species is essential for appropriate treatment of Malassezia-related skin infections, fungaemia and nosocomial outbreaks in neonates, children and adults and can be life-saving for those patients. Ma-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been reported to be a rapid and reliable diagnostic tool to identify clinically important yeasts, but so far no data have been reported on identification of Malassezia isolates with this technique. To create an extensive database of main mass spectra (MSPs) that will allow quick identification of Malassezia species by MALDI-TOF MS. An in-house library of 113 MSPs was created from 48 reference strains from the CBS-KNAW yeast collection. The in-house library was challenged with two test sets of Malassezia strains, namely 165 reference strains from the CBS collection and 338 isolates collected in Greece, Italy, Sweden and Thailand. MALDI-TOF MS allowed correct identification of all 14 Malassezia spp. MALDI-TOF MS results were concordant with those of sequence analyses of the internal transcribed spacers (ITS1/ITS2) and the D1/D2 domains of the large subunit of the ribosomal DNA. Implementation of the MALDI-TOF MS system as a routine identification tool will contribute to correct identification of Malassezia yeasts with minimal effort and in a short turnaround time, which is especially important for the rapid identification of Malassezia in skin diseases and nosocomial outbreaks. © 2013 British Association of Dermatologists.

PTR-3-TOF a novel in-situ instrument for studying the lifecycle of reactive organic carbon in the atmosphere

NASA Astrophysics Data System (ADS)

Hansel, Armin; Breitenlechner, Martin; Fischer, Lukas; Hainer, Markus

2017-04-01

Existing proton transfer reaction time of flight (PTR-TOF) instruments are known to detect volatile organic compounds (VOCs) and could in principle also detect highly oxidized organic compounds such as low volatility organic compounds (LVOC) but PTR-TOF inlets were not optimized to avoid wall losses of such low volatility compounds. In addition PTR-TOF is not sensitive enough to quantify second order and even higher order oxidation products at atmospherically relevant concentrations. To solve this problem, as well as to enable bridging the gap in understanding how atmospherically relevant BVOC form SVOC, LVOC and even ELVOC, we developed the PTR3, a compact and field deployable ultrasensitive instrument based on chemical ionization mass spectrometry. Here we report first results from PTR-3-TOF measurements at Hyytiälä where we measured concentrations and fluxes of precursor gases (BVOC) and their oxidation products: semi and low volatile organic compounds. The recently developed PTR-3-TOF instrument uses a discharge ion source coupled to a contact free inlet system running at high sample flow rates through the novel reaction chamber at 80 mbar. The PTR-3 front part is coupled to TOFWERK's newest Long-TOF mass analyzer. The first prototype has sensitivities of up to 20.000 cps per ppb and a mass resolution of 8.000 m/Δm. The instrument has been successfully tested at CERN for the CLOUD campaign in 2015. During pure α-pinene ozonolysis experiments at low NOx conditions we observed in total several hundred peaks in the mass spectrum, including α-Pinene present in the ppb range, first and higher order oxidation products present in the ppt range and highly oxydized α-pinene monomers and dimers (e.g., C20H30O18H+; m/z = 559.1506 Th) in the low ppq range and even sub-ppq range. The advantage of this new technology based on positive ion chemistry is the capability to measure precursor gases as well as condensing- and even nucleating vapors.

Measurement of cosmic muon angular distribution and vertical integrated flux by 2 m × 2 m RPC stack at IICHEP-Madurai

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pethuraj, S.; Datar, V.M.; Majumder, G.

2017-09-01

The 50 kton INO-ICAL is a proposed underground high energy physics experiment at Theni, India (9{sup o}57' N , 77{sup o}16' E ) to study the neutrino oscillation parameters using atmospheric neutrinos. The Resistive Plate Chamber (RPC) has been chosen as the active detector element for the ICAL detector. An experimental setup consisting of 12 layers of glass RPCs of size 2 m × 2 m has been built at IICHEP, Madurai to study the long term stability and performance of RPCs which are produced on a large scale in Indian industry. In this paper, the studies on the performancemore » of RPCs are presented along with the angular distribution of muons at Madurai (9{sup o}56' N ,78{sup o}00' E and Altitude ≈ 160 m from sea level).« less

Evaluation of Three MALDI-TOF Mass Spectrometry Libraries for the Identification of Filamentous Fungi in Three Clinical Microbiology Laboratories in Manitoba, Canada.

PubMed

Stein, Markus; Tran, Vanessa; Nichol, Kimberly A; Lagacé-Wiens, Philippe; Pieroni, Peter; Adam, Heather J; Turenne, Christine; Walkty, Andrew J; Normand, Anne-Cécile; Hendrickx, Marijke; Piarroux, Renaud; Karlowsky, James A

2018-06-12

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is commonly used by clinical microbiology laboratories to identify bacterial pathogens and yeasts, but not for the identification of moulds. Recent progress in extraction protocols and the composition of comparative libraries support potential application of MALDI-TOF MS for mould identification in clinical microbiology laboratories. We evaluated the performance of the Bruker Microflex ™ MALDI-TOF MS instrument (Billerica, MA, USA) to identify clinical isolates and reference strains of moulds using three libraries, the Bruker mould library, the National Institutes of Health (NIH) library, and the Mass Spectrometry Identification (MSI) online library, and compared those results to conventional (morphological) and molecular (18S/ITS; gold standard) identification methods. All three libraries demonstrated greater accuracy in genus identification (≥94.9%) than conventional methods (86.4%). MALDI-TOF MS identified 73.3% of isolates to species-level compared to only 31.7% by conventional methods. The MSI library demonstrated the highest rate of species-level identification (72.0%) compared to NIH (19.5%) and Bruker (13.6%) libraries. Greater than 20% of moulds remained unidentified to species-level by all three MALDI-TOF MS libraries primarily because of library limitations or imperfect spectra. The overall identification rate of each MALDI-TOF MS library depended on the number of species and the number of spectra representing each species in the library. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

SELDI-TOF MS of quadruplicate urine and serum samples to evaluate changes related to storage conditions.

PubMed

Traum, Avram Z; Wells, Meghan P; Aivado, Manuel; Libermann, Towia A; Ramoni, Marco F; Schachter, Asher D

2006-03-01

Proteomic profiling with SELDI-TOF MS has facilitated the discovery of disease-specific protein profiles. However, multicenter studies are often hindered by the logistics required for prompt deep-freezing of samples in liquid nitrogen or dry ice within the clinic setting prior to shipping. We report high concordance between MS profiles within sets of quadruplicate split urine and serum samples deep-frozen at 0, 2, 6, and 24 h after sample collection. Gage R&R results confirm that deep-freezing times are not a statistically significant source of SELDI-TOF MS variability for either blood or urine.

Exploring Hamiltonian dielectric solvent molecular dynamics

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-09-01

Hamiltonian dielectric solvent (HADES) is a recent method [7,25], which enables Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric continua. Sample simulations of an α-helical decapeptide with and without explicit solvent demonstrate the high efficiency of HADES-MD. Addressing the folding of this peptide by replica exchange MD we study the properties of HADES by comparing melting curves, secondary structure motifs and salt bridges with explicit solvent results. Despite the unoptimized ad hoc parametrization of HADES, calculated reaction field energies correlate well with numerical grid solutions of the dielectric Poisson equation.

Gold patterned biochips for on-chip immuno-MALDI-TOF MS: SPR imaging coupled multi-protein MS analysis.

PubMed

Kim, Young Eun; Yi, So Yeon; Lee, Chang-Soo; Jung, Yongwon; Chung, Bong Hyun

2012-01-21

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analysis of immuno-captured target protein efficiently complements conventional immunoassays by offering rich molecular information such as protein isoforms or modifications. Direct immobilization of antibodies on MALDI solid support enables both target enrichment and MS analysis on the same plate, allowing simplified and potentially multiplexing protein MS analysis. Reliable on-chip immuno-MALDI-TOF MS for multiple biomarkers requires successful adaptation of antibody array biochips, which also must accommodate consistent reaction conditions on antibody arrays during immuno-capture and MS analysis. Here we developed a facile fabrication process of versatile antibody array biochips for reliable on-chip MALDI-TOF-MS analysis of multiple immuno-captured proteins. Hydrophilic gold arrays surrounded by super-hydrophobic surfaces were formed on a gold patterned biochip via spontaneous chemical or protein layer deposition. From antibody immobilization to MALDI matrix treatment, this hydrophilic/phobic pattern allowed highly consistent surface reactions on each gold spot. Various antibodies were immobilized on these gold spots both by covalent coupling or protein G binding. Four different protein markers were successfully analyzed on the present immuno-MALDI biochip from complex protein mixtures including serum samples. Tryptic digests of captured PSA protein were also effectively detected by on-chip MALDI-TOF-MS. Moreover, the present MALDI biochip can be directly applied to the SPR imaging system, by which antibody and subsequent antigen immobilization were successfully monitored.

Contrast Enhancement in TOF cerebral angiography at 7 T using Saturation and MT pulses under SAR constraints: impact of VERSE and sparse pulses

PubMed Central

Schmitter, Sebastian; Bock, Michael; Johst, Sören; Auerbach, Edward J.; Uğurbil, Kâmil; Van de Moortele, Pierre-François

2011-01-01

Cerebral 3D time of flight (TOF) angiography significantly benefits from ultra high fields, mainly due to higher SNR and to longer T1 relaxation time of static brain tissues, however, SAR significantly increases with B0. Thus, additional RF pulses commonly used at lower field strengths to improve TOF contrast such as saturation of venous signal and improved background suppression by magnetization transfer typically cannot be used at higher fields. In this work we aimed at reducing SAR for each RF pulse category in a TOF sequence. We use the VERSE principle for the slab selective TOF excitation as well as the venous saturation RF pulses. Additionally, MT pulses are implemented by sparsely applying the pulses only during acquisition of the central k-space lines to limit their SAR contribution. Image quality, angiographic contrast and SAR reduction were investigated as a function of VERSE parameters and of the total number of MT pulses applied. Based on these results, a TOF protocol was generated that increases the angiographic contrast by more than 50% and reduces subcutaneous fat signal while keeping the resulting SAR within regulatory limits. PMID:22139829

Understanding the Changes to Biomass Surface Characteristics after Ammonia and Organosolv Pretreatments by Using Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tolbert, Allison K.; Yoo, Chang Geun; Ragauskas, Arthur J.

Surface characteristic changes to poplar after ammonia and organosolv pretreatments were investigated by means of time-of-flight secondary-ion mass spectrometry (TOF-SIMS) analysis. Whereas normalized total polysaccharides and lignin contents on the surface differed from bulk chemical compositions, the surface cellulose ions detected by TOF-SIMS showed the same value trend as the cellulose content in the biomass. In addition, the lignin syringyl/guaiacyl ratio according to TOF-SIMS results showed the same trend as the ratio measured by means of NMR spectroscopic analysis, even though the ratio scales for each method were different. A similar correlation was determined between the surface cellulose and glucosemore » release after enzymatic hydrolysis. Lastly, these results demonstrate that surface characterization using TOF-SIMS can provide important information about the effects of pretreatment on biomass properties and its hydrolysis.« less

Understanding the Changes to Biomass Surface Characteristics after Ammonia and Organosolv Pretreatments by Using Time-of-Flight Secondary-Ion Mass Spectrometry (TOF-SIMS)

DOE PAGES

Tolbert, Allison K.; Yoo, Chang Geun; Ragauskas, Arthur J.

2017-03-20

Surface characteristic changes to poplar after ammonia and organosolv pretreatments were investigated by means of time-of-flight secondary-ion mass spectrometry (TOF-SIMS) analysis. Whereas normalized total polysaccharides and lignin contents on the surface differed from bulk chemical compositions, the surface cellulose ions detected by TOF-SIMS showed the same value trend as the cellulose content in the biomass. In addition, the lignin syringyl/guaiacyl ratio according to TOF-SIMS results showed the same trend as the ratio measured by means of NMR spectroscopic analysis, even though the ratio scales for each method were different. A similar correlation was determined between the surface cellulose and glucosemore » release after enzymatic hydrolysis. Lastly, these results demonstrate that surface characterization using TOF-SIMS can provide important information about the effects of pretreatment on biomass properties and its hydrolysis.« less

GC-TOF/MS-based metabolomic profiling of estrogen deficiency-induced obesity in ovariectomized rats

PubMed Central

Ma, Bo; Zhang, Qi; Wang, Guang-ji; A, Ji-ye; Wu, Di; Liu, Ying; Cao, Bei; Liu, Lin-sheng; Hu, Ying-ying; Wang, Yong-lu; Zheng, Ya-ya

2011-01-01

Aim: To explore the alteration of endogenous metabolites and identify potential biomarkers using metabolomic profiling with gas chromatography coupled a time-of-flight mass analyzer (GC/TOF-MS) in a rat model of estrogen-deficiency-induced obesity. Methods: Twelve female Sprague-Dawley rats six month of age were either sham-operated or ovariectomized (OVX). Rat blood was collected, and serum was analyzed for biomarkers using standard colorimetric methods with commercial assay kits and a metabolomic approach with GC/TOF-MS. The data were analyzed using multivariate statistical techniques. Results: A high body weight and body mass index inversely correlated with serum estradiol (E2) in the OVX rats compared to the sham rats. Estrogen deficiency also significantly increased serum total cholesterol, triglycerides, and low-density lipoprotein cholesterol. Utilizing GC/TOF-MS-based metabolomic analysis and the partial least-squares discriminant analysis, the OVX samples were discriminated from the shams. Elevated levels of cholesterol, glycerol, glucose, arachidonic acid, glutamic acid, glycine, and cystine and reduced alanine levels were observed. Serum glucose metabolism, energy metabolism, lipid metabolism, and amino acid metabolism were involved in estrogen-deficiency-induced obesity in OVX rats. Conclusion: The series of potential biomarkers identified in the present study provided fingerprints of rat metabolomic changes during obesity and an overview of multiple metabolic pathways during the progression of obesity involving glucose metabolism, lipid metabolism, and amino acid metabolism. PMID:21293480

Identification and Characterization of Cell Wall Proteins of a Toxic Dinoflagellate Alexandrium catenella Using 2-D DIGE and MALDI TOF-TOF Mass Spectrometry

PubMed Central

Wang, Da-Zhi; Dong, Hong-Po; Li, Cheng; Xie, Zhang-Xian; Lin, Lin; Hong, Hua-Sheng

2011-01-01

The cell wall is an important subcellular component of dinoflagellate cells with regard to various aspects of cell surface-associated ecophysiology, but the full range of cell wall proteins (CWPs) and their functions remain to be elucidated. This study identified and characterized CWPs of a toxic dinoflagellate, Alexandrium catenella, using a combination of 2D fluorescence difference gel electrophoresis (DIGE) and MALDI TOF-TOF mass spectrometry approaches. Using sequential extraction and temperature shock methods, sequentially extracted CWPs and protoplast proteins, respectively, were separated from A. catenella. From the comparison between sequentially extracted CWPs labeled with Cy3 and protoplast proteins labeled with Cy5, 120 CWPs were confidently identified in the 2D DIGE gel. These proteins gave positive identification of protein orthologues in the protein database using de novo sequence analysis and homology-based search. The majority of the prominent CWPs identified were hypothetical or putative proteins with unknown function or no annotation, while cell wall modification enzymes, cell wall structural proteins, transporter/binding proteins, and signaling and defense proteins were tentatively identified in agreement with the expected role of the extracellular matrix in cell physiology. This work represents the first attempt to investigate dinoflagellate CWPs and provides a potential tool for future comprehensive characterization of dinoflagellate CWPs and elucidation of their physiological functions. PMID:21904561

Surface and adsorbate structural analysis from time-of-flight scattering and recoiling spectrometry (TOF-SARS)

NASA Astrophysics Data System (ADS)

Rabalais, J. W.; Bu, H.; Roux, C.

1992-02-01

The methods of obtaining surface structural information from low energy ion scattering spectrometry are described. These methods include measurements of backscattering, forwardscattering, and recoiling intensities vs beam incident α, beam exit β, crystal azimuthal δ, and scattering Θ angles. References are provided which give examples of each different kind of measurement. The technique of time-of-flight scattering and recoiling spectrometry (TOF-SARS), which collects both scattered.and recoiled neutrals and ions simultaneously, is described. TOF-SARS data for the three surface phases, clean Ni{110}-(1 × 1), Ni{110}-(1 × 2)-H missing row, and Ni{110}-(2 × 1)-O missing row, are used to illustrate some of the structural measurements.

Polyphasic Approach Including MALDI-TOF MS/MS Analysis for Identification and Characterisation of Fusarium verticillioides in Brazilian Corn Kernels

PubMed Central

Chang, Susane; Porto Carneiro-Leão, Mariele; Ferreira de Oliveira, Benny; Souza-Motta, Cristina; Lima, Nelson; Santos, Cledir; Tinti de Oliveira, Neiva

2016-01-01

Fusarium verticillioides is considered one of the most important global sources of fumonisins contamination in food and feed. Corn is one of the main commodities produced in the Northeastern Region of Brazil. The present study investigated potential mycotoxigenic fungal strains belonging to the F. verticillioides species isolated from corn kernels in 3 different Regions of the Brazilian State of Pernambuco. A polyphasic approach including classical taxonomy, molecular biology, MALDI-TOF MS and MALDI-TOF MS/MS for the identification and characterisation of the F. verticillioides strains was used. Sixty F. verticillioides strains were isolated and successfully identified by classical morphology, proteomic profiles of MALDI-TOF MS, and by molecular biology using the species-specific primers VERT-1 and VERT-2. FUM1 gene was further detected for all the 60 F. verticillioides by using the primers VERTF-1 and VERTF-2 and through the amplification profiles of the ISSR regions using the primers (GTG)5 and (GACA)4. Results obtained from molecular analysis shown a low genetic variability among these isolates from the different geographical regions. All of the 60 F. verticillioides isolates assessed by MALDI-TOF MS/MS presented ion peaks with the molecular mass of the fumonisin B1 (721.83 g/mol) and B2 (705.83 g/mol). PMID:26927172

Characterisation of the aerobic bacterial flora of boid snakes: application of MALDI-TOF mass spectrometry.

PubMed

Plenz, Bastian; Schmidt, Volker; Grosse-Herrenthey, Anke; Krüger, Monika; Pees, Michael

2015-03-14

The aim of this study was to identify aerobic bacterial isolates from the respiratory tract of boids with matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry (MALDI-TOF MS). From 47 boid snakes, swabs from the oral cavity, tracheal wash samples and, in cases in which postmortem examination was performed, pulmonary tissue samples were taken. Each snake was classified as having inflammation of the respiratory tract and/or oral cavity, or without evidence of inflammation based on combination of clinical, cytological and histopathological findings. Samples collected from the respiratory tract and oral cavity were inoculated onto routine media and bacteria were cultured aerobically. All morphologically distinct individual colonies obtained were analysed using MALDI-TOF MS. Unidentified isolates detected in more than three snakes were selected for further 16S rDNA PCR and sequencing. Among all examined isolates (n=243), 49 per cent (n=119) could be sufficiently speciated using MALDI-TOF MS. Molecular biology revealed several bacterial species that have not been previously described in reptiles. With an average of 6.3 different isolates from the respiratory tract and/or oral cavity, boids with inflammatory disease harboured significantly more bacterial species than boids without inflammatory disease (average 2.8 isolates). British Veterinary Association.

MALDI-TOF mass spectrometry following short incubation on a solid medium is a valuable tool for rapid pathogen identification from positive blood cultures.

PubMed

Kohlmann, Rebekka; Hoffmann, Alexander; Geis, Gabriele; Gatermann, Sören

2015-01-01

Rapid identification of the causative microorganism is a key element in appropriate antimicrobial therapy of bloodstream infections. Whereas traditional analysis of positive blood cultures requires subculture over at least 16-24h prior to pathogen identification by, e.g. matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), sample preparation procedures enabling direct MALDI-TOF MS, i.e. without preceding subculture, are associated with additional effort and costs. Hence, we integrated an alternative MALDI-TOF MS approach in diagnostic routine using a short incubation on a solid medium. Positive blood cultures were routinely plated on chocolate agar plates and incubated for 4h (37 °C, 5% CO2). Subsequently, MALDI-TOF MS using a Microflex LT instrument (Bruker Daltonics) and direct smear method was performed once per sample. For successful identification of bacteria at species level, score cut-off values were used as proposed by the manufacturer (≥ 2.0) and in a modified form (≥ 1.5 for MALDI-TOF MS results referring to Gram-positive cocci and ≥ 1.7 for MALDI-TOF MS results referring to bacteria other than Gram-positive cocci). Further data analysis also included an assessment of the clinical impact of the MALDI-TOF MS result. Applying the modified score cut-off values, our approach led to an overall correct species identification in 69.5% with misidentification in 3.4% (original cut-offs: 49.2% and 1.8%, respectively); for Gram-positive cocci, correct identification in 68.4% (100% for Staphylococcus aureus and enterococci, 80% for beta-hemolytic streptococci), for Gram-negative bacteria, correct identification in 97.6%. In polymicrobial blood cultures, in 72.7% one of the pathogens was correctly identified. Results were not reliable for Gram-positive rods and yeasts. The approach was easy to implement in diagnostic routine. In cases with available clinical data and successful pathogen identification, in 51.1% our

MALDI-TOF mass spectrometry provides high accuracy in identification of Salmonella at species level but is limited to type or subtype Salmonella serovars.

PubMed

Kang, Lin; Li, Nan; Li, Ping; Zhou, Yang; Gao, Shan; Gao, Hongwei; Xin, Wenwen; Wang, Jinglin

2017-04-01

Salmonella can cause global foodborne illnesses in humans and many animals. The current diagnostic gold standard used for detecting Salmonella infection is microbiological culture followed by serological confirmation tests. However, these methods are complicated and time-consuming. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis offers some advantages in rapid identification, for example, simple and fast sample preparation, fast and automated measurement, and robust and reliable identification up to genus and species levels, possibly even to the strain level. In this study, we established a reference database for species identification using whole-cell MALDI-TOF MS; the database consisted of 12 obtained main spectra of the Salmonella culture collection strains belonged to seven serotypes. Eighty-two clinical isolates of Salmonella were identified using established database, and partial 16S rDNA gene sequencing and serological method were used as comparison. We found that MALDI-TOF mass spectrometry provided high accuracy in identification of Salmonella at species level but was limited to type or subtype Salmonella serovars. We also tried to find serovar-specific biomarkers and failed. Our study demonstrated that (a) MALDI-TOF MS was suitable for identification of Salmonella at species level with high accuracy and (b) that MALDI-TOF MS method presented in this study was not useful for serovar assignment of Salmonella currently, because of its low matching with serological method and (c) MALDI-TOF MS method presented in this study was not suitable to subtype S. typhimurium because of its low discriminatory ability.

Evaluation of two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems for the identification of Candida species.

PubMed

Lacroix, C; Gicquel, A; Sendid, B; Meyer, J; Accoceberry, I; François, N; Morio, F; Desoubeaux, G; Chandenier, J; Kauffmann-Lacroix, C; Hennequin, C; Guitard, J; Nassif, X; Bougnoux, M-E

2014-02-01

Candida spp. are responsible for severe infections in immunocompromised patients and those undergoing invasive procedures. The accurate identification of Candida species is important because emerging species can be associated with various antifungal susceptibility spectra. Conventional methods have been developed to identify the most common pathogens, but have often failed to identify uncommon species. Several studies have reported the efficiency of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for the identification of clinically relevant Candida species. In this study, we evaluated two commercially available MALDI-TOF systems, Andromas™ and Bruker Biotyper™, for Candida identification in routine diagnosis. For this purpose, we investigated 1383 Candida isolates prospectively collected in eight hospital laboratories during routine practice. MALDI-TOF MS results were compared with those obtained using conventional phenotypic methods. Analysis of rDNA gene sequences with internal transcribed regions or D1-D2 regions is considered the reference standard for identification. Both MALDI-TOF MS systems could accurately identify 98.3% of the isolates at the species level (1359/1383 for Andromas™; 1360/1383 for Bruker Biotyper™) vs. 96.5% for conventional techniques. Furthermore, whereas conventional methods failed to identify rare or emerging species, these were correctly identified by MALDI-TOF MS. Both MALDI-TOF MS systems are accurate and cost-effective alternatives to conventional methods for mycological identification of clinically relevant Candida species and should improve the diagnosis of fungal infections as well as patient management. © 2013 The Authors Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

The potential of combining ion trap/MS/MS and TOF/MS for identification of emerging contaminants

USGS Publications Warehouse

Ferrer, I.; Furlong, E.T.; Heine, C.E.; Thurman, E.M.

2002-01-01

The use of a method combining ion trap tandem mass spectrometry (MS/MS) and time of flight mass spectrometry (TOF/MS) for identification of emerging contaminates was discussed. The two tools together complemented each other in sensitivity, fragmentation and accurate mass determination. Liquid chromatography/electrospray ionization/ion-trap tandem mass spectrometry (LC/ESI/MS/MS), in positive ion mode of operation, was used to separate and identify specific compounds. Diagnostic fragment ions were obtained for a polyethyleneglycol(PEG) homolog by ion trap MS/MS, and fragments were measured by TOF/MS. It was observed that the combined method gave an exact mass measurement that differed from the calculated mass.

ToF diagnostic of Tin resonant laser photoionization in SPES laser offline laboratory

NASA Astrophysics Data System (ADS)

Scarpa, D.; Fedorov, D.; Andrighetto, A.; Mariotti, E.; Nicolosi, P.; Sottili, L.; Tomaselli, A.; Cecchi, R.; Stiaccini, L.

2016-09-01

Tin is the principal element of interest in the SPES ISOL facility, which is under construction at Legnaro INFN Laboratories. Atomic nuclei have a shell structure in which nuclei with \\textquoteleft magic numbers\\textquoteright of protons and neutrons are analogous to the noble gasses in atomic physics. In particular, recent theoretical studies, reveal double-magic nature of radioactive 132Sn. For this reason the nuclear physics community demonstrated, in the last years, a huge interest to produce and study this radioactive neutron rich isotope. Experiments on Tin laser resonant ionization have been performed in the offline SPES laser laboratory to investigate the capability of the new home-made Time of Flight (ToF) mass spectrometer. Several three-step, two color ionization schemes have been tested by comparing fast and slow optogalvanic signals from a Tin Hollow Cathode Lamp (HCL) and Time of Flight signals from the spectrometer. By scanning the wavelength of one of the two dye lasers across the specific resonance, comparisons of ionization signals from both the ToF and the HCL have been made, finding perfect agreement. Furthermore, with the mass spectrometer, resolved peaks of all the natural Tin isotopes have been detected. The natural abundances extracted from these measurements are in agreement with the table values for Tin isotopes. This work, with comparison of OGE and ToF signals, confirm the fully functional SPES offline laser laboratory capability in order to develop scheme studies also for the other possible Radioactive Ion Beam (RIB) elements.

Novel, improved sample preparation for rapid, direct identification from positive blood cultures using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry.

PubMed

Schubert, Sören; Weinert, Kirsten; Wagner, Chris; Gunzl, Beatrix; Wieser, Andreas; Maier, Thomas; Kostrzewa, Markus

2011-11-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used for rapid and reliable identification of bacteria and yeast grown on agar plates. Moreover, MALDI-TOF MS also holds promise for bacterial identification from blood culture (BC) broths in hospital laboratories. The most important technical step for the identification of bacteria from positive BCs by MALDI-TOF MS is sample preparation to remove blood cells and host proteins. We present a method for novel, rapid sample preparation using differential lysis of blood cells. We demonstrate the efficacy and ease of use of this sample preparation and subsequent MALDI-TOF MS identification, applying it to a total of 500 aerobic and anaerobic BCs reported to be positive by a Bactec 9240 system. In 86.5% of all BCs, the microorganism species were correctly identified. Moreover, in 18/27 mixed cultures at least one isolate was correctly identified. A novel method that adjusts the score value for MALDI-TOF MS results is proposed, further improving the proportion of correctly identified samples. The results of the present study show that the MALDI-TOF MS-based method allows rapid (<20 minutes) bacterial identification directly from positive BCs and with high accuracy. Copyright © 2011 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Semi-quantitative MALDI-TOF for antimicrobial susceptibility testing in Staphylococcus aureus.

PubMed

Maxson, Tucker; Taylor-Howell, Cheryl L; Minogue, Timothy D

2017-01-01

Antibiotic resistant bacterial infections are a significant problem in the healthcare setting, in many cases requiring the rapid administration of appropriate and effective antibiotic therapy. Diagnostic assays capable of quickly and accurately determining the pathogen resistance profile are therefore crucial to initiate or modify care. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) is a standard method for species identification in many clinical microbiology laboratories and is well positioned to be applied towards antimicrobial susceptibility testing. One recently reported approach utilizes semi-quantitative MALDI-TOF MS for growth rate analysis to provide a resistance profile independent of resistance mechanism. This method was previously successfully applied to Gram-negative pathogens and mycobacteria; here, we evaluated this method with the Gram-positive pathogen Staphylococcus aureus. Specifically, we used 35 strains of S. aureus and four antibiotics to optimize and test the assay, resulting in an overall accuracy rate of 95%. Application of the optimized assay also successfully determined susceptibility from mock blood cultures, allowing both species identification and resistance determination for all four antibiotics within 3 hours of blood culture positivity.

MALDI-TOF MS Andromas strategy for the routine identification of bacteria, mycobacteria, yeasts, Aspergillus spp. and positive blood cultures.

PubMed

Bille, E; Dauphin, B; Leto, J; Bougnoux, M-E; Beretti, J-L; Lotz, A; Suarez, S; Meyer, J; Join-Lambert, O; Descamps, P; Grall, N; Mory, F; Dubreuil, L; Berche, P; Nassif, X; Ferroni, A

2012-11-01

All organisms usually isolated in our laboratory are now routinely identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) using the Andromas software. The aim of this study was to describe the use of this strategy in a routine clinical microbiology laboratory. The microorganisms identified included bacteria, mycobacteria, yeasts and Aspergillus spp. isolated on solid media or extracted directly from blood cultures. MALDI-TOF MS was performed on 2665 bacteria isolated on solid media, corresponding to all bacteria isolated during this period except Escherichia coli grown on chromogenic media. All acquisitions were performed without extraction. After a single acquisition, 93.1% of bacteria grown on solid media were correctly identified. When the first acquisition was not contributory, a second acquisition was performed either the same day or the next day. After two acquisitions, the rate of bacteria identified increased to 99.2%. The failures reported on 21 strains were due to an unknown profile attributed to new species (9) or an insufficient quality of the spectrum (12). MALDI-TOF MS has been applied to 162 positive blood cultures. The identification rate was 91.4%. All mycobacteria isolated during this period (22) were correctly identified by MALDI-TOF MS without any extraction. For 96.3% and 92.2% of yeasts and Aspergillus spp., respectively, the identification was obtained with a single acquisition. After a second acquisition, the overall identification rate was 98.8% for yeasts (160/162) and 98.4% (63/64) for Aspergillus spp. In conclusion, the MALDI-TOF MS strategy used in this work allows a rapid and efficient identification of all microorganisms isolated routinely. © 2011 The Authors. Clinical Microbiology and Infection © 2011 European Society of Clinical Microbiology and Infectious Diseases.

Detection of Staphylococcus aureus Delta-Toxin Production by Whole-Cell MALDI-TOF Mass Spectrometry

PubMed Central

Gagnaire, Julie; Dauwalder, Olivier; Boisset, Sandrine; Khau, David; Freydière, Anne-Marie; Ader, Florence; Bes, Michèle; Lina, Gerard; Tristan, Anne; Reverdy, Marie-Elisabeth; Marchand, Adrienne; Geissmann, Thomas; Benito, Yvonne; Durand, Géraldine; Charrier, Jean-Philippe; Etienne, Jerome; Welker, Martin; Van Belkum, Alex; Vandenesch, François

2012-01-01

The aim of the present study was to detect the Staphylococcus aureus delta-toxin using Whole-Cell (WC) Matrix Assisted Laser Desorption Ionization - Time-of-Flight (MALDI-TOF) mass spectrometry (MS), correlate delta-toxin expression with accessory gene regulator (agr) status, and assess the prevalence of agr deficiency in clinical isolates with and without resistance to methicillin and glycopeptides. The position of the delta-toxin peak in the mass spectrum was identified using purified delta-toxin and isogenic wild type and mutant strains for agr-rnaIII, which encodes delta-toxin. Correlation between delta-toxin production and agr RNAIII expression was assessed by northern blotting. A series of 168 consecutive clinical isolates and 23 unrelated glycopeptide-intermediate S. aureus strains (GISA/heterogeneous GISA) were then tested by WC-MALDI-TOF MS. The delta-toxin peak was detected at 3005±5 Thomson, as expected for the naturally formylated delta toxin, or at 3035±5 Thomson for its G10S variant. Multivariate analysis showed that chronicity of S. aureus infection and glycopeptide resistance were significantly associated with delta-toxin deficiency (p = 0.048; CI 95%: 1.01–10.24; p = 0.023; CI 95%: 1.20–12.76, respectively). In conclusion, the S. aureus delta-toxin was identified in the WC-MALDI-TOF MS spectrum generated during routine identification procedures. Consequently, agr status can potentially predict infectious complications and rationalise application of novel virulence factor-based therapies. PMID:22792394

Introduction to Time of Flight Positron Annihilation Induced Auger Spectroscopy (TOF-PAES)

NASA Astrophysics Data System (ADS)

Joglekar, Prasad; Kalaskar, Sushant; Shastry, Karthik; Satyal, Suman; Weiss, Alex

2009-10-01

Time of flight- positron annihilation induced auger electron spectroscopy (TOF-PAES) is extremely surface selective with close to 95% of the PAES signal stemming from the top-most atomic layer. In PAES, a beam of low energy (1eV -- 25eV) positrons is made incident on a surface where they become trapped in an image potential well. A fraction (up to several percent) of the positrons in the surface state annihilate with the core electrons of atoms at the surface resulting in core-holes. Electrons in higher levels can fill these core-hole via an Auger transition in which the energy associated with this filling the core hole is transferred to another electron which can leave the atom and the surface. The energy of the outgoing (Auger) electrons is characteristic of the energy levels of the atom and can be used to identify the specific element taking part in the transition. In this talk I will present a brief review of how the TOF PAES technique can be used to obtain Auger spectra that is completely free of secondary electron background.

PTR-TOF-MS measurements of atmospheric VOCs during the CALNEX 2010 campaign

NASA Astrophysics Data System (ADS)

Vlasenko, A. L.; Li, S.; Bon, D.; Gilman, J. B.; Kuster, W. C.; de Gouw, J. A.

2010-12-01

During the CALNEX 2010 study, in-situ volatile organic compounds (VOCs) measurements were made aboard the WHOI research vessel Atlantis by a high resolution proton transfer mass spectrometer (PTR-TOF-MS, Ionicon Analytik). The PTR-TOF-MS was deployed along with a GC-FID system during cruise along the California coast and inside port areas to characterize atmospheric levels and chemical transformation of the extensive set of VOCs in marine boundary layer, in particular, in situations where outflows of pollutants from the major urban centers along the coast occur, and to probe the interactions of the anthropogenic pollutants with marine atmosphere. One minute average scans were collected over a period of 24 days. Several offshore outflow episodes were identified by the increasing mixing ratios of aromatic compounds, such as benzene, toluene and C8-aromatics. Preliminary analysis suggests a relatively rapid removal of these species as a result of photochemical aging over a time scale of hours during sunrise. The observed rates of removal correspond reasonably well with those expected from OH photochemistry. Data demonstrating all of these conclusions will be shown.

Fast identification of dermatophytes by MALDI-TOF/MS using direct transfer of fungal cells on ground steel target plates.

PubMed

da Cunha, Keith C; Riat, Arnaud; Normand, Anne-Cecile; Bosshard, Philipp P; de Almeida, Margarete T G; Piarroux, Renaud; Schrenzel, Jacques; Fontao, Lionel

2018-05-15

Dermatophytes cause human infections limited to keratinized tissues. We showed that the direct transfer method allows reliable identification of non-dermatophytes mould and yeast by MALDI-TOF/MS. We aimed at assessing whether the direct transfer method can be used for dermatophytes and whether an own mass spectra library would be superior to the Bruker library. We used the Bruker Biotyper to build a dermatophyte mass spectra library and assessed its performance by 1/ testing a panel of mass spectrum produced with strains genotypically identified and, 2/ comparing MALDI-TOF/MS identification to morphology-based methods. Identification of dermatophytes using the Bruker library is poor. Our library provided 97% concordance between ITS sequencing and MALDI-TOF/MS analysis with a panel of 1104 spectra corresponding to 276 strains. Direct transfer method using unpolished target plates allowed proper identification of 85% of dermatophytes clinical isolates most of which were common dermatophytes. A homemade dermatophyte MSP library is a prerequisite for accurate identification of species absent in the Bruker library but it also improves identification of species already listed in the database. The direct deposit method can be used to identify the most commonly found dermatophytes such as T. rubrum and T. interdigitale/mentagrophytes by MALDI-TOF/MS. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Rapid Characterization of Microalgae and Microalgae Mixtures Using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS)

PubMed Central

Barbano, Duane; Diaz, Regina; Zhang, Lin; Sandrin, Todd; Gerken, Henri; Dempster, Thomas

2015-01-01

Current molecular methods to characterize microalgae are time-intensive and expensive. Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) may represent a rapid and economical alternative approach. The objectives of this study were to determine whether MALDI-TOF MS can be used to: 1) differentiate microalgae at the species and strain levels and 2) characterize simple microalgal mixtures. A common protein extraction sample preparation method was used to facilitate rapid mass spectrometry-based analysis of 31 microalgae. Each yielded spectra containing between 6 and 56 peaks in the m/z 2,000 to 20,000 range. The taxonomic resolution of this approach appeared higher than that of 18S rDNA sequence analysis. For example, two strains of Scenedesmus acutus differed only by two 18S rDNA nucleotides, but yielded distinct MALDI-TOF mass spectra. Mixtures of two and three microalgae yielded relatively complex spectra that contained peaks associated with members of each mixture. Interestingly, though, mixture-specific peaks were observed at m/z 11,048 and 11,230. Our results suggest that MALDI-TOF MS affords rapid characterization of individual microalgae and simple microalgal mixtures. PMID:26271045

Unexpected materials in a Rembrandt painting characterized by high spatial resolution cluster-TOF-SIMS imaging.

PubMed

Sanyova, Jana; Cersoy, Sophie; Richardin, Pascale; Laprévote, Olivier; Walter, Philippe; Brunelle, Alain

2011-02-01

The painting materials of the Portrait of Nicolaes van Bambeeck (Royal Museums of Fine Arts of Belgium, Brussels, inv. 155) painted by Rembrandt van Rijn in 1641 has been studied using high resolution cluster-TOF-SIMS imaging. In the first step, a moderate spatial resolution (2 μm) was used to characterize the layer structure and the chemical composition of each layer on account of a high mass resolution. Then, in the second step, and despite a low mass resolution, the cluster primary ion beam was focused well below 1 μm in order to reveal smaller structures in the painting sample. The study confirmed the presence of starch in the second ground layer, which is quite surprising and, at least for Rembrandt paintings, has never been reported before. TOF-SIMS also indicated the presence of proteins, which, added to the size and shape of lake particles, suggests that it was manufactured from shearings (waste of textile manufacturing) of dyed wool, used as the source of the dyestuff. The analyses have also shown various lead carboxylates, being the products of the interaction between lead white and the oil of the binding medium. These findings considerably contribute to the understanding of Rembrandt's studio practice and thus demonstrate the importance and potential of cluster-TOF-SIMS imaging in the characterization on a submicrometer scale of artist painting materials.

Structural Characterization of Ginsenosides from Flower Buds of Panax ginseng by RRLC-Q-TOF MS.

PubMed

Wu, Wei; Lu, Ziyan; Teng, Yaran; Guo, Yingying; Liu, Shuying

2016-02-01

Ginseng flower bud as a part of Panax ginseng has received much attention as a valuable functional food with medicinal potential. A few studies focused on systematic and comprehensive studies on its major ingredients. This study aims to rapidly characterize ginsenosides in ginseng flower buds and provide scientific basis for developing functional food, exploiting pharmaceutical effects and making full use of ginseng resources. A rapid resolution liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry (RRLC-Q-TOF-MS) method was developed for rapid qualitative and quantitative analysis of ginsenosides in ginseng flower buds. The compounds were identified by comparing retention time of the reference standards, accurate mass measurement and the fragment ions obtained from RRLC-Q-TOF-MS/MS analyses. A total of 14 kinds of ginsenosides were identified and 5 kinds of malonyl-ginsenosides were first tentatively identified in ginseng flower buds. Ten kinds of main ginsenosides were quantitatively analyzed. The developed RRLC-Q-TOF-MS method was demonstrated as an effective analytical means for rapid characterization of the ginsenosides in flower buds of P. ginseng. The research result is valuable for quality control, assessment of authenticity and stability evaluation of ginseng flower buds. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Comparison between MALDI-TOF MS and FilmArray Blood Culture Identification panel for rapid identification of yeast from positive blood culture.

PubMed

Paolucci, M; Foschi, C; Tamburini, M V; Ambretti, S; Lazzarotto, T; Landini, M P

2014-09-01

In this study we evaluated MALDI-TOF MS and FilmArray methods for the rapid identification of yeast from positive blood cultures. FilmArray correctly identified 20/22 of yeast species, while MALDI-TOF MS identified 9/22. FilmArray is a reliable and rapid identification system for the direct identification of yeasts from positive blood cultures. Copyright © 2014 Elsevier B.V. All rights reserved.

Biosynthesis of staphylococcal enterotoxin A by genetic engineering technology and determination of staphylococcal enterotoxin A in water by HPLC-ESI-TOF.

PubMed

Li, Hong-Na; Yuan, Fei; Luo, Yun-Jing; Wang, Jian-Feng; Zhang, Chuan-Bin; Zhou, Wei-E; Ren, Zhi-Qin; Wu, Wen-Jie; Zhang, Feng

2017-08-01

Staphylococcal enterotoxin A (SEA) was the major virulence factor of Staphylococcus aureus and a biomarker of S. aureus. To establish a fast, low cost, high accuracy, reliable, and simple method for detecting S. aureus, SEA was analyzed by HPLC-ESI-TOF. SEA was not yet commercially available in universal, so SEA was prepared before it was analyzed by HPLC-ESI-TOF. The result showed that high purified SEA was successfully prepared and SEA has normal distribution in mass spectra. A large amount of recombinant SEA (rSEA) was obtained by engineering technology and was purified by Ni affinity chromatography column, and the expression and purity of rSEA and SEA were analyzed by SDS-PAGE. The factors effected on ionization of SEA were studied, and the qualitative analysis of SEA by HPLC-ESI-TOF. The result showed that large amount of SEs expressed within a short time at 28 °C or thereabouts, and there was no impurity bands in electrophorogram after rSEA was purified by Ni affinity chromatography column. In addition, the SEA which had homologous AA sequence with wild SEA was made by rSEA. The retention of SEA in column and ionization of SEA in ESI-TOF were studied for qualitative analysis of S. aureus. The result showed that the content of formic acid in mobile phase was an important factor for ionization of SEs in ESI-TOF. And the result provided theoretical foundation for qualitative detection of S. aureus. [SEs + nH + + mNH 4 + ] n+m+ was shown on ESI-TOF spectra when SEA was detected by ESI-TOF in positive ion mode, and the numerical value of n+m was less than or equal to the number of basic amino acids in SEs. This method was applied to determine SEA in water samples preliminarily, and the detection limit of SEA in spiked water sample was 3 mg/kg. The limit of detection of 3 mg/kg was low sensitivity for low molecular weight matters, but it was high sensitivity for SEA which had a high molecular weight of 27 kDa. Of SEA, 3 mg/kg was equivalent to 10 -4 �

Study of rat hypothalamic proteome by HPLC/ESI ion trap and HPLC/ESI-Q-TOF MS.

PubMed

Iqbal, Javed; Li, Wang; Ullah, Kaleem; Hasan, Murtaza; Linna, Guo; Awan, Umer; Zhang, Yongqian; Batool, Sajida; Qing, Hong; Deng, Yulin

2013-08-01

The proteomic profile of hypothalamus, a key organ of CNS, is explored here by employing two widely used MS techniques, i.e. HPLC/ESI-ion trap and HPLC/ESI-quadrupole-TOF MS. Strong cation exchange is used for the fractionation of peptides and protein search engine MASCOT is employed for data query. One hundred and thirty six proteins with 10 973 peptides were identified by HPLC/ESI-ion trap MS, while 140 proteins with 32 183 peptides were characterized by HPLC/ESI-quadrupole-TOF MS. Among the total 198 proteins identified in both experiments, 78 proteins were common in both sets of conditions. The rest of the 120 proteins were identified distinctly in both MS strategies, i.e. 58 unique proteins were found using the quadrupole-TOF while 62 were found with the HPLC/ESI-ion trap. Moreover, these proteins were classified into groups based on their functions performed in the body. Results presented here identified some important signal and cellular defense proteins inevitable for survival in stressed conditions. Additionally, it is also shown that any single MS strategy is not reliable for good results due to loss of data depending on sensitivity of the instrument used. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Validation of LC–TOF-MS Screening for Drugs, Metabolites, and Collateral Compounds in Forensic Toxicology Specimens

PubMed Central

Guale, Fessessework; Shahreza, Shahriar; Walterscheid, Jeffrey P.; Chen, Hsin-Hung; Arndt, Crystal; Kelly, Anna T.; Mozayani, Ashraf

2013-01-01

Liquid chromatography time-of-flight mass spectrometry (LC–TOF-MS) analysis provides an expansive technique for identifying many known and unknown analytes. This study developed a screening method that utilizes automated solid-phase extraction to purify a wide array of analytes involving stimulants, benzodiazepines, opiates, muscle relaxants, hypnotics, antihistamines, antidepressants and newer synthetic “Spice/K2” cannabinoids and cathinone “bath salt” designer drugs. The extract was applied to LC–TOF-MS analysis, implementing a 13 min chromatography gradient with mobile phases of ammonium formate and methanol using positive mode electrospray. Several common drugs and metabolites can share the same mass and chemical formula among unrelated compounds, but they are structurally different. In this method, the LC–TOF-MS was able to resolve many isobaric compounds by accurate mass correlation within 15 ppm mass units and a narrow retention time interval of less than 10 s of separation. Drug recovery yields varied among spiked compounds, but resulted in overall robust area counts to deliver an average match score of 86 when compared to the retention time and mass of authentic standards. In summary, this method represents a rapid, enhanced screen for blood and urine specimens in postmortem, driving under the influence, and drug facilitated sexual assault forensic toxicology casework. PMID:23118149

Validation of LC-TOF-MS screening for drugs, metabolites, and collateral compounds in forensic toxicology specimens.

PubMed

Guale, Fessessework; Shahreza, Shahriar; Walterscheid, Jeffrey P; Chen, Hsin-Hung; Arndt, Crystal; Kelly, Anna T; Mozayani, Ashraf

2013-01-01

Liquid chromatography time-of-flight mass spectrometry (LC-TOF-MS) analysis provides an expansive technique for identifying many known and unknown analytes. This study developed a screening method that utilizes automated solid-phase extraction to purify a wide array of analytes involving stimulants, benzodiazepines, opiates, muscle relaxants, hypnotics, antihistamines, antidepressants and newer synthetic "Spice/K2" cannabinoids and cathinone "bath salt" designer drugs. The extract was applied to LC-TOF-MS analysis, implementing a 13 min chromatography gradient with mobile phases of ammonium formate and methanol using positive mode electrospray. Several common drugs and metabolites can share the same mass and chemical formula among unrelated compounds, but they are structurally different. In this method, the LC-TOF-MS was able to resolve many isobaric compounds by accurate mass correlation within 15 ppm mass units and a narrow retention time interval of less than 10 s of separation. Drug recovery yields varied among spiked compounds, but resulted in overall robust area counts to deliver an average match score of 86 when compared to the retention time and mass of authentic standards. In summary, this method represents a rapid, enhanced screen for blood and urine specimens in postmortem, driving under the influence, and drug facilitated sexual assault forensic toxicology casework.

Identification of Acinetobacter species: is Bruker biotyper MALDI-TOF mass spectrometry a good alternative to molecular techniques?

PubMed

Alvarez-Buylla, Adela; Culebras, Esther; Picazo, Juan J

2012-03-01

Acinetobacter spp. has become a leading cause of nosocomial infection in recent years. Phenotypic similarities between the species in the genus have made it difficult to identify them clearly using routine diagnostic methods. Consequently, more relevant species have been grouped together as Acinetobacter calcoaceticus-Acinetobacter baumannii complex (A. baumannii, A. calcoaceticus, Acinetobacter genospecies 3 and A. genospecies 13TU). However, there are other species that may also have clinical significance. The aims of this study were to establish the usefulness of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Acinetobacter species by comparison with two molecular techniques, as well as determine the role of species other than A. baumannii play in nosocomial infections.The study sample comprised 109 clinical isolates of Acinetobacter. They were all identified using MALDI-TOF MS. Thirty-one isolates of these were also tested using comparator amplification of bla(OXA51-like) and sequencing of the rpoB gene. Different score values in MALDI-TOF MS revealed 87 A. baumannii, 19 A. genospecies 3, 1 Acinetobacter junii, 1 Acinetobacter baylyi and 1 Acinetobacter tjernbergiae. Amplification of bla(OXA-51)(-like) showed products in 85 isolates. Sequencing of the rpoB gene allowed us to identify all the 31 isolates analyzed: 16 were consistent with the results of spectrometry and 15 were not. This work showed that molecular techniques are still needed to identify the different species of clinical interest within the genus Acinetobacter. Although, MALDI-TOF MS could be useful to identify A. baumannii but not other species in the genus. Copyright © 2012 Elsevier B.V. All rights reserved.

Semi Quantitative MALDI TOF for Antimicrobial Susceptibility Testing in Staphylococcus aureus

DTIC Science & Technology

2017-08-31

Semi- quantitative MALDI-TOF for antimicrobial susceptibility testing in Staphylococcus 1 aureus 2 3 4 Tucker Maxson,a Cheryl L. Taylor-Howell,a...Timothy D. Minoguea# 5 6 Diagnostic Systems Division, United States Army Medical Research Institute of Infectious 7 Disease, Fort Detrick, MD...USAa 8 9 Running Title: Quantitative MALDI for AST in S. aureus 10 #Address correspondence to Timothy D. Minogue, timothy.d.minogue.civ@mail.mil

First in situ TOF-PET study using digital photon counters for proton range verification.

PubMed

Cambraia Lopes, P; Bauer, J; Salomon, A; Rinaldi, I; Tabacchini, V; Tessonnier, T; Crespo, P; Parodi, K; Schaart, D R

2016-08-21

Positron emission tomography (PET) is the imaging modality most extensively tested for treatment monitoring in particle therapy. Optimal use of PET in proton therapy requires in situ acquisition of the relatively strong (15)O signal due to its relatively short half-life (~2 min) and high oxygen content in biological tissues, enabling shorter scans that are less sensitive to biological washout. This paper presents the first performance tests of a scaled-down in situ time-of-flight (TOF) PET system based on digital photon counters (DPCs) coupled to Cerium-doped Lutetium Yttrium Silicate (LYSO:Ce) crystals, providing quantitative results representative of a dual-head tomograph that complies with spatial constraints typically encountered in clinical practice (2  ×  50°, of 360°, transaxial angular acceptance). The proton-induced activity inside polymethylmethacrylate (PMMA) and polyethylene (PE) phantoms was acquired within beam pauses (in-beam) and immediately after irradiation by an actively-delivered synchrotron pencil-beam, with clinically relevant 125.67 MeV/u, 4.6  ×  10(8) protons s(-1), and 10(10) total protons. 3D activity maps reconstructed with and without TOF information are compared to FLUKA simulations, demonstrating the benefit of TOF-PET to reduce limited-angle artefacts using a 382 ps full width at half maximum coincidence resolving time. The time-dependent contributions from different radionuclides to the total count-rate are investigated. We furthermore study the impact of the acquisition time window on the laterally integrated activity depth-profiles, with emphasis on 2 min acquisitions starting at different time points. The results depend on phantom composition and reflect the differences in relative contributions from the radionuclides originating from carbon and oxygen. We observe very good agreement between the shapes of the simulated and measured activity depth-profiles for post-beam protocols. However, our results

First in situ TOF-PET study using digital photon counters for proton range verification

NASA Astrophysics Data System (ADS)

Cambraia Lopes, P.; Bauer, J.; Salomon, A.; Rinaldi, I.; Tabacchini, V.; Tessonnier, T.; Crespo, P.; Parodi, K.; Schaart, D. R.

2016-08-01

Positron emission tomography (PET) is the imaging modality most extensively tested for treatment monitoring in particle therapy. Optimal use of PET in proton therapy requires in situ acquisition of the relatively strong 15O signal due to its relatively short half-life (~2 min) and high oxygen content in biological tissues, enabling shorter scans that are less sensitive to biological washout. This paper presents the first performance tests of a scaled-down in situ time-of-flight (TOF) PET system based on digital photon counters (DPCs) coupled to Cerium-doped Lutetium Yttrium Silicate (LYSO:Ce) crystals, providing quantitative results representative of a dual-head tomograph that complies with spatial constraints typically encountered in clinical practice (2  ×  50°, of 360°, transaxial angular acceptance). The proton-induced activity inside polymethylmethacrylate (PMMA) and polyethylene (PE) phantoms was acquired within beam pauses (in-beam) and immediately after irradiation by an actively-delivered synchrotron pencil-beam, with clinically relevant 125.67 MeV/u, 4.6  ×  108 protons s-1, and 1010 total protons. 3D activity maps reconstructed with and without TOF information are compared to FLUKA simulations, demonstrating the benefit of TOF-PET to reduce limited-angle artefacts using a 382 ps full width at half maximum coincidence resolving time. The time-dependent contributions from different radionuclides to the total count-rate are investigated. We furthermore study the impact of the acquisition time window on the laterally integrated activity depth-profiles, with emphasis on 2 min acquisitions starting at different time points. The results depend on phantom composition and reflect the differences in relative contributions from the radionuclides originating from carbon and oxygen. We observe very good agreement between the shapes of the simulated and measured activity depth-profiles for post-beam protocols. However, our results also

First beam test of a liquid Cherenkov detector prototype for a future TOF measurements at the Super-FRS

NASA Astrophysics Data System (ADS)

Kuzminchuk-Feuerstein, Natalia; Ferber, Nadine; Rozhkova, Elena; Kaufeld, Ingo; Voss, Bernd

2017-09-01

In order to separate and identify fragmentation products with the Super-Fragment Separator (SuperFRS) at FAIR a high resolving power detector system is required for position and Time-Of-Flight (TOF) measurements. The TOF detector is used to measure the velocity of the particles and hence, in conjunction with their momentum or energy, to determine their mass and hence their identity. Aiming to develop a system with a precision down to about 50 ps in time and resistant to a high radiation rate of relativistic heavy ions of up to 107 per spill (at the second focal plane), we have shown a conceptual design for a Cherenkov detector envisioned for the future TOF measurements employing Iodine Naphthalene (C10H7I) as a fluid radiator. The application of a liquid radiator allows the circulation of the active material and therefore to greatly reduce the effects of the degradation of the optical performance expected after exposure to the high ion rates at the Super-FRS. The prototype of a TOF-Cherenkov detector was designed, constructed and its key-properties have been investigated in measurements with heavy ions at CaveC at GSI. These measurements were performed with nickel ions at 300-1500 MeV/u and ion-beam intensities of up to 4 × 106 ions/spill of 8 s. As a first result a maximum detection efficiency of 70% and a timing resolution of 267 ps (σ) was achieved. We report the first attempt of time measurements with a Cherenkov detector based on a liquid radiator. Further optimization is required.

Identification of filamentous fungi isolates by MALDI-TOF mass spectrometry: clinical evaluation of an extended reference spectra library.

PubMed

Becker, Pierre T; de Bel, Annelies; Martiny, Delphine; Ranque, Stéphane; Piarroux, Renaud; Cassagne, Carole; Detandt, Monique; Hendrickx, Marijke

2014-11-01

The identification of filamentous fungi by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) relies mainly on a robust and extensive database of reference spectra. To this end, a large in-house library containing 760 strains and representing 472 species was built and evaluated on 390 clinical isolates by comparing MALDI-TOF MS with the classical identification method based on morphological observations. The use of MALDI-TOF MS resulted in the correct identification of 95.4% of the isolates at species level, without considering LogScore values. Taking into account the Brukers' cutoff value for reliability (LogScore >1.70), 85.6% of the isolates were correctly identified. For a number of isolates, microscopic identification was limited to the genus, resulting in only 61.5% of the isolates correctly identified at species level while the correctness reached 94.6% at genus level. Using this extended in-house database, MALDI-TOF MS thus appears superior to morphology in order to obtain a robust and accurate identification of filamentous fungi. A continuous extension of the library is however necessary to further improve its reliability. Indeed, 15 isolates were still not represented while an additional three isolates were not recognized, probably because of a lack of intraspecific variability of the corresponding species in the database. © The Author 2014. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A UPLC-ESI-Q-TOF method for rapid and reliable identification and quantification of major indole alkaloids in Catharanthus roseus.

PubMed

Jeong, Won Tae; Lim, Heung Bin

2018-03-30

We developed a novel ultra performance liquid chromatography-quadrupole time-of-flight (UPLC-Q-TOF) mass spectrometry method that allows sensitive, rapid, and reliable detection and identification of six representative indole alkaloids (vincristine, vinblastine, ajmalicine, catharanthine, serpentine, and vindoline) that exhibit physiological activity in Catharanthus roseus (C. roseus). The alkaloids were eluted on a C18 column with acetonitrile and water containing 0.1% formic acid and 10 mM ammonium acetate, and separated with good resolution within 13 min. Electrospray ionization-Q-TOF (ESI-Q-TOF) analysis was performed to characterize the molecules and their fragment ions, and the characteristic ions and fragmentation patterns were used as to identify the alkaloids. The proposed analytical method was verified in reference to the ICH guidelines and the results showed excellent linearity (R 2  > 0.9988), limit of detection (1 ng/mL to 10 ng/mL), limit of quantification (3 ng/mL to 30 ng/mL), intra-day and inter-day precisions, and extraction recovery rates (92.8% to 104.1%) for all components. The validated UPLC-Q-TOF method was applied to the analysis of extracts from the root, stem, and leaves of C. roseus, allowing the identification of six alkaloids by comparison of retention times, molecular ions, and fragmentation patterns with those of reference compounds. Sixteen additional indole alkaloids were tentatively identified by comparison of chromatograms to chemical databases and literature reports. The contents of bis-indole alkaloids (vincristine and vinblastine) were high in the aerial parts, while the contents of mono-indole alkaloids (ajmalicine, catharanthine, serpentine, and vindoline) were high in the roots. The present results demonstrate that the proposed UPLC-Q-TOF method can be useful for the investigation of phytochemical constituents of medicinal plants. Copyright © 2018 Elsevier B.V. All rights reserved.

Evaluation of MALDI-TOF-MS for the Identification of Yeast Isolates Causing Bloodstream Infection.

PubMed

Turhan, Ozge; Ozhak-Baysan, Betil; Zaragoza, Oscar; Er, Halil; Sarıtas, Zubeyde Eres; Ongut, Gozde; Ogunc, Dilara; Colak, Dilek; Cuenca-Estrella, Manuel

2017-04-01

Infections due to Candida species are major causes of morbidity and mortality in humans, causing a diverse spectrum of clinical disease ranging from superficial and mucosal infections to invasive disease. Several authors have demonstrated that mortality is closely linked to both timing of therapy and/or source control. The rapid identification of pathogenic species is helpful to start timely and effective antifungal therapy. The aim of this study was to assess the performance of the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system for the correct and rapid identification of yeast isolates causing bloodstream infection. Between January 2014 and January 2015, a total of 117 yeast like organisms isolated from blood culture samples of 117 episodes from 102 patients who had blood stream infections were included in the study. The isolates were identified by MALDI-TOF MS. The results were compared with those obtained by the standard mycological methods and/or sequence analysis. One hundred and seventeen yeast isolates including 115 Candida spp and two non-Candida yeasts were analysed. The Biotyper correctly identified 115 (98.3%) isolates to the genus level and 102 (87.2%) isolates to the species level using the manufacturer's recommended cutoff scores. The Bruker Biotyper is a rapid, easy, inexpensive, and highly reliable system for the identification of yeast isolates. Early identification with MALDI-TOF MS would save time for determination of antifungal susceptibility and proper treatment strategy. The expansion of the database of the library by addition of less common species will improve the performance of the system.

Feasibility of matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) networking in university hospitals in Brussels.

PubMed

Martiny, D; Cremagnani, P; Gaillard, A; Miendje Deyi, V Y; Mascart, G; Ebraert, A; Attalibi, S; Dediste, A; Vandenberg, O

2014-05-01

The mutualisation of analytical platforms might be used to address rising healthcare costs. Our study aimed to evaluate the feasibility of networking a unique matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) system for common use in several university hospitals in Brussels, Belgium. During a one-month period, 1,055 successive bacterial isolates from the Brugmann University Hospital were identified on-site using conventional techniques; these same isolates were also identified using a MALDI-TOF MS system at the Porte de Hal Laboratory by sending target plates and identification projects via transportation and the INFECTIO_MALDI software (Infopartner, Nancy, France), respectively. The occurrence of transmission problems (<2 %) and human errors (<1 %) suggested that the system was sufficiently robust to be implemented in a network. With a median time-to-identification of 5 h and 11 min (78 min, min-max: 154-547), MALDI-TOF MS networking always provided a faster identification result than conventional techniques, except when chromogenic culture media and oxidase tests were used (p < 0.0001). However, the limited clinical benefits of the chromogenic culture media do not support their extra cost. Our financial analysis also suggested that MALDI-TOF MS networking could lead to substantial annual cost savings. MALDI-TOF MS networking presents many advantages, and few conventional techniques (optochin and oxidase tests) are required to ensure the same quality in patient care from the distant laboratory. Nevertheless, such networking should not be considered unless there is a reorganisation of workflow, efficient communication between teams, qualified technologists and a reliable IT department and helpdesk to manage potential connectivity problems.

Microorganism Identification Based On MALDI-TOF-MS Fingerprints

NASA Astrophysics Data System (ADS)

Elssner, Thomas; Kostrzewa, Markus; Maier, Thomas; Kruppa, Gary

Advances in MALDI-TOF mass spectrometry have enabled the ­development of a rapid, accurate and specific method for the identification of bacteria directly from colonies picked from culture plates, which we have named the MALDI Biotyper. The picked colonies are placed on a target plate, a drop of matrix solution is added, and a pattern of protein molecular weights and intensities, "the protein fingerprint" of the bacteria, is produced by the MALDI-TOF mass spectrometer. The obtained protein mass fingerprint representing a molecular signature of the microorganism is then matched against a database containing a library of previously measured protein mass fingerprints, and scores for the match to every library entry are produced. An ID is obtained if a score is returned over a pre-set threshold. The sensitivity of the techniques is such that only approximately 104 bacterial cells are needed, meaning that an overnight culture is sufficient, and the results are obtained in minutes after culture. The improvement in time to result over biochemical methods, and the capability to perform a non-targeted identification of bacteria and spores, potentially makes this method suitable for use in the detect-to-treat timeframe in a bioterrorism event. In the case of white-powder samples, the infectious spore is present in sufficient quantity in the powder so that the MALDI Biotyper result can be obtained directly from the white powder, without the need for culture. While spores produce very different patterns from the vegetative colonies of the corresponding bacteria, this problem is overcome by simply including protein fingerprints of the spores in the library. Results on spores can be returned within minutes, making the method suitable for use in the "detect-to-protect" timeframe.

Comparing Novel Multi-Gap Resistive Plate Chamber Models

NASA Astrophysics Data System (ADS)

Stien, Haley; EIC PID Consortium Collaboration

2016-09-01

Investigating nuclear structure has led to the fundamental theory of Quantum Chromodynamics. An Electron Ion Collider (EIC) is a proposed accelerator that would further these investigations. In order to prepare for the EIC, there is an active detector research and development effort. One specific goal is to achieve better particle identification via improved Time of Flight (TOF) detectors. A promising option is the Multi-Gap Resistive Plate Chamber (mRPC). These detectors are similar to the more traditional RPCs, but their active gas gaps have dividers to form several thinner gas gaps. These very thin and accurately defined gas gaps improve the timing resolution of the chamber, so the goal is to build an mRPC with the thinnest gaps to achieve the best possible timing resolution. Two different construction techniques have been employed to make two mRPCs. The first technique is to physically separate the gas gaps with sheets of glass that are .2mm thick. The second technique is to 3D print the layered gas gaps. A comparison of these mRPCs and their performances will be discussed and the latest data presented. This research was supported by US DOE MENP Grant DE-FG02-03ER41243.

Application of proteotyping Strain Solution™ ver. 2 software and theoretically calculated mass database in MALDI-TOF MS typing of Salmonella serotype.

PubMed

Ojima-Kato, Teruyo; Yamamoto, Naomi; Nagai, Satomi; Shima, Keisuke; Akiyama, Yumi; Ota, Junji; Tamura, Hiroto

2017-12-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based microbial identification is a popular analytical method. Strain Solution proteotyping software available for MALDI-TOF MS has great potential for the precise and detailed discrimination of microorganisms at serotype- or strain-level, beyond the conventional mass fingerprinting approaches. Here, we constructed a theoretically calculated mass database of Salmonella enterica subspecies enterica consisting of 12 biomarker proteins: ribosomal proteins S8, L15, L17, L21, L25, and S7, Mn-cofactor-containing superoxide dismutase (SodA), peptidyl-prolyl cis-trans isomerase C (PPIase C), and protein Gns, and uncharacterized proteins YibT, YaiA, and YciF, that can allow serotyping of Salmonella. Strain Solution ver. 2 software with the novel database constructed in this study demonstrated that 109 strains (94%), including the major outbreak-associated serotypes, Enteritidis, Typhimurium, and Infantis, could be correctly identified from others by colony-directed MALDI-TOF MS using 116 strains belonging to 23 kinds of typed and untyped serotypes of S. enterica from culture collections, patients, and foods. We conclude that Strain Solution ver. 2 software integrated with the accurate mass database will be useful for the bacterial proteotyping by MALDI-TOF MS-based microbial classification in the clinical and food safety fields.

Rapid and reliable identification of Gram-negative bacteria and Gram-positive cocci by deposition of bacteria harvested from blood cultures onto the MALDI-TOF plate.

PubMed

Barnini, Simona; Ghelardi, Emilia; Brucculeri, Veronica; Morici, Paola; Lupetti, Antonella

2015-06-18

Rapid identification of the causative agent(s) of bloodstream infections using the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) methodology can lead to increased empirical antimicrobial therapy appropriateness. Herein, we aimed at establishing an easier and simpler method, further referred to as the direct method, using bacteria harvested by serum separator tubes from positive blood cultures and placed onto the polished steel target plate for rapid identification by MALDI-TOF. The results by the direct method were compared with those obtained by MALDI-TOF on bacteria isolated on solid media. Identification of Gram-negative bacilli was 100 % concordant using the direct method or MALDI-TOF on isolated bacteria (96 % with score > 2.0). These two methods were 90 % concordant on Gram-positive cocci (32 % with score > 2.0). Identification by the SepsiTyper method of Gram-positive cocci gave concordant results with MALDI-TOF on isolated bacteria in 87 % of cases (37 % with score > 2.0). The direct method herein developed allows rapid identification (within 30 min) of Gram-negative bacteria and Gram-positive cocci from positive blood cultures and can be used to rapidly report reliable and accurate results, without requiring skilled personnel or the use of expensive kits.

Typing of vancomycin-resistant enterococci with MALDI-TOF mass spectrometry in a nosocomial outbreak setting.

PubMed

Holzknecht, B J; Dargis, R; Pedersen, M; Pinholt, M; Christensen, J J

2018-03-23

To investigate the usefulness of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) typing as a first-line epidemiological tool in a nosocomial outbreak of vancomycin-resistant Enterococcus faecium (VREfm). Fifty-five VREfm isolates, previously characterized by whole-genome sequencing (WGS), were included and analysed by MALDI-TOF MS. To take peak reproducibility into account, ethanol/formic acid extraction and other steps of the protocol were conducted in triplicate. Twenty-seven spectra were generated per isolate, and spectra were visually inspected to determine discriminatory peaks. The presence or absence of these was recorded in a peak scheme. Nine discriminatory peaks were identified. A characteristic pattern of these could distinguish between the three major WGS groups: WGS I, WGS II and WGS III. Only one of 38 isolates belonging to WGS I, WGS II or WGS III was misclassified. However, ten of the 17 isolates not belonging to WGS I, II or III displayed peak patterns indistinguishable from those of the outbreak strain. Using visual inspection of spectra, MALDI-TOF MS typing proved to be useful in differentiating three VREfm outbreak clones from each other. However, as non-outbreak isolates could not be reliably differentiated from outbreak clones, the practical value of this typing method for VREfm outbreak management was limited in our setting. Copyright © 2018 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Rapid Screening of Ergot Alkaloids in Sclerotia by MALDI-TOF Mass Spectrometry.

PubMed

Sivagnanam, Kumaran; Komatsu, Emy; Patrick, Susan; Rampitsch, Christoph; Perreault, Hélène; Gräfenhan, Tom

2016-07-01

Ergot is a common disease of wheat and other cereal grains that is predominantly caused by Claviceps purpurea in the field, often affecting crop yield in addition to the environment. Infected grain can be contaminated with dark sclerotia, which contain fungal metabolites such as ergot alkaloids. The occurrence of ergot alkaloids in cereal grain is a major health concern for humans and livestock. Effective and rapid screening of these mycotoxins is crucial for producers, processors, and consumers of cereal-based food and feed grain. Established methods of ergot alkaloid screening based on LC-MS or GC-MS require laborious processes. A novel method using matrix-assisted laser desorption ionization (MALDI)-time-of-flight (TOF) MS was developed to identify four ergot alkaloids. Using dihydroxybenzoic acid as the matrix, ergosine, ergocornine, ergocryptine, and ergocristine were readily detected in individual sclerotia of C. purpurea. The accuracy of the identified ergot alkaloids was further confirmed by tandem MS analysis. MALDI-TOF MS is suitable for high-throughput screening of ergot alkaloids because it permits rapid and accurate identification, simple sample preparation, and no derivatization or chromatographic separation.

Automated High-Throughput Permethylation for Glycosylation Analysis of Biologics Using MALDI-TOF-MS.

PubMed

Shubhakar, Archana; Kozak, Radoslaw P; Reiding, Karli R; Royle, Louise; Spencer, Daniel I R; Fernandes, Daryl L; Wuhrer, Manfred

2016-09-06

Monitoring glycoprotein therapeutics for changes in glycosylation throughout the drug's life cycle is vital, as glycans significantly modulate the stability, biological activity, serum half-life, safety, and immunogenicity. Biopharma companies are increasingly adopting Quality by Design (QbD) frameworks for measuring, optimizing, and controlling drug glycosylation. Permethylation of glycans prior to analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) is a valuable tool for glycan characterization and for screening of large numbers of samples in QbD drug realization. However, the existing protocols for manual permethylation and liquid-liquid extraction (LLE) steps are labor intensive and are thus not practical for high-throughput (HT) studies. Here we present a glycan permethylation protocol, based on 96-well microplates, that has been developed into a kit suitable for HT work. The workflow is largely automated using a liquid handling robot and includes N-glycan release, enrichment of N-glycans, permethylation, and LLE. The kit has been validated according to industry analytical performance guidelines and applied to characterize biopharmaceutical samples, including IgG4 monoclonal antibodies (mAbs) and recombinant human erythropoietin (rhEPO). The HT permethylation enabled glycan characterization and relative quantitation with minimal side reactions: the MALDI-TOF-MS profiles obtained were in good agreement with hydrophilic liquid interaction chromatography (HILIC) and ultrahigh performance liquid chromatography (UHPLC) data. Automated permethylation and extraction of 96 glycan samples was achieved in less than 5 h and automated data acquisition on MALDI-TOF-MS took on average less than 1 min per sample. This automated and HT glycan preparation and permethylation showed to be convenient, fast, and reliable and can be applied for drug glycan profiling and clinical glycan biomarker studies.

Direct screening of herbal blends for new synthetic cannabinoids by MALDI-TOF MS.

PubMed

Gottardo, Rossella; Chiarini, Anna; Dal Prà, Ilaria; Seri, Catia; Rimondo, Claudia; Serpelloni, Giovanni; Armato, Ubaldo; Tagliaro, Franco

2012-01-01

Since 2004, a number of herbal blends containing different synthetic compounds mimicking the pharmacological activity of cannabinoids and displaying a high toxicological potential have appeared in the market. Their availability is mainly based on the so-called "e-commerce", being sold as legal alternatives to cannabis and cannabis derivatives. Although highly selective, sensitive, accurate, and quantitative methods based on GC-MS and LC-MS are available, they lack simplicity, rapidity, versatility and throughput, which are required for product monitoring. In this context, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) offers a simple and rapid operation with high throughput. Thus, the aim of the present work was to develop a MALDI-TOF MS method for the rapid qualitative direct analysis of herbal blend preparations for synthetic cannabinoids to be used as front screening of confiscated clandestine preparations. The sample preparation was limited to herbal blend leaves finely grinding in a mortar and loading onto the MALDI plate followed by addition of 2 µl of the matrix/surfactant mixture [α-cyano-4-hydroxy-cinnamic acid/cetyltrimethylammonium bromide (CTAB)]. After drying, the sample plate was introduced into the ion source for analysis. MALDI-TOF conditions were as follows: mass spectra were analyzed in the range m/z 150-550 by averaging the data from 50 laser shots and using an accelerating voltage of 20 kV. The described method was successfully applied to the screening of 31 commercial herbal blends, previously analyzed by GC-MS. Among the samples analyzed, 21 contained synthetic cannabinoids (namely JWH-018, JWH-073, JWH-081, JWH-250, JWH-210, JWH-019, and AM-694). All the results were in agreement with GC-MS, which was used as the reference technique. Copyright © 2012 John Wiley & Sons, Ltd.

The influence of culture conditions on the identification of Mycobacterium species by MALDI-TOF MS profiling.

PubMed

Balážová, Tereza; Makovcová, Jitka; Šedo, Ondrej; Slaný, Michal; Faldyna, Martin; Zdráhal, Zbyněk

2014-04-01

Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) represents a simple reliable approach for rapid bacterial identification based on specific peptide/protein fingerprints. However, cell-wall characteristics of mycobacterial species, and their well known stability, complicate MALDI-TOF MS profiling analysis. In this study, we tested two recently published protocols for inactivation and disruption of mycobacteria, and we also examined the influence of different culture conditions (four culture media and five cultivation times) on mass spectral quality and the discriminatory power of the method. We found a significant influence of sample pretreatment method and culture medium on species identification and differentiation for a total of 10 strains belonging to Mycobacterium phlei and Mycobacterium smegmatis. Optimum culture conditions yielding the highest identification success rate against the BioTyper database (Bruker Daltonics) and permitting the possibility of automatic acquisition of mass spectra were found to be distinct for the two mycobacterial species examined. Similarly, individual changes in growth conditions had diverse effects on the two species. For these reasons, thorough control over cultivation conditions should always be employed to maximize the performance and discriminatory power of MALDI-TOF MS profiling, and cultivation conditions must be optimized separately for individual groups of mycobacterial species/strains. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Geena 2, improved automated analysis of MALDI/TOF mass spectra.

PubMed

Romano, Paolo; Profumo, Aldo; Rocco, Mattia; Mangerini, Rosa; Ferri, Fabio; Facchiano, Angelo

2016-03-02

Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of

Reducing time to identification of positive blood cultures with MALDI-TOF MS analysis after a 5-h subculture.

PubMed

Verroken, A; Defourny, L; Lechgar, L; Magnette, A; Delmée, M; Glupczynski, Y

2015-02-01

Speeding up the turn-around time of positive blood culture identifications is essential in order to optimize the treatment of septic patients. Several sample preparation techniques have been developed allowing direct matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification of positive blood cultures. Yet, the hands-on time restrains their routine workflow. In this study, we evaluated an approach whereby MALDI-TOF MS identification without any additional steps was carried out on short subcultured colonies from positive blood bottles with the objective of allowing results reporting on the day of positivity detection. Over a 7-month period in 2012, positive blood cultures detected by 9 am with an automated system were inoculated onto a Columbia blood agar and processed after a 5-h incubation on a MALDI-TOF MicroFlex platform (Bruker Daltonik GmbH). Single-spotted colonies were covered with 1 μl formic acid and 1 μl matrix solution. The results were compared to the validated identification techniques. A total of 925 positive blood culture bottles (representing 470 bacteremic episodes) were included. Concordant identification was obtained in 727 (81.1 %) of the 896 monomicrobial blood cultures, with failure being mostly observed with anaerobes and yeasts. In 17 episodes of polymicrobic bacteremia, the identification of one of the two isolates was achieved in 24/29 (82.7 %) positive cultures. Routine implementation of MALDI-TOF MS identification on young positive blood subcultures provides correct results to the clinician in more than 80 % of the bacteremic episodes and allows access to identification results on the day of blood culture positivity detection, potentially accelerating the implementation of targeted clinical treatments.

Development of a Direct Headspace Collection Method from Arabidopsis Seedlings Using HS-SPME-GC-TOF-MS Analysis

PubMed Central

Kusano, Miyako; Iizuka, Yumiko; Kobayashi, Makoto; Fukushima, Atsushi; Saito, Kazuki

2013-01-01

Plants produce various volatile organic compounds (VOCs), which are thought to be a crucial factor in their interactions with harmful insects, plants and animals. Composition of VOCs may differ when plants are grown under different nutrient conditions, i.e., macronutrient-deficient conditions. However, in plants, relationships between macronutrient assimilation and VOC composition remain unclear. In order to identify the kinds of VOCs that can be emitted when plants are grown under various environmental conditions, we established a conventional method for VOC profiling in Arabidopsis thaliana (Arabidopsis) involving headspace-solid-phase microextraction-gas chromatography-time-of-flight-mass spectrometry (HS-SPME-GC-TOF-MS). We grew Arabidopsis seedlings in an HS vial to directly perform HS analysis. To maximize the analytical performance of VOCs, we optimized the extraction method and the analytical conditions of HP-SPME-GC-TOF-MS. Using the optimized method, we conducted VOC profiling of Arabidopsis seedlings, which were grown under two different nutrition conditions, nutrition-rich and nutrition-deficient conditions. The VOC profiles clearly showed a distinct pattern with respect to each condition. This study suggests that HS-SPME-GC-TOF-MS analysis has immense potential to detect changes in the levels of VOCs in not only Arabidopsis, but other plants grown under various environmental conditions. PMID:24957989

Evaluation of MALDI-TOF mass spectrometry for differentiation of Pichia kluyveri strains isolated from traditional fermentation processes.

PubMed

De la Torre González, Francisco Javier; Gutiérrez Avendaño, Daniel Oswaldo; Gschaedler Mathis, Anne Christine; Kirchmayr, Manuel Reinhart

2018-06-06

Non- Saccharomyces yeasts are widespread microorganisms and some time ago were considered contaminants in the beverage industry. However, nowadays they have gained importance for their ability to produce aromatic compounds, which in alcoholic beverages improves aromatic complexity and therefore the overall quality. Thus, identification and differentiation of the species involved in fermentation processes is vital and can be classified in traditional methods and techniques based on molecular biology. Traditional methods, however, can be expensive, laborious and/or unable to accurately discriminate on strain level. In the present study, a total of 19 strains of Pichia kluyveri isolated from mezcal, tejuino and cacao fermentations were analyzed with rep-PCR fingerprinting and matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). The comparative analysis between MS spectra and rep-PCR patterns obtained from these strains showed a high similarity between both methods. However, minimal differences between the obtained rep-PCR and MALDI-TOF MS clusters could be observed. The data shown suggests that MALDI-TOF MS is a promising alternative technique for rapid, reliable and cost-effective differentiation of natives yeast strains isolated from different traditional fermented foods and beverages. This article is protected by copyright. All rights reserved.

Recognition of Clostridium difficile PCR-ribotypes 001, 027 and 126/078 using an extended MALDI-TOF MS system.

PubMed

Reil, M; Erhard, M; Kuijper, E J; Kist, M; Zaiss, H; Witte, W; Gruber, H; Borgmann, S

2011-11-01

During the last decade, Clostridium difficile infection (CDI) increased markedly inside as well as outside of hospitals. In association with the occurrence of new hypervirulent C. difficile strains, CDI became more important. Until now typing of C. difficile strains has been enabled by PCR-ribotyping. However, this method is restricted to specialized laboratories combined with high maintenance cost. Therefore, we tested MALDI-TOF mass spectrometry for typing of C. difficile to provide a fast method for surveillance of CDI. Using a standard set of 25 different C. difficile PCR ribotypes a database was made by different mass spectra recorded in the SARAMIS software (AnagnosTec, Zossen, Germany). The database was validated with 355 C. difficile strains belonging to 29 different PCR ribotypes collected prospectively from all submitted feces samples in 2009. The most frequent PCR ribotypes were type 001 (70%), 027 (4.8%) and 078/126 (4.7%). All three types were recognized by MALDI-TOF MS. We conclude that an extended MALDI-TOF system was capable to recognize specific markers for ribotypes 001, 027 and 078/126 allowing an effective identification of these strains.

High-accuracy determination of the neutron flux in the new experimental area n_TOF-EAR2 at CERN

NASA Astrophysics Data System (ADS)

Sabaté-Gilarte, M.; Barbagallo, M.; Colonna, N.; Gunsing, F.; Žugec, P.; Vlachoudis, V.; Chen, Y. H.; Stamatopoulos, A.; Lerendegui-Marco, J.; Cortés-Giraldo, M. A.; Villacorta, A.; Guerrero, C.; Damone, L.; Audouin, L.; Berthoumieux, E.; Cosentino, L.; Diakaki, M.; Finocchiaro, P.; Musumarra, A.; Papaevangelou, T.; Piscopo, M.; Tassan-Got, L.; Aberle, O.; Andrzejewski, J.; Bécares, V.; Bacak, M.; Baccomi, R.; Balibrea, J.; Barros, S.; Bečvář, F.; Beinrucker, C.; Belloni, F.; Billowes, J.; Bosnar, D.; Brugger, M.; Caamaño, M.; Calviño, F.; Calviani, M.; Cano-Ott, D.; Cardella, R.; Casanovas, A.; Castelluccio, D. M.; Cerutti, F.; Chiaveri, E.; Cortés, G.; Deo, K.; Domingo-Pardo, C.; Dressler, R.; Dupont, E.; Durán, I.; Fernández-Domínguez, B.; Ferrari, A.; Ferreira, P.; Frost, R. J. W.; Furman, V.; Göbel, K.; García, A. R.; Gawlik, A.; Gheorghe, I.; Glodariu, T.; Gonçalves, I. F.; González, E.; Goverdovski, A.; Griesmayer, E.; Harada, H.; Heftrich, T.; Heinitz, S.; Hernández-Prieto, A.; Heyse, J.; Jenkins, D. G.; Jericha, E.; Käppeler, F.; Kadi, Y.; Katabuchi, T.; Kavrigin, P.; Ketlerov, V.; Khryachkov, V.; Kimura, A.; Kivel, N.; Kokkoris, M.; Krtička, M.; Leal-Cidoncha, E.; Lederer, C.; Leeb, H.; Licata, M.; Lo Meo, S.; Lonsdale, S. J.; Losito, R.; Macina, D.; Marganiec, J.; Martínez, T.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Matteucci, F.; Maugeri, E. A.; Mendoza, E.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Mirea, M.; Montesano, S.; Nolte, R.; Oprea, A.; Palomo-Pinto, F. R.; Paradela, C.; Patronis, N.; Pavlik, A.; Perkowski, J.; Porras, J. I.; Praena, J.; Quesada, J. M.; Rajeev, K.; Rauscher, T.; Reifarth, R.; Riego-Perez, A.; Robles, M. S.; Rout, P. C.; Rubbia, C.; Ryan, J. A.; Saxena, A.; Schillebeeckx, P.; Schmidt, S.; Schumann, D.; Sedyshev, P.; Smith, A. G.; Suryanarayana, S. V.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tsinganis, A.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vlastou, R.; Wallner, A.; Warren, S.; Weigand, M.; Wolf, C.; Woods, P. J.; Weiss, C.; Wright, T.

2017-10-01

A new high flux experimental area has recently become operational at the n_TOF facility at CERN. This new measuring station, n_TOF-EAR2, is placed at the end of a vertical beam line at a distance of approximately 20m from the spallation target. The characterization of the neutron beam, in terms of flux, spatial profile and resolution function, is of crucial importance for the feasibility study and data analysis of all measurements to be performed in the new area. In this paper, the measurement of the neutron flux, performed with different solid-state and gaseous detection systems, and using three neutron-converting reactions considered standard in different energy regions is reported. The results of the various measurements have been combined, yielding an evaluated neutron energy distribution in a wide energy range, from 2meV to 100MeV, with an accuracy ranging from 2%, at low energy, to 6% in the high-energy region. In addition, an absolute normalization of the n_TOF-EAR2 neutron flux has been obtained by means of an activation measurement performed with 197Au foils in the beam.

Advantage of MALDI-TOF-MS over biochemical-based phenotyping for microbial identification illustrated on industrial applications.

PubMed

Urwyler, S K; Glaubitz, J

2016-02-01

Fast microbial identification is becoming increasingly necessary in industry to improve microbial control and reduce biocide consumption. We compared the performances of two systems based on MALDI-TOF MS (VITEK MS and BIOTYPER) and two based on biochemical testing (BIOLOG, VITEK 2 Compact) with genetic methods for the identification of environmental bacteria. At genus level both MALDI-TOF MS-based systems showed the lowest number of false (4%) and approx. 60% correct identifications. In contrast, the biochemical-based systems assigned 25% of the genera incorrectly. The differences were even more apparent at the species level. The BIOTYPER was most conservative, where assigning a species led to the lowest percentage of species identifications (54%) but also to the least wrong assignments (4%). The other three systems showed higher levels of false assignments: 8·7, 40 and 46% respectively. The genus identification performance on four industrial products of the BIOTYPER could be increased up to 94·3% (average 88% of 167 isolates) by evolving the database in a product specific manner. Comparison of the bacterial population in the example of paints, and raw materials used therein, at different production steps demonstrated unequivocally that the contamination of the final paint product originated not from the main raw material. MALDI-TOF-MS has revolutionized speed and precision of microbial identification for clinical isolates outperforming conventional methods. In contrast, few performance studies have been published so far focusing on suitability for particularly industrial applications, geomicrobiology and environmental analytics. This study evaluates the performance of this proteomic phenotyping on such industrial isolates in comparison with biochemical-based phenotyping and genotyping. Further the study exemplifies the power of MALDI-TOF-MS to trace cost-efficiently the dominating cultivable bacterial species throughout an industrial paint production process

Work flow analysis of around-the-clock processing of blood culture samples and integrated MALDI-TOF mass spectrometry analysis for the diagnosis of bloodstream infections.

PubMed

Schneiderhan, Wilhelm; Grundt, Alexander; Wörner, Stefan; Findeisen, Peter; Neumaier, Michael

2013-11-01

Because sepsis has a high mortality rate, rapid microbiological diagnosis is required to enable efficient therapy. The effectiveness of MALDI-TOF mass spectrometry (MALDI-TOF MS) analysis in reducing turnaround times (TATs) for blood culture (BC) pathogen identification when available in a 24-h hospital setting has not been determined. On the basis of data from a total number of 912 positive BCs collected within 140 consecutive days and work flow analyses of laboratory diagnostics, we evaluated different models to assess the TATs for batch-wise and for immediate response (real-time) MALDI-TOF MS pathogen identification of positive BC results during the night shifts. The results were compared to TATs from routine BC processing and biochemical identification performed during regular working hours. Continuous BC incubation together with batch-wise MALDI-TOF MS analysis enabled significant reductions of up to 58.7 h in the mean TATs for the reporting of the bacterial species. The TAT of batch-wise MALDI-TOF MS analysis was inferior by a mean of 4.9 h when compared to the model of the immediate work flow under ideal conditions with no constraints in staff availability. Together with continuous cultivation of BC, the 24-h availability of MALDI-TOF MS can reduce the TAT for microbial pathogen identification within a routine clinical laboratory setting. Batch-wise testing of positive BC loses a few hours compared to real-time identification but is still far superior to classical BC processing. Larger prospective studies are required to evaluate the contribution of rapid around-the-clock pathogen identification to medical decision-making for septicemic patients.

Multicenter evaluation of the Sepsityper™ extraction kit and MALDI-TOF MS for direct identification of positive blood culture isolates using the BD BACTEC™ FX and VersaTREK(®) diagnostic blood culture systems.

PubMed

Schieffer, K M; Tan, K E; Stamper, P D; Somogyi, A; Andrea, S B; Wakefield, T; Romagnoli, M; Chapin, K C; Wolk, D M; Carroll, K C

2014-04-01

(i) Evaluation of delayed time to blood culture extraction by the Sepsityper kit and impact of shipping pellets off-site for MALDI-TOF MS analysis. (ii) Comparison of Sepsityper and laboratory-developed extraction methods from a literature review. Using two blood culture systems (BD BACTEC and VersaTREK), we extracted 411 positive blood cultures using the Sepsityper kit to mimic a potential protocol for institutions without a MALDI-TOF MS. Extracted pellets were shipped and analysed on the Bruker UltraflexIII. Successful extraction of 358 (87·1%) samples was determined by the presence of detectable proteins. MALDI-TOF MS correctly identified 332 (80·8%) samples. Delayed time to extraction did not affect Sepsityper extraction or MALDI-TOF MS accuracy. The extracted pellets remain stable and provide accurate results by MALDI-TOF MS when shipped at room temperature to off-site reference laboratories. This is the first study to show that institutions without a MALDI-TOF MS can take advantage of this innovative technology by shipping a volume of blood to an off-site laboratory for extraction and MALDI-TOF MS analysis. We also performed a literature review to compare various extraction methods. © 2014 The Society for Applied Microbiology.

Matrix-Assisted Laser Desorption Ionization–Time of Flight (MALDI-TOF) Mass Spectrometry for Detection of Antibiotic Resistance Mechanisms: from Research to Routine Diagnosis

PubMed Central

Chudáčková, Eva; Walková, Radka

2013-01-01

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has been successfully applied as an identification procedure in clinical microbiology and has been widely used in routine laboratory practice because of its economical and diagnostic benefits. The range of applications of MALDI-TOF MS has been growing constantly, from rapid species identification to labor-intensive proteomic studies of bacterial physiology. The purpose of this review is to summarize the contribution of the studies already performed with MALDI-TOF MS concerning antibiotic resistance and to analyze future perspectives in this field. We believe that current research should continue in four main directions, including the detection of antibiotic modifications by degrading enzymes, the detection of resistance mechanism determinants through proteomic studies of multiresistant bacteria, and the analysis of modifications of target sites, such as ribosomal methylation. The quantification of antibiotics is suggested as a new approach to study influx and efflux in bacterial cells. The results of the presented studies demonstrate that MALDI-TOF MS is a relevant tool for the detection of antibiotic resistance and opens new avenues for both clinical and experimental microbiology. PMID:23297261

Heterotrophic monitoring at a drinking water treatment plant by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry after different drinking water treatments.

PubMed

Sala-Comorera, Laura; Blanch, Anicet R; Vilaró, Carles; Galofré, Belén; García-Aljaro, Cristina

2017-10-01

The aim of this work was to assess the suitability of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) for routine heterotrophic monitoring in a drinking water treatment plant. Water samples were collected from raw surface water and after different treatments during two campaigns over a 1-year period. Heterotrophic bacteria were studied and isolates were identified by MALDI-TOF MS. Moreover, the diversity index and the coefficient of population similarity were also calculated using biochemical fingerprinting of the populations studied. MALDI-TOF MS enabled us to characterize and detect changes in the bacterial community composition throughout the water treatment plant. Raw water showed a large and diverse population which was slightly modified after initial treatment steps (sand filtration and ultrafiltration). Reverse osmosis had a significant impact on the microbial diversity, while the final chlorination step produced a shift in the composition of the bacterial community. Although MALDI-TOF MS could not identify all the isolates since the available MALDI-TOF MS database does not cover all the bacterial diversity in water, this technique could be used to monitor bacterial changes in drinking water treatment plants by creating a specific protein profile database for tracking purposes.

Field performance and identification capability of the Innsbruck PTR-TOF

NASA Astrophysics Data System (ADS)

Graus, M.; Müller, M.; Hansel, A.

2009-04-01

Over the last one and a half decades Proton Transfer Reaction Mass Spectrometry (PTR-MS) [1, 2] has gained recognition as fast on-line sensor for monitoring volatile organic compounds (VOC) in the atmosphere. Sample collection is very straight forward and the fact that no pre-concentration is needed is of particular advantage for compounds that are notoriously difficult to pre-concentrate and/or analyze by gas chromatographic (GC) methods. Its ionization method is very versatile, i.e. all compounds that perform exothermic proton transfer with hydronium ions - and most VOCs do so - are readily ionized, producing quasi-molecular ions VOC.H+. In the quasi-molecular ion the elemental composition of the analyte compound is conserved and allows, in combination with some background knowledge of the sample, conclusions about the identity of that compound. De Gouw and Warneke (2007) [3] summarized the applicability of PTR-MS in atmospheric chemistry but they also pointed out shortcomings in the identification capabilities. Goldstein and Galbally (2007) [4] addressed the multitude of VOCs potentially present in the atmosphere and they emphasized the gasphase-to-aerosol partitioning of organic compounds (volatile and semi-volatile) in dependence of carbon-chain length and oxygen containing functional groups. In collaboration with Ionicon and assisted by TOFWERK we developed a PTR time-of-flight (PTR-TOF) instrument that allows for the identification of the atomic composition of oxygenated hydrocarbons by exact-mass determination. A detection limit in the low pptv range was achieved at a time resolution of one minute, one-second detection limit is in the sub-ppbv range. In 2008 the Innsbruck PTR-TOF was field deployed in the icebreaker- and helicopter based Arctic Summer Cloud Ocean Study (ASCOS) to characterize the organic trace gas composition of the High Arctic atmosphere. During the six-week field campaign the PTR-TOF was run without problems even under harsh conditions in

Rapid Genotyping of Single Nucleotide Polymorphisms Influencing Warfarin Drug Response by Surface-Enhanced Laser Desorption and Ionization Time-of-Flight (SELDI-TOF) Mass Spectrometry

PubMed Central

Yang, Shangbin; Xu, LiHui; Wu, Haifeng M.

2010-01-01

Warfarin exhibits significant interindividual variability in dosing requirements. Different drug responses are partly attributed to the single nucleotide polymorphisms (SNPs) that influence either drug action or drug metabolism. Rapid genotyping of these SNPs helps clinicians to choose appropriate initial doses to quickly achieve anticoagulation effects and to prevent complications. We report a novel application of surface-enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF MS) in the rapid genotyping of SNPs that impact warfarin efficacy. The SNPs were first amplified by PCR and then underwent single base extension to generate the specific SNP product. Next, genetic variants displaying different masses were bound to Q10 anionic proteinChips and then genotyped by using SELDI-TOF MS in a multiplex fashion. SELDI-TOF MS offered unique properties of on-chip sample enrichment and clean-ups, which streamlined the testing procedures and eliminated many tedious experimental steps required by the conventional MS-based method. The turn-around time for genotyping three known warfarin-related SNPs, CYP2C9*2, CYP2C9*3, and VKORC1 3673G>A by SELDI-TOF MS was less than 5 hours. The analytical accuracy of this method was confirmed both by bidirectional DNA sequencing and by comparing the genotype results (n = 189) obtained by SELDI-TOF MS to reports from a clinical reference laboratory. This new multiplex genotyping method provides an excellent clinical laboratory platform to promote personalized medicine in warfarin therapy. PMID:20075209

Rapid genotyping of single nucleotide polymorphisms influencing warfarin drug response by surface-enhanced laser desorption and ionization time-of-flight (SELDI-TOF) mass spectrometry.

PubMed

Yang, Shangbin; Xu, LiHui; Wu, Haifeng M

2010-03-01

Warfarin exhibits significant interindividual variability in dosing requirements. Different drug responses are partly attributed to the single nucleotide polymorphisms (SNPs) that influence either drug action or drug metabolism. Rapid genotyping of these SNPs helps clinicians to choose appropriate initial doses to quickly achieve anticoagulation effects and to prevent complications. We report a novel application of surface-enhanced laser desorption and ionization time-of-flight mass spectrometry (SELDI-TOF MS) in the rapid genotyping of SNPs that impact warfarin efficacy. The SNPs were first amplified by PCR and then underwent single base extension to generate the specific SNP product. Next, genetic variants displaying different masses were bound to Q10 anionic proteinChips and then genotyped by using SELDI-TOF MS in a multiplex fashion. SELDI-TOF MS offered unique properties of on-chip sample enrichment and clean-ups, which streamlined the testing procedures and eliminated many tedious experimental steps required by the conventional MS-based method. The turn-around time for genotyping three known warfarin-related SNPs, CYP2C9*2, CYP2C9*3, and VKORC1 3673G>A by SELDI-TOF MS was less than 5 hours. The analytical accuracy of this method was confirmed both by bidirectional DNA sequencing and by comparing the genotype results (n = 189) obtained by SELDI-TOF MS to reports from a clinical reference laboratory. This new multiplex genotyping method provides an excellent clinical laboratory platform to promote personalized medicine in warfarin therapy.

Identification of clinical isolates of Aspergillus, including cryptic species, by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

PubMed

Vidal-Acuña, M Reyes; Ruiz-Pérez de Pipaón, Maite; Torres-Sánchez, María José; Aznar, Javier

2017-12-08

An expanded library of matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been constructed using the spectra generated from 42 clinical isolates and 11 reference strains, including 23 different species from 8 sections (16 cryptic plus 7 noncryptic species). Out of a total of 379 strains of Aspergillus isolated from clinical samples, 179 strains were selected to be identified by sequencing of beta-tubulin or calmodulin genes. Protein spectra of 53 strains, cultured in liquid medium, were used to construct an in-house reference database in the MALDI-TOF MS. One hundred ninety strains (179 clinical isolates previously identified by sequencing and the 11 reference strains), cultured on solid medium, were blindy analyzed by the MALDI-TOF MS technology to validate the generated in-house reference database. A 100% correlation was obtained with both identification methods, gene sequencing and MALDI-TOF MS, and no discordant identification was obtained. The HUVR database provided species level (score of ≥2.0) identification in 165 isolates (86.84%) and for the remaining 25 (13.16%) a genus level identification (score between 1.7 and 2.0) was obtained. The routine MALDI-TOF MS analysis with the new database, was then challenged with 200 Aspergillus clinical isolates grown on solid medium in a prospective evaluation. A species identification was obtained in 191 strains (95.5%), and only nine strains (4.5%) could not be identified at the species level. Among the 200 strains, A. tubingensis was the only cryptic species identified. We demonstrated the feasibility and usefulness of the new HUVR database in MALDI-TOF MS by the use of a standardized procedure for the identification of Aspergillus clinical isolates, including cryptic species, grown either on solid or liquid media. © The Author 2017. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For

Simultaneous reconstruction of the activity image and registration of the CT image in TOF-PET

NASA Astrophysics Data System (ADS)

Rezaei, Ahmadreza; Michel, Christian; Casey, Michael E.; Nuyts, Johan

2016-02-01

Previously, maximum-likelihood methods have been proposed to jointly estimate the activity image and the attenuation image or the attenuation sinogram from time-of-flight (TOF) positron emission tomography (PET) data. In this contribution, we propose a method that addresses the possible alignment problem of the TOF-PET emission data and the computed tomography (CT) attenuation data, by combining reconstruction and registration. The method, called MLRR, iteratively reconstructs the activity image while registering the available CT-based attenuation image, so that the pair of activity and attenuation images maximise the likelihood of the TOF emission sinogram. The algorithm is slow to converge, but some acceleration could be achieved by using Nesterov’s momentum method and by applying a multi-resolution scheme for the non-rigid displacement estimation. The latter also helps to avoid local optima, although convergence to the global optimum cannot be guaranteed. The results are evaluated on 2D and 3D simulations as well as a respiratory gated clinical scan. Our experiments indicate that the proposed method is able to correct for possible misalignment of the CT-based attenuation image, and is therefore a very promising approach to suppressing attenuation artefacts in clinical PET/CT. When applied to respiratory gated data of a patient scan, it produced deformations that are compatible with breathing motion and which reduced the well known attenuation artefact near the dome of the liver. Since the method makes use of the energy-converted CT attenuation image, the scale problem of joint reconstruction is automatically solved.

GyrB sequence analysis and MALDI-TOF MS as identification tools for plant pathogenic Clavibacter.

PubMed

Zaluga, Joanna; Heylen, Kim; Van Hoorde, Koenraad; Hoste, Bart; Van Vaerenbergh, Johan; Maes, Martine; De Vos, Paul

2011-09-01

The bacterial genus Clavibacter has only one species, Clavibacter michiganensis, containing five subspecies. All five are plant pathogens, among which three are recognized as quarantine pests (mentioned on the EPPO A2 list). Prevention of their introduction and epidemic outbreaks requires a reliable and accurate identification. Currently, identification of these bacteria is time consuming and often problematic, mainly because of cross-reactions with other plant-associated bacteria in immunological tests and false-negative results in PCR detection methods. Furthermore, distinguishing closely related subspecies is not straightforward. This study aimed at evaluating the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and a fragment of the gyrB sequence for the reliable and fast identification of the Clavibacter subspecies. Amplification and sequencing of gyrB using a single primer set had sufficient resolution and specificity to identify each subspecies based on both sequence similarities in cluster analyses and specific signatures within the sequences. All five subspecies also generated distinct and reproducible MALDI-TOF MS profiles, with unique and specific ion peaks for each subspecies, which could be used as biomarkers for identification. Results from both methods were in agreement and were able to distinguish the five Clavibacter subspecies from each other and from representatives of closely related Rathayibacter, Leifsonia or Curtobacterium species. Our study suggests that proteomic analysis using MALDI-TOF MS and gyrB sequence are powerful diagnostic tools for the accurate identification of Clavibacter plant pathogens. Copyright © 2011 Elsevier GmbH. All rights reserved.

A 32 mm  ×  32 mm  ×  22 mm monolithic LYSO:Ce detector with dual-sided digital photon counter readout for ultrahigh-performance TOF-PET and TOF-PET/MRI

NASA Astrophysics Data System (ADS)

Borghi, Giacomo; Peet, Bart Jan; Tabacchini, Valerio; Schaart, Dennis R.

2016-07-01

New applications for positron emission tomography (PET) and combined PET/magnetic resonance imaging (MRI) are currently emerging, for example in the fields of neurological, breast, and pediatric imaging. Such applications require improved image quality, reduced dose, shorter scanning times, and more precise quantification. This can be achieved by means of dedicated scanners based on ultrahigh-performance detectors, which should provide excellent spatial resolution, precise depth-of-interaction (DOI) estimation, outstanding time-of-flight (TOF) capability, and high detection efficiency. Here, we introduce such an ultrahigh-performance TOF/DOI PET detector, based on a 32 mm  ×  32 mm  ×  22 mm monolithic LYSO:Ce crystal. The 32 mm  ×  32 mm front and back faces of the crystal are coupled to a digital photon counter (DPC) array, in so-called dual-sided readout (DSR) configuration. The fully digital detector offers a spatial resolution of ~1.1 mm full width at half maximum (FWHM)/~1.2 mm mean absolute error, together with a DOI resolution of ~2.4 mm FWHM, an energy resolution of 10.2% FWHM, and a coincidence resolving time of 147 ps FWHM. The time resolution closely approaches the best results (135 ps FWHM) obtained to date with small crystals made from the same material coupled to the same DPC arrays, illustrating the excellent correction for optical and electronic transit time spreads that can be achieved in monolithic scintillators using maximum-likelihood techniques for estimating the time of interaction. The performance barely degrades for events with missing data (up to 6 out of 32 DPC dies missing), permitting the use of almost all events registered under realistic acquisition conditions. Moreover, the calibration procedures and computational methods used for position and time estimation follow recently made improvements that make them fast and practical, opening up realistic perspectives for using DSR monolithic

Identification of coryneform Actinomyces neuii by MALDI-TOF MS: 5 case reports and review of literature.

PubMed

De Vreese, K; Verhaegen, J

2013-01-01

We describe five cases of Actinomyces neuii, isolated from different clinical specimens over a period of five months (from June to October 2011), followed by a review of literature on infections with this micro-organism. All Actinomyces neuii strains were cultured or subcultured on horse blood agar. Identification took place using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Identification was confirmed by conventional biochemical tests and API Coryne test strips (BioMérieux SA). Susceptibility testing was performed on Mueller-Hinton agar supplemented with horse blood, using E-tests (BioMérieux SA). The minimal inhibitory concentrations were determined after 24 and 48 hours of incubation in a 5% CO2 environment. Isolation of this micro-organism was associated with abscesses in two patients and chronic osteomyelitis in one patient. The remaining two patients had positive blood cultures which grew Actinomyces neuii, either as contamination or as catheter-related infection. All Actinomyces neuii identifications were obtained by MALDI-TOF MS and were confirmed by conventional biochemical and API Coryne tests. Identification of one isolate was also confirmed by 16S rRNA sequencing. All strains were susceptible to penicillin. One strain showed heteroresistance for macrolides and lincosamides. Minimal inhibitory concentrations were more reliable and easier to read after 48 hours of incubation, as compared to 24 hours. MALDI-TOF MS analysis allows rapid and reliable identification of Actinomyces neuii, even at subspecies level.

MALDI-TOF-MS with PLS Modeling Enables Strain Typing of the Bacterial Plant Pathogen Xanthomonas axonopodis

NASA Astrophysics Data System (ADS)

Sindt, Nathan M.; Robison, Faith; Brick, Mark A.; Schwartz, Howard F.; Heuberger, Adam L.; Prenni, Jessica E.

2018-02-01

Matrix-assisted desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) is a fast and effective tool for microbial species identification. However, current approaches are limited to species-level identification even when genetic differences are known. Here, we present a novel workflow that applies the statistical method of partial least squares discriminant analysis (PLS-DA) to MALDI-TOF-MS protein fingerprint data of Xanthomonas axonopodis, an important bacterial plant pathogen of fruit and vegetable crops. Mass spectra of 32 X. axonopodis strains were used to create a mass spectral library and PLS-DA was employed to model the closely related strains. A robust workflow was designed to optimize the PLS-DA model by assessing the model performance over a range of signal-to-noise ratios (s/n) and mass filter (MF) thresholds. The optimized parameters were observed to be s/n = 3 and MF = 0.7. The model correctly classified 83% of spectra withheld from the model as a test set. A new decision rule was developed, termed the rolled-up Maximum Decision Rule (ruMDR), and this method improved identification rates to 92%. These results demonstrate that MALDI-TOF-MS protein fingerprints of bacterial isolates can be utilized to enable identification at the strain level. Furthermore, the open-source framework of this workflow allows for broad implementation across various instrument platforms as well as integration with alternative modeling and classification algorithms.

Real-time observation of coadsorption layers on Ru(001) using a temperature-programmed ESDIAD/TOF system

NASA Astrophysics Data System (ADS)

Sasaki, T.; Itai, Y.; Iwasawa, Y.

1997-11-01

For the purpose of utilizing ESDIAD as a real-time probe for surface processes, we have developed an instrument which can measure ESDIAD images and time of flight (TOF) spectra of desorbing ions in temperature-programmed surface processes. TOF measurements are carried out to identify the mass and to determine the kinetic energy distribution of the desorbed ions. This temperature-programmed (TP-) ESDIAD/TOF system was used to observe coadsorption layers of methylamine and CO on Ru(001) which have been previously studied by our group using LEED, TPD and HREELS, also drawing upon a comparison of findings with the coadsorption system of CO and ammonia. ESDIAD images acquired for temperature-programmed surface processes in real time were found to provide new insight into the dynamic behaviour of the coadsorption layers. As to the pure adsorption of ammonia and methylamine, the second and the first (chemisorbed) layers can be easily discriminated in their different ESD detection efficiency due to the difference in neutralization rate. The intensity change of H + ions with temperature shows the process of the decomposition of methylamine to be dependent on CO coverage. The intensity of O + originating from CO changes due to the change of CO adsorption site in the reaction process. The angular distribution of H + ions which correspond to CH2NH…Ru species appears at 250-300 K in the presence of high CO pre-coverage.

LC-MS-MS-TOF analysis of oxygenated organic compounds in ambient aerosol

NASA Astrophysics Data System (ADS)

Roempp, A.; Moortgat, G.

2003-04-01

Ambient aerosol samples were taken at different sites across Europe. The fine mode aerosol was collected on quartz filters at flow rates of 160 L/min and 500 L/min. These samples were analyzed for organic acids (C>4) by an HPLC system coupled to a hybrid mass spectrometer. The mass spectrometer consists of a quadrupole mass analyzer, a quadrupole collision cell and a time-of-flight mass analyzer (TOF). Analytes were identified by standards when available or MS-MS experiments and exact mass measurements utilizing the high mass resolution of the TOF instrument. Monoterpenes (alpha-pinene, beta-pinene, sabinene, limonene, 3-carene) were ozonolyzed in the laboratory and compared with field samples. Besides the commonly measured organic acids (pinic, pinonic and norpinic acid) sabinic, caric and caronic acid were identified for the first time in ambient aerosol. In addition, nearly all samples showed significant concentrations of newly identified keto dicarboxylic acids (C9 - C12). Laboratory experiments were used to investigate the formation mechanisms of these compounds. By comparing laboratory measurements of wood combustion and field samples from the Eastern Mediterranean region, nitrocatechol was identified as a possible tracer for biomass burning. The data obtained is used to determine the role of biogenic sources in secondary organic aerosol formation.

Identification and High-Resolution Imaging of α-Tocopherol from Human Cells to Whole Animals by TOF-SIMS Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Bruinen, Anne L.; Fisher, Gregory L.; Balez, Rachelle; van der Sar, Astrid M.; Ooi, Lezanne; Heeren, Ron M. A.

2018-06-01

A unique method for identification of biomolecular components in different biological specimens, while preserving the capability for high speed 2D and 3D molecular imaging, is employed to investigate cellular response to oxidative stress. The employed method enables observing the distribution of the antioxidant α-tocopherol and other molecules in cellular structures via time-of-flight secondary ion mass spectrometry (TOF-SIMS (MS1)) imaging in parallel with tandem mass spectrometry (MS2) imaging, collected simultaneously. The described method is employed to examine a network formed by neuronal cells differentiated from human induced pluripotent stem cells (iPSCs), a model for investigating human neurons in vitro. The antioxidant α-tocopherol is identified in situ within different cellular layers utilizing a 3D TOF-SIMS tandem MS imaging analysis. As oxidative stress also plays an important role in mediating inflammation, the study was expanded to whole body tissue sections of M. marinum-infected zebrafish, a model organism for tuberculosis. The TOF-SIMS tandem MS imaging results reveal an increased presence of α-tocopherol in response to the pathogen. [Figure not available: see fulltext.

Comparison of TOF MRA, Contrast-Enhanced MRA and Subtracted CTA from CTP in Residue Evaluation of Treated Intracranial Aneurysms.

PubMed

Dündar, Tolga Turan; Aralaşmak, Ayşe; Özdemir, Hüseyin; Seyithanoğlu, Mehmet Hakan; Uysal, Ömer; Toprak, Hüseyin; Kitiş, Serkan; Özek, Erdinç; Alkan, Alpay

2017-10-18

To compare effectiveness of contrast-enhanced MRA (CE-MRA), 3D-Time-of-flight MRA (3D-TOF-MRA) and subtracted CTA from CTP (sub-CTA) in residue evaluation of intracranial aneurysms treated either with coiling or clipping. Sixteen treated aneurysms, which were evaluated with three methods within two weeks after the operation, were enrolled. The success of each imaging techniques in demonstration of residue aneurysm and nearby vessels was compared by Fisher\\'s Exact Test. The differences among three was evaluated by Cochran\\'s Q test (p ≤ 0.05). Perfusion abnormality was noted in % 81 of clipped and none of coiled patients. Vessel visualization in the vicinity of aneurysm was better in sub-CTA, followed by CE-MRA. In clipped aneurysms, sub-CTA revealed residue aneurysms in % 16,7 of the patients while 3D-TOF-MRA and CE-MRA revealed none. In coiled aneurysms, CE-MRA revealed residue aneurysms in 100 %, and TOF-MRA in 33,3 % while sub-CTA revealed none. Although dramatic differences were noted in the evaluation of residue aneurysm as well as nearby vessel visualization, no statistical significance noted due to very few patients in subcategories Conclusion: This is first study comparing the effectiveness of CE-MRA, 3D-TOF MRA and sub-CTA in residue aneurysms evaluation. Vessel visualization in the vicinity of aneurysm was better in sub-CTA in all regardless of coiling or clipping. Residue aneurysms were more commonly revealed by CE-MRA in coiled patients and more commonly and better shown by sub-CTA in clipped patients in addition of showing perfusion abnormality that's is more common in clipped patients.

Rapid identification of microorganisms from positive blood cultures by MALDI-TOF mass spectrometry subsequent to very short-term incubation on solid medium.

PubMed

Idelevich, E A; Schüle, I; Grünastel, B; Wüllenweber, J; Peters, G; Becker, K

2014-10-01

Rapid identification of the causative microorganism is important for appropriate antimicrobial therapy of bloodstream infections. Bacteria from positive blood culture (BC) bottles are not readily available for identification by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Lysis and centrifugation procedures suggested for direct MALDI-TOF MS from positive BCs without previous culture are associated with additional hands-on processing time and costs. Here, we describe an alternative approach applying MALDI-TOF MS from bacterial cultures incubated very briefly on solid medium. After plating of positive BC broth on Columbia blood agar (n = 165), MALDI-TOF MS was performed after 1.5, 2, 3, 4, 5, 6, 7, 8, 12 and (for control) 24 h of incubation until reliable identification to the species level was achieved (score ≥2.0). Mean incubation time needed to achieve species-level identification was 5.9 and 2.0 h for Gram-positive aerobic cocci (GPC, n = 86) and Gram-negative aerobic rods (GNR, n = 42), respectively. Short agar cultures with incubation times ≤2, ≤4, ≤6, ≤8 and ≤12 h yielded species identification in 1.2%, 18.6%, 64.0%, 96.5%, 98.8% of GPC, and in 76.2%, 95.2%, 97.6%, 97.6%, 97.6% of GNR, respectively. Control species identification at 24 h was achieved in 100% of GPC and 97.6% of GNR. Ethanol/formic acid protein extraction performed for an additional 34 GPC isolates cultivated from positive BCs showed further reduction in time to species identification (3.1 h). MALDI-TOF MS using biomass subsequent to very short-term incubation on solid medium allows very early and reliable bacterial identification from positive BCs without additional time and cost expenditure. © 2014 The Authors Clinical Microbiology and Infection © 2014 European Society of Clinical Microbiology and Infectious Diseases.

Nuclear data activities at the n_TOF facility at CERN

NASA Astrophysics Data System (ADS)

Gunsing, F.; Aberle, O.; Andrzejewski, J.; Audouin, L.; Bécares, V.; Bacak, M.; Balibrea-Correa, J.; Barbagallo, M.; Barros, S.; Bečvář, F.; Beinrucker, C.; Belloni, F.; Berthoumieux, E.; Billowes, J.; Bosnar, D.; Brugger, M.; Caamaño, M.; Calviño, F.; Calviani, M.; Cano-Ott, D.; Cardella, R.; Casanovas, A.; Castelluccio, D. M.; Cerutti, F.; Chen, Y. H.; Chiaveri, E.; Colonna, N.; Cortés-Giraldo, M. A.; Cortés, G.; Cosentino, L.; Damone, L. A.; Deo, K.; Diakaki, M.; Domingo-Pardo, C.; Dressler, R.; Dupont, E.; Durán, I.; Fernández-Domínguez, B.; Ferrari, A.; Ferreira, P.; Finocchiaro, P.; Frost, R. J. W.; Furman, V.; Ganesan, S.; García, A. R.; Gawlik, A.; Gheorghe, I.; Glodariu, T.; Gonçalves, I. F.; González, E.; Goverdovski, A.; Griesmayer, E.; Guerrero, C.; Göbel, K.; Harada, H.; Heftrich, T.; Heinitz, S.; Hernández-Prieto, A.; Heyse, J.; Jenkins, D. G.; Jericha, E.; Käppeler, F.; Kadi, Y.; Katabuchi, T.; Kavrigin, P.; Ketlerov, V.; Khryachkov, V.; Kimura, A.; Kivel, N.; Kokkoris, M.; Krtička, M.; Leal-Cidoncha, E.; Lederer, C.; Leeb, H.; Lerendegui, J.; Licata, M.; Lo Meo, S.; Lonsdale, S. J.; Losito, R.; Macina, D.; Marganiec, J.; Martínez, T.; Masi, A.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Matteucci, F.; Maugeri, E. A.; Mazzone, A.; Mendoza, E.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Mirea, M.; Montesano, S.; Musumarra, A.; Nolte, R.; Oprea, A.; Palomo-Pinto, F. R.; Paradela, C.; Patronis, N.; Pavlik, A.; Perkowski, J.; Porras, I.; Praena, J.; Quesada, J. M.; Rajeev, K.; Rauscher, T.; Reifarth, R.; Riego-Perez, A.; Robles, M.; Rout, P.; Radeck, D.; Rubbia, C.; Ryan, J. A.; Sabaté-Gilarte, M.; Saxena, A.; Schillebeeckx, P.; Schmidt, S.; Schumann, D.; Sedyshev, P.; Smith, A. G.; Stamatopoulos, A.; Suryanarayana, S. V.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tarrío, D.; Tassan-Got, L.; Tsinganis, A.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vlachoudis, V.; Vlastou, R.; Wallner, A.; Warren, S.; Weigand, M.; Weiss, C.; Wolf, C.; Woods, P. J.; Wright, T.; Žugec, P.

2016-10-01

Nuclear data in general, and neutron-induced reaction cross sections in particular, are important for a wide variety of research fields. They play a key role in the safety and criticality assessment of nuclear technology, not only for existing power reactors but also for radiation dosimetry, medical applications, the transmutation of nuclear waste, accelerator-driven systems, fuel cycle investigations and future reactor systems as in Generation IV. Applications of nuclear data are also related to research fields as the study of nuclear level densities and stellar nucleosynthesis. Simulations and calculations of nuclear technology applications largely rely on evaluated nuclear data libraries. The evaluations in these libraries are based both on experimental data and theoretical models. Experimental nuclear reaction data are compiled on a worldwide basis by the international network of Nuclear Reaction Data Centres (NRDC) in the EXFOR database. The EXFOR database forms an important link between nuclear data measurements and the evaluated data libraries. CERN's neutron time-of-flight facility n_TOF has produced a considerable amount of experimental data since it has become fully operational with the start of the scientific measurement programme in 2001. While for a long period a single measurement station (EAR1) located at 185 m from the neutron production target was available, the construction of a second beam line at 20 m (EAR2) in 2014 has substantially increased the measurement capabilities of the facility. An outline of the experimental nuclear data activities at CERN's neutron time-of-flight facility n_TOF will be presented.

MALDI-TOF mass spectrometry proteomic phenotyping of clinically relevant fungi.

PubMed

Putignani, Lorenza; Del Chierico, Federica; Onori, Manuela; Mancinelli, Livia; Argentieri, Marta; Bernaschi, Paola; Coltella, Luana; Lucignano, Barbara; Pansani, Laura; Ranno, Stefania; Russo, Cristina; Urbani, Andrea; Federici, Giorgio; Menichella, Donato

2011-03-01

Proteomics is particularly suitable for characterising human pathogens with high life cycle complexity, such as fungi. Protein content and expression levels may be affected by growth states and life cycle morphs and correlate to species and strain variation. Identification and typing of fungi by conventional methods are often difficult, time-consuming and frequently, for unusual species, inconclusive. Proteomic phenotypes from MALDI-TOF MS were employed as analytical and typing expression profiling of yeast, yeast-like species and strain variants in order to achieve a microbial proteomics population study. Spectra from 303 clinical isolates were generated and processed by standard pattern matching with a MALDI-TOF Biotyper (MT). Identifications (IDs) were compared to a reference biochemical-based system (Vitek-2) and, when discordant, MT IDs were verified with genotyping IDs, obtained by sequencing the 25-28S rRNA hypervariable D2 region. Spectra were converted into virtual gel-like formats, and hierarchical clustering analysis was performed for 274 Candida profiles to investigate species and strain typing correlation. MT provided 257/303 IDs consistent with Vitek-2 ones. However, amongst 26/303 discordant MT IDs, only 5 appeared "true". No MT identification was achieved for 20/303 isolates for incompleteness of database species variants. Candida spectra clustering agreed with identified species and topology of Candida albicans and Candida parapsilosis specific dendrograms. MT IDs show a high analytical performance and profiling heterogeneity which seems to complement or even outclass existing typing tools. This variability reflects the high biological complexity of yeasts and may be properly exploited to provide epidemiological tracing and infection dispersion patterns.

Short communication: Evaluation of MALDI-TOF mass spectrometry and a custom reference spectra expanded database for the identification of bovine-associated coagulase-negative staphylococci.

PubMed

Cameron, M; Perry, J; Middleton, J R; Chaffer, M; Lewis, J; Keefe, G P

2018-01-01

This study evaluated MALDI-TOF mass spectrometry and a custom reference spectra expanded database for the identification of bovine-associated coagulase-negative staphylococci (CNS). A total of 861 CNS isolates were used in the study, covering 21 different CNS species. The majority of the isolates were previously identified by rpoB gene sequencing (n = 804) and the remainder were identified by sequencing of hsp60 (n = 56) and tuf (n = 1). The genotypic identification was considered the gold standard identification. Using a direct transfer protocol and the existing commercial database, MALDI-TOF mass spectrometry showed a typeability of 96.5% (831/861) and an accuracy of 99.2% (824/831). Using a custom reference spectra expanded database, which included an additional 13 in-house created reference spectra, isolates were identified by MALDI-TOF mass spectrometry with 99.2% (854/861) typeability and 99.4% (849/854) accuracy. Overall, MALDI-TOF mass spectrometry using the direct transfer method was shown to be a highly reliable tool for the identification of bovine-associated CNS. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Basic performance of Mg co-doped new scintillator used for TOF-DOI-PET systems

NASA Astrophysics Data System (ADS)

Kobayashi, Takahiro; Yamamoto, Seiichi; Okumura, Satoshi; Yeom, Jung Yeol; Kamada, Kei; Yoshikawa, Akira

2017-01-01

Phoswich depth-of-interaction (DOI) detectors utilizing multiple scintillators with different decay time are a useful device for developing a high spatial resolution, high sensitivity PET scanner. However, in order to apply pulse shape discrimination (PSD), there are not many combinations of scintillators for which phoswich technique can be implemented. Ce doped Gd3Ga3Al2O12 (GFAG) is a recently developed scintillator with a fast decay time. This scintillator is similar to Ce doped Gd3Al2Ga3O12 (GAGG), which is a promising scintillator for PET detector with high light yield. By stacking these scintillators, it may be possible to realize a high spatial resolution and high timing resolution phoswich DOI detector. Such phoswich DOI detector may be applied to time-of-flight (TOF) systems with high timing performance. Therefore, in this study, we tested the basic performance of the new scintillator -GFAG for use in a TOF phoswich detector. The measured decay time of a GFAG element of 2.9 mmx2.9 mmx10 mm in dimension, which was optically coupled to a photomultiplier tube (PMT), was faster (66 ns) than that of same sized GAGG (103 ns). The energy resolution of the GFAG element was 5.7% FWHM which was slightly worse than that of GAGG with 4.9% FWHM for 662 keV gamma photons without saturation correction. Then we assembled the GFAG and the GAGG crystals in the depth direction to form a 20 mm long phoswich element (GFAG/GAGG). By pulse shape analysis, the two types of scintillators were clearly resolved. Measured timing resolution of a pair of opposing GFAG/GAGG phoswich scintillator coupled to Silicon Photomultipliers (Si-PM) was good with coincidence resolving time of 466 ps FWHM. These results indicate that the GFAG combined with GAGG can be a candidate for TOF-DOI-PET systems.

DOI Determination by Rise Time Discrimination in Single-Ended Readout for TOF PET Imaging

PubMed Central

Wiener, R.I.; Surti, S.; Karp, J.S.

2013-01-01

Clinical TOF PET systems achieve detection efficiency using thick crystals, typically of thickness 2–3cm. The resulting dispersion in interaction depths degrades spatial resolution for increasing radial positions due to parallax error. Furthermore, interaction depth dispersion results in time pickoff dispersion and thus in degraded timing resolution, and is therefore of added concern in TOF scanners. Using fast signal digitization, we characterize the timing performance, pulse shape and light output of LaBr3:Ce, CeBr3 and LYSO. Coincidence timing resolution is shown to degrade by ~50ps/cm for scintillator pixels of constant cross section and increasing length. By controlling irradiation depth in a scintillator pixel, we show that DOI-dependence of time pickoff is a significant factor in the loss of timing performance in thick detectors. Using the correlated DOI-dependence of time pickoff and charge collection, we apply a charge-based correction to the time pickoff, obtaining improved coincidence timing resolution of <200ps for a uniform 4×4×30mm3 LaBr3 pixel. In order to obtain both DOI identification and improved timing resolution, we design a two layer LaBr3[5%Ce]/LaBr3[30%Ce] detector of total size 4×4×30mm3, exploiting the dependence of scintillator rise time on [Ce] in LaBr3:Ce. Using signal rise time to determine interaction layer, excellent interaction layer discrimination is achieved, while maintaining coincidence timing resolution of <250ps and energy resolution <7% using a R4998 PMT. Excellent layer separation and timing performance is measured with several other commercially-available TOF photodetectors, demonstrating the practicality of this design. These results indicate the feasibility of rise time discrimination as a technique for measuring event DOI while maintaining sensitivity, timing and energy performance, in a well-known detector architecture. PMID:24403611

DOI Determination by Rise Time Discrimination in Single-Ended Readout for TOF PET Imaging.

PubMed

Wiener, R I; Surti, S; Karp, J S

2013-06-01

Clinical TOF PET systems achieve detection efficiency using thick crystals, typically of thickness 2-3cm. The resulting dispersion in interaction depths degrades spatial resolution for increasing radial positions due to parallax error. Furthermore, interaction depth dispersion results in time pickoff dispersion and thus in degraded timing resolution, and is therefore of added concern in TOF scanners. Using fast signal digitization, we characterize the timing performance, pulse shape and light output of LaBr 3 :Ce, CeBr 3 and LYSO. Coincidence timing resolution is shown to degrade by ~50ps/cm for scintillator pixels of constant cross section and increasing length. By controlling irradiation depth in a scintillator pixel, we show that DOI-dependence of time pickoff is a significant factor in the loss of timing performance in thick detectors. Using the correlated DOI-dependence of time pickoff and charge collection, we apply a charge-based correction to the time pickoff, obtaining improved coincidence timing resolution of <200ps for a uniform 4×4×30mm 3 LaBr 3 pixel. In order to obtain both DOI identification and improved timing resolution, we design a two layer LaBr 3 [5%Ce]/LaBr 3 [30%Ce] detector of total size 4×4×30mm 3 , exploiting the dependence of scintillator rise time on [Ce] in LaBr 3 :Ce. Using signal rise time to determine interaction layer, excellent interaction layer discrimination is achieved, while maintaining coincidence timing resolution of <250ps and energy resolution <7% using a R4998 PMT. Excellent layer separation and timing performance is measured with several other commercially-available TOF photodetectors, demonstrating the practicality of this design. These results indicate the feasibility of rise time discrimination as a technique for measuring event DOI while maintaining sensitivity, timing and energy performance, in a well-known detector architecture.

Quantifying accessible sites and reactivity on titania–silica (photo)catalysts: Refining TOF calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eaton, Todd R.; Campos, Michael P.; Gray, Kimberly A.

2014-01-01

It can be difficult to determine the number of active atoms accessible to the fluid phase in mixed oxide catalysts, as required for obtaining true turnover frequencies (TOF). Here, we utilize the selective titration of surface Ti atoms with phenylphosphonic acid (PPA) on TiO 2–SiO 2 materials to estimate the number of reactant-accessible sites. TiO 2–SiO 2 composites were synthesized over a range of Ti loadings from grafting of titanocene dichloride (Cp 2TiCl 2) or tetraethoxy orthotitanate (TEOT) on SiO 2 and sol–gel co-hydrolysis of Si and Ti alkoxides. The materials were characterized by DRUV–vis, XRD, BET, and XANES. Despitemore » the significant morphological and electronic differences, materials prepared by Cp 2TiCl 2 and TEOT yielded a near-constant TOF of 0.14 h -1 (±0.04) across Ti loadings, for benzyl alcohol photooxidation, when normalizing rates by sites titrated by PPA. The fraction of Ti atoms titrated by PPA was strongly dependent on synthesis method and surface density. PPA titration and benzyl alcohol photooxidation may be useful measures of surface accessibility in other supported oxides.« less

[Serum pharmacochemistry of Qinbai Qingfei concentrated pellets based on UPLC-Q-TOF-MS].

PubMed

Liu, Ye; Wei, Wen-Feng; Huo, Jin-Hai; Wang, Wei-Ming

2017-02-01

To analyze the main components of Qinbai Qingfei concentrated pellets in rat serum with UPLC-Q-TOF-MS technology and serum pharmacochemistry theory. After gavage administration with Qinbai Qingfei concentrated pellets, blood was collected from hepatic portal vein. ACQUITY UPLC BEH C₁₈(2.1 mm×100 mm, 1.7 μm) was used, with 0.1% formic acid agueous solution(A)-0.1%formic acid and acetonitrile(B) as the mobile phase for gradient elution. The flow rate was 0.3 mL•min⁻¹, the column temperature was maintained at 35 ℃. Through the comparative analysis fingerprints of Qinbai Qingfei concentrated pellets, drug containing-serum and blank serum, and with the help Peakview and Metabolitepilot software, components in serum were defined. A total of 28 compounds were identified, including 18 prototypes and 10 metabolites. As a result, UPLC-Q-TOF-MS technology and serum pharmacochemistry theory were applied to comprehensively expound Qinbai Qingfei concentrated pellets'constituents migrating to rat serum, and provide scientific basis for further studies for in vivo metabolic process and effective material base. Copyright© by the Chinese Pharmaceutical Association.

Performance studies towards a TOF-PET sensor using Compton scattering at plastic scintillators

NASA Astrophysics Data System (ADS)

Kuramoto, M.; Nakamori, T.; Gunji, S.; Kamada, K.; Shoji, Y.; Yoshikawa, A.; Aoki, T.

2018-01-01

We have developed a sensor head for a time-of-flight (TOF) PET scanner using plastic scintillators that have a very fast timing property. Given the very small cross section of photoelectric absorption in plastic scintillators at 511 keV, we use Compton scattering in order to compensate for detection efficiency. The detector will consist of two layers of scatterers and absorbers which are made of plastic and inorganic scintillators such as GAGG:Ce, respectively. Signals are read by monolithic Multi Pixel Photon Counters, and with energy deposits and interaction time stamps are being acquired. The scintillators are built to be capable of resolving interaction position in three dimensions, so that our system has also a function of depth-of-interaction (DOI) PET scanners. TOF resolution of ~ 200 ps (FWHM) is achieved in both cases of using the leading-edge discriminator and time-walk correction and using a configuration sensitive to DOI. Both the position resolution and spectroscopy are demonstrated using the prototype data acquisition system, with Compton scattering events subsequently being obtained. We also demonstrated that the background rejection technique using the Compton cone constraint could be valid with our system.

Classification of illicit heroin by UPLC-Q-TOF analysis of acidic and neutral manufacturing impurities.

PubMed

Liu, Cuimei; Hua, Zhendong; Bai, Yanping

2015-12-01

The illicit manufacture of heroin results in the formation of trace levels of acidic and neutral manufacturing impurities that provide valuable information about the manufacturing process used. In this work, a new ultra performance liquid chromatography-quadrupole-time of flight mass spectrometry (UPLC-Q-TOF) method; that features high resolution, mass accuracy and sensitivity for profiling neutral and acidic heroin manufacturing impurities was developed. After the UPLC-Q-TOF analysis, the retention times and m/z data pairs of acidic and neutral manufacturing impurities were detected, and 19 peaks were found to be evidently different between heroin samples from "Golden Triangle" and "Golden Crescent". Based on the data set of these 19 impurities in 150 authentic heroin samples, classification of heroin geographic origins was successfully achieved utilizing partial least squares discriminant analysis (PLS-DA). By analyzing another data set of 267 authentic heroin samples, the developed discrimiant model was validated and proved to be accurate and reliable. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

MALDI-TOF to compare polysaccharide profiles from commercial health supplements of different mushroom species.

PubMed

López-García, Marta; García, María Sonia Dopico; Vilariño, José Manuel López; Rodríguez, María Victoria González

2016-05-15

In this work MALDI-TOF mass spectroscopy was investigated to characterise the β-glucan profiles of several commercial health supplements, without any derivatisation or purification pre-treatment. The effect of two solvents (water and dimethyl sulfoxide) and two MALDI matrices (2,5-dihydroxybenzoic acid and 2',4',6'-trihydroxyacetophenone) was first evaluated on dextran standards. MALDI-TOF was found as a useful and quick technique to obtain structural information of diverse food supplements based on mushroom extracts. The MALDI polysaccharide profiles of 5 supplements from different mushroom species were qualitatively similar showing [Glucan+Na](+) cations with a peak-to-peak mass difference of 16 Da consistent with the repeating unit of the β-(1→3)-glucan. The profiles strongly depended on the sample solvent used, with m/z values around 5000-8000 for water and 2000 for dimethyl sulfoxide; differences between samples were revealed in the molecular weight of the aqueous preparation, with the highest values for Maitake and Cordyceps species. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multi-spectroscopic analysis of cholesterol gallstone using TOF-SIMS, FTIR and UV-Vis spectroscopy

NASA Astrophysics Data System (ADS)

Jaswal, Brij Bir S.; Kumar, Vinay; Swart, H. C.; Sharma, Jitendra; Rai, Pradeep K.; Singh, Vivek K.

2015-10-01

For the first time, spatial distribution of major and trace elements has been studied in cholesterol gallstones using time-of-flight secondary mass ion mass spectrometry (TOF-SIMS). The TOF-SIMS has been used to study the elemental constituents of the center and surface parts of the gallstone sample. We have classified the gallstone sample using Fourier transform spectroscopy. The detected elements in cholesterol gallstone sample were carbon (C), hydrogen (H), calcium (Ca), sodium (Na), potassium (K), strontium (Sr), copper (Cu), iron (Fe), chromium (Cr), mercury (Hg) and lead (Pb). The detected molecules in the cholesterol gallstone were CH3 +, CO3 +, CaCO3 + and C3H+. Our results revealed that the contents of these elements in cholesterol gallstone were higher in the center part than that in the surface part. In the present paper, we have also presented the UV-Vis spectroscopic studies of the center and surface parts of the gallstone sample which indicated the presence of a higher content of cholesterol in the surface part and bilirubin in the center part.

Comparison among four proposed direct blood culture microbial identification methods using MALDI-TOF MS.

PubMed

Bazzi, Ali M; Rabaan, Ali A; El Edaily, Zeyad; John, Susan; Fawarah, Mahmoud M; Al-Tawfiq, Jaffar A

Matrix-assisted laser desorption-ionization time-of-flight (MALDI-TOF) mass spectrometry facilitates rapid and accurate identification of pathogens, which is critical for sepsis patients. In this study, we assessed the accuracy in identification of both Gram-negative and Gram-positive bacteria, except for Streptococcus viridans, using four rapid blood culture methods with Vitek MALDI-TOF-MS. We compared our proposed lysis centrifugation followed by washing and 30% acetic acid treatment method (method 2) with two other lysis centrifugation methods (washing and 30% formic acid treatment (method 1); 100% ethanol treatment (method 3)), and picking colonies from 90 to 180min subculture plates (method 4). Methods 1 and 2 identified all organisms down to species level with 100% accuracy, except for Streptococcus viridans, Streptococcus pyogenes, Enterobacter cloacae and Proteus vulgaris. The latter two were identified to genus level with 100% accuracy. Each method exhibited excellent accuracy and precision in terms of identification to genus level with certain limitations. Copyright © 2016 King Saud Bin Abdulaziz University for Health Sciences. Published by Elsevier Ltd. All rights reserved.

Identification of isoquercitrin metabolites produced by human intestinal bacteria using UPLC-Q-TOF/MS.

PubMed

Lu, Linling; Qian, Dawei; Yang, Jing; Jiang, Shu; Guo, Jianming; Shang, Er-xin; Duan, Jin-ao

2013-04-01

In this paper, ultraperformance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS) and the MetaboLynx™ software combined with mass defect filtering were applied to identity the metabolites of isoquercitrin using an intestinal mixture of bacteria and 96 isolated strains from human feces. The human incubated samples collected for 72 h in the anaerobic incubator and extracted with ethyl acetate were analyzed by UPLC-Q-TOF/MS within 10 min. The parent compound and five metabolites were identified by eight isolated strains, including Bacillus sp. 17, Veillonella sp. 23 and 32 and Bacteroides sp. 40, 41, 56, 75 and 88 in vitro. The results indicate that quercetin, acetylated isoquercitrin, dehydroxylated isoquercitrin, hydroxylated quercetin and hydroxymethylated quercetin are the major metabolites of isoquercitrin. Furthermore, a possible metabolic pathway for the biotransformation of isoquercitrin was established in intestinal flora. This study will be helpful for understanding the metabolic route of isoquercitrin and the role of different intestinal bacteria in the metabolism of natural compounds. Copyright © 2012 John Wiley & Sons, Ltd.

The measurement programme at the neutron time-of-flight facility n_TOF at CERN

NASA Astrophysics Data System (ADS)

Gunsing, F.; Aberle, O.; Andrzejewski, J.; Audouin, L.; Bécares, V.; Bacak, M.; Balibrea-Correa, J.; Barbagallo, M.; Barros, S.; Bečvář, F.; Beinrucker, C.; Belloni, F.; Berthoumieux, E.; Billowes, J.; Bosnar, D.; Brown, A.; Brugger, M.; Caamaño, M.; Calviño, F.; Calviani, M.; Cano-Ott, D.; Cardella, R.; Casanovas, A.; Castelluccio, D. M.; Cerutti, F.; Chen, Y. H.; Chiaveri, E.; Colonna, N.; Cortés-Giraldo, M. A.; Cortés, G.; Cosentino, L.; Damone, L. A.; Deo, K.; Diakaki, M.; Domingo-Pardo, C.; Dressler, R.; Dupont, E.; Durán, I.; Fernández-Domínguez, B.; Ferrari, A.; Ferreira, P.; Finocchiaro, P.; Frost, R. J. W.; Furman, V.; Ganesan, S.; García, A. R.; Gawlik, A.; Gheorghe, I.; Gilardoni, S.; Glodariu, T.; Gonçalves, I. F.; González, E.; Goverdovski, A.; Griesmayer, E.; Guerrero, C.; Göbel, K.; Harada, H.; Heftrich, T.; Heinitz, S.; Hernández-Prieto, A.; Heyse, J.; Jenkins, D. G.; Jericha, E.; Käppeler, F.; Kadi, Y.; Kalamara, A.; Katabuchi, T.; Kavrigin, P.; Ketlerov, V.; Khryachkov, V.; Kimura, A.; Kivel, N.; Kokkoris, M.; Krtička, M.; Kurtulgil, D.; Leal-Cidoncha, E.; Lederer, C.; Leeb, H.; Lerendegui, J.; Licata, M.; Meo, S. Lo; Lonsdale, S. J.; Losito, R.; Macina, D.; Marganiec, J.; Martínez, T.; Masi, A.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Matteucci, F.; Maugeri, E. A.; Mazzone, A.; Mendoza, E.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Mirea, M.; Montesano, S.; Musumarra, A.; Nolte, R.; Negret, A.; Oprea, A.; Palomo-Pinto, F. R.; Paradela, C.; Patronis, N.; Pavlik, A.; Perkowski, J.; Porras, I.; Praena, J.; Quesada, J. M.; Radeck, D.; Rajeev, K.; Rauscher, T.; Reifarth, R.; Riego-Perez, A.; Robles, M.; Rout, P.; Rubbia, C.; Ryan, J. A.; Sabaté-Gilarte, M.; Saxena, A.; Schillebeeckx, P.; Schmidt, S.; Schumann, D.; Sedyshev, P.; Smith, A. G.; Sosnin, N. V.; Stamatopoulos, A.; Suryanarayana, S. V.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tarrío, D.; Tassan-Got, L.; Tsinganis, A.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vlachoudis, V.; Vlastou, R.; Wallner, A.; Warren, S.; Weigand, M.; Weiss, C.; Wolf, C.; Woods, P. J.; Wright, T.; Žugec, P.

2017-09-01

Neutron-induced reaction cross sections are important for a wide variety of research fields ranging from the study of nuclear level densities, nucleosynthesis to applications of nuclear technology like design, and criticality and safety assessment of existing and future nuclear reactors, radiation dosimetry, medical applications, nuclear waste transmutation, accelerator-driven systems and fuel cycle investigations. Simulations and calculations of nuclear technology applications largely rely on evaluated nuclear data libraries. The evaluations in these libraries are based both on experimental data and theoretical models. CERN's neutron time-of-flight facility n_TOF has produced a considerable amount of experimental data since it has become fully operational with the start of its scientific measurement programme in 2001. While for a long period a single measurement station (EAR1) located at 185 m from the neutron production target was available, the construction of a second beam line at 20 m (EAR2) in 2014 has substantially increased the measurement capabilities of the facility. An outline of the experimental nuclear data activities at n_TOF will be presented.

[Identification of chemical constituents in Sinopodophylli Fructus by HPLC-DAD-ESI-IT-TOF-MSn].

PubMed

Wang, Ai-Hua; Ma, Li-Man; Fan, Shan-Shan; Liu, Guang-Xue; Xu, Feng; Shang, Ming-Ying; Cai, Shao-Qing

2018-01-01

This experiment was performed to analyze and identify the chemical constituents of Sinopodophylli Fructus by HPLC-DAD-ESI-IT-TOF-MSn. The analysis was performed on an Agilent Zorbax SB-C₁₈ (4.6 mm×250 mm, 5 μm) column.The mobile phase consisted of 0.1% formic acid was used for gradient at a flow rate of 1.0 mL·min⁻¹. Electrospray ionization ion trap time-of-flight multistage mass spectrometry was applied for qualitative analysis under positive and negative ion modes. The results indicated that 54 compounds consisted of 18 lignans and 36 flavonoids from Xiaoyelian had been detected by their HRMS data, the information of literature and reference substance. Among them, 27 compounds were reported in Sinopodophylli Fructus for the first time. In conclusion, an HPLC-DAD-ESI-IT-TOF-MSn method was established to qualitative analysis of Xiaoyelian in this study, which will provide the evidence for evaluating the quality of Xiaoyelian herbs, clarifying the mechanism, and guiding the development of pharmacological active ingredients. Copyright© by the Chinese Pharmaceutical Association.

MALDI-TOF mass spectrometry-based identification of group A Streptococcus isolated from areas of the 2011 scarlet fever outbreak in china.

PubMed

Xiao, Di; You, Yuanhai; Bi, Zhenwang; Wang, Haibin; Zhang, Yongchan; Hu, Bin; Song, Yanyan; Zhang, Huifang; Kou, Zengqiang; Yan, Xiaomei; Zhang, Menghan; Jin, Lianmei; Jiang, Xihong; Su, Peng; Bi, Zhenqiang; Luo, Fengji; Zhang, Jianzhong

2013-03-01

There was a dramatic increase in scarlet fever cases in China from March to July 2011. Group A Streptococcus (GAS) is the only pathogen known to cause scarlet fever. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) coupled to Biotyper system was used for GAS identification in 2011. A local reference database (LRD) was constructed, evaluated and used to identify GAS isolates. The 75 GAS strains used to evaluate the LRD were all identified correctly. Of the 157 suspected β-hemolytic strains isolated from 298 throat swab samples, 127 (100%) and 120 (94.5%) of the isolates were identified as GAS by the MALDI-TOF MS system and the conventional bacitracin sensitivity test method, respectively. All 202 (100%) isolates were identified at the species level by searching the LRD, while 182 (90.1%) were identified by searching the original reference database (ORD). There were statistically significant differences with a high degree of credibility at species level (χ(2)=6.052, P<0.05 between the LRD and ORD). The test turnaround time was shortened 36-48h, and the cost of each sample is one-tenth of the cost of conventional methods. Establishing a domestic database is the most effective way to improve the identification efficiency using a MALDI-TOF MS system. MALDI-TOF MS is a viable alternative to conventional methods and may aid in the diagnosis and surveillance of GAS. Copyright © 2013 Elsevier B.V. All rights reserved.

MALDI-TOF Mass Spectrometry as a Useful Tool for Identification of Enterococcus spp. from Wild Birds and Differentiation of Closely Related Species.

PubMed

Stępień-Pyśniak, Dagmara; Hauschild, Tomasz; Różański, Paweł; Marek, Agnieszka

2017-06-28

The aim of this study was to explore the accuracy and feasibility of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) in identifying bacteria from environmental sources, as compared with rpoA gene sequencing, and to evaluate the occurrence of bacteria of the genus Enterococcus in wild birds. In addition, a phyloproteomic analysis of certain Enterococcus species with spectral relationships was performed. The enterococci were isolated from 25 species of wild birds in central Europe (Poland). Proteomic (MALDI-TOF MS) and genomic ( rpoA gene sequencing) methods were used to identify all the isolates. Using MALDI-TOF MS, all 54 (100%) isolates were identified as Enterococcus spp. Among these, 51 (94.4%) isolates were identified to the species level (log(score) > or =2.0), and three isolates (5.6%) were identified at a level of probable genus identification (log(score) 1.88-1.927). Phylogenetic analysis based on rpoA sequences confirmed that all enterococci had been correctly identified. Enterococcus faecalis was the most prevalent enterococcal species (50%) and Enterococcus faecium (33.3%) the second most frequent species, followed by Enterococcus hirae (9.3%), Enterococcus durans (3.7%), and Enterococcus casseliflavus (3.7%). The phyloproteomic analysis of the spectral profiles of the isolates showed that MALDI-TOF MS is able to differentiate among similar species of the genus Enterococcus .

Analysis of TOF-SIMS spectra from fullerene compounds

NASA Astrophysics Data System (ADS)

Kato, N.; Yamashita, Y.; Iida, S.; Sanada, N.; Kudo, M.

2008-12-01

We analyzed TOF-SIMS spectra obtained from three different size of fullerenes (C 60, C 70 and C 84) by using Ga +, Au + and Au 3+ primary ion beams and investigated the fragmentation patterns, the enhancement of secondary ion yields and the restraint of fragmentation by using cluster primary ion beams compared with monoatomic primary ion beams. In the TOS-SIMS spectra from C 70 and C 84, it was found that a fragment ion, identified as C 60+ ( m/ z = 720), showed a relatively high intensity compared with that of other fragment ions related to C 2 depletion. It was also found that the Au 3+ bombardment caused intensity enhancement of intact molecules (C 60+, C 70+ and C 84+) and restrained the fragmentation due to C 2 depletion.

Erratum: Correction to: The sTOF, a Favorable Geometry for a Time-of-Flight Analyzer

NASA Astrophysics Data System (ADS)

Murphy, Daniel M.

2018-05-01

In the article "The sTOF, a Favorable Geometry for a Time-of-Flight Analyzer", the electric sectors in the prototype analyzer used to generate the data in Figure 4 were mistakenly listed as having a radius of 165 mm. The correct size is a diameter of 165 mm.

Detection of Listeria monocytogenes from selective enrichment broth using MALDI-TOF Mass Spectrometry.

PubMed

Jadhav, Snehal; Sevior, Danielle; Bhave, Mrinal; Palombo, Enzo A

2014-01-31

Conventional methods used for primary detection of Listeria monocytogenes from foods and subsequent confirmation of presumptive positive samples involve prolonged incubation and biochemical testing which generally require four to five days to obtain a result. In the current study, a simple and rapid proteomics-based MALDI-TOF MS approach was developed to detect L. monocytogenes directly from selective enrichment broths. Milk samples spiked with single species and multiple species cultures were incubated in a selective enrichment broth for 24h, followed by an additional 6h secondary enrichment. As few as 1 colony-forming unit (cfu) of L. monocytogenes per mL of initial selective broth culture could be detected within 30h. On applying the same approach to solid foods previously implicated in listeriosis, namely chicken pâté, cantaloupe and Camembert cheese, detection was achieved within the same time interval at inoculation levels of 10cfu/mL. Unlike the routine application of MALDI-TOF MS for identification of bacteria from solid media, this study proposes a cost-effective and time-saving detection scheme for direct identification of L. monocytogenes from broth cultures.This article is part of a Special Issue entitled: Trends in Microbial Proteomics. Globally, foodborne diseases are major causes of illness and fatalities in humans. Hence, there is a continual need for reliable and rapid means for pathogen detection from food samples. Recent applications of MALDI-TOF MS for diagnostic microbiology focused on detection of microbes from clinical specimens. However, the current study has emphasized its use as a tool for detecting the major foodborne pathogen, Listeria monocytogenes, directly from selective enrichment broths. This proof-of-concept study proposes a detection scheme that is more rapid and simple compared to conventional methods of Listeria detection. Very low levels of the pathogen could be identified from different food samples post-enrichment in

The use of PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) to detect bacterial and fungal colonization in healthy military service members.

PubMed

Vetor, Ryan; Murray, Clinton K; Mende, Katrin; Melton-Kreft, Rachel; Akers, Kevin S; Wenke, Joseph; Spirk, Tracy; Guymon, Charles; Zera, Wendy; Beckius, Miriam L; Schnaubelt, Elizabeth R; Ehrlich, Garth; Vento, Todd J

2016-07-22

The role of microbial colonization in disease is complex. Novel molecular tools to detect colonization offer theoretical improvements over traditional methods. We evaluated PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) as a screening tool to study colonization of healthy military service members. We assessed 101 healthy Soldiers using PCR/ESI-TOF-MS on nares, oropharynx, and groin specimens for the presence of gram-positive and gram-negative bacteria (GNB), fungi, and antibiotic resistance genes. A second set of swabs was processed by traditional culture, followed by identification using the BD Phoenix automated system; comparison between PCR/ESI-TOF-MS and culture was carried out only for GNB. Using PCR/ESI-TOF-MS, at least one colonizing organism was found on each individual: mean (SD) number of organisms per subject of 11.8(2.8). The mean number of organisms in the nares, groin and oropharynx was 3.8(1.3), 3.8(1.4) and 4.2(2), respectively. The most commonly detected organisms were aerobic gram-positive bacteria: primarily coagulase-negative Staphylococcus (101 subjects: 341 organisms), Streptococcus pneumoniae (54 subjects: 57 organisms), Staphylococcus aureus (58 subjects: 80 organisms) and Nocardia asteroides (45 subjects: 50 organisms). The mecA gene was found in 96 subjects. The most commonly found GNB was Haemophilus influenzae (20 subjects: 21 organisms) and the most common anaerobe was Propionibacterium acnes (59 subjects). Saccharomyces species (30 subjects) were the most common fungi detected. Only one GNB (nares E. coli) was identified in the same subject by both diagnostic systems. PCR/ESI-TOF-MS detected common colonizing organisms and identified more typically-virulent bacteria in asymptomatic, healthy adults. PCR/ESI-TOF-MS appears to be a useful method for detecting bacterial and fungal organisms, but further clinical correlation and validation studies are needed.

Visualizing Antimicrobials in Bacterial Biofilms: Three-Dimensional Biochemical Imaging Using TOF-SIMS.

PubMed

Davies, Sarah K; Fearn, Sarah; Allsopp, Luke P; Harrison, Freya; Ware, Ecaterina; Diggle, Stephen P; Filloux, Alain; McPhail, David S; Bundy, Jacob G

2017-01-01

Bacterial biofilms are groups of bacteria that exist within a self-produced extracellular matrix, adhering to each other and usually to a surface. They grow on medical equipment and inserts such as catheters and are responsible for many persistent infections throughout the body, as they can have high resistance to many antimicrobials. Pseudomonas aeruginosa is an opportunistic pathogen that can cause both acute and chronic infections and is used as a model for research into biofilms. Direct biochemical methods of imaging of molecules in bacterial biofilms are of high value in gaining a better understanding of the fundamental biology of biofilms and biochemical gradients within them. Time of flight-secondary-ion mass spectrometry (TOF-SIMS) is one approach, which combines relatively high spatial resolution and sensitivity and can perform depth profiling analysis. It has been used to analyze bacterial biofilms but has not yet been used to study the distribution of antimicrobials (including antibiotics and the antimicrobial metal gallium) within biofilms. Here we compared two methods of imaging of the interior structure of P. aeruginosa in biological samples using TOF-SIMS, looking at both antimicrobials and endogenous biochemicals: cryosectioning of tissue samples and depth profiling to give pseudo-three-dimensional (pseudo-3D) images. The sample types included both simple biofilms grown on glass slides and bacteria growing in tissues in an ex vivo pig lung model. The two techniques for the 3D imaging of biofilms are potentially valuable complementary tools for analyzing bacterial infection. IMPORTANCE Modern analytical techniques are becoming increasingly important in the life sciences; imaging mass spectrometry offers the opportunity to gain unprecedented amounts of information on the distribution of chemicals in samples-both xenobiotics and endogenous compounds. In particular, simultaneous imaging of antibiotics (and other antimicrobial compounds) and bacterium

Matrix normalized MALDI-TOF quantification of a fluorotelomer-based acrylate polymer.

PubMed

Rankin, Keegan; Mabury, Scott A

2015-05-19

The degradation of fluorotelomer-based acrylate polymers (FTACPs) has been hypothesized to serve as a source of the environmental contaminants, perfluoroalkyl carboxylates (PFCAs). Studies have relied on indirect measurement of presumed degradation products to evaluate the environmental fate of FTACPs; however, this approach leaves a degree of uncertainty. The present study describes the development of a quantitative matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry method as the first direct analysis method for FTACPs. The model FTACP used in this study was poly(8:2 FTAC-co-HDA), a copolymer of 8:2 fluorotelomer acrylate (8:2 FTAC) and hexadecyl acrylate (HDA). Instead of relying on an internal standard polymer, the intensities of 40 poly(8:2 FTAC-co-HDA) signals (911-4612 Da) were normalized to the signal intensity of a matrix-sodium cluster (659 Da). We termed this value the normalized polymer response (P(N)). By using the same dithranol solution for the sample preparation of poly(8:2 FTAC-co-HDA) standards, calibration curves with coefficient of determinations (R(2)) typically >0.98 were produced. When poly(8:2 FTAC-co-HDA) samples were prepared with the same dithranol solution as the poly(8:2 FTAC-co-HDA) standards, quantification to within 25% of the theoretical concentration was achieved. This approach minimized the sample-to-sample variability that typically plagues MALDI-TOF, and is the first method developed to directly quantify FTACPs.

Rapid analysis of the main components of the total glycosides of Ranunculus japonicus by UPLC/Q-TOF-MS.

PubMed

Rui, Wen; Chen, Hongyuan; Tan, Yuzhi; Zhong, Yanmei; Feng, Yifan

2010-05-01

A rapid method for the analysis of the main components of the total glycosides of Ranunculus japonicus (TGOR) was developed using ultra-performance liquid chromatography with quadrupole-time-of-flight mass spectrometry (UPLC/Q-TOF-MS). The separation analysis was performed on a Waters Acquity UPLC system and the accurate mass of molecules and their fragment ions were determined by Q-TOF MS. Twenty compounds, including lactone glycosides, flavonoid glycosides and flavonoid aglycones, were identified and tentatively deduced on the basis of their elemental compositions, MS/MS data and relevant literature. The results demonstrated that lactone glycosides and flavonoids were the main constituents of TGOR. Furthermore, an effective and rapid pattern was established allowing for the comprehensive and systematic characterization of the complex samples.

Investigation of practical initial attenuation image estimates in TOF-MLAA reconstruction for PET/MR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Ju-Chieh, E-mail: chengjuchieh@gmail.com; Y

Purpose: Time-of-flight joint attenuation and activity positron emission tomography reconstruction requires additional calibration (scale factors) or constraints during or post-reconstruction to produce a quantitative μ-map. In this work, the impact of various initializations of the joint reconstruction was investigated, and the initial average mu-value (IAM) method was introduced such that the forward-projection of the initial μ-map is already very close to that of the reference μ-map, thus reducing/minimizing the offset (scale factor) during the early iterations of the joint reconstruction. Consequently, the accuracy and efficiency of unconstrained joint reconstruction such as time-of-flight maximum likelihood estimation of attenuation and activity (TOF-MLAA)more » can be improved by the proposed IAM method. Methods: 2D simulations of brain and chest were used to evaluate TOF-MLAA with various initial estimates which include the object filled with water uniformly (conventional initial estimate), bone uniformly, the average μ-value uniformly (IAM magnitude initialization method), and the perfect spatial μ-distribution but with a wrong magnitude (initialization in terms of distribution). 3D GATE simulation was also performed for the chest phantom under a typical clinical scanning condition, and the simulated data were reconstructed with a fully corrected list-mode TOF-MLAA algorithm with various initial estimates. The accuracy of the average μ-values within the brain, chest, and abdomen regions obtained from the MR derived μ-maps was also evaluated using computed tomography μ-maps as the gold-standard. Results: The estimated μ-map with the initialization in terms of magnitude (i.e., average μ-value) was observed to reach the reference more quickly and naturally as compared to all other cases. Both 2D and 3D GATE simulations produced similar results, and it was observed that the proposed IAM approach can produce quantitative μ-map/emission when the

Evaluation of MALDI-TOF mass spectrometry for identification of environmental yeasts and development of supplementary database.

PubMed

Agustini, Bruna Carla; Silva, Luciano Paulino; Bloch, Carlos; Bonfim, Tania M B; da Silva, Gildo Almeida

2014-06-01

Yeast identification using traditional methods which employ morphological, physiological, and biochemical characteristics can be considered a hard task as it requires experienced microbiologists and a rigorous control in culture conditions that could implicate in different outcomes. Considering clinical or industrial applications, the fast and accurate identification of microorganisms is a crescent demand. Hence, molecular biology approaches has been extensively used and, more recently, protein profiling using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has proved to be an even more efficient tool for taxonomic purposes. Nonetheless, concerning to mass spectrometry, data available for the differentiation of yeast species for industrial purpose is limited and reference databases commercially available comprise almost exclusively clinical microorganisms. In this context, studies focusing on environmental isolates are required to extend the existing databases. The development of a supplementary database and the assessment of a commercial database for taxonomic identifications of environmental yeast are the aims of this study. We challenge MALDI-TOF MS to create protein profiles for 845 yeast strains isolated from grape must and 67.7 % of the strains were successfully identified according to previously available manufacturer database. The remaining 32.3 % strains were not identified due to the absence of a reference spectrum. After matching the correct taxon for these strains by using molecular biology approaches, the spectra concerning the missing species were added in a supplementary database. This new library was able to accurately predict unidentified species at first instance by MALDI-TOF MS, proving it is a powerful tool for the identification of environmental yeasts.

MALDI-TOF identification of Gram-negative bacteria directly from blood culture bottles containing charcoal: Sepsityper® kits versus centrifugation-filtration method.

PubMed

Riederer, Kathleen; Cruz, Kristian; Shemes, Stephen; Szpunar, Susan; Fishbain, Joel T

2015-06-01

Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry has dramatically altered the way microbiology laboratories identify clinical isolates. Direct blood culture (BC) detection may be hampered, however, by the presence of charcoal in BC bottles currently in clinical use. This study evaluates an in-house process for extraction and MALDI-TOF identification of Gram-negative bacteria directly from BC bottles containing charcoal. Three hundred BC aliquots were extracted by a centrifugation-filtration method developed in our research laboratory with the first 96 samples processed in parallel using Sepsityper® kits. Controls were colonies from solid media with standard phenotypic and MALDI-TOF identification. The identification of Gram-negative bacteria was successful more often via the in-house method compared to Sepsityper® kits (94.7% versus 78.1%, P≤0.0001). Our in-house centrifugation-filtration method was further validated for isolation and identification of Gram-negative bacteria (95%; n=300) directly from BC bottles containing charcoal. Copyright © 2015 Elsevier Inc. All rights reserved.

MALDI-TOF mass spectrometry: avoidance of artifacts and analysis of caffeine-precipitated SII thearubigins from 15 commercial black teas.

PubMed

Drynan, J Warren; Clifford, Michael N; Obuchowicz, Jacek; Kuhnert, Nikolai

2012-05-09

Thearubigins are the quantitatively major phenolic compounds in black tea, accounting for some 60-70% of the solids in a typical black tea infusion. MALDI-TOF mass spectra for caffeine-precipitated SII thearubigins (SII CTRs) from 15 different commercial teas support previous conclusions that SII CTRs are polyhydroxylated oligomers (rather than polymers) of catechins and catechin gallates in redox equilibrium with their quinone counterparts. Some 4500 peaks were revealed in a mass range from m/z 500 to 2100. Polyphenols are redox-susceptible and readily generate artifacts during MALDI-TOF analysis when the matrix is also redox-susceptible. Of the nine matrices evaluated, 3',4',5'-trihydroxyacetophenone (F) provided the best compromise between signal intensity and redox artifact formation.

An advanced LC-MS (Q-TOF) technique for the detection of amino acids in atmospheric aerosols

EPA Science Inventory

Methodology for detection of native (underivitized) amino acids in atmospheric aerosols has been developed. This article describes the use of LC-MS (Q-TOF) and microwave-assisted gas phase hydrolysis for detection of free and combined amino acids in aerosols collected in a Southe...

Modeling of charged particles trajectories in order to optimize the design of a new, higher resolution, Time of flight- Positron Annihilation Induced Auger Electron Spectroscopy (TOF PAES) System

NASA Astrophysics Data System (ADS)

Joglekar, Prasad; Lim, L.; Satyal, Suman; Kalaskar, Sushant; Shastry, K.; Weiss, Alex

2011-03-01

Time of Flight Positron Annihilation Induced~Auger Electron Spectroscopy~(TOF PAES) is a surface analytical technique with high surface selectivity. TOF PAES is used to study elemental composition, surface defects, and various energy loss mechanisms. Positrons incident on the sample surface at low energies can be trapped in an image-potential well just above the surface Prior to annihilation. Consequently it is possible to use positron annihilation related signals to selectively probe the top-most atomic layer. This poster presents the results of modeling of the charge particle beam transport system performed in connection with the optimization of the the design of the new TOF-PAES system currently under construction at U T Arlington. The system will incorporate a 2 m long drift tube in order to achieve better energy resolution than our previous TOF-PAES system design which used a 1 m long drift tube NSF DMR 0907679, Welch Foundation Y 1100.

Characterization of paliperidone photodegradation products by LC-Q-TOF multistage mass spectrometry.

PubMed

Skibiński, Robert; Komsta, Łukasz; Inglot, Tadeusz

2016-06-01

The photodegradation of paliperidone in aqueous and methanol media under UVA and UVC irradiation was investigated. The identification and structural elucidation of its photodegradation products were performed by the use of the reversed-phase liquid chromatography coupled with accurate mass hybrid Q-TOF mass spectrometry and an atmospheric pressure chemical ionization source. Five degradation products were found and their masses were obtained with high accuracy (1.10-5.26 ppm) based on the TOF (MS) spectra. For the structural elucidation of unknown degradation products MS/MS spectra were also registered. However, for the identification of the main photodegradation product (3-{2-[4-(6-fluoro-1,3-benzoxazol-2-yl)piperidin-1-yl]ethyl}-9-hydroxy-2-methyl-6,7,8,9-tetrahydro-4H-pyrido[1,2-a]pyrimidin-4-one) in-source fragmentation connected with collision-induced dissociation was used and MS(3) spectra were finally performed. The photodegradation of paliperidone yields the first-order kinetics in all tested conditions. The aqueous medium was in this case much less stable than the methanol solvent regardless of the irradiation source. Additionally, the toxicity of the analyzed photodegradation products was predicted by the use of ECOSAR software and comparable values of LC50 for the main degradants and the parent compound were obtained. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Comparative analysis of Gram's stain, PNA-FISH and Sepsityper with MALDI-TOF MS for the identification of yeast direct from positive blood cultures.

PubMed

Gorton, Rebecca L; Ramnarain, P; Barker, K; Stone, N; Rattenbury, S; McHugh, T D; Kibbler, C C

2014-10-01

Fungaemia diagnosis could be improved by reducing the time to identification of yeast from blood cultures. This study aimed to evaluate three rapid methods for the identification of yeast direct from blood cultures; Gram's stain analysis, the AdvanDX Peptide Nucleic Acid in Situ Hybridisation Yeast Traffic Light system (PNA-FISH YTL) and Bruker Sepsityper alongside matrix-assisted laser desorption ionisation time of flight mass spectrometry (MALDI-TOF MS). Fifty blood cultures spiked with a known single yeast strain were analysed by blinded operators experienced in each method. Identifications were compared with MALDI-TOF MS CHROMagar Candida culture and ITS rRNA sequence-based identifications. On first attempt, success rates of 96% (48/50) and 76% (36/50) were achieved using PNA-FISH YTL and Gram's stain respectively. MALDI-TOF MS demonstrated a success rate of 56% (28/50) when applying manufacturer's species log score thresholds and 76% (38/50) using in-house parameters, including lowering the species log score threshold to >1.5. In conclusion, PNA-FISH YTL demonstrated a high success rate successfully identifying yeast commonly encountered in fungaemia. Sepsityper(™) with MALDI-TOF MS was accurate but increased sensitivity is required. Due to the misidentification of commonly encountered yeast Gram's stain analysis demonstrated limited utility in this setting. © 2014 Blackwell Verlag GmbH.

Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

NASA Astrophysics Data System (ADS)

Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

2015-11-01

Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADES can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved—up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.

[Changes of chemical constituents in Rubiae Radix et Rhizoma before and after carbonized by UPLC-Q-TOF-MS method].

PubMed

Chen, Yi; Shan, Ming-Qiu; Wang, Hai-Li; Xue, Lu; Zhang, Li; Ding, An-Wei

2017-03-01

In order to explore the effect on chemical constituents after carbonized, the changes of chemical constituents in raw and carbonized Rubiae Radix et Rhizoma were analyzed by UPLC-Q-TOF-MS. The research also used principal component analysis(PCA) and orthogonal partial least squares discriminant analysis(OPLS-DA) for data statistics to find out the main differences on components before and after carbonized. The accurate m/z values of Q-TOF-MS and Q-TOF-MS-MS fragments were applied to identify the structures. The results showed that 6 more discrepant constituents were existed between raw and carbonized Rubiae Radix et Rhizoma. Three constituents were selected as the main discrepant components according to the peak area (276 nm) and identified, as lucidin, xanthopurpurin and 1,3,6-trihydroxy-2-methylanthraquinone. After carbonized, contents of xanthopurpurin and 1,3,6-trihydroxy-2-methylanthraquinone were observably increasing, while lucidin was obviously decreasing. They could be used as the chemical markers for the differentiation between raw and carbonized Rubiae Radix et Rhizoma. The results of this experiment played an important role in the study of processing principle of carbonized Rubiae Radix et Rhizoma. It also provided important evidences for the interpretation of effective material based on carbonized Rubiae Radix et Rhizoma. Copyright© by the Chinese Pharmaceutical Association.

Evaluation of MALDI-TOF mass spectrometry for the competitiveness analysis of selected indigenous cowpea (Vigna unguiculata L. Walp.) Bradyrhizobium strains from Kenya.

PubMed

Ndungu, Samuel Mathu; Messmer, Monika M; Ziegler, Dominik; Thuita, Moses; Vanlauwe, Bernard; Frossard, Emmanuel; Thonar, Cécile

2018-06-01

Cowpea N 2 fixation and yield can be enhanced by selecting competitive and efficient indigenous rhizobia. Strains from contrasting agro-ecologies of Kilifi and Mbeere (Kenya) were screened. Two pot experiments were established consisting of 13 Bradyrhizobium strains; experiment 1 (11 Mbeere + CBA + BK1 from Burkina Faso), experiment 2 (12 Kilifi + CBA). Symbiotic effectiveness was assessed (shoot biomass, SPAD index and N uptake). Nodule occupancy of 13 simultaneously co-inoculated strains in each experiment was analyzed by matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry (MS) to assess competitiveness. Strains varied in effectiveness and competitiveness. The four most efficient strains were further evaluated in a field trial in Mbeere during the 2014 short rains. Strains from bacteroids of cowpea nodules from pot and field experiments were accurately identified as Bradyrhizobium by MALDI-TOF based on the SARAMIS™ database. In the field, abundant indigenous populations 7.10 × 10 3 rhizobia g -1 soil, outcompeted introduced strains. As revealed by MALDI-TOF, indigenous strains clustered into six distinct groups (I, II, III, IV, V and VI), group III were most abundant occupying 80% of nodules analyzed. MALDI-TOF was rapid, affordable and reliable to identify Bradyrhizobium strains directly from nodule suspensions in competition pot assays and in the field with abundant indigenous strains thus, its suitability for future competition assays. Evaluating strain competitiveness and then symbiotic efficacy is proposed in bioprospecting for potential cowpea inoculant strains.

MALDI-TOF mass spectrometry for early identification of bacteria grown in blood culture bottles.

PubMed

Zabbe, Jean-Benoît; Zanardo, Laura; Mégraud, Francis; Bessède, Emilie

2015-08-01

This note reports an interesting way to rapidly identify bacteria grown from blood culture bottles. Chocolate agar plates were inoculated with 1 drop of the positive blood bottle medium. After a 3-hour incubation, the growth veil was submitted to MALDI-TOF mass spectrometry: 77% of the bacteria present have been correctly identified. Copyright © 2015 Elsevier B.V. All rights reserved.

SPAD array based TOF SoC design for unmanned vehicle

NASA Astrophysics Data System (ADS)

Pan, An; Xu, Yuan; Xie, Gang; Huang, Zhiyu; Zheng, Yanghao; Shi, Weiwei

2018-03-01

As for the requirement of unmanned-vehicle mobile Lidar system, this paper presents a SoC design based on pulsed TOF depth image sensor. This SoC has a detection range of 300m and detecting resolution of 1.5cm. Pixels are made of SPAD. Meanwhile, SoC adopts a structure of multi-pixel sharing TDC, which significantly reduces chip area and improve the fill factor of light-sensing surface area. SoC integrates a TCSPC module to achieve the functionality of receiving each photon, measuring photon flight time and processing depth information in one chip. The SOC is designed in the SMIC 0.13μm CIS CMOS technology

MALDI-TOF MS as a Tool To Detect a Nosocomial Outbreak of Extended-Spectrum-β-Lactamase- and ArmA Methyltransferase-Producing Enterobacter cloacae Clinical Isolates in Algeria

PubMed Central

Khennouchi, Nour Chems el Houda; Loucif, Lotfi; Boutefnouchet, Nafissa; Allag, Hamoudi

2015-01-01

Enterobacter cloacae is among the most important pathogens responsible for nosocomial infections and outbreaks. In this study, 77 Enterobacter isolates were collected: 27 isolates from Algerian hospitals (in Constantine, Annaba, and Skikda) and 50 isolates from Marseille, France. All strains were identified by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). Antibiotic susceptibility testing was performed by the disk diffusion method. PCR was used to detect extended-spectrum-beta-lactamase (ESBL)-encoding, fluoroquinolone resistance-encoding, and aminoglycoside-modifying enzyme (AME) genes. Epidemiological typing was performed using MALDI-TOF MS with data mining approaches, along with multilocus sequence typing (MLST). Sixty-eight isolates (27 from Algeria, 41 from Marseille) were identified by MALDI-TOF MS as E. cloacae. Resistance to antibiotics in the Algerian isolates was significantly higher than that in the strains from Marseille, especially for beta-lactams and aminoglycosides. Eighteen of the 27 Algerian isolates and 11 of the 41 Marseille isolates possessed at least one ESBL-encoding gene: blaCTX-M and/or blaTEM. AME genes were detected in 20 of the 27 Algerian isolates and 8 of the 41 Marseille isolates [ant(2″)-Ia, aac(6′)-Ib-cr, aadA1, aadA2, and armA]. Conjugation experiments showed that armA was carried on a transferable plasmid. MALDI-TOF typing showed three separate clusters according to the geographical distribution and species level. An MLST-based phylogenetic tree showed a clade of 14 E. cloacae isolates from a urology unit clustering together in the MALDI-TOF dendrogram, suggesting the occurrence of an outbreak in this unit. In conclusion, the ability of MALDI-TOF to biotype strains was confirmed, and surveillance measures should be implemented, especially for Algerian patients hospitalized in France. PMID:26239991

An Improved In-house MALDI-TOF MS Protocol for Direct Cost-Effective Identification of Pathogens from Blood Cultures.

PubMed

Zhou, Menglan; Yang, Qiwen; Kudinha, Timothy; Sun, Liying; Zhang, Rui; Liu, Chang; Yu, Shuying; Xiao, Meng; Kong, Fanrong; Zhao, Yupei; Xu, Ying-Chun

2017-01-01

Background: Bloodstream infection is a major cause of morbidity and mortality in hospitalized patients worldwide. Delays in the identification of microorganisms often leads to a poor prognosis. The application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) directly to blood culture (BC) broth can potentially identify bloodstream infections earlier, and facilitate timely management. Methods: We developed an "in-house" (IH) protocol for direct MALDI-TOF MS based identification of organisms in positive BCs. The IH protocol was initially evaluated and improved with spiked BC samples, and its performance was compared with the commercial Sepsityper™ kit using both traditional and modified cut-off values. We then studied in parallel the performance of the IH protocol and the colony MS identifications in positive clinical BC samples using only modified cut-off values. All discrepancies were investigated by "gold standard" of gene sequencing. Results: In 54 spiked BC samples, the IH method showed comparable results with Sepsityper™ after applying modified cut-off values. Specifically, accurate species and genus level identification was achieved in 88.7 and 3.9% of all the clinical monomicrobial BCs (284/301, 94.4%), respectively. The IH protocol exhibited superior performance for Gram negative bacteria than for Gram positive bacteria (92.8 vs. 82.4%). For anaerobes and yeasts, accurate species identification was achieved in 80.0 and 90.0% of the cases, respectively. For polymicrobial cultures (17/301, 5.6%), MALDI-TOF MS correctly identified a single species present in all the polymicrobial BCs under the Standard mode, while using the MIXED method, two species were correctly identified in 52.9% of the samples. Comparisons based on BC bottle type, showed that the BACTEC™ Lytic/10 Anaerobic/F culture vials performed the best. Conclusion: Our study provides a novel and effective sample preparation method for MALDI-TOF MS

[Evaluation of Brodifacoum-induced Toxicity by Metabonomics Approach Based on HPLC-TOF-MS].

PubMed

Yan, H; Zhuo, X Y; Shen, B H; Xiang, P; Shen, M

2017-06-01

To analyse the metabolic changes in urine of rats with brodifacoum intoxication, and to reveal the molecular mechanism of brodifacoum-induced toxicity on rats. By establishing a brodifacoum poisoning rats model, the urine metabolic profiling data of rats were acquired using high performance liquid chromatography-time of flight mass spectrometry （HPLC-TOF-MS）. The orthogonal partial least squares analysis-discrimination analysis （OPLS-DA） was applied for the multivariate statistics and the discovery of differential metabolites closely related to toxicity of brodifacoum. OPLS-DA score plot showed that the urinary metabolic at different time points before and after drug administration had good similarity within time period and presented clustering phenomenon. Comparing the urine samples of rats before drug administration with which after drug administration, twenty-two metabolites related to brodifacoum-induced toxicity were selected. The toxic effect of brodifacoum worked by disturbing the metabolic pathways in rats such as tricarboxylic cycle, glycolysis, sphingolipid metabolism and tryptophan metabolism, and the toxicity of brodifacoum is characterized of accumulation effect. The metabonomic method based on urine HPLC-TOF-MS can provide a novel insight into the study on molecular mechanism of brodifacoum-induced toxicity. Copyright© by the Editorial Department of Journal of Forensic Medicine

Multielement analysis of interplanetary dust particles using TOF-SIMS

NASA Technical Reports Server (NTRS)

Stephan, T.; Kloeck, W.; Jessberger, E. K.; Rulle, H.; Zehnpfenning, J.

1993-01-01

Sections of three stratospheric particles (U2015G1, W7029*A27, and L2005P9) were analyzed with TOF-SIMS (Time Of Flight-Secondary Ion Mass Spectrometry) continuing our efforts to investigate the element distribution in interplanetary dust particles (IDP's) with high lateral resolution (approximately 0.2 micron), to examine possible atmospheric contamination effects, and to further explore the abilities of this technique for element analysis of small samples. The samples, previously investigated with SXRF (synchrotron X-ray fluorescence analysis), are highly enriched in Br (Br/Fe: 59 x CI, 9.2 x CI, and 116 x CI, respectively). U2015G1 is the IDP with the by far highest Zn/Fe-ratio (81 x CI) ever reported in chondritic particles.

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry applied to virus identification

PubMed Central

Calderaro, Adriana; Arcangeletti, Maria-Cristina; Rodighiero, Isabella; Buttrini, Mirko; Gorrini, Chiara; Motta, Federica; Germini, Diego; Medici, Maria-Cristina; Chezzi, Carlo; De Conto, Flora

2014-01-01

Virus detection and/or identification traditionally rely on methods based on cell culture, electron microscopy and antigen or nucleic acid detection. These techniques are good, but often expensive and/or time-consuming; furthermore, they not always lead to virus identification at the species and/or type level. In this study, Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) was tested as an innovative tool to identify human polioviruses and to identify specific viral protein biomarkers in infected cells. The results revealed MALDI-TOF MS to be an effective and inexpensive tool for the identification of the three poliovirus serotypes. The method was firstly applied to Sabin reference strains, and then to isolates from different clinical samples, highlighting its value as a time-saving, sensitive and specific technique when compared to the gold standard neutralization assay and casting new light on its possible application to virus detection and/or identification. PMID:25354905

A TOF-SIMS Investigation of the Volatile Inventory of Lithic and Mineral Clasts in Lunar Regolith Samples

NASA Astrophysics Data System (ADS)

Tartèse, R.; Lyon, I. C.

2017-07-01

The lunar regolith offers a key record to characterise the transfer of volatiles across the solar system for the past 4.5 billion years. We tackle this issue by investigating the volatile inventory of lunar regolith samples using TOF-SIMS.

Multilocus phylogeny and MALDI-TOF analysis of the plant pathogenic species Alternaria dauci and relatives.

PubMed

Brun, Sophie; Madrid, Hugo; Gerrits Van Den Ende, Bert; Andersen, Birgitte; Marinach-Patrice, Carine; Mazier, Dominique; De Hoog, G Sybren

2013-01-01

The genus Alternaria includes numerous phytopathogenic species, many of which are economically relevant. Traditionally, identification has been based on morphology, but is often hampered by the tendency of some strains to become sterile in culture and by the existence of species-complexes of morphologically similar taxa. This study aimed to assess if strains of four closely-related plant pathogens, i.e., accurately Alternaria dauci (ten strains), Alternaria porri (six), Alternaria solani (ten), and Alternaria tomatophila (ten) could be identified using multilocus phylogenetic analysis and Matrix-Assisted Laser Desorption Ionisation Time of Flight (MALDI-TOF) profiling of proteins. Phylogenetic analyses were performed on three loci, i.e., the internal transcribed spacer (ITS) region of rRNA, and the glyceraldehyde-3-phosphate dehydrogenase (gpd) and Alternaria major antigen (Alt a 1) genes. Phylogenetic trees based on ITS sequences did not differentiate strains of A. solani, A. tomatophila, and A. porri, but these three species formed a clade separate from strains of A. dauci. The resolution improved in trees based on gpd and Alt a 1, which distinguished strains of the four species as separate clades. However, none provided significant bootstrap support for all four species, which could only be achieved when results for the three loci were combined. MALDI-TOF-based dendrograms showed three major clusters. The first comprised all A. dauci strains, the second included five strains of A. porri and one of A. solani, and the third included all strains of A. tomatophila, as well as all but one strain of A. solani, and one strain of A. porri. Thus, this study shows the usefulness of MALDI-TOF mass spectrometry as a promising tool for identification of these four species of Alternaria which are closely-related plant pathogens. Copyright © 2012 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Differentiation in MALDI-TOF MS and FTIR spectra between two pathovars of Xanthomonas oryzae

NASA Astrophysics Data System (ADS)

Ge, Mengyu; Li, Bin; Wang, Li; Tao, Zhongyun; Mao, Shengfeng; Wang, Yangli; Xie, Guanlin; Sun, Guochang

2014-12-01

Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc) strains are closely related phenotypically and genetically, which make it difficult to differentiate between the two pathovars based on phenotypic and DNA-based methods. In this study, a fast and accurate method was developed based on the differences in MALDI-TOF MS and FTIR spectra between the two pathovars. MALDI-TOF MS analysis revealed that 9 and 10 peaks are specific to Xoo and Xoc, respectively, which can be used as biomarkers to identify and differentiate the two closely related pathovars. Furthermore, FTIR analysis showed that there is a significant difference in both the band frequencies and absorption intensity of various functional groups between the two pathovars. In particular, the 6 peaks at 3433, 2867, 1273, 1065, 983 and 951 cm-1 were specific to the Xoo strains, while one peak at 1572 cm-1 was specific to the Xoc strains. Overall, this study gives the first attempt to identify and differentiate the two pathovars of X. oryzae based on mass and FTIR spectra, which will be helpful for the early detection and prevention of the two rice diseases caused by both X. oryzae pathovars.

Fast detection of Piscirickettsia salmonis in Salmo salar serum through MALDI-TOF-MS profiling.

PubMed

Olate, Verónica R; Nachtigall, Fabiane M; Santos, Leonardo S; Soto, Alex; Araya, Macarena; Oyanedel, Sandra; Díaz, Verónica; Marchant, Vanessa; Rios-Momberg, Mauricio

2016-03-01

Piscirickettsia salmonis is a pathogenic bacteria known as the aetiological agent of the salmonid rickettsial syndrome and causes a high mortality in farmed salmonid fishes. Detection of P. salmonis in farmed fishes is based mainly on molecular biology and immunohistochemistry techniques. These techniques are in most of the cases expensive and time consuming. In the search of new alternatives to detect the presence of P. salmonis in salmonid fishes, this work proposed the use of MALDI-TOF-MS to compare serum protein profiles from Salmo salar fish, including experimentally infected and non-infected fishes using principal component analysis (PCA). Samples were obtained from a controlled bioassay where S. salar was challenged with P. salmonis in a cohabitation model and classified according to the presence or absence of the bacteria by real time PCR analysis. MALDI spectra of the fish serum samples showed differences in its serum protein composition. These differences were corroborated with PCA analysis. The results demonstrated that the use of both MALDI-TOF-MS and PCA represents a useful tool to discriminate the fish status through the analysis of salmonid serum samples. Copyright © 2016 John Wiley & Sons, Ltd.

MALDI-TOF Mass Spectrometry Enables a Comprehensive and Fast Analysis of Dynamics and Qualities of Stress Responses of Lactobacillus paracasei subsp. paracasei F19

PubMed Central

Schott, Ann-Sophie; Behr, Jürgen; Quinn, Jennifer; Vogel, Rudi F.

2016-01-01

Lactic acid bacteria (LAB) are widely used as starter cultures in the manufacture of foods. Upon preparation, these cultures undergo various stresses resulting in losses of survival and fitness. In order to find conditions for the subsequent identification of proteomic biomarkers and their exploitation for preconditioning of strains, we subjected Lactobacillus (Lb.) paracasei subsp. paracasei TMW 1.1434 (F19) to different stress qualities (osmotic stress, oxidative stress, temperature stress, pH stress and starvation stress). We analysed the dynamics of its stress responses based on the expression of stress proteins using MALDI-TOF mass spectrometry (MS), which has so far been used for species identification. Exploiting the methodology of accumulating protein expression profiles by MALDI-TOF MS followed by the statistical evaluation with cluster analysis and discriminant analysis of principle components (DAPC), it was possible to monitor the expression of low molecular weight stress proteins, identify a specific time point when the expression of stress proteins reached its maximum, and statistically differentiate types of adaptive responses into groups. Above the specific result for F19 and its stress response, these results demonstrate the discriminatory power of MALDI-TOF MS to characterize even dynamics of stress responses of bacteria and enable a knowledge-based focus on the laborious identification of biomarkers and stress proteins. To our knowledge, the implementation of MALDI-TOF MS protein profiling for the fast and comprehensive analysis of various stress responses is new to the field of bacterial stress responses. Consequently, we generally propose MALDI-TOF MS as an easy and quick method to characterize responses of microbes to different environmental conditions, to focus efforts of more elaborate approaches on time points and dynamics of stress responses. PMID:27783652

Identification and Characterization of Lipopeptides from Bacillus subtilis B1 Against Sapstain Fungus of Rubberwood Through MALDI-TOF-MS and RT-PCR.

PubMed

Sajitha, K L; Dev, Suma Arun; Maria Florence, E J

2016-07-01

Bacillus subtilis is a potent biocontrol agent producing a wide array of antifungal lipopeptides for the inhibition of fungal growth. B. subtilis B1 isolated from market-available compost provided an efficient control of rubberwood sapstain fungus, Lasiodiplodia theobromae. The current study is aimed to identify and characterize the lipopeptides responsible for the biocontrol of rubberwood sapstain fungus by Bacillus subtilis B1. The bacterial whole-cell surface extract from the dual culture of B. subtilis B1 and sapstain fungus (L. theobromae) was analysed using MALDI-TOF-MS. The protonated as well as sodium, potassium adducts of homologues of iturin C, surfactin, bacillomycin D and fengycin A and B were identified and expression of the lipopeptide biosynthetic genes could be confirmed through RT-PCR. This is the first report of mycobacillin and trimethylsilyl derivative of bacilysin during antagonism through MALDI-TOF-MS. MALDI-TOF-MS with RT-PCR offered easy platforms to characterize the antifungal lipopeptides. The identification of antifungal lipopeptides can lead to the formulation of prospective biocontrol by-products which have wide-scale utility.

Assessment of MALDI-TOF MS biotyping for Borrelia burgdorferi sl detection in Ixodes ricinus

PubMed Central

Boyer, Pierre H.; Boulanger, Nathalie; Nebbak, Amira; Collin, Elodie; Jaulhac, Benoit; Almeras, Lionel

2017-01-01

Matrix Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has been demonstrated to be useful for tick identification at the species level. More recently, this tool has been successfully applied for the detection of bacterial pathogens directly in tick vectors. The present work has assessed the detection of Borrelia burgdorferi sensu lato in Ixodes ricinus tick vector by MALDI-TOF MS. To this aim, experimental infection model of I. ricinus ticks by B. afzelii was carried out and specimens collected in the field were also included in the study. Borrelia infectious status of I. ricinus ticks was molecularly controlled using half-idiosome to classify specimens. Among the 39 ticks engorged on infected mice, 14 were confirmed to be infected by B. afzelii. For field collection, 14.8% (n = 12/81) I. ricinus ticks were validated molecularly as infected by B. burgdorferi sl. To determine the body part allowing the detection of MS protein profile changes between non-infected and B. afzelii infected specimens, ticks were dissected in three compartments (i.e. 4 legs, capitulum and half-idiosome) prior to MS analysis. Highly reproducible MS spectra were obtained for I. ricinus ticks according to the compartment tested and their infectious status. However, no MS profile change was found when paired body part comparison between non-infected and B. afzelii infected specimens was made. Statistical analyses did not succeed to discover, per body part, specific MS peaks distinguishing Borrelia-infected from non-infected ticks whatever their origins, laboratory reared or field collected. Despite the unsuccessful of MALDI-TOF MS to classify tick specimens according to their B. afzelii infectious status, this proteomic tool remains a promising method for rapid, economic and accurate identification of tick species. Moreover, the singularity of MS spectra between legs and half-idiosome of I. ricinus could be used to reinforce this proteomic identification

Rapid identification and typing of Yersinia pestis and other Yersinia species by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry

PubMed Central

2010-01-01

Background Accurate identification is necessary to discriminate harmless environmental Yersinia species from the food-borne pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis and from the group A bioterrorism plague agent Yersinia pestis. In order to circumvent the limitations of current phenotypic and PCR-based identification methods, we aimed to assess the usefulness of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) protein profiling for accurate and rapid identification of Yersinia species. As a first step, we built a database of 39 different Yersinia strains representing 12 different Yersinia species, including 13 Y. pestis isolates representative of the Antiqua, Medievalis and Orientalis biotypes. The organisms were deposited on the MALDI-TOF plate after appropriate ethanol-based inactivation, and a protein profile was obtained within 6 minutes for each of the Yersinia species. Results When compared with a 3,025-profile database, every Yersinia species yielded a unique protein profile and was unambiguously identified. In the second step of analysis, environmental and clinical isolates of Y. pestis (n = 2) and Y. enterocolitica (n = 11) were compared to the database and correctly identified. In particular, Y. pestis was unambiguously identified at the species level, and MALDI-TOF was able to successfully differentiate the three biotypes. Conclusion These data indicate that MALDI-TOF can be used as a rapid and accurate first-line method for the identification of Yersinia isolates. PMID:21073689

Rapid identification and typing of Yersinia pestis and other Yersinia species by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry.

PubMed

Ayyadurai, Saravanan; Flaudrops, Christophe; Raoult, Didier; Drancourt, Michel

2010-11-12

Accurate identification is necessary to discriminate harmless environmental Yersinia species from the food-borne pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis and from the group A bioterrorism plague agent Yersinia pestis. In order to circumvent the limitations of current phenotypic and PCR-based identification methods, we aimed to assess the usefulness of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) protein profiling for accurate and rapid identification of Yersinia species. As a first step, we built a database of 39 different Yersinia strains representing 12 different Yersinia species, including 13 Y. pestis isolates representative of the Antiqua, Medievalis and Orientalis biotypes. The organisms were deposited on the MALDI-TOF plate after appropriate ethanol-based inactivation, and a protein profile was obtained within 6 minutes for each of the Yersinia species. When compared with a 3,025-profile database, every Yersinia species yielded a unique protein profile and was unambiguously identified. In the second step of analysis, environmental and clinical isolates of Y. pestis (n = 2) and Y. enterocolitica (n = 11) were compared to the database and correctly identified. In particular, Y. pestis was unambiguously identified at the species level, and MALDI-TOF was able to successfully differentiate the three biotypes. These data indicate that MALDI-TOF can be used as a rapid and accurate first-line method for the identification of Yersinia isolates.

Identification of the inflow zone of unruptured cerebral aneurysms: comparison of 4D flow MRI and 3D TOF MRA data.

PubMed

Futami, K; Sano, H; Misaki, K; Nakada, M; Ueda, F; Hamada, J

2014-07-01

The hemodynamics of the inflow zone of cerebral aneurysms may be a key factor in coil compaction and recanalization after endovascular coil embolization. We performed 4D flow MR imaging in conjunction with 3D TOF MRA and compared their ability to identify the inflow zone of unruptured cerebral aneurysms. This series comprised 50 unruptured saccular cerebral aneurysms in 44 patients. Transluminal color-coded 3D MRA images were created by selecting the signal-intensity ranges on 3D TOF MRA images that corresponded with both the luminal margin and the putative inflow. 4D flow MR imaging demonstrated the inflow zone and yielded inflow velocity profiles for all 50 aneurysms. In 18 of 24 lateral-projection aneurysms (75%), the inflow zone was located distally on the aneurysmal neck. The maximum inflow velocity ranged from 285 to 922 mm/s. On 4D flow MR imaging and transluminal color-coded 3D MRA studies, the inflow zone of 32 aneurysms (64%) was at a similar location. In 91% of aneurysms whose neck section plane angle was <30° with respect to the imaging section direction on 3D TOF MRA, depiction of the inflow zone was similar on transluminal color-coded 3D MRA and 4D flow MR images. 4D flow MR imaging can demonstrate the inflow zone and provide inflow velocity profiles. In aneurysms whose angle of the neck-section plane is obtuse vis-a-vis the imaging section on 3D TOF MRA scans, transluminal color-coded 3D MRA may depict the inflow zone reliably. © 2014 by American Journal of Neuroradiology.

LC-UV assay method and UPLC/Q-TOF-MS characterisation of saponins from Ilex paraguariensis A. St. Hil. (mate) unripe fruits.

PubMed

Peixoto, Maria Paula Garofo; Kaiser, Samuel; Verza, Simone Gasparin; de Resende, Pedro Ernesto; Treter, Janine; Pavei, Cabral; Borré, Gustavo Luís; Ortega, George González

2012-01-01

Ilex paraguariensis A. St. Hil. (mate) is known in several South American countries because of the use of its leaves in stimulant herbal beverages. High saponin contents were reported in mate leaves and unripe fruits that possess a dissimilar composition. Two LC-UV methods previously reported for mate saponins assay focused on mate leaves and the quantification of the less polar saponin fraction in mate fruits. To develop and validate a LC-UV method to assay the total content of saponins in unripe mate fruits and characterise the chemical structure of triterpenic saponins by UPLC/Q-TOF-MS. From unripe fruits of mate a crude ethanolic extract was prepared (EX40) and the mate saponin fraction (MSF) purified by solid phase extraction. The LC-UV method was validated using ilexoside II as external standard. UPLC/Q-TOF-MS was adjusted from the LC-UV method to obtain the fragmentation patterns of the main saponins present in unripe fruits. Both LC-UV and UPLC/Q-TOF-MS methods indicate a wide range of Ilex saponins polarity. The ilexoside II and total saponin content of EX40 were 8.20% (w/w) and 47.60% (w/w), respectively. The total saponin content in unripe fruits was 7.28% (w/w). The saponins present in MSF characterised by UPLC/Q-TOF-MS are derived mainly from ursolic/oleanolic, acetyl ursolic or pomolic acid. The validated LC-UV method was shown to be linear, precise, accurate and to cover several saponins previously isolated from Ilex species and could be applied for the quality control of unripe fruit saponins. Copyright © 2011 John Wiley & Sons, Ltd.

Application of MALDI-TOF MS fingerprinting as a quick tool for identification and clustering of foodborne pathogens isolated from food products.

PubMed

Elbehiry, Ayman; Marzouk, Eman; Hamada, Mohamed; Al-Dubaib, Musaad; Alyamani, Essam; Moussa, Ihab M; AlRowaidhan, Anhar; Hemeg, Hassan A

2017-10-01

Foodborne pathogens can be associated with a wide variety of food products and it is very important to identify them to supply safe food and prevent foodborne infections. Since traditional techniques are timeconsuming and laborious, this study was designed for rapid identification and clustering of foodborne pathogens isolated from various restaurants in Al-Qassim region, Kingdom of Saudi Arabia (KSA) using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Sixty-nine bacterial and thirty-two fungal isolates isolated from 80 food samples were used in this study. Preliminary identification was carried out through culture and BD Phoenix™ methods. A confirmatory identification technique was then performed using MALDI-TOF MS. The BD Phoenix results revealed that 97% (67/69 isolates) of bacteria were correctly identified as 75% Enterobacter cloacae, 95.45% Campylobacter jejuni and 100% for Escherichia coli, Salmonella enterica, Staphylococcus aureus, Acinetobacter baumannii, and Klebsiella pneumoniae. While 94.44% (29/32 isolates) of fungi were correctly identified as 77.77% Alternaria alternate, 88.88% Aspergillus niger and 100% for Aspergillus flavus, Penicillium digitatum, Candida albicans and Debaryomyces hansenii. However, all bacterial and fungal isolates were 100% properly identified by MALDI-TOF MS fingerprinting with a score value ≥2.00. A gel view illustrated that the spectral peaks for the identified isolates fluctuate between 3,000 and 10,000 Da. The results of main spectra library (MSP) dendrogram showed that the bacterial and fungal isolates matched with 19 and 9 reference strains stored in the Bruker taxonomy, respectively. Our results indicated that MALDI-TOF MS is a promising technique for fast and accurate identification of foodborne pathogens.

Comprehensive MALDI-TOF biotyping of the non-redundant Harvard Pseudomonas aeruginosa PA14 transposon insertion mutant library.

PubMed

Oumeraci, Tonio; Jensen, Vanessa; Talbot, Steven R; Hofmann, Winfried; Kostrzewa, Markus; Schlegelberger, Brigitte; von Neuhoff, Nils; Häussler, Susanne

2015-01-01

Pseudomonas aeruginosa is a gram-negative bacterium that is ubiquitously present in the aerobic biosphere. As an antibiotic-resistant facultative pathogen, it is a major cause of hospital-acquired infections. Its rapid and accurate identification is crucial in clinical and therapeutic environments. In a large-scale MALDI-TOF mass spectrometry-based screen of the Harvard transposon insertion mutant library of P. aeruginosa strain PA14, intact-cell proteome profile spectra of 5547 PA14 transposon mutants exhibiting a plethora of different phenotypes were acquired and analyzed. Of all P. aeruginosa PA14 mutant profiles 99.7% were correctly identified as P. aeruginosa with the Biotyper software on the species level. On the strain level, 99.99% of the profiles were mapped to five different individual P. aeruginosa Biotyper database entries. A principal component analysis-based approach was used to determine the most important discriminatory mass features between these Biotyper groups. Although technical replicas were consistently categorized to specific Biotyper groups in 94.2% of the mutant profiles, biological replicas were not, indicating that the distinct proteotypes are affected by growth conditions. The PA14 mutant profile collection presented here constitutes the largest coherent P. aeruginosa MALDI-TOF spectral dataset publicly available today. Transposon insertions in thousands of different P. aeruginosa genes did not affect species identification from MALDI-TOF mass spectra, clearly demonstrating the robustness of the approach. However, the assignment of the individual spectra to sub-groups proved to be non-consistent in biological replicas, indicating that the differentiation between biotyper groups in this nosocomial pathogen is unassured.

Analysis of E. rutaecarpa Alkaloids Constituents In Vitro and In Vivo by UPLC-Q-TOF-MS Combined with Diagnostic Fragment

PubMed Central

Yang, Shenshen; Tian, Meng; Yuan, Lei; Deng, Haoyue; Wang, Lei; Li, Aizhu; Hou, Zhiguo; Li, Yubo

2016-01-01

Evodia rutaecarpa (Juss.) Benth. (Rutaceae) dried ripe fruit is used for dispelling colds, soothing liver, and analgesia. Pharmacological research has proved that alkaloids are the main active ingredients of E. rutaecarpa. This study aimed to rapidly classify and identify the alkaloids constituents of E. rutaecarpa by using UPLC-Q-TOF-MS coupled with diagnostic fragments. Furthermore, the effects of the material base of E. rutaecarpa bioactive ingredients in vivo were examined such that the transitional components in the blood of rats intragastrically given E. rutaecarpa were analyzed and identified. In this study, the type of alcohol extraction of E. rutaecarpa and the corresponding blood sample were used for the analysis by UPLC-Q-TOF-MS in positive ion mode. After reviewing much of the literature and collected information on the fragments, we obtained some diagnostic fragments of the alkaloids. Combining the diagnostic fragments with the technology of UPLC-Q-TOF-MS, we identified the compounds of E. rutaecarpa and blood samples and compared the ion fragment information with that of the alkaloids in E. rutaecarpa. A total of 17 alkaloids components and 6 blood components were identified. The proposed method was rapid, accurate, and sensitive. Therefore, this technique can reliably and practically analyze the chemical constituents in traditional Chinese medicine (TCM). PMID:27446630

NACE-ESI-TOF MS to reveal phenolic compounds from olive oil: introducing enriched olive oil directly inside capillary.

PubMed

Gómez-Caravaca, Ana María; Carrasco-Pancorbo, Alegría; Segura-Carretero, Antonio; Fernández-Gutiérrez, Alberto

2009-09-01

Most CE methods for the analysis of phenols from olive oil use an aqueous electrolyte separation medium, although the importance of NACE is obvious, as this kind of CE seems to be more compatible with the hydrophobic olive oil matrix and could facilitate its direct injection. In the current work we develop a method involving SPE and NACE coupled to ESI-TOF MS. All the CE and ESI-TOF MS parameters were optimized in order to maximize the number of phenolic compounds detected and the sensitivity in their determination. Electrophoretic separation was carried out using a CE buffer system consisting of 25 mM NH(4)OAc/AcH in methanol/ACN (1/1 v/v) at an apparent pH value of 5.0. We studied in depth the effect of the nature and concentration of different electrolytes dissolved in different organic solvents and other experimental and instrumental CE variables. The results were compared with those obtained by CZE (with aqueous buffers) coupled to ESI-TOF MS; both methods offered to the analyst the chance to study phenolic compounds of different families (such as phenolic alcohols, lignans, complex phenols, flavonoids, etc.) from virgin olive oil by injecting methanolic extracts with efficient and fast CE separations. In the case of NACE method, we also studied the direct injection of the investigated matrix introducing a plug of olive oil directly into the capillary.

A laser desorption ionization/matrix-assisted laser desorption ionization target system applicable for three distinct types of instruments (LinTOF/curved field RTOF, LinTOF/RTOF and QqRTOF) with different performance characteristics from three vendors.

PubMed

Rados, Edita; Pittenauer, Ernst; Frank, Johannes; Varmuza, Kurt; Allmaier, Günter

2018-04-30

We have developed a target system which enables the use of only one target (i.e. target preparation set) for three different laser desorption ionization (LDI)/matrix-assisted laser desorption ionization (MALDI) mass spectrometric instruments. The focus was on analysing small biomolecules with LDI for future use of the system for the study of meteorite samples (carbonaceous chondrites) using devices with different mass spectrometric performance characteristics. Three compounds were selected due to their potential presence in meteoritic chondrites: tryptophan, 2-deoxy-d-ribose and triphenylene. They were prepared (with and without MALDI matrix, i.e. MALDI and LDI) and analysed with three different mass spectrometers (LinTOF/curved field RTOF, LinTOF/RTOF and QqRTOF). The ion sources of two of the instruments were run at high vacuum, and one at intermediate pressure. Two devices used a laser wavelength of 355 nm and one a wavelength of 337 nm. The developed target system operated smoothly with all devices. Tryptophan, 2-deoxy-d-ribose and triphenylene showed similar desorption/ionization behaviour for all instruments using the LDI mode. Interestingly, protonated tryptophan could be observed only with the LinTOF/curved field RTOF device in LDI and MALDI mode, while sodiated molecules were observed with all three instruments (in both ion modes). Deprotonated tryptophan was almost completely obscured by matrix ions in the MALDI mode whereas LDI yielded abundant deprotonated molecules. The presented target system allowed successful analyses of the three compounds using instruments from different vendors with only one preparation showing different analyser performance characteristics. The elemental composition with the QqRTOF analyser and the high-energy 20 keV collision-induced dissociation fragmentation will be important in identifying unknown compounds in chondrites. © 2018 The Authors. Rapid Communications in Mass Spectrometry Published by John Wiley & Sons Ltd.

Study on Chemical Constituents in Polygoni Cuspidati Folium and its Preparation by UPLC-ESI-Q-TOF-MS/MS.

PubMed

Wang, Xin; Qin, Yao; Li, Guang-Quan; Chen, Shuai; Ma, Jing-Qi; Guo, Yan-Lei; Luo, Wei-Zao

2018-03-15

A rapid and credible analytical method was developed using online UPLC-ESI-Q-TOF-MS/MS to identify chemical constituents in Polygoni cuspidati folium and its preparation. By accurate mass measurements within 6.5 ppm error for [M-H]- ion in routine analysis, 26 chemical constituents, including tannin, derivatives of phenylpropionic acid, stilbene, flavonoid, anthraquinone, torachryson and its derivatives, were identified or tentatively characterized. Among them, five constituents (compounds 19-23) were firstly reported in Polygoni cuspidati folium, other 17 constituents were coexisting in both Polygoni cuspidati folium and its preparation. Fragmentation behaviors of different categories of constituents were also investigated to confirm the results. This established UPLC-ESI-Q-TOF-MS/MS method, with reliance and efficiency for the identification the major constituents, would be the basis for quality control of Polygoni cuspidati folium and its preparation.

A novel PFIB sample preparation protocol for correlative 3D X-ray CNT and FIB-TOF-SIMS tomography.

PubMed

Priebe, Agnieszka; Audoit, Guillaume; Barnes, Jean-Paul

2017-02-01

We present a novel sample preparation method that allows correlative 3D X-ray Computed Nano-Tomography (CNT) and Focused Ion Beam Time-Of-Flight Secondary Ion Mass Spectrometry (FIB-TOF-SIMS) tomography to be performed on the same sample. In addition, our invention ensures that samples stay unmodified structurally and chemically between the subsequent experiments. The main principle is based on modifying the topography of the X-ray CNT experimental setup before FIB-TOF-SIMS measurements by incorporating a square washer around the sample. This affects the distribution of extraction field lines and therefore influences the trajectories of secondary ions that are now guided more efficiently towards the detector. As the result, secondary ion detection is significantly improved and higher, i.e. statistically better, signals are obtained. Copyright © 2016 Elsevier B.V. All rights reserved.

Fish proteins as targets of ferrous-catalyzed oxidation: identification of protein carbonyls by fluorescent labeling on two-dimensional gels and MALDI-TOF/TOF mass spectrometry.

PubMed

Pazos, Manuel; da Rocha, Angela Pereira; Roepstorff, Peter; Rogowska-Wrzesinska, Adelina

2011-07-27

Protein oxidation in fish meat is considered to affect negatively the muscle texture. An important source of free radicals taking part in this process is Fenton's reaction dependent on ferrous ions present in the tissue. The aim of this study was to investigate the susceptibility of cod muscle proteins in sarcoplasmic and myofibril fractions to in vitro metal-catalyzed oxidation and to point out protein candidates that might play a major role in the deterioration of fish quality. Extracted control proteins and proteins subjected to free radicals generated by Fe(II)/ascorbate mixture were labeled with fluorescein-5-thiosemicarbazide (FTSC) to tag carbonyl groups and separated by two-dimensional gel electrophoresis. Consecutive visualization of protein carbonyl levels by capturing the FTSC signal and total protein levels by capturing the SyproRuby staining signal allowed us to quantify the relative change in protein carbonyl levels corrected for changes in protein content. Proteins were identified using MALDI-TOF/TOF mass spectrometry and homology-based searches. The results show that freshly extracted cod muscle proteins exhibit a detectable carbonylation background and that the incubation with Fe(II)/ascorbate triggers a further oxidation of both sarcoplasmic and myofibril proteins. Different proteins exhibited various degrees of sensitivity to oxidation processes. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), nucleoside diphosphate kinase B (NDK), triosephosphate isomerase, phosphoglycerate mutase, lactate dehydrogenase, creatine kinase, and enolase were the sarcoplasmic proteins most vulnerable to ferrous-catalyzed oxidation. Moreover, NDK, phosphoglycerate mutase, and GAPDH were identified in several spots differing by their pI, and those forms showed different susceptibilities to metal-catalyzed oxidation, indicating that post-translational modifications may change the resistance of proteins to oxidative damage. The Fe(II)/ascorbate treatment significantly

Evaluation of MALDI-TOF mass spectrometry and Sepsityper Kit™ for the direct identification of organisms from sterile body fluids in a Canadian pediatric hospital.

PubMed

Tadros, Manal; Petrich, Astrid

2013-01-01

Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) can be used to identify bacteria directly from positive blood and sterile fluid cultures. The authors evaluated a commercially available kit - the Sepsityper Kit (Bruker Daltonik, Germany) - and MALDI-TOF MS for the rapid identification of organisms from 80 flagged positive blood culture broths, of which 73 (91.2%) were blood culture specimens and seven (8.7%) were cerebrospinal fluid specimens, in comparison with conventional identification methods. Correct identification to the genus and species levels was obtained in 75 of 80 (93.8%) and 39 of 50 (78%) blood culture broths, respectively. Applying the blood culture analysis module, a newly developed software tool, improved the species identification of Gram-negative organisms from 94.7% to 100% and of Gram-positive organisms from 66.7% to 70%. MALDI-TOF MS is a promising tool for the direct identification of organisms cultured from sterile sites.

MALDI-TOF mass spectrometry applied to identifying species of insect-pathogenic fungi from the Metarhizium anisopliae complex

USDA-ARS?s Scientific Manuscript database

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has proven to be a powerful tool for taxonomic resolution of microorganisms. In this proof-of-concept study, we assessed the effectiveness of this technique to track the current gene sequence-based phylogenet...

MALDI-TOF MS Versus VITEK®2: Comparison of Systems for the Identification of Microorganisms Responsible for Bacteremia.

PubMed

Febbraro, Filomena; Rodio, Donatella Maria; Puggioni, Gianluca; Antonelli, Guido; Pietropaolo, Valeria; Trancassini, Maria

2016-12-01

We evaluated the reliability and accuracy of the combined use of MALDI-TOF MS and classical ID VITEK 2 to identify monomicrobial infection in blood culture bottles. In total, 70 consecutive positive blood cultures were included in this study. Positive blood culture bottles were subjected to Gram staining and subcultured on solid media. Isolates grown from such culture media were used for classical ID using VITEK 2 system. In parallel, an aliquot was subjected to a lysing-centrifugation method and used for the identification with the MALDI-TOF system. Results evidenced the correct genus and species identification of 91.4 % of microorganisms responsible for bacteremia with an agreement to the species and the genus level. If compared with the standard method VITEK 2 , our simple and cost-effective sample preparation method would be very useful for rapid identification of microorganisms using blood culture bottles. In fact, the direct method showed rapid and reliable results, especially for the gram-negative group.

Determination of Curcuminoids in Curcuma longa Linn. by UPLC/Q-TOF-MS: An Application in Turmeric Cultivation.

PubMed

Ashraf, Kamran; Mujeeb, Mohd; Ahmad, Altaf; Ahmad, Niyaz; Amir, Mohd

2015-09-01

Cucuma longa Linn. (Fam-Zingiberaceae) is a valued medicinal plant contains curcuminoids (curcumin, demethoxycurcumin and bisdemethoxycurcumin) as major bioactive constituents. Previously reported analytical methods for analysis of curcuminoids were found to suffer from low resolution, lower sensitivity and longer analytical times. In this study, a rapid, sensitive, selective high-throughput ultra high performance liquid chromatography-tandem mass spectrometry (UPLC/Q-TOF-MS) method was developed and validated for the quantification of curcuminoids with an aim to reduce analysis time and enhance efficiency. UPLC/Q-TOF-MS analysis showed large variation (1.408-5.027% w/w) of curcuminoids among different samples with respect to their occurrence of metabolite and their concentration. The results showed that Erode (south province) contains highest quantity of curcuminoids and concluded to be the superior varieties. The results obtained here could be valuable for devising strategies for cultivating this medicinal plant. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

GPU-Accelerated Forward and Back-Projections with Spatially Varying Kernels for 3D DIRECT TOF PET Reconstruction.

PubMed

Ha, S; Matej, S; Ispiryan, M; Mueller, K

2013-02-01

We describe a GPU-accelerated framework that efficiently models spatially (shift) variant system response kernels and performs forward- and back-projection operations with these kernels for the DIRECT (Direct Image Reconstruction for TOF) iterative reconstruction approach. Inherent challenges arise from the poor memory cache performance at non-axis aligned TOF directions. Focusing on the GPU memory access patterns, we utilize different kinds of GPU memory according to these patterns in order to maximize the memory cache performance. We also exploit the GPU instruction-level parallelism to efficiently hide long latencies from the memory operations. Our experiments indicate that our GPU implementation of the projection operators has slightly faster or approximately comparable time performance than FFT-based approaches using state-of-the-art FFTW routines. However, most importantly, our GPU framework can also efficiently handle any generic system response kernels, such as spatially symmetric and shift-variant as well as spatially asymmetric and shift-variant, both of which an FFT-based approach cannot cope with.

GPU-Accelerated Forward and Back-Projections With Spatially Varying Kernels for 3D DIRECT TOF PET Reconstruction

NASA Astrophysics Data System (ADS)

Ha, S.; Matej, S.; Ispiryan, M.; Mueller, K.

2013-02-01

We describe a GPU-accelerated framework that efficiently models spatially (shift) variant system response kernels and performs forward- and back-projection operations with these kernels for the DIRECT (Direct Image Reconstruction for TOF) iterative reconstruction approach. Inherent challenges arise from the poor memory cache performance at non-axis aligned TOF directions. Focusing on the GPU memory access patterns, we utilize different kinds of GPU memory according to these patterns in order to maximize the memory cache performance. We also exploit the GPU instruction-level parallelism to efficiently hide long latencies from the memory operations. Our experiments indicate that our GPU implementation of the projection operators has slightly faster or approximately comparable time performance than FFT-based approaches using state-of-the-art FFTW routines. However, most importantly, our GPU framework can also efficiently handle any generic system response kernels, such as spatially symmetric and shift-variant as well as spatially asymmetric and shift-variant, both of which an FFT-based approach cannot cope with.

The application of Gaussian mixture models for signal quantification in MALDI-TOF mass spectrometry of peptides.

PubMed

Spainhour, John Christian G; Janech, Michael G; Schwacke, John H; Velez, Juan Carlos Q; Ramakrishnan, Viswanathan

2014-01-01

Matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) coupled with stable isotope standards (SIS) has been used to quantify native peptides. This peptide quantification by MALDI-TOF approach has difficulties quantifying samples containing peptides with ion currents in overlapping spectra. In these overlapping spectra the currents sum together, which modify the peak heights and make normal SIS estimation problematic. An approach using Gaussian mixtures based on known physical constants to model the isotopic cluster of a known compound is proposed here. The characteristics of this approach are examined for single and overlapping compounds. The approach is compared to two commonly used SIS quantification methods for single compound, namely Peak Intensity method and Riemann sum area under the curve (AUC) method. For studying the characteristics of the Gaussian mixture method, Angiotensin II, Angiotensin-2-10, and Angiotenisn-1-9 and their associated SIS peptides were used. The findings suggest, Gaussian mixture method has similar characteristics as the two methods compared for estimating the quantity of isolated isotopic clusters for single compounds. All three methods were tested using MALDI-TOF mass spectra collected for peptides of the renin-angiotensin system. The Gaussian mixture method accurately estimated the native to labeled ratio of several isolated angiotensin peptides (5.2% error in ratio estimation) with similar estimation errors to those calculated using peak intensity and Riemann sum AUC methods (5.9% and 7.7%, respectively). For overlapping angiotensin peptides, (where the other two methods are not applicable) the estimation error of the Gaussian mixture was 6.8%, which is within the acceptable range. In summary, for single compounds the Gaussian mixture method is equivalent or marginally superior compared to the existing methods of peptide quantification and is capable of quantifying overlapping (convolved) peptides within the

Evaluation of repetitive-PCR and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid strain typing of Bacillus coagulans.

PubMed

Sato, Jun; Nakayama, Motokazu; Tomita, Ayumi; Sonoda, Takumi; Hasumi, Motomitsu; Miyamoto, Takahisa

2017-01-01

In order to establish rapid and accurate typing method for Bacillus coagulans strains which is important for controlling in some canned foods and tea-based beverages manufacturing because of the high-heat resistance of the spores and high tolerance of the vegetative cells to catechins and chemicals, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and repetitive-PCR (rep-PCR) were evaluated. For this purpose, 28 strains of B. coagulans obtained from various culture collections were tested. DNA sequence analyses of the genes encoding 16S rRNA and DNA gyrase classified the test strains into two and three groups, respectively, regardless of their phenotypes. Both MALDI-TOF MS and rep-PCR methods classified the test strains in great detail. Strains classified in each group showed similar phenotypes, such as carbohydrate utilization determined using API 50CH. In particular, the respective two pairs of strains which showed the same metabolic characteristic were classified into the same group by both MALDI-TOF MS and rep-PCR methods separating from the other strains. On the other hand, the other strains which have the different profiles of carbohydrate utilization were separated into different groups by these methods. These results suggested that the combination of MALDI-TOF MS and rep-PCR analyses was advantageous for the rapid and detailed typing of bacterial strains in respect to both phenotype and genotype.

Ellagitannin composition of blackberry as determined by HPLC-ESI-MS and MALDI-TOF-MS.

PubMed

Hager, Tiffany J; Howard, Luke R; Liyanage, Rohana; Lay, Jackson O; Prior, Ronald L

2008-02-13

Blackberries ( Rubus sp.) were evaluated by high-performance liquid chromatography-electrospray ionization-mass spectrometry (HPLC-ESI-MS) and matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF-MS) to identify the ellagitannins present in flesh, torus (receptacle tissue), and seeds. Most ellagitannins were present (or detectable) only in seed tissues. Ellagitannins identified by HPLC-ESI-MS in the seeds included pedunculagin, casuarictin/potentillin, castalagin/vescalagin, lambertianin A/sanguiin H-6, lambertianin C, and lambertianin D. For several of the ellagitannins, isomeric separation was also obtained. The MALDI-TOF-MS analysis was primarily utilized to evaluate and identify high molecular mass (>1000 Da) ellagitannins. The MALDI analysis verified the presence of the ellagitannins identified by HPLC-ESI-MS including lambertianin A/sanguiin H-6, lambertianin C, and lambertianin D, but the analysis also indicated the presence of several other compounds that were most likely ellagitannins based on the patterns observed in the masses (i.e., loss or addition of a gallic acid moiety to a known ellagitannin). This study determined the presence of several possible isomeric forms of ellagitannins previously unidentified in fruit and presents a possible analytical HPLC method for the analysis of the major ellagitannins present in the fruit.

UPLC-Q-TOF-MS analysis of non-volatile migrants from new active packaging materials.

PubMed

Aznar, M; Rodriguez-Lafuente, A; Alfaro, P; Nerin, C

2012-10-01

Ultra-performance liquid chromatography (UPLC) coupled to mass spectrometry (MS) is a useful tool in the analysis of non-volatile compounds, and the use of a quadrupole-time-of-flight (Q-TOF) mass analyzer allows a high sensitivity and accuracy when acquiring full fragment mode, providing a high assurance of correct identification of unknown compounds. In this work, UPLC-Q-TOF-MS technology has been applied to the analysis of non-volatile migrants from new active packaging materials. The materials tested were based on polypropylene (PP), ethylene-vinyl alcohol copolymer (EVOH), and poly(ethylene terephthalate) (PET). The active packaging materials studied were one PP film containing a natural antioxidant, and two PP/EVOH films, two PET/EVOH films and one coextruded PP/EVOH/PP film containing natural antimicrobials. The chemical structure of several compounds was unequivocally identified. The analysis revealed the migration of some of the active substances used in the manufacture of active packaging, such as caffeine (0.07 ± 0.01 μg/g), carvacrol (0.31 ± 0.03 μg/g) and citral (0.20 ± 0.01 μg/g). Unintentionally added substances were also found, such as citral reaction compounds, or citral impurities present in the raw materials.

Effect of ecosystem type and fire on chemistry of WEOM as measured by LDI-TOF-MS and NMR.

PubMed

Crecelius, Anna C; Vitz, Jürgen; Näthe, Kerstin; Meyer, Stefanie; Michalzik, Beate; Schubert, Ulrich S

2017-01-01

Soil organic matter (SOM) and its water-soluble components play an important role in terrestrial carbon cycling and associated ecosystem functions. Chemically, they are complex mixtures of organic compounds derived from decomposing plant material, microbial residues, as well as root exudates, and soil biota. To test the effect of the ecosystem type (forest and grassland) and fires events on the chemistry of dissolved organic matter (DOM), we applied a combination of laser-desorption/ionization time-of-flight mass spectrometry (LDI-TOF-MS) and 2D ( 1 H and 13 C) nuclear magnetic resonance (NMR) spectroscopy to water-extractable organic matter (WEOM) from a range of top soil samples. The aim was to assess the suitability of LDI-TOF-MS for the rapid characterization of WEOM. Therefore, we evaluated the effects of sample (pH and dilution) conditions and use of positive or negative reflector mode to identify the conditions under which LDI-TOF-MS best distinguished between WEOM from different sources. Thirty-six samples were measured with both analytical techniques and their chemical patterns were statistically evaluated to distinguish firstly the effect of the type of ecosystem (forest versus grassland) on WEOM characteristics, and secondly the impact of fire on the chemical composition of WEOM. The nonmetric multidimensional scaling (NMDS) analysis of the most suitable experimental LDI-TOF-MS conditions showed a clear separation between the type of vegetation and fire-induced changes, mostly reflecting the presence of poly(ethylene glycol) in grassland soils. Discrimination among WEOM from different vegetation types was preserved in the fire treated samples. The calculation of the relative abundance of certain functional structures in the WEOM samples revealed a common composition of forest and grassland WEOM, with polysaccharides and proteins making up to 60%. The compositional impact of forest fire on WEOM was more pronounced compared to the one of grassland, leading

Rapid Characterization of Constituents in Tribulus terrestris from Different Habitats by UHPLC/Q-TOF MS.

PubMed

Zheng, Wei; Wang, Fangxu; Zhao, Yang; Sun, Xinguang; Kang, Liping; Fan, Ziquan; Qiao, Lirui; Yan, Renyi; Liu, Shuchen; Ma, Baiping

2017-11-01

A strategy for rapid identification of the chemical constituents from crude extracts of Tribulus terrestris was proposed using an informatics platform for the UHPLC/Q-TOF MS E data analyses. This strategy mainly utilizes neutral losses, characteristic fragments, and in-house library to rapidly identify the structure of the compounds. With this strategy, rapid characterization of the chemical components of T. terrestris from Beijing, China was successfully achieved. A total of 82 steroidal saponins and nine flavonoids were identified or tentatively identified from T. terrestris. Among them, 15 new components were deduced based on retention times and characteristic MS fragmentation patterns. Furthermore, the chemical components of T. terrestris, including the other two samples from Xinjiang Uygur Autonomous region, China, and Rome, Italy, were also identified with this strategy. Altogether, 141 chemical components were identified from these three samples, of which 39 components were identified or tentatively identified as new compounds, including 35 groups of isomers. It demonstrated that this strategy provided an efficient protocol for the rapid identification of chemical constituents in complex samples such as traditional Chinese medicines (TCMs) by UHPLC/Q-TOF MS E with informatics platform. Graphical Abstract ᅟ.

[Fast identification of constituents of Lagotis brevituba by using UPLC-Q-TOF-MS/MS method].

PubMed

Xie, Jing; Zhang, Li; Zeng, Jin-Xiang; Li, Min; Wang, Juan; Xie, Xiong-Xiong; Zhong, Guo-Yue; Luo, Guang-Ming; Yuan, Jin-Bin; Liang, Jian

2017-06-01

The chemical constituents of Lagotis brevituba were rapidly determined and analyzed by using ultra performance liquid chromatography tandem quadrupole time of flight mass spectrometry (UPLC-Q-TOF-MS/MS) method, providing material basis for the clinical application of L. brevituba. The separation was performed on UPLC YMC-Triart C₁₈ (2.1 mm×100 mm, 1.9 μm) column, with acetonitrile-water containing 0.2% formic acid as mobile phase for gradient elution. The flow rate was 0.4 mL•min-1 gradient elution and column temperature was 40 ℃, the injection volume was 2 μL. ESI ion source was used to ensure the data collected in a negative ion mode. The chemical components of L. brevituba were identified through retention time, exact relative molecular mass, cleavage fragments of MS/MS and reported data. The results showed that a total of 22 compounds were identified, including 11 flavones, 6 phenylethanoid glycosides, 1 iridoid glucosides, and 4 organic acid. The UPLC-Q-TOF-MS/MS method could fast identify the chemical components of L. brevituba, providing valuable information about L. brevituba for its clinical application. Copyright© by the Chinese Pharmaceutical Association.

Rapid Characterization of Constituents in Tribulus terrestris from Different Habitats by UHPLC/Q-TOF MS

NASA Astrophysics Data System (ADS)

Zheng, Wei; Wang, Fangxu; Zhao, Yang; Sun, Xinguang; Kang, Liping; Fan, Ziquan; Qiao, Lirui; Yan, Renyi; Liu, Shuchen; Ma, Baiping

2017-08-01

A strategy for rapid identification of the chemical constituents from crude extracts of Tribulus terrestris was proposed using an informatics platform for the UHPLC/Q-TOF MSE data analyses. This strategy mainly utilizes neutral losses, characteristic fragments, and in-house library to rapidly identify the structure of the compounds. With this strategy, rapid characterization of the chemical components of T. terrestris from Beijing, China was successfully achieved. A total of 82 steroidal saponins and nine flavonoids were identified or tentatively identified from T. terrestris. Among them, 15 new components were deduced based on retention times and characteristic MS fragmentation patterns. Furthermore, the chemical components of T. terrestris, including the other two samples from Xinjiang Uygur Autonomous region, China, and Rome, Italy, were also identified with this strategy. Altogether, 141 chemical components were identified from these three samples, of which 39 components were identified or tentatively identified as new compounds, including 35 groups of isomers. It demonstrated that this strategy provided an efficient protocol for the rapid identification of chemical constituents in complex samples such as traditional Chinese medicines (TCMs) by UHPLC/Q-TOF MSE with informatics platform. [Figure not available: see fulltext.

Use of MALDI-TOF Mass Spectrometry for the Fast Identification of Gram-Positive Fish Pathogens

PubMed Central

Assis, Gabriella B. N.; Pereira, Felipe L.; Zegarra, Alexandra U.; Tavares, Guilherme C.; Leal, Carlos A.; Figueiredo, Henrique C. P.

2017-01-01

Gram-positive cocci, such as Streptococcus agalactiae, Lactococcus garvieae, Streptococcus iniae, and Streptococcus dysgalactiae subsp. dysgalactiae, are found throughout the world, particularly in outbreaks in farmed fish, and are thus associated with high economic losses, especially in the cultivation of Nile Tilapia. The aim of this study was to evaluate the efficacy of matrix-assisted laser desorption ionization (MALDI)-time of flight (TOF) mass spectrometry (MS) as an alternative for the diagnosis of these pathogens. One hundred and thirty-one isolates from Brazilian outbreaks assisted by the national authority were identified using a MALDI Biotyper from Bruker Daltonics. The results showed an agreement with respect to identification (Kappa = 1) between this technique and 16S ribosomal RNA gene sequencing for S. agalactiae and L. garvieae. However, for S. iniae and S. dysgalactiae subsp. dysgalactiae, perfect agreement was only achieved after the creation of a custom main spectra profile, as well as further comparisons with 16S ribosomal RNA and multilocus sequence analysis. MALDI-TOF MS was shown to be an efficient technology for the identification of these Gram-positive pathogens, yielding a quick and precise diagnosis. PMID:28848512

MALDI-TOF MS for the identification of veterinary non-C. neoformans-C. gattii Cryptococcus spp. isolates from Italy.

PubMed

Danesi, Patrizia; Drigo, Ilenia; Iatta, Roberta; Firacative, Carolina; Capelli, Gioia; Cafarchia, Claudia; Meyer, Wieland

2014-08-01

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) offers an effective alternative to phenotypic and molecular methods for the rapid identification of microorganisms. Our aim in this study was to create an in-house library for a set of strains of nine uncommonly reported human and animal cryptococcal species, including Cryptococcus adeliensis, C. albidosimilis, C. albidus, C. aureus, C. carnescens, C. laurentii, C. magnus, C. victoriae and C. uniguttulatus, and to use this library to make timely and correct identifications using MALDI-TOF MS for use in routine laboratory diagnostics. Protein extracts obtained via the formic acid extraction method of 62 veterinary non-C. neoformans-C. gattii cryptococcal isolates were studied. The obtained mass spectra correctly grouped all 62 studied isolates according to species identification previously obtained by internal transcribe spacer sequence analysis. The in-house database was than exported and successfully uploaded to the Microflex LT (Maldi Biotyper; Bruker Daltonics) instrument at a different diagnostic laboratory in Italy. Scores >2.7 obtained from isolates reanalyzed in the latter laboratory supported the high reproducibility of the method. The possibility of creating and transferring an in-house library adds to the usefulness MALDI-TOF MS an important tool for the rapid and inexpensive identification of pathogenic and saprophytic fungi as required for differential diagnosis of human and animal mycoses. © The Author 2014. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

TOF-SIMS investigation of Streptomyces coelicolor, a mycelial bacterium

NASA Astrophysics Data System (ADS)

Vaidyanathan, Seetharaman; Fletcher, John S.; Lockyer, Nicholas P.; Vickerman, John C.

2008-12-01

Streptomyces coelicolor is a mycelial microorganism that produces several secondary metabolites, including antibiotics. The physiology of the organism has largely been investigated in liquid cultures due to ease of monitoring different physiological parameters and more homogeneous culture conditions. However, solid cultures reflect the natural physiology of the microorganism better, given that in its natural state it grows in the soil. Imaging mass spectrometry with TOF-SIMS and C 60+ primary ion beams offers a potential route to studying chemical changes at the molecular level, both intracellular and extracellular that can help in understanding the natural physiology of the microorganism. Here, we report the application of the technique for studying the lateral distribution of the chemical species detected in a population, grown in both liquid and solid cultures. The capability of the technique for studying biological systems with minimal system intervention is demonstrated.

Optimization of analytical and pre-analytical conditions for MALDI-TOF-MS human urine protein profiles.

PubMed

Calvano, C D; Aresta, A; Iacovone, M; De Benedetto, G E; Zambonin, C G; Battaglia, M; Ditonno, P; Rutigliano, M; Bettocchi, C

2010-03-11

Protein analysis in biological fluids, such as urine, by means of mass spectrometry (MS) still suffers for insufficient standardization in protocols for sample collection, storage and preparation. In this work, the influence of these variables on healthy donors human urine protein profiling performed by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) was studied. A screening of various urine sample pre-treatment procedures and different sample deposition approaches on the MALDI target was performed. The influence of urine samples storage time and temperature on spectral profiles was evaluated by means of principal component analysis (PCA). The whole optimized procedure was eventually applied to the MALDI-TOF-MS analysis of human urine samples taken from prostate cancer patients. The best results in terms of detected ions number and abundance in the MS spectra were obtained by using home-made microcolumns packed with hydrophilic-lipophilic balance (HLB) resin as sample pre-treatment method; this procedure was also less expensive and suitable for high throughput analyses. Afterwards, the spin coating approach for sample deposition on the MALDI target plate was optimized, obtaining homogenous and reproducible spots. Then, PCA indicated that low storage temperatures of acidified and centrifuged samples, together with short handling time, allowed to obtain reproducible profiles without artifacts contribution due to experimental conditions. Finally, interesting differences were found by comparing the MALDI-TOF-MS protein profiles of pooled urine samples of healthy donors and prostate cancer patients. The results showed that analytical and pre-analytical variables are crucial for the success of urine analysis, to obtain meaningful and reproducible data, even if the intra-patient variability is very difficult to avoid. It has been proven how pooled urine samples can be an interesting way to make easier the comparison between

A UPLC-TOF/MS-based metabolomics study of rattan stems of Schisandra chinensis effects on Alzheimer's disease rats model.

PubMed

Yang, Bing-You; Tan, Jin-Yan; Liu, Yan; Liu, Bo; Jin, Shuang; Guo, Hong-Wei; Kuang, Hai-Xue

2018-02-01

A UPLC-TOF/MS-based metabolomics method was established to explore the therapeutic mechanisms of rattan stems of S. chinensis (SCS) in Alzheimer's disease (AD). Experimental AD model was induced by intra-hippocampal Aβ 1-42 injection in rats. Cognitive function and oxidative stress condition in brain of AD rats were assessed using Morris water maze tests and antioxidant assays [malondialdehyde (MDA), superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px)], respectively. UPLC-TOF/MS combined with multivariate statistical analysis were conducted to study the changes in metabolic networks in serum of rats. The results indicated that the AD model was established successfully and the inducement of Aβ 1-42 caused a decline in spatial learning and memory of rats. The injection of Aβ 1-42 in rat brains significantly elevated the level of MDA, and reduced SOD and GSH-Px activities. In addition, SCS showed significant anti-AD effects on model rats. A total of 30 metabolites were finally identified as potential biomarkers of AD and 14 of them had a significant recovery compared with the AD model after SCS administration. Changes in AD metabolite profiling were restored to different levels through the regulation of 13 pathways. This is first report on the use of the UPLC-TOF/MS-based serum metabolomics method to investigate therapeutic effects of SCS on AD, and enrich potential biomarkers and metabolic networks of AD. Copyright © 2017 John Wiley & Sons, Ltd.

Identification and susceptibility testing of microorganism by direct inoculation from positive blood culture bottles by combining MALDI-TOF and Vitek-2 Compact is rapid and effective.

PubMed

Romero-Gómez, María-Pilar; Gómez-Gil, Rosa; Paño-Pardo, Jose Ramón; Mingorance, Jesús

2012-12-01

The objective of this study was to evaluate the reliability and accuracy of the combined use of MALDI-TOF MS bacterial identification and the Vitek-2 Compact antimicrobial susceptibility testing (AST) directly from positive blood cultures. Direct identification by MALDI-TOF MS and AST were performed in parallel to the standard methods in all positively flagged blood cultures bottles during the study period. Three hundred and twenty four monomicrobial positive blood cultures were included in the present study, with 257 Gram-negative and 67 Gram-positive isolates. MALDI-TOF MS identification directly from blood bottles reported the correct identification for Enterobacteriaceae in 97.7%, non-fermentative Gram-negative bacilli 75.0%, Staphylococcus aureus 75.8%, coagulase negative staphylococci 63.3% and enterococci 63.3%. A total 6156 isolate/antimicrobial agent combinations were tested. Enterobacteriaceae group and non-fermentative Gram-negative Bacilli showed an agreement of 96.67% and 92.30%, respectively, for the Gram-positive cocci the overall agreement found was 97.84%. We conclude that direct identification by MALDI-TOF and inoculation of Vitek-2 Compact AST with positive blood culture bottles yielded very good results and decreased time between initial inoculation of blood culture media and determination of the antibiotic susceptibility for Gram-negative rods and Gram-positive cocci causing bacteremia. Copyright © 2012 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

Comparative evaluation of the identification of rapidly growing non-tuberculous mycobacteria by mass spectrometry (MALDI-TOF MS), GenoType Mycobacterium CM/AS assay and partial sequencing of the rpoβ gene with phylogenetic analysis as a reference method.

PubMed

Costa-Alcalde, José Javier; Barbeito-Castiñeiras, Gema; González-Alba, José María; Aguilera, Antonio; Galán, Juan Carlos; Pérez-Del-Molino, María Luisa

2018-06-02

The American Thoracic Society and the Infectious Diseases Society of America recommend that clinically significant non-tuberculous mycobacteria (NTM) should be identified to the species level in order to determine their clinical significance. The aim of this study was to evaluate identification of rapidly growing NTM (RGM) isolated from clinical samples by using MALDI-TOF MS and a commercial molecular system. The results were compared with identification using a reference method. We included 46 clinical isolates of RGM and identified them using the commercial molecular system GenoType ® CM/AS (Hain, Lifescience, Germany), MALDI-TOF MS (Bruker) and, as reference method, partial rpoβ gene sequencing followed by BLAST and phylogenetic analysis with the 1093 sequences available in the GeneBank. The degree of agreement between GenoType ® and MALDI-TOF MS and the reference method, partial rpoβ sequencing, was 27/43 (62.8%) and 38/43 cases (88.3%) respectively. For all the samples correctly classified by GenoType ® , we obtained the same result with MALDI-TOF MS (27/27). However, MALDI-TOF MS also correctly identified 68.75% (11/16) of the samples that GenoType ® had misclassified (p=0.005). MALDI-TOF MS classified significantly better than GenoType ® . When a MALDI-TOF MS score >1.85 was achieved, MALDI-TOF MS and partial rpoβ gene sequencing were equivalent. GenoType ® was not able to distinguish between species belonging to the M. fortuitum complex. MALDI-TOF MS methodology is simple, rapid and associated with lower consumable costs than GenoType ® . The partial rpoβ sequencing methods with BLAST and phylogenetic analysis were not able to identify some RGM unequivocally. Therefore, sequencing of additional regions would be indicated in these cases. Copyright © 2018 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Usefulness and accuracy of MALDI-TOF mass spectrometry as a supplementary tool to identify mosquito vector species and to invest in development of international database.

PubMed

Raharimalala, F N; Andrianinarivomanana, T M; Rakotondrasoa, A; Collard, J M; Boyer, S

2017-09-01

Arthropod-borne diseases are important causes of morbidity and mortality. The identification of vector species relies mainly on morphological features and/or molecular biology tools. The first method requires specific technical skills and may result in misidentifications, and the second method is time-consuming and expensive. The aim of the present study is to assess the usefulness and accuracy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as a supplementary tool with which to identify mosquito vector species and to invest in the creation of an international database. A total of 89 specimens belonging to 10 mosquito species were selected for the extraction of proteins from legs and for the establishment of a reference database. A blind test with 123 mosquitoes was performed to validate the MS method. Results showed that: (a) the spectra obtained in the study with a given species differed from the spectra of the same species collected in another country, which highlights the need for an international database; (b) MALDI-TOF MS is an accurate method for the rapid identification of mosquito species that are referenced in a database; (c) MALDI-TOF MS allows the separation of groups or complex species, and (d) laboratory specimens undergo a loss of proteins compared with those isolated in the field. In conclusion, MALDI-TOF MS is a useful supplementary tool for mosquito identification and can help inform vector control. © 2017 The Royal Entomological Society.

Evaluation of repetitive-PCR and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for rapid strain typing of Bacillus coagulans

PubMed Central

Nakayama, Motokazu; Tomita, Ayumi; Sonoda, Takumi; Hasumi, Motomitsu; Miyamoto, Takahisa

2017-01-01

In order to establish rapid and accurate typing method for Bacillus coagulans strains which is important for controlling in some canned foods and tea-based beverages manufacturing because of the high-heat resistance of the spores and high tolerance of the vegetative cells to catechins and chemicals, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and repetitive-PCR (rep-PCR) were evaluated. For this purpose, 28 strains of B. coagulans obtained from various culture collections were tested. DNA sequence analyses of the genes encoding 16S rRNA and DNA gyrase classified the test strains into two and three groups, respectively, regardless of their phenotypes. Both MALDI-TOF MS and rep-PCR methods classified the test strains in great detail. Strains classified in each group showed similar phenotypes, such as carbohydrate utilization determined using API 50CH. In particular, the respective two pairs of strains which showed the same metabolic characteristic were classified into the same group by both MALDI-TOF MS and rep-PCR methods separating from the other strains. On the other hand, the other strains which have the different profiles of carbohydrate utilization were separated into different groups by these methods. These results suggested that the combination of MALDI-TOF MS and rep-PCR analyses was advantageous for the rapid and detailed typing of bacterial strains in respect to both phenotype and genotype. PMID:29020109

Development and validation of TOF-SIMS and CLSM imaging method for cytotoxicity study of ZnO nanoparticles in HaCaT cells.

PubMed

Lee, Pei-Ling; Chen, Bo-Chia; Gollavelli, Ganesh; Shen, Sin-Yu; Yin, Yu-Sheng; Lei, Shiu-Ling; Jhang, Cian-Ling; Lee, Woan-Ruoh; Ling, Yong-Chien

2014-07-30

Zinc oxide nanoparticles (ZnO NPs) exhibit novel physiochemical properties and have found increasing use in sunscreen products and cosmetics. The potential toxicity is of increasing concern due to their close association with human skin. A time-of-flight secondary ion mass spectrometry (TOF-SIMS) and confocal laser scanning microscopy (CLSM) imaging method was developed and validated for rapid and sensitive cytotoxicity study of ZnO NPs using human skin equivalent HaCaT cells as a model system. Assorted material, chemical, and toxicological analysis methods were used to confirm their shape, size, crystalline structure, and aggregation properties as well as dissolution behavior and effect on HaCaT cell viability in the presence of various concentrations of ZnO NPs in aqueous media. Comparative and correlative analyses of aforementioned results with TOF-SIMS and CLSM imaging results exhibit reasonable and acceptable outcome. A marked drop in survival rate was observed with 50μg/ml ZnO NPs. The CLSM images reveal the absorption and localization of ZnO NPs in cytoplasm and nuclei. The TOF-SIMS images demonstrate elevated levels of intracellular ZnO concentration and associated Zn concentration-dependent (40)Ca/(39)K ratio, presumably caused by the dissolution behavior of ZnO NPs. Additional validation by using stable isotope-labeled (68)ZnO NPs as tracers under the same experimental conditions yields similar cytotoxicity effect. The imaging results demonstrate spatially-resolved cytotoxicity relationship between intracellular ZnO NPs, (40)Ca/(39)K ratio, phosphocholine fragments, and glutathione fragments. The trend of change in TOF-SIMS spectra and images of ZnO NPs treated HaCaT cells demonstrate the possible mode of actions by ZnO NP involves cell membrane disruption, cytotoxic response, and ROS mediated apoptosis. Copyright © 2014 Elsevier B.V. All rights reserved.

Optimized MLAA for quantitative non-TOF PET/MR of the brain

NASA Astrophysics Data System (ADS)

Benoit, Didier; Ladefoged, Claes N.; Rezaei, Ahmadreza; Keller, Sune H.; Andersen, Flemming L.; Højgaard, Liselotte; Hansen, Adam E.; Holm, Søren; Nuyts, Johan

2016-12-01

For quantitative tracer distribution in positron emission tomography, attenuation correction is essential. In a hybrid PET/CT system the CT images serve as a basis for generation of the attenuation map, but in PET/MR, the MR images do not have a similarly simple relationship with the attenuation map. Hence attenuation correction in PET/MR systems is more challenging. Typically either of two MR sequences are used: the Dixon or the ultra-short time echo (UTE) techniques. However these sequences have some well-known limitations. In this study, a reconstruction technique based on a modified and optimized non-TOF MLAA is proposed for PET/MR brain imaging. The idea is to tune the parameters of the MLTR applying some information from an attenuation image computed from the UTE sequences and a T1w MR image. In this MLTR algorithm, an {αj} parameter is introduced and optimized in order to drive the algorithm to a final attenuation map most consistent with the emission data. Because the non-TOF MLAA is used, a technique to reduce the cross-talk effect is proposed. In this study, the proposed algorithm is compared to the common reconstruction methods such as OSEM using a CT attenuation map, considered as the reference, and OSEM using the Dixon and UTE attenuation maps. To show the robustness and the reproducibility of the proposed algorithm, a set of 204 [18F]FDG patients, 35 [11C]PiB patients and 1 [18F]FET patient are used. The results show that by choosing an optimized value of {αj} in MLTR, the proposed algorithm improves the results compared to the standard MR-based attenuation correction methods (i.e. OSEM using the Dixon or the UTE attenuation maps), and the cross-talk and the scale problem are limited.

Elemental, Isotopic, and Organic Analysis on Mars with Laser TOF-MS

NASA Technical Reports Server (NTRS)

Brinckerhoff, W. B.; Cornish, T. J.

2000-01-01

The in-depth landed exploration of Mars will require increasingly sophisticated robotic analytical tools for both in situ composition science [1] and reconnaissance for sample return [2]. Beyond dust, rock surfaces, and topsoil, samples must be accessed within rocks and ice, well below surface soil, and possibly in elevated deposit layers. A range of spatial scales will be studied, and for the most information-rich microscopic analyses, samples must be acquired, prepared, and positioned with high precision. In some cases samples must also be brought into a vacuum chamber. After expending such resources, it will be important to apply techniques that provide a wide range of information about the samples. Microscopy, mineralogy, and molecular/organic, elemental, and isotopic analyses are all needed, at a minimum, to begin to address the in situ goals at Mars. These techniques must work as an efficient suite to provide layers of data, each layer helping to determine if further analysis on a given sample is desired. In the spirit of broad-band and efficient data collection, we are developing miniature laser time-of-flight mass spectrometers (TOF-MS) for elemental, isotopic, and molecular/organic microanalysis of unprepared solid samples. Laser TOF-MS uses a pulsed laser to volatilize and ionize material from a small region on the sample. The laser energy and focus can be adjusted for atomic and molecular content, sampling area, and depth. Ions travel through the instrument and are detected at a sequence of times proportional to the square root of their mass-to- charge ratios. Thus, each laser pulse produces a complete mass spectrum (in less than 50 microseconds). These instruments can now be significantly miniaturized (potentially to the size of a soda can) without a loss in performance. This effort is reviewed here with an emphasis on applications to Mars exploration.

Shiga Toxin 2 Subtypes of Enterohemorrhagic E. coli O157:H- E32511 Analyzed by RT-qPCR and Top-Down Proteomics Using MALDI-TOF-TOF-MS

NASA Astrophysics Data System (ADS)

Fagerquist, Clifton K.; Zaragoza, William J.

2015-05-01

We have measured the relative abundance of the B-subunits and mRNA transcripts of two Stx2 subtypes present in Shiga toxin-producing Escherichia coli (STEC) O157:H- strain E32511 using matrix-assisted laser desorption/ionization time-of-flight-time-of-flight tandem mass spectrometry (MALDI-TOF-TOF-MS/MS) with post source decay (PSD) and real time-quantitative polymerase chain reaction (RT-qPCR). Stx2a and Stx2c in STEC strain E32511 were quantified from the integrated peak area of their singly charged disulfide-intact B-subunit ions at m/z ~7819 and m/z ~7774, respectively. We found that the Stx2a subtype was 21-fold more abundant than the Stx2c subtype. The two amino acid substitutions (16D ↔ 16 N and 24D ↔ 24A) that distinguish Stx2a from Stx2c not only result in a mass difference of 45 Da between their respective B-subunits but also result in distinctly different fragmentation channels by MS/MS-PSD because both substitutions involve an aspartic acid (D) residue. Importantly, these two substitutions have also been linked to differences in subtype toxicity. We measured the relative abundances of mRNA transcripts using RT-qPCR and determined that the stx2a transcript is 13-fold more abundant than stx2c transcript. In silico secondary structure analysis of the full mRNA operons of stx2a and stx2c suggest that transcript structural differences may also contribute to a relative increase of Stx2a over Stx2c. In consequence, toxin expression may be under both transcriptional and post-transcriptional control.

The applied research of MRI with ASSET-EPI-FLAIR combined with 3D TOF MRA sequences in the assessment of patients with acute cerebral infarction.

PubMed

Lin, Zhichao; Guo, Zexiong; Qiu, Lin; Yang, Wanyoug; Lin, Mingxia

2016-12-01

Background To extend the time window for thrombolysis, reducing the time for diagnosis and detection of acute cerebral infarction seems to be warranted. Purpose To evaluate the feasibility of implementing an array spatial sensitivity technique (ASSET)-echo-planar imaging (EPI)-fluid attenuated inversion recovery (FLAIR) (AE-FLAIR) sequence into an acute cerebral infarction magnetic resonance (MR) evaluation protocol, and to assess the diagnostic value of AE-FLAIR combined with three-dimensional time-of-flight MR angiography (3D TOF MRA). Material and Methods A total of 100 patients (68 men, 32 women; age range, 44-82 years) with acute cerebral infarction, including 50 consecutive uncooperative and 50 cooperative patients, were evaluated with T1-weighted (T1W) imaging, T2-weighted (T2W) imaging, FLAIR, diffusion-weighted imaging (DWI), 3D TOF, EPI-FLAIR, and AE-FLAIR. Conventional FLAIR, EPI-FLAIR, and AE-FLAIR were assessed by two observers independently for image quality. The optimized group (AE-FLAIR and 3D TOF) and the control group (T1W imaging, T2W imaging, conventional FLAIR, DWI, and 3D TOF) were compared for evaluation time and diagnostic accuracy. Results One hundred and twenty-five lesions were detected and images having adequate diagnostic image quality were in 73% of conventional FLAIR, 62% of EPI-FLAIR, and 89% of AE-FLAIR. The detection time was 12 ± 1 min with 76% accuracy and 4 ± 0.5 min with 100% accuracy in the control and the optimized groups, respectively. Inter-observer agreements of κ = 0.78 and κ = 0.81 were for the optimized group and control group, respectively. Conclusion With reduced acquisition time and better image quality, AE-FLAIR combined with 3D TOF may be used as a rapid diagnosis tool in patients with acute cerebral infarction, especially in uncooperative patients.

Discovery of human urinary biomarkers of aronia-citrus juice intake by HPLC-q-TOF-based metabolomic approach.

PubMed

Llorach, Rafael; Medina, Sonia; García-Viguera, Cristina; Zafrilla, Pilar; Abellán, José; Jauregui, Olga; Tomás-Barberán, Francisco A; Gil-Izquierdo, Angel; Andrés-Lacueva, Cristina

2014-06-01

Metabolomics has emerged in the field of food and nutrition sciences as a powerful tool for doing profiling approaches. In this context, HPLC-q-TOF-based metabolomics approach was applied to unveil changes in the urinary metabolome in human subjects (n = 51, 23 men and 28 women) after regular aronia-citrus juice (AC-juice) intake (250 mL/day) during 16 weeks compared to individuals given a placebo beverage. Samples were analyzed by HPLC-q-TOF followed by multivariate data analysis (orthogonal signal filtering-partial least square discriminant analysis) that discriminated relevant mass features related to AC-juice intake. The results showed that biomarkers of AC-juice intake including metabolites coming from metabolism of food components as proline betaine, ferulic acid, and two unknown mercapturate derivatives were identified. Discovery of new biomarkers of food intake will help in the building up of the food metabolome and facilitate future insights into the mechanisms of action of dietary components in population health. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Investigation of anodic TiO2 nanotube composition with high spatial resolution AES and ToF SIMS

NASA Astrophysics Data System (ADS)

Dronov, Alexey; Gavrilin, Ilya; Kirilenko, Elena; Dronova, Daria; Gavrilov, Sergey

2018-03-01

High resolution Scanning Auger Electron Spectroscopy (AES) and Time-of-Flight Secondary Ion Mass-Spectrometry (ToF SIMS) were used to investigate structure and elemental composition variation of both across an array of TiO2 nanotubes (NTs) and single tube of an array. The TiO2 NT array was grown by anodic oxidation of Ti foil in fluorine-containing ethylene glycol electrolyte. It was found that the studied anodic TiO2 nanotubes have a layered structure with rather sharp interfaces. The differences in AES depth profiling results of a single tube with the focused primary electron beam (point analysis) and over an area of 75 μm in diameter of a nanotube array with the defocused primary electron beam are discussed. Depth profiling by ToF SIMS was carried out over approximately the same size of a nanotube array to determine possible ionic fragments in the structure. The analysis results show that the combination of both mentioned methods is useful for a detailed analysis of nanostructures with complex morphology and multi-layered nature.

Characterization of nucleosides and nucleobases in natural Cordyceps by HILIC-ESI/TOF/MS and HILIC-ESI/MS.

PubMed

Zhao, Heng-Qiang; Wang, Xiao; Li, Hong-Mei; Yang, Bin; Yang, Hong-Jun; Huang, Luqi

2013-08-15

A method combining hydrophilic interaction chromatography (HILIC) and electrospray ionization mass spectrometry (ESI-MS) was developed for the characterization and determination of natural Cordyceps. Separation was achieved on a Waters Xbridge Amide column with gradient elution. Identification of 15 target nucleosides and nucleobases was based on retention time, UV spectra and mass measurements of the protonated molecules ([M+H]⁺) and main fragment ions (ESI-TOF/MS). Eight non-target compounds were tentatively identified by ESI-TOF/MS. The 15 target compounds were quantified by HILIC-ESI-MS/MS using time-programmed selective ion monitoring or multiple reaction monitoring in positive-ion mode under optimized mass conditions. This technique showed good linearity, repeatability and recovery. This approach was also successfully implemented in the analysis of nucleosides and nucleobases in 12 batches of natural Cordyceps samples that were collected from different regions in China. The developed HILIC-ESI-MS method exhibited clear advantages in identifying and determining highly polar bioactive components in Cordyceps, as well as their quality control.

Development and characterization of a rapid polymerizing collagen for soft tissue augmentation

PubMed Central

Devore, Dale; Zhu, Jiaxun; Brooks, Robert; McCrate, Rebecca Rone; Grant, David A.

2015-01-01

Abstract A liquid collagen has been developed that fibrilizes upon injection. Rapid polymerizing collagen (RPC) is a type I porcine collagen that undergoes fibrillization upon interaction with ionic solutions, such as physiological solutions. The ability to inject liquid collagen would be beneficial for many soft tissue augmentation applications. In this study, RPC was synthesized and characterized as a possible dermal filler. Transmission electron microscopy, ion induced RPC fibrillogenesis tests, collagenase resistance assay, and injection force studies were performed to assess RPC's physicochemical properties. An in vivo study was performed which consisted of a 1‐, 3‐, and 6‐month study where RPC was injected into the ears of miniature swine. The results demonstrated that the liquid RPC requires low injection force (<7 N); fibrillogenesis and banding of collagen occurs when RPC is injected into ionic solutions, and RPC has enhanced resistance to collagenase breakdown. The in vivo study demonstrated long‐term biocompatibility with low irritation scores. In conclusion RPC possesses many of the desirable properties of a soft tissue augmentation material. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 758–767, 2016. PMID:26488368

A tail like no other. The RPC-MAG view of Rosetta's tail excursion at comet 67P/Churyumov-Gerasimenko

NASA Astrophysics Data System (ADS)

Volwerk, Martin; Goetz, Charlotte; Richter, Ingo; Delva, Magda; Ostaszewski, Katharina; Schwingenschuh, Konrad; Glassmeier, Karl-Heinz

2018-06-01

Context. The Rosetta Plasma Consortium (RPC) magnetometer (MAG) data during the tail excursion in March-April 2016 are used to investigate the magnetic structure of and activity in the tail region of the weakly outgassing comet 67P/Churyumov-Gerasimenko (67P). Aims: The goal of this study is to compare the large scale (near) tail structure with that of earlier missions to strong outgassing comets, and the small scale turbulent energy cascade (un)related to the singing comet phenomenon. Methods: The usual methods of space plasma physics are used to analyse the magnetometer data, such as minimum variance analysis, spectral analysis, and power law fitting. Also the cone angle and clock angle of the magnetic field are calculated to interpret the data. Results: It is found that comet 67P does not have a classical draped magnetic field and no bi-lobal tail structure at this late stage of the mission when the comet is already at 2.7 AU distance from the Sun. The main magnetic field direction seems to be more across the tail direction, which may implicate an asymmetric pick-up cloud. During periods of singing comet activity the propagation direction of the waves is at large angles with respect to the magnetic field and to the radial direction towards the comet. Turbulent cascade of magnetic energy from large to small scales is different in the presence of singing as without it.

Rapid identification of moulds and arthroconidial yeasts from positive blood cultures by MALDI-TOF mass spectrometry.

PubMed

de Almeida, João N; Sztajnbok, Jaques; da Silva, Afonso Rafael; Vieira, Vinicius Adriano; Galastri, Anne Layze; Bissoli, Leandro; Litvinov, Nadia; Del Negro, Gilda Maria Barbaro; Motta, Adriana Lopes; Rossi, Flávia; Benard, Gil

2016-11-01

Moulds and arthroconidial yeasts are potential life-threatening agents of fungemia in immunocompromised patients. Fast and accurate identification (ID) of these pathogens hastens initiation of targeted antifungal therapy, thereby improving the patients' prognosis. We describe a new strategy that enabled the identification of moulds and arthroconidial yeasts directly from positive blood cultures by MALDI-TOF mass spectrometry (MS). Positive blood cultures (BCs) with Gram staining showing hyphae and/or arthroconidia were prospectively selected and submitted to an in-house protein extraction protocol. Mass spectra were obtained by Vitek MS™ system, and identifications were carried out with in the research use only (RUO) mode with an extended database (SARAMIS™ [v.4.12] plus in-house database). Fusarium solani, Fusarium verticillioides, Exophiala dermatitidis, Saprochaete clavata, and Trichosporon asahii had correct species ID by MALDI-TOF MS analysis of positive BCs. All cases were related to critically ill patients with high mortality fungemia and direct ID from positive BCs was helpful for rapid administration of targeted antifungal therapy. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Two tumor models of curative adoptive chemoimmunotherapy using tumor-infiltrated spleen cells with potent antitumor cytotoxicity stimulated by antigen-sharing tumors.

PubMed

Laude, M; Russo, K L; Mokyr, M B; Dray, S

1993-07-01

Previously we have established curative protocols for adoptive chemoimmunotherapy (ACIT) of mice bearing different plasmacytomas that are known to bear cross-reacting antigens: (a) the cure of mice bearing an early-stage, nonpalpable MOPC-315 tumor by a very low dose of cyclophosphamide (10 mg/kg) and cultured MOPC-315-tumor-infiltrated (TI) spleen cells (25 x 10(6)) and (b) the cure of mice bearing a late-stage, relatively drug-resistant, highly metastatic RPC-5 tumor with cyclophosphamide (100 mg/kg) and cultured RPC-5 TI spleen cells (25 x 10(6) - 50 x 10(6)). In both models, the spleen cells were obtained from mice bearing a late-stage tumor and were cultured for 5 days in the presence of polyethyleneglycol 6000 and autochthonous tumor cells as a source of tumor antigen. Here we show that RPC-5 tumor cells could substitute for MOPC-315 tumor cells in the 5-day culture of MOPC-315 TI spleen cells so that they became curative in ACIT for mice bearing an early-stage MOPC-315 tumor. Similarly, MOPC-315 tumor cells could substitute for RPC-5 tumor cells in the 5-day culture of RPC-5 TI spleen cells so that they became curative in ACIT of mice bearing a late-stage RPC-5 tumor. In addition, RPC-5 TI spleen cells cultured with either MOPC-315 or RPC-5 tumor cells were effective in curing all mice bearing an early-stage MOPC-315 tumor by ACIT. However, MOPC-315 TI spleen cells whether cultured with MOPC-315 or RPC-5 tumor cells, were much less effective than cultured RPC-5 TI spleen cells in curing mice bearing a late-stage RPC-5 tumor by ACIT (although the survival of these mice was extended significantly). Interestingly, whereas RPC-5 TI spleen cells cultured with either MOPC-315 or RPC-5 tumor cells were as effective as MOPC-315 TI spleen cells cultured under the same conditions in lysing MOPC-315 tumor cells in vitro, MOPC-315 TI spleen cells that had been cultured with either MOPC-315 or RPC-5 tumor cells exerted a much weaker in vitro cytotoxic T lymphocyte

Phenolic antioxidants (hydrolyzable tannins, flavonols, and anthocyanins) identified by LC-ESI-MS and MALDI-QIT-TOF MS from Rosa chinensis flowers.

PubMed

Cai, Yi-Zhong; Xing, Jie; Sun, Mei; Zhan, Zhao-Qi; Corke, Harold

2005-12-28

Rosa chinensis (Yuejihua) is a well-known ornamental plant, and its flowers are commonly used in traditional Chinese medicine. Methanolic crude extracts of dried R. chinensis flowers were used for simultaneous determination of phenolic constituents by liquid chromatography-mass spectrometry (LC-MS) and matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry (MALDI-QIT-TOF MS). A total of 36 known and unknown phenolics were identified as hydrolyzable tannins, flavonols, and anthocyanins, mainly including gallotannins (mono-, di-, or trigalloylglucopyranosides), ellagitannins, quercetin, quercetin/kaempferol mono- and diglycosides, and cyanidin/pelargonidin diglycosides. MALDI-QIT-TOF MS was applied not only to verify most phenolics isolated and identified by LC-MS but also to tentatively identify two ellagitannins (rugosins B and C) not isolated and unidentified by LC-MS. This study is the first to demonstrate the rapid and successful use of MALDI-QIT-TOF MS and LC-MS to directly and simultaneously identify phenolics in the crude extracts of R. chinensis flowers without any purification. The antioxidant activity of the crude extracts from R. chinensis flowers was also measured with three assay methods. The results showed that the phenolic antioxidants from R. chinensis flowers exhibited very strong radical scavenging effect and antioxidant power. High levels of flavonols and hydrolyzable tannins might be important bioactive principles in the dried R. chinensis flowers.

Systematic and comprehensive strategy for metabolite profiling in bioanalysis using software-assisted HPLC-Q-TOF: magnoflorine as an example.

PubMed

Tian, Xiaoting; Zhang, Yucheng; Li, Zhixiong; Hu, Pei; Chen, Mingcang; Sun, Zhaolin; Lin, Yunfei; Pan, Guoyu; Huang, Chenggang

2016-03-01

Metabolite profiling plays a crucial role in drug discovery and development, and HPLC-Q-TOF has evolved into a powerful and effective high-resolution analytical tool for metabolite detection. However, traditional empirical identification is laborious and incomplete. This paper presents a systematic and comprehensive strategy for elucidating metabolite structures using software-assisted HPLC-Q-TOF that takes full advantage of data acquisition, data processing, and data mining technologies, especially for high-throughput metabolite screening. This strategy has been successfully applied in the study of magnoflorine metabolism based on our previous report of its poor bioavailability and drug-drug interactions. In this report, 23 metabolites of magnoflorine were tentatively identified with detailed fragmentation pathways in rat biological samples (urine, feces, plasma, and various organs) after i.p. or i.g. administration, and for most of these metabolites, the metabolic sites were determined. The phase I biotransformations of magnoflorine (M1-M7, M10-M14) consist of demethylation, dehydrogenation, hydroxylation, methylene to ketone transformation, N-ring opening, and dehydroxylation. The phase II biotransformations (M8, M9, and M15-M23) consist of methylation, acetylation, glucuronidation, and N-acetylcysteine conjugation. The results indicate that the extensive metabolism and wide tissue distribution of magnoflorine and its metabolites may partly contribute to its poor bioavailability and drug-drug interaction, and i.p. administration should thus be a suitable approach for isolating magnoflorine metabolites. In summary, this strategy could provide an efficient, rapid, and reliable method for the structural characterization of drug metabolites and may be applicable for general Q-TOF users.

HPLC, NMR and MALDI-TOF MS analysis of condensed tannins from Lithocarpus glaber leaves with potent free radical scavenging activity.

PubMed

Zhang, Liang Liang; Lin, Yi Ming

2008-12-04

Using acid-catalyzed degradation in the presence of cysteamine, the condensed tannins from Lithocarpus glaber leaves were characterized, following thiolysis, by means of reversed-phase HPLC, 13C-NMR and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) analyses. The thiolysis reaction products showed the presence of the procyanidin (PC) and prodelphinidin (PD) structures. The 13C-NMR spectrum revealed that the condensed tannins were comprised of PD (72.4%) and PC (27.6%), and with a greater content of cis configuration rather than the trans configuration of C2-C3. The MALDI-TOF MS analysis proved the presence of PD units, and the maximum degree of polymerization (DP) was an undecamer. The antioxidant activity of condensed tannins from L. glaber leaves was evaluated by using a free radical scavenging activity assay.

Eddy covariance VOC emission and deposition fluxes above grassland using PTR-TOF

NASA Astrophysics Data System (ADS)

Ruuskanen, T. M.; Müller, M.; Schnitzhofer, R.; Karl, T.; Graus, M.; Bamberger, I.; Hörtnagl, L.; Brilli, F.; Wohlfahrt, G.; Hansel, A.

2011-01-01

Eddy covariance (EC) is the preferable technique for flux measurements since it is the only direct flux determination method. It requires a continuum of high time resolution measurements (e.g. 5-20 Hz). For volatile organic compounds (VOC) soft ionization via proton transfer reaction has proven to be a quantitative method for real time mass spectrometry; here we use a proton transfer reaction time of flight mass spectrometer (PTR-TOF) for 10 Hz EC measurements of full mass spectra up to m/z 315. The mass resolution of the PTR-TOF enabled the identification of chemical formulas and separation of oxygenated and hydrocarbon species exhibiting the same nominal mass. We determined 481 ion mass peaks from ambient air concentration above a managed, temperate mountain grassland in Neustift, Stubai Valley, Austria. During harvesting we found significant fluxes of 18 compounds distributed over 43 ions, including protonated parent compounds, as well as their isotopes and fragments and VOC-H+ - water clusters. The dominant BVOC fluxes were methanol, acetaldehyde, ethanol, hexenal and other C6 leaf wound compounds, acetone, acetic acid, monoterpenes and sequiterpenes. The smallest reliable fluxes we determined were less than 0.1 nmol m-2 s-1, as in the case of sesquiterpene emissions from freshly cut grass. Terpenoids, including mono- and sesquiterpenes, were also deposited to the grassland before and after the harvesting. During cutting, total VOC emission fluxes up to 200 nmolC m-2 s-1 were measured. Methanol emissions accounted for half of the emissions of oxygenated VOCs and a third of the carbon of all measured VOC emissions during harvesting.

VOC Emission and Deposition Eddy Covariance Fluxes above Grassland using PTR-TOF

NASA Astrophysics Data System (ADS)

Ruuskanen, T. M.; Müller, M.; Schnitzhofer, R.; Karl, T.; Graus, M.; Bamberger, I.; Hörtnagl, L.; Brilli, F.; Wohlfahrt, G.; Hansel, A.

2010-12-01

Eddy covariance (EC) is the preferable technique for flux measurements since it is the only direct flux determination method. It requires a continuum of high time resolution measurements (e.g. 5-20 Hz). For volatile organic compounds (VOC) soft ionization via proton transfer reaction has proven to be a quantitative method for real time mass spectrometry; here we use a proton transfer reaction time of flight mass spectrometer (PTR-TOF) for 10 Hz EC measurements of full mass spectra up to m/z 315. The mass resolution of the PTR-TOF enabled the identification of chemical formulas and separation of oxygenated and hydrocarbon species exhibiting the same nominal mass. We determined 481 ion mass peaks from ambient air concentration above a managed, temperate mountain grassland in Neustift, Stubai Valley, Austria. During harvesting we found significant fluxes of 18 compounds distributed over 43 ions, including protonated parent compounds, as well as their isotopes and fragments and VOC-H+ - water clusters. The dominant BVOC fluxes were methanol, acetaldehyde, ethanol, hexenal and other C6 leaf wound compounds, acetone, acetic acid, monoterpenes and sequiterpenes. The smallest reliable fluxes we determined were less than 0.1 nmol m-2 s-1, as in the case of sesquiterpene emissions from freshly cut grass. Terpenoids, including mono- and sesquiterpenes, were also deposited to the grassland before and after the harvesting. During cutting, total VOC emission fluxes up to 200 nmolC m-2 s-1 were measured. Methanol emissions accounted for half of the emissions of oxygenated VOCs and a third of the carbon of all measured VOC emissions during harvesting.

Eddy covariance VOC emission and deposition fluxes above grassland using PTR-TOF

NASA Astrophysics Data System (ADS)

Ruuskanen, T. M.; Müller, M.; Schnitzhofer, R.; Karl, T.; Graus, M.; Bamberger, I.; Hörtnagl, L.; Brilli, F.; Wohlfahrt, G.; Hansel, A.

2010-09-01

Eddy covariance (EC) is the preferable technique for flux measurements since it is the only direct flux determination method. It requires a continuum of high time resolution measurements (e.g. 5-20 Hz). For volatile organic compounds (VOC) soft ionization via proton transfer reaction has proven to be a quantitative method for real time mass spectrometry; here we use a proton transfer reaction time of flight mass spectrometer (PTR-TOF) for 10 Hz EC measurements of full mass spectra up to m/z 315. The mass resolution of the PTR-TOF enabled the identification of chemical formulas and separation of oxygenated and hydrocarbon species exhibiting the same nominal mass. We determined 481 ion mass peaks from ambient air concentration above a managed, temperate mountain grassland in Neustift, Stubai Valley, Austria. During harvesting we found significant fluxes of 18 compounds distributed over 43 ions, including protonated parent compounds, as well as their isotopes and fragments and VOC-H+-water clusters. The dominant BVOC fluxes were methanol, acetaldehyde, ethanol, hexenal and other C6 leaf wound compounds, acetone, acetic acid, monoterpenes and sequiterpenes. The smallest reliable fluxes we determined were less than 0.1 nmol m-2 s-1, as in the case of sesquiterpene emissions from freshly cut grass. Terpenoids, including mono- and sesquiterpenes, were also deposited to the grassland before and after the harvesting. During cutting, total VOC emission fluxes up to 200 nmol C m-2 s-1 were measured. Methanol emissions accounted for half of the emissions of oxygenated VOCs and a third of the carbon of all measured VOC emissions during harvesting.

Mapping hard magnetic recording disks by TOF-SIMS

NASA Astrophysics Data System (ADS)

Spool, A.; Forrest, J.

2008-12-01

Mapping of hard magnetic recording disks by TOF-SIMS was performed both to produce significant analytical results for the understanding of the disk surface and the head disk interface in hard disk drives, and as an example of a macroscopic non-rectangular mapping problem for the technique. In this study, maps were obtained by taking discrete samples of the disk surface at set intervals in R and Θ. Because both in manufacturing, and in the disk drive, processes that may affect the disk surface are typically circumferential in nature, changes in the surface are likely to be blurred in the Θ direction. An algorithm was developed to determine the optimum relative sampling ratio in R and Θ. The results confirm what the experience of the analysts suggested, that changes occur more rapidly on disks in the radial direction, and that more sampling in the radial direction is desired. The subsequent use of statistical methods principle component analysis (PCA), maximum auto-correlation factors (MAF), and the algorithm inverse distance weighting (IDW) are explored.

Characterization of bioactive compounds of Annona cherimola L. leaves using a combined approach based on HPLC-ESI-TOF-MS and NMR.

PubMed

Díaz-de-Cerio, Elixabet; Aguilera-Saez, Luis Manuel; Gómez-Caravaca, Ana María; Verardo, Vito; Fernández-Gutiérrez, Alberto; Fernández, Ignacio; Arráez-Román, David

2018-06-01

Annona cherimola Mill. (cherimoya) has widely been used as food crop. The leaves of this tree possess several health benefits, which are, in general, attributed mainly to its bioactive composition. However, literature concerning a comprehensive characterization based on a combined approach, which consists of nuclear magnetic resonance (NMR) and high-performance liquid chromatography coupled with time-of-flight mass spectrometry (HPLC-TOF-MS), from these leaves is scarce. Thus, the aim of this work was to study the polar profile of full extracts of cherimoya leaves by using these tools. Thus, a total of 77 compounds have been characterized, 12 of which were identified by both techniques. Briefly, 23 compounds were classified as amino acids, organic acids, carbohydrates, cholines, phenolic acid derivatives, and flavonoids by NMR, while 66 metabolites were divided into sugars, amino acids, phenolic acids and derivatives, flavonoids, phenylpropanoids, and other polar compounds by HPLC-TOF-MS. It is worth mentioning that different solvent mixtures were tested and the total phenolic content in the extracts quantified (TPC via HPLC-TOF-MS). The tendency observed was EtOH/water 80/20 (v/v) (17.0 ± 0.2 mg TPC/g leaf dry weight (d.w.)) ≥ acetone/water 70/30 (v/v) (16.1 ± 0.7 mg TPC/g leaf d.w.) > EtOH/water 70/30 (v/v) (14.0 ± 0.3 mg TPC/g leaf d.w.) > acetone/water 80/20 (v/v) (13.5 ± 0.4 mg TPC/g leaf d.w.). Importantly, flavonoids derivatives were between 63 and 76% of the TPC in those extracts. Major compounds were sucrose, glucose (α and β), and proline, and chlorogenic acid and rutin for NMR and HPLC-TOF-MS, respectively. Graphical abstract The combined use of LC-HRMS and NMR is a potential synergic combination for a comprehensive metabolite composition of cherimoya leaves.

Small is different: RPC observations of a small scale comet interacting with the solar wind

NASA Astrophysics Data System (ADS)

Nilsson, Hans; Burch, James L.; Carr, Christopher M.; Eriksson, Anders I.; Glassmeier, Karl-Heinz; Henri, Pierre; Rosetta Plasma Consortium Team

2016-10-01

Rosetta followed comet 67P from low activity at more than 3 AU heliocentric distance to peak activity at perihelion and then out again. We study the evolution of the dynamic plasma environment using data from the Rosetta Plasma Consortium (RPC). Observations of cometary plasma began in August 2014, at a distance of 100 km from the comet nucleus and at 3.6 AU from the Sun. As the comet approached the Sun, outgassing from the comet increased, as did the density of the cometary plasma. Measurements showed a highly heterogeneous cold ion environment, permeated by the solar wind. The solar wind was deflected due to the mass loading from newly added cometary plasma, with no discernible slowing down. The magnetic field magnitude increased significantly above the background level, and strong low frequency waves were observed in the magnetic field, a.k.a. the "singing comet". Electron temperatures were high, leading to a frequently strongly negative spacecraft potential. In mid to late April 2015 the solar wind started to disappear from the observation region. This was associated with a solar wind deflection reaching nearly 180°, indicating that mass loading became efficient enough to form a solar wind-free region. Accelerated water ions, moving mainly in the anti-sunward direction, kept being observed also after the solar wind disappearance. Plasma boundaries began to form and a collisionopause was tentatively identified in the ion and electron data. At the time around perihelion, a diamagnetic cavity was also observed, at a surprisingly large distance from the comet. In late 2016 the solar wind re-appeared at the location of Rosetta, allowing for studies of asymmetry of the comet ion environment with respect to perihelion. A nightside excursion allowed us to get a glimpse of the electrodynamics of the innermost part of the plasma tail. Most of these phenomena are dependent on the small-scale physics of comet 67P, since for most of the Rosetta mission the solar wind

SU-E-P-02: Imaging and Radiation Oncology Core (IROC) Houston QA Center (RPC) Credentialing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amador, C; Keith, T; Nguyen, T

2014-06-01

Purpose: To provide information pertaining to IROC Houston QA Center's (RPC) credentialing process for institutions participating in NCI-sponsored clinical trials. Methods: IROC Houston issues credentials for NCI sponsored study groups. Requirements for credentialing might include any combination of questionnaires, knowledge assessment forms, benchmarks, or phantom irradiations. Credentialing requirements for specific protocols can be found on IROC Houston's website (irochouston.mdanderson.org). The website also houses the credentialing status inquiry (CSI) form. Once an institution has reviewed the protocol's credentialing requirements, a CSI form should be completed and submitted to IROC Houston. This form is used both to request whether requirements have beenmore » met as well as to notify IROC Houston that the institution requests credentialing for a specific protocol. IROC Houston will contact the institution to discuss any delinquent requirements. Once the institution has met all requirements IROC Houston issues a credentialing letter to the institution and will inform study groups and other IROC offices of the credentials. Institutions can all phone the IROC Houston office to initiate credentialing or ask any credentialing related questions. Results: Since 2010 IROC has received 1313 credentialing status inquiry forms. We received 317 in 2010, 266 in 2011, 324 in 2012, and 406 in 2013. On average we receive 35 phone calls per week with multiple types of credentialing questions. Decisions regarding credentialing status are based on the protocol specifications and previous completed credentialing by the institution. In some cases, such as for general IMRT credentialing, up to 5 sites may be credentialed based on the credentialing of one main center. Each of these situations is handled individually. Conclusion: IROC Houston will issue radiation therapy credentials for the NCI trials in the National Clinical Trials Network. Credentialing requirements and the

A Silicon Nanomembrane Detector for Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) of Large Proteins

PubMed Central

Park, Jonghoo; Blick, Robert H.

2013-01-01

We describe a MALDI-TOF ion detector based on freestanding silicon nanomembrane technology. The detector is tested in a commercial MALDI-TOF mass spectrometer with equimolar mixtures of proteins. The operating principle of the nanomembrane detector is based on phonon-assisted field emission from these silicon nanomembranes, in which impinging ion packets excite electrons in the nanomembrane to higher energy states. Thereby the electrons can overcome the vacuum barrier and escape from the surface of the nanomembrane via field emission. Ion detection is demonstrated of apomyoglobin (16,952 Da), aldolase (39,212 Da), bovine serum albumin (66,430 Da), and their equimolar mixtures. In addition to the three intact ions, a large number of fragment ions are also revealed by the silicon nanomembrane detector, which are not observable with conventional detectors. PMID:24152929

A silicon nanomembrane detector for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) of large proteins.

PubMed

Park, Jonghoo; Blick, Robert H

2013-10-11

We describe a MALDI-TOF ion detector based on freestanding silicon nanomembrane technology. The detector is tested in a commercial MALDI-TOF mass spectrometer with equimolar mixtures of proteins. The operating principle of the nanomembrane detector is based on phonon-assisted field emission from these silicon nanomembranes, in which impinging ion packets excite electrons in the nanomembrane to higher energy states. Thereby the electrons can overcome the vacuum barrier and escape from the surface of the nanomembrane via field emission. Ion detection is demonstrated of apomyoglobin (16,952 Da), aldolase (39,212 Da), bovine serum albumin (66,430 Da), and their equimolar mixtures. In addition to the three intact ions, a large number of fragment ions are also revealed by the silicon nanomembrane detector, which are not observable with conventional detectors.

MALDI-TOF MS performance compared to direct examination, culture, and 16S rDNA PCR for the rapid diagnosis of bone and joint infections.

PubMed

Lallemand, E; Coiffier, G; Arvieux, C; Brillet, E; Guggenbuhl, P; Jolivet-Gougeon, A

2016-05-01

The rapid identification of bacterial species involved in bone and joint infections (BJI) is an important element to optimize the diagnosis and care of patients. The aim of this study was to evaluate the usefulness of matrix-assisted laser desorption ionization mass spectrometry (MALDI-TOF MS) for the rapid diagnosis of bone infections, directly on synovial fluid (SF) or on crushed osteoarticular samples (CS). From January to October 2013, we prospectively analyzed 111 osteoarticular samples (bone and joint samples, BJS) from 78 patients in care at the University Hospital of Rennes, France. The diagnosis procedure leading to the sample collection was linked to a suspicion of infection, inflammatory disease, arthritis, or for any bone or joint abnormalities. Standard bacteriological diagnosis and molecular biology analysis [16S rRNA polymerase chain reaction (PCR) and sequencing] were conducted. In addition, analysis by MALDI-TOF MS was performed directly on the osteoarticular samples, as soon as the amount allowed. Culture, which remains the gold standard for the diagnosis of BJI, has the highest sensitivity (85.9 %) and remains necessary to test antimicrobial susceptibility. The 16S rDNA PCR results were positive in the group with positive BJI (28.6 %) and negative in the group without infection. Direct examination remains insensitive (31.7 %) but more effective than MALDI-TOF MS directly on the sample (6.3 %). The specificity was 100 % in all cases, except for culture (74.5 %). Bacterial culture remains the gold standard, especially enrichment in blood bottles. Direct analysis of bone samples with MALDI-TOF MS is not useful, possibly due to the low inoculum of BJS.

Effects of rumen-protected Capsicum oleoresin on productivity and responses to a glucose tolerance test in lactating dairy cows.

PubMed

Oh, J; Harper, M; Giallongo, F; Bravo, D M; Wall, E H; Hristov, A N

2017-03-01

The objective of this experiment was to investigate the effects of rumen-protected Capsicum oleoresin (RPC) supplementation on feed intake, milk yield and composition, nutrient utilization, fecal microbial ecology, and responses to a glucose tolerance test in lactating dairy cows. Nine multiparous Holstein cows were used in a replicated 3 × 3 Latin square design balanced for residual effects with three 28-d periods. Each period consisted of 14 d for adaptation and 14 d for data collection and sampling. Treatments were 0 (control), 100, and 200 mg of RPC/cow per day. They were mixed with a small portion of the total mixed ration and top-dressed. Glucose tolerance test was conducted once during each experimental period by intravenous administration of glucose at a rate of 0.3 g/kg of body weight. Dry matter intake was not affected by RPC. Milk yield tended to increase for RPC treatments compared to the control. Feed efficiency was linearly increased by RPC supplementation. Concentrations of fat, true protein, and lactose in milk were not affected by RPC. Apparent total-tract digestibility of dry matter, organic matter, and crude protein was linearly increased, and fecal nitrogen excretion was linearly decreased by RPC supplementation. Rumen-protected Capsicum oleoresin did not affect the composition of fecal bacteria. Glucose concentration in serum was not affected by RPC supplementation post glucose challenge. However, compared to the control, RPC decreased serum insulin concentration at 5, 10, and 40 min post glucose challenge. The area under the insulin concentration curve was also decreased 25% by RPC. Concentration of nonesterified fatty acids and β-hydroxybutyrate in serum were not affected by RPC following glucose administration. In this study, RPC tended to increase milk production and increased feed efficiency in dairy cows. In addition, RPC decreased serum insulin concentration during the glucose tolerance test, but glucose concentration was not affected

Use of matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant.

PubMed

Sala-Comorera, Laura; Vilaró, Carles; Galofré, Belén; Blanch, Anicet R; García-Aljaro, Cristina

2016-10-01

The study of bacterial communities throughout a drinking water treatment plant could provide a basic understanding of the effects of water processing that could then be used to improve the management of such plants. However, it is necessary to develop new analytical techniques that are sufficiently efficient, robust and fast for their effective and useful application in routine analysis. The aim of this study is therefore to assess the performance of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), as compared to the PhenePlate™ system, for routine analysis in a drinking water treatment plant. To this end we studied a total of 277 colonies isolated in different seasons and from different points throughout the water treatment process, including: raw water, sand filtration, ultrafiltration, reverse osmosis and chlorination. The colonies were analysed using MALDI-TOF MS by direct deposition of the cells on the plate. The colonies were also biochemically fingerprinted using the PhenePlate™ system, clustered according to their similarity and a representative strain was selected for 16S rRNA gene sequencing and API ® gallery-based identification. The use of MALDI-TOF MS was reliable compared to the PhenePlate™ system and has the advantage of being faster and relatively cheap. Bacteria typing by MALDI-TOF MS is therefore a promising method to replace conventional routine phenotypic methods for the identification of bacteria in drinking water laboratories, thanks to its robustness. The major limiting factor for MALDI-TOF MS is the lack of a suitable mass spectra database; although each laboratory can develop its own library. This methodology will provide a tracking tool for companies to use in risk management and the detection of possible failures in both the water treatment processes and the distribution network, as well as offering characterization of the intrinsic microbial populations. Copyright © 2016 Elsevier Gmb

The use of HPLC-Q-TOF-MS for comprehensive screening of drugs and psychoactive substances in hair samples and several "legal highs" products.

PubMed

Aszyk, Justyna; Kot-Wasik, Agata

Non-targeted screening of drugs present in herbal products, known as "legal high" drugs and in hair as a biological matrix commonly used in toxicological investigations was accomplished with the use of high pressure liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (HPLC-Q-TOF-MS). In total, 25 and 14 therapeutical drugs and psychoactive substances/metabolites were detected in investigated hair samples and herbal products, respectively. We demonstrate that the HPLC-Q-TOF methodology seems to be a powerful tool in the qualitative analysis applied in identification of these designer drugs, thus enabling a laboratory to stay-up-to-date with the drugs that are being sold as legal high products on black market.

Rapid identification and simultaneous analysis of multiple constituents from Rheum tanguticum Maxim. ex Balf. by UPLC/Q-TOF-MS.

PubMed

Gao, Liang-Liang; Guo, Tao; Xu, Xu-Dong; Yang, Jun-Shan

2017-07-01

Rhubarb contains biologically active compounds such as anthraquinones, anthrones, stilbenes and tannins. A rapid and efficient UPLC/Q-TOF-MS/MS method was developed and applied towards identifying the constituents of Rheum tanguticum Maxim. ex Balf. for the first time. Chemical constituents were separated and investigated by UPLC/Q-TOF-MS/MS in the negative ion mode. The ESI-MS 2 fragmentation pathways of four types of compounds were interpreted, providing a very useful guidance for the characterisation of different types of compounds. Based on the exact mass information, fragmentation characteristic and LC retention time of 7 reference standards, 30 constituents were tentatively identified from the methanol extract of R. tanguticum. Among them, seven compounds were described for the first time from R. tanguticum and two from the genus Rheum were described for the first time. The analytical tool used here is valuable for the rapid separation and identification of multiple and minor constituents in methanol extracts of R. tanguticum.

Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry.

PubMed

Parker, Laurie; Engel-Hall, Aaron; Drew, Kevin; Steinhardt, George; Helseth, Donald L; Jabon, David; McMurry, Timothy; Angulo, David S; Kron, Stephen J

2008-04-01

Despite advances in methods and instrumentation for analysis of phosphopeptides using mass spectrometry, it is still difficult to quantify the extent of phosphorylation of a substrate because of physiochemical differences between unphosphorylated and phosphorylated peptides. Here we report experiments to investigate those differences using MALDI-TOF mass spectrometry for a set of synthetic peptides by creating calibration curves of known input ratios of peptides/phosphopeptides and analyzing their resulting signal intensity ratios. These calibration curves reveal subtleties in sequence-dependent differences for relative desorption/ionization efficiencies that cannot be seen from single-point calibrations. We found that the behaviors were reproducible with a variability of 5-10% for observed phosphopeptide signal. Although these data allow us to begin addressing the issues related to modeling these properties and predicting relative signal strengths for other peptide sequences, it is clear that this behavior is highly complex and needs to be further explored. John Wiley & Sons, Ltd

Investigating quantitation of phosphorylation using MALDI-TOF mass spectrometry

PubMed Central

Parker, Laurie; Engel-Hall, Aaron; Drew, Kevin; Steinhardt, George; Helseth, Donald L.; Jabon, David; McMurry, Timothy; Angulo, David S.; Kron, Stephen J.

2010-01-01

Despite advances in methods and instrumentation for analysis of phosphopeptides using mass spectrometry, it is still difficult to quantify the extent of phosphorylation of a substrate due to physiochemical differences between unphosphorylated and phosphorylated peptides. Here we report experiments to investigate those differences using MALDI-TOF mass spectrometry for a set of synthetic peptides by creating calibration curves of known input ratios of peptides/phosphopeptides and analyzing their resulting signal intensity ratios. These calibration curves reveal subtleties in sequence-dependent differences for relative desorption/ionization efficiencies that cannot be seen from single-point calibrations. We found that the behaviors were reproducible with a variability of 5–10% for observed phosphopeptide signal. Although these data allow us to begin addressing the issues related to modeling these properties and predicting relative signal strengths for other peptide sequences, it is clear this behavior is highly complex and needs to be further explored. PMID:18064576

Characterizing ICF Neutron Scintillation Diagnostics on the nTOF line at SUNY Geneseo

NASA Astrophysics Data System (ADS)

Lawson-Keister, Pat; Padawar-Curry, Jonah; Visca, Hannah; Fletcher, Kurt; Padalino, Stephen; Sangster, T. Craig; Regan, Sean

2015-11-01

Neutron scintillator diagnostics for ICF and HEDP can be characterized using the neutron time-of-flight (nTOF) line on Geneseo's 1.7 MV tandem Pelletron accelerator. Neutron signals can be differentiated from gamma signals by employing coincidence methods. A 1.8-MeV beam of deuterons incident on a deuterated polyethylene target produces neutrons via the 2H(d,n)3He reaction. Neutrons emerging at a lab angle of 88° have an energy of 2.96 MeV; the 3He ions associated with these neutrons are detected at a scattering angle of 43° using a surface barrier detector. The time of flight of the neutron can be measured by using the 3He detection as a ``start'' signal and the scintillation detection as a ``stop'' signal. This time of flight requirement is used to identify the 2.96-MeV neutron signals in the scintillator. To measure the light curve produced by these monoenergetic neutrons, two photomultiplier (PMT) tubes are attached to the scintillator. The full aperture PMT establishes the nTOF coincidence. The other PMT is fitted with a pinhole to collect single events. The time between the full aperture PMT signal and the arrival of the signal in the pinhole PMT is used to determine the light curve for the scintillator. This system will enable the neutron response of various scintillators to be compared. Supported in part by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.

Highly efficient classification and identification of human pathogenic bacteria by MALDI-TOF MS.

PubMed

Hsieh, Sen-Yung; Tseng, Chiao-Li; Lee, Yun-Shien; Kuo, An-Jing; Sun, Chien-Feng; Lin, Yen-Hsiu; Chen, Jen-Kun

2008-02-01

Accurate and rapid identification of pathogenic microorganisms is of critical importance in disease treatment and public health. Conventional work flows are time-consuming, and procedures are multifaceted. MS can be an alternative but is limited by low efficiency for amino acid sequencing as well as low reproducibility for spectrum fingerprinting. We systematically analyzed the feasibility of applying MS for rapid and accurate bacterial identification. Directly applying bacterial colonies without further protein extraction to MALDI-TOF MS analysis revealed rich peak contents and high reproducibility. The MS spectra derived from 57 isolates comprising six human pathogenic bacterial species were analyzed using both unsupervised hierarchical clustering and supervised model construction via the Genetic Algorithm. Hierarchical clustering analysis categorized the spectra into six groups precisely corresponding to the six bacterial species. Precise classification was also maintained in an independently prepared set of bacteria even when the numbers of m/z values were reduced to six. In parallel, classification models were constructed via Genetic Algorithm analysis. A model containing 18 m/z values accurately classified independently prepared bacteria and identified those species originally not used for model construction. Moreover bacteria fewer than 10(4) cells and different species in bacterial mixtures were identified using the classification model approach. In conclusion, the application of MALDI-TOF MS in combination with a suitable model construction provides a highly accurate method for bacterial classification and identification. The approach can identify bacteria with low abundance even in mixed flora, suggesting that a rapid and accurate bacterial identification using MS techniques even before culture can be attained in the near future.

Analysis of Bacterial Lipooligosaccharides by MALDI-TOF MS with Traveling Wave Ion Mobility

NASA Astrophysics Data System (ADS)

Phillips, Nancy J.; John, Constance M.; Jarvis, Gary A.

2016-07-01

Lipooligosaccharides (LOS) are major microbial virulence factors displayed on the outer membrane of rough-type Gram-negative bacteria. These amphipathic glycolipids are comprised of two domains, a core oligosaccharide linked to a lipid A moiety. Isolated LOS samples are generally heterogeneous mixtures of glycoforms, with structural variability in both domains. Traditionally, the oligosaccharide and lipid A components of LOS have been analyzed separately following mild acid hydrolysis, although important acid-labile moieties can be cleaved. Recently, an improved method was introduced for analysis of intact LOS by MALDI-TOF MS using a thin layer matrix composed of 2,4,6-trihydroxyacetophenone (THAP) and nitrocellulose. In addition to molecular ions, the spectra show in-source "prompt" fragments arising from regiospecific cleavage between the lipid A and oligosaccharide domains. Here, we demonstrate the use of traveling wave ion mobility spectrometry (TWIMS) for IMS-MS and IMS-MS/MS analyses of intact LOS from Neisseria spp. ionized by MALDI. Using IMS, the singly charged prompt fragments for the oligosaccharide and lipid A domains of LOS were readily separated into resolved ion plumes, permitting the extraction of specific subspectra, which led to increased confidence in assigning compositions and improved detection of less abundant ions. Moreover, IMS separation of precursor ions prior to collision-induced dissociation (CID) generated time-aligned, clean MS/MS spectra devoid of fragments from interfering species. Incorporating IMS into the profiling of intact LOS by MALDI-TOF MS exploits the unique domain structure of the molecule and offers a new means of extracting more detailed information from the analysis.

Development and characterization of a rapid polymerizing collagen for soft tissue augmentation.

PubMed

Devore, Dale; Zhu, Jiaxun; Brooks, Robert; McCrate, Rebecca Rone; Grant, David A; Grant, Sheila A

2016-03-01

A liquid collagen has been developed that fibrilizes upon injection. Rapid polymerizing collagen (RPC) is a type I porcine collagen that undergoes fibrillization upon interaction with ionic solutions, such as physiological solutions. The ability to inject liquid collagen would be beneficial for many soft tissue augmentation applications. In this study, RPC was synthesized and characterized as a possible dermal filler. Transmission electron microscopy, ion induced RPC fibrillogenesis tests, collagenase resistance assay, and injection force studies were performed to assess RPC's physicochemical properties. An in vivo study was performed which consisted of a 1-, 3-, and 6-month study where RPC was injected into the ears of miniature swine. The results demonstrated that the liquid RPC requires low injection force (<7 N); fibrillogenesis and banding of collagen occurs when RPC is injected into ionic solutions, and RPC has enhanced resistance to collagenase breakdown. The in vivo study demonstrated long-term biocompatibility with low irritation scores. In conclusion RPC possesses many of the desirable properties of a soft tissue augmentation material. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 758-767, 2016. © 2015 The authors journal of biomedical materials research part a published by wiley periodicals, inc.

The Phantom Menace for Patients with Hepatobiliary Diseases: Shewanella haliotis, Often Misidentified as Shewanella algae in Biochemical Tests and MALDI-TOF Analysis.

PubMed

Byun, Jung-Hyun; Park, Hyunwoong; Kim, Sunjoo

2017-03-24

Although Shewanella algae has been known to have weak pathogenicity, case reports on infections with this species have been steadily increasing. S. algae and S. haliotis are difficult to distinguish from each other with conventional phenotypic methods. We reviewed the microbiological and clinical features of S. algae and S. haliotis infections at our institute. Bacterial culture and identification reports from patient samples from 2010 to 2014 were reviewed to screen the cases of Shewanella infections. In addition to conventional biochemical tests, 16S rRNA gene sequence analysis and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry were performed for 19 stored bacterial isolates. Medical records were reviewed for clinical characteristics and laboratory findings. All isolates were identified as S. algae by using VITEK 2. MALDI-TOF also identified all isolates as S. algae with a 99.9 confidence value. In contrast, 16S rRNA analysis identified 10 isolates as S. algae and 9 isolates as S. haliotis. Both S. algae (60%) and S. haliotis (77%) infections were strongly associated with diseases of the hepatobiliary tract and pancreas. To distinguish between S. algae and S. haliotis, 16S rRNA gene sequence analysis seems more accurate than biochemical tests or MALDI-TOF. Patients with underlying diseases in the hepatobiliary tract and pancreas seem to be susceptible to these marine pathogens.

High Throughput Detection of Tetracycline Residues in Milk Using Graphene or Graphene Oxide as MALDI-TOF MS Matrix

NASA Astrophysics Data System (ADS)

Liu, Junyan; Liu, Yang; Gao, Mingxia; Zhang, Xiangmin

2012-08-01

In this work, a new pre-analysis method for tetracyclines (TCs) detection from the milk samples was established. As a good accomplishment for the existing accurate quantification strategies for TCs detection, the new pre-analysis method was demonstrated to be simple, sensitive, fast, cost effective, and high throughput, which would do a great favor to the routine quality pre-analysis of TCs from milk samples. Graphene or graphene oxide was utilized, for the first time, as a duel-platform to enrich and detect the TCs by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). All together, four TCs were chosen as models: tetracycline, oxytetracycline, demeclocycline, and chlortetracycline. Due to the excellent electronic, thermal, and mechanical properties, graphene and graphene oxide were successfully applied as matrices for MALDI-TOF MS with free background inference in low mass range. Meanwhile, graphene or graphene oxide has a large surface area and strong interaction force with the analytes. By taking the advantage of these features, TCs were effectively enriched with the limit of detection (LOD) as low as 2 nM.

[Infections as a preoperative problem in patients with tetralogy of Fallot (TOF) associated with complete atrioventricular canal septal defect (AVC)].

PubMed

Szydłowski, Lesław; Marek-Szydłowska, Teresa; Rudziński, Andrzej; Pajak, Jacek; Morka, Jacek; Stołtny, Ludwik

2004-01-01

Tetralogy of Fallot (TOF) coexisting with atrioventricular canal septal defect (AVC) is a rare combination of anomalies. Additionally, in cases with concomitant Down syndrome, recurrent infections can be a serious problem in patients (pts.) waiting for cardiosurgery treatment. The purpose of the study was an analysis of types of infections and other factors complicating the preoperative period in those patients. The study group consisted of 17 pts. with TOF and AVC aged from 1 day to 9 years (mean 9.4 month). In this group there were 11 pts. with Down syndrome. All of them were subjected to physical examinations, blood analysis, ECG, chest X-ray and echocardiographic study. Additionally, in 8 pts. we performed catheterization. The signs of different types of infection were analyzed and results were compared in two groups: with and without Down syndrome. The differences were observed in the frequency of recurrent or chronic infections (21 v/s 4), time of hospitalization before surgery (17 v/s 9 days), necessity (11 v/s 3) and duration of antibiotic therapy (19 v/s 7 days) in the two studied groups. Elevated body temperature of unknown etiology was noted in 8 cases with Down syndrome, compared to 1 patient without trisomy 21. Also, the children with Down syndrome had to wait 11 days longer (19 v/s 8) for discharge after operation. Infections in children with TOF, AVC and Down syndrome significantly complicate the natural course of this anomaly. Prolonged preoperation time is characteristic of Down syndrome pts. compared to patients without chromosomal abnormalities.

Detection of nitro-organic and peroxide explosives in latent fingermarks by DART- and SALDI-TOF-mass spectrometry.

PubMed

Rowell, Frederick; Seviour, John; Lim, Angelina Yimei; Elumbaring-Salazar, Cheryl Grace; Loke, Jason; Ma, Jan

2012-09-10

The ability of two mass spectrometric methods, surface-assisted laser desorption/ionization-time of flight-mass spectrometry (SALDI-TOF-MS) and direct analysis in real time (DART-MS), to detect the presence of seven common explosives (six nitro-organic- and one peroxide-type) in spiked latent fingermarks has been examined. It was found that each explosive could be detected with nanogram sensitivity for marks resulting from direct finger contact with a glass probe by DART-MS or onto stainless steel target plates using SALDI-TOF-MS for marks pre-dusted with one type of commercial black magnetic powder. These explosives also could be detected in latent marks lifted from six common surfaces (paper, plastic bag, metal drinks can, wood laminate, adhesive tape and white ceramic tile) whereas no explosive could be detected in equivalent pre-dusted marks on the surface of a commercial lifting tape by the DART-MS method due to high background interference from the tape material. The presence of TNT and Tetryl could be detected in pre-dusted latent fingermarks on a commercial lifting tape for up to 29 days sealed and stored under ambient conditions. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

3M™ Molecular detection system versus MALDI-TOF mass spectrometry and molecular techniques for the identification of Escherichia coli 0157:H7, Salmonella spp. &Listeria spp.

PubMed

Loff, Marché; Mare, Louise; de Kwaadsteniet, Michele; Khan, Wesaal

2014-06-01

The aim of this study was to compare standard selective plating, conventional PCR (16S rRNA and species specific primers), MALDI-TOF MS and the 3M™ Molecular Detection System for the routine detection of the pathogens Listeria, Salmonella and Escherichia coli 0157:H7 in wastewater and river water samples. MALDI-TOF MS was able to positively identify 20/21 (95%) of the E. coli isolates obtained at genus and species level, while 16S rRNA sequencing only correctly identified 6/21 (28%) as E. coli strains. None of the presumptive positive Listeria spp. and Salmonella spp. isolates obtained by culturing on selective media were positively identified by MALDI-TOF and 16S rRNA analysis. The species-specific E. coli 0157:H7 PCR described in this present study, was not able to detect any E. coli 0157:H7 strains in the wastewater and river water samples analysed. However, E. coli strains, Listeria spp., L. monocytogenes and Salmonella spp. were detected using species specific PCR. Escherichia coli 0157:H7, Listeria spp. and Salmonella spp. were also sporadically detected throughout the sampling period in the wastewater and river water samples analysed by the 3M™ Molecular Detection System. MALDI-TOF MS, which is a simple, accurate and cost-effective detection method, efficiently identified the culturable organisms, while in the current study both species specific PCR (Listeria spp. and Salmonella spp.) and 3M™ Molecular Detection System could be utilised for the direct routine analysis of pathogens in water sources. Copyright © 2014 Elsevier B.V. All rights reserved.

Protein adsorption/desorption and antibody binding stoichiometry on silicon interferometric biosensors examined with TOF-SIMS

NASA Astrophysics Data System (ADS)

Gajos, Katarzyna; Budkowski, Andrzej; Petrou, Panagiota; Pagkali, Varvara; Awsiuk, Kamil; Rysz, Jakub; Bernasik, Andrzej; Misiakos, Konstantinos; Raptis, Ioannis; Kakabakos, Sotirios

2018-06-01

Time-of-flight secondary ion mass spectrometry has been employed to examine, with biomolecular discrimination, sensing arm areas (20 μm × 600 μm) of integrated onto silicon chips Mach-Zehnder interferometers aiming to optimize their biofunctionalization with regard to indirect immunochemical (competitive) detection of ochratoxin A. Sensing areas are examined after: modification with (3-aminopropyl)triethoxysilane, spotting of OTA-ovalbumin conjugate (probe) from solutions with different concentration, blocking with bovine serum albumin, reaction with OTA-specific mouse monoclonal antibody followed by goat anti-mouse IgG secondary antibody. Component mass loadings of all proteins involved in immunodetection are determined from TOF-SIMS micro-analysis combined with ellipsometry of planar surfaces. These data show that partial desorption of surface-bound probe and blocking protein takes place upon primary immunoreaction to a degree that depends on probe concentration in spotting solution. Taking into account this desorption, apparent binding stoichiometry of both antibodies in immune complexes formed onto chip surface is determined more accurately than the respective evaluation based on real-time sensor response. In addition, mass loadings for probe and secondary antibody is observed to saturate for optimum probe concentrations. Also, principal component analysis of TOF-SIMS data could resolve both immunoreactions and biofunctionalization and discriminate surfaces prepared with optimum probe concentrations from those prepared using suboptimum ones.

Evaluating Factor XIII Specificity for Glutamine-Containing Substrates Using a MALDI-TOF Mass Spectrometry Assay

PubMed Central

Doiphode, Prakash G.; Malovichko, Marina V.; Mouapi, Kelly Njine; Maurer, Muriel C.

2014-01-01

Activated Factor XIII (FXIIIa) catalyzes the formation of γ-glutamyl-ε-lysyl cross-links within the fibrin blood clot network. Although several cross-linking targets have been identified, the characteristic features that define FXIIIa substrate specificity are not well understood. To learn more about how FXIIIa selects its targets, a matrix-assisted laser desorption ionization – time of flight mass spectrometry (MALDI-TOF MS) based assay was developed that could directly follow the consumption of a glutamine-containing substrate and the formation of a cross-linked product with glycine ethylester. This FXIIIa kinetics assay is no longer reliant on a secondary coupled reaction, on substrate labeling, or on detecting the final deacylation portion of the transglutaminase reaction. With the MALDI-TOF MS assay, glutamine-containing peptides derived from α2-antiplasmin, S. Aureus fibronectin binding protein A, and thrombin activatable fibrinolysis inhibitor were examined directly. Results suggest that the FXIIIa active site surface responds to changes in substrate residues following the reactive glutamine. The P-1 substrate position is sensitive to charge character and the P-2 and P-3 to the broad FXIIIa substrate specificity pockets. The more distant P-8 to P-11 region serves as a secondary substrate anchoring point. New knowledge on FXIIIa specificity may be used to design better substrates or inhibitors of this transglutaminase. PMID:24751466

Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli.

PubMed

Christner, Martin; Trusch, Maria; Rohde, Holger; Kwiatkowski, Marcel; Schlüter, Hartmut; Wolters, Manuel; Aepfelbacher, Martin; Hentschke, Moritz

2014-01-01

In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Specific peaks in the outbreak strain's spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow.

Comparison of MALDI-TOF MS, nucleic acid hybridization and the MPT64 immunochromatographic test for the identification of M. tuberculosis and non-tuberculosis Mycobacterium species.

PubMed

Şamlı, Asuman; İlki, Arzu

2016-10-01

Mycobacteria are an important cause of morbidity in humans. Rapid and accurate mycobacterial identification is important for improving patient outcomes. However, identification of Mycobacterium species is not easy, due to the slow and fastidious growth of mycobacteria. Recently, biochemical, sequencing, and probing methods have come to be used for identification. This study compared the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of M.tuberculosis and non-tuberculosis Mycobacteria (NTM) to those of nucleic acid hybridization (NAH) and the MPT64 immunochromatographic test. A total of 69 isolates from Marmara University Hospital, Microbiology Laboratory obtained between 2012 and 2013 were included in our study. All strains were grown on Lowenstein-Jensen and Middlebrook 7H9 medium. Among the 69 isolates, 56 (81%) were isolated as Mycobacterium tuberculosis complex (MTC), and 13 (19%) were isolated as NTM by the MPT64 ICT. NAH was able to identify all isolates to the species level. The isolated NTM included M. intracellulare (n:5), M. lentiflavum (n:3), M. xenopi (n:2), M. malmoense (n:1), M. abscessus (n:1), and M. avium (n:1). MALDI-TOF MS identified 88% of the mycobacterial isolates. All M. tuberculosis strains were identified correctly, but the ratio was 38.5% for NTM. Mycobacterial identification using MALDI-TOF MS takes 45 minutes and costs 3 Euro/test, whereas mycobacterial identification using NAH takes 6-7 hours and costs 30 Euro/test. In conclusion, MALDI-TOF MS has the potential to identify mycobacteria in the clinical laboratory setting by reducing identification turnaround time and laboratory costs for isolate referral.

Insight into Identification of Acinetobacter Species by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the Clinical Laboratory

NASA Astrophysics Data System (ADS)

Li, Xiuyuan; Tang, Yanyan; Lu, Xinxin

2018-04-01

Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ 2 = 41.336, P < 0.001. The species similar in 16 rDNA were discriminative from the mass spectra, such as A. baumannii & A. junii, A. pittii & A. calcoaceticus, and A. nosocomialis & A. seifertii. Therefore, using MALDI-TOF MS to identify Acinetobacter strains isolated from clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. [Figure not available: see fulltext.

Insight into Identification of Acinetobacter Species by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the Clinical Laboratory.

PubMed

Li, Xiuyuan; Tang, Yanyan; Lu, Xinxin

2018-04-09

Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ 2  = 41.336, P < 0.001. The species similar in 16 rDNA were discriminative from the mass spectra, such as A. baumannii & A. junii, A. pittii & A. calcoaceticus, and A. nosocomialis & A. seifertii. Therefore, using MALDI-TOF MS to identify Acinetobacter strains isolated from clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. Graphical Abstract ᅟ.

Comparative proteomic profiles of Aspergillus fumigatus and Aspergillus lentulus strains by surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS)

PubMed Central

2011-01-01

Background Surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS) was applied to analyze the protein profiles in both somatic and metabolic extracts of Aspergillus species. The study was carried out on some Aspergillus species within the Fumigati section (Aspergillus fumigatus wild-types and natural abnormally pigmented mutants, and Aspergillus lentulus). The aim was to validate whether mass spectrometry protein profiles can be used as specific signatures to discriminate different Aspergillus species or even mutants within the same species. Results The growth conditions and the SELDI-TOF parameters were determined to generate characteristic protein profiles of somatic and metabolic extracts of Aspergillus fumigatus strains using five different ProteinChips®, eight growth conditions combining two temperatures, two media and two oxygenation conditions. Nine strains were investigated: three wild-types and four natural abnormally pigmented mutant strains of A. fumigatus and two strains of A. lentulus. A total of 242 fungal extracts were prepared. The spectra obtained are protein signatures linked to the physiological states of fungal strains depending on culture conditions. The best resolutions were obtained using the chromatographic surfaces CM10, NP20 and H50 with fractions of fungi grown on modified Sabouraud medium at 37°C in static condition. Under these conditions, the SELDI-TOF analysis allowed A. fumigatus and A. lentulus strains to be grouped into distinct clusters. Conclusions SELDI-TOF analysis distinguishes A. fumigatus from A. lentulus strains and moreover, permits separate clusters of natural abnormally pigmented A. fumigatus strains to be obtained. In addition, this methodology allowed us to point out fungal components specifically produced by a wild-type strain or natural mutants. It offers attractive potential for further studies of the Aspergillus biology or pathogenesis. PMID:21798007

Comparative proteomic profiles of Aspergillus fumigatus and Aspergillus lentulus strains by surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS).

PubMed

Pinel, Claudine; Arlotto, Marie; Issartel, Jean-Paul; Berger, François; Pelloux, Hervé; Grillot, Renée; Symoens, Françoise

2011-07-28

Surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS) was applied to analyze the protein profiles in both somatic and metabolic extracts of Aspergillus species. The study was carried out on some Aspergillus species within the Fumigati section (Aspergillus fumigatus wild-types and natural abnormally pigmented mutants, and Aspergillus lentulus). The aim was to validate whether mass spectrometry protein profiles can be used as specific signatures to discriminate different Aspergillus species or even mutants within the same species. The growth conditions and the SELDI-TOF parameters were determined to generate characteristic protein profiles of somatic and metabolic extracts of Aspergillus fumigatus strains using five different ProteinChips®, eight growth conditions combining two temperatures, two media and two oxygenation conditions. Nine strains were investigated: three wild-types and four natural abnormally pigmented mutant strains of A. fumigatus and two strains of A. lentulus. A total of 242 fungal extracts were prepared. The spectra obtained are protein signatures linked to the physiological states of fungal strains depending on culture conditions. The best resolutions were obtained using the chromatographic surfaces CM10, NP20 and H50 with fractions of fungi grown on modified Sabouraud medium at 37 °C in static condition. Under these conditions, the SELDI-TOF analysis allowed A. fumigatus and A. lentulus strains to be grouped into distinct clusters. SELDI-TOF analysis distinguishes A. fumigatus from A. lentulus strains and moreover, permits separate clusters of natural abnormally pigmented A. fumigatus strains to be obtained. In addition, this methodology allowed us to point out fungal components specifically produced by a wild-type strain or natural mutants. It offers attractive potential for further studies of the Aspergillus biology or pathogenesis. © 2011 Pinel et al; licensee BioMed Central Ltd.

Identification of Low Molecular Weight Glutenin Alleles by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) in Common Wheat (Triticum aestivum L.).

PubMed

Wang, Aili; Liu, Li; Peng, Yanchun; Islam, Shahidul; Applebee, Marie; Appels, Rudi; Yan, Yueming; Ma, Wujun

2015-01-01

Low molecular weight glutenin subunits (LMW-GS) play an important role in determining dough properties and breadmaking quality. However, resolution of the currently used methodologies for analyzing LMW-GS is rather low which prevents an efficient use of genetic variations associated with these alleles in wheat breeding. The aim of the current study is to evaluate and develop a rapid, simple, and accurate method to differentiate LMW-GS alleles using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. A set of standard single LMW-GS allele lines as well as a suite of well documented wheat cultivars were collected from France, CIMMYT, and Canada. Method development and optimization were focused on protein extraction procedures and MALDI-TOF instrument settings to generate reproducible diagnostic spectrum peak profiles for each of the known wheat LMW-GS allele. Results revealed a total of 48 unique allele combinations among the studied genotypes. Characteristic MALDI-TOF peak patterns were obtained for 17 common LMW-GS alleles, including 5 (b, a or c, d, e, f), 7 (a, b, c, d or i, f, g, h) and 5 (a, b, c, d, f) patterns or alleles for the Glu-A3, Glu-B3, and Glu-D3 loci, respectively. In addition, some reproducible MALDI-TOF peak patterns were also obtained that did not match with any known alleles. The results demonstrated a high resolution and throughput nature of MALDI-TOF technology in analyzing LMW-GS alleles, which is suitable for application in wheat breeding programs in processing a large number of wheat lines with high accuracy in limited time. It also suggested that the variation of LMW-GS alleles is more abundant than what has been defined by the current nomenclature system that is mainly based on SDS-PAGE system. The MALDI-TOF technology is useful to differentiate these variations. An international joint effort may be needed to assign allele symbols to these newly identified alleles and determine their effects on end

Identification of Low Molecular Weight Glutenin Alleles by Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF-MS) in Common Wheat (Triticum aestivum L.)

PubMed Central

Islam, Shahidul; Applebee, Marie; Appels, Rudi; Yan, Yueming; Ma, Wujun

2015-01-01

Low molecular weight glutenin subunits (LMW-GS) play an important role in determining dough properties and breadmaking quality. However, resolution of the currently used methodologies for analyzing LMW-GS is rather low which prevents an efficient use of genetic variations associated with these alleles in wheat breeding. The aim of the current study is to evaluate and develop a rapid, simple, and accurate method to differentiate LMW-GS alleles using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. A set of standard single LMW-GS allele lines as well as a suite of well documented wheat cultivars were collected from France, CIMMYT, and Canada. Method development and optimization were focused on protein extraction procedures and MALDI-TOF instrument settings to generate reproducible diagnostic spectrum peak profiles for each of the known wheat LMW-GS allele. Results revealed a total of 48 unique allele combinations among the studied genotypes. Characteristic MALDI-TOF peak patterns were obtained for 17 common LMW-GS alleles, including 5 (b, a or c, d, e, f), 7 (a, b, c, d or i, f, g, h) and 5 (a, b, c, d, f) patterns or alleles for the Glu-A3, Glu-B3, and Glu-D3 loci, respectively. In addition, some reproducible MALDI-TOF peak patterns were also obtained that did not match with any known alleles. The results demonstrated a high resolution and throughput nature of MALDI-TOF technology in analyzing LMW-GS alleles, which is suitable for application in wheat breeding programs in processing a large number of wheat lines with high accuracy in limited time. It also suggested that the variation of LMW-GS alleles is more abundant than what has been defined by the current nomenclature system that is mainly based on SDS-PAGE system. The MALDI-TOF technology is useful to differentiate these variations. An international joint effort may be needed to assign allele symbols to these newly identified alleles and determine their effects on end

Importance of establishing radiation protection culture in Radiology Department.

PubMed

Ploussi, Agapi; Efstathopoulos, Efstathios P

2016-02-28

The increased use of ionization radiation for diagnostic and therapeutic purposes, the rapid advances in computed tomography as well as the high radiation doses delivered by interventional procedures have raised serious safety and health concerns for both patients and medical staff and have necessitated the establishment of a radiation protection culture (RPC) in every Radiology Department. RPC is a newly introduced concept. The term culture describes the combination of attitudes, beliefs, practices and rules among the professionals, staff and patients regarding to radiation protection. Most of the time, the challenge is to improve rather than to build a RPC. The establishment of a RPC requires continuing education of the staff and professional, effective communication among stakeholders of all levels and implementation of quality assurance programs. The RPC creation is being driven from the highest level. Leadership, professionals and associate societies are recognized to play a vital role in the embedding and promotion of RPC in a Medical Unit. The establishment of a RPC enables the reduction of the radiation dose, enhances radiation risk awareness, minimizes unsafe practices, and improves the quality of a radiation protection program. The purpose of this review paper is to describe the role and highlight the importance of establishing a strong RPC in Radiology Departments with an emphasis on promoting RPC in the Interventional Radiology environment.

Effect of Modified Red Pottery Clay on the Moisture Absorption Behavior and Weatherability of Polyethylene-Based Wood-Plastic Composites

PubMed Central

Li, Qingde; Gao, Xun; Cheng, Wanli; Han, Guangping

2017-01-01

Red pottery clay (RPC) was modified using a silane coupling agent, and the modified RPC (mRPC) was then used to enhance the performance of high-density polyethylene-based wood-plastic composites. The effect of the mRPC content on the performances of the composites was investigated through Fourier transform infrared spectrometry, differential mechanical analysis (DMA) and ultraviolet (UV)-accelerated aging tests. After adding the mRPC, a moisture adsorption hysteresis was observed. The DMA results indicated that the mRPC effectively enhanced the rigidity and elasticity of the composites. The mRPC affected the thermal gravimetric, leading to a reduction of the thermal degradation rate and a right-shift of the thermal degradation peak; the initial thermal degradation temperature was increased. After 3000 h of UV-accelerated aging, the flexural strength and impact strength both declined. For aging time between 0 and 1000 h, the increase in amplitude of ΔL* (luminescence) and ΔE* (color) reached a maximum; the surface fading did not became obvious. ΔL* and ΔE* increased more significantly between 1000 and 2000 h. These characterization results indicate that the chromophores of the mRPC became briefly active. However, when the aging times were higher than 2000 h, the photo-degradation reaction was effectively prevented by adding the mRPC. The best overall enhancement was observed for an mRPC mass percentage of 5%, with a storage modulus of 3264 MPa and an increase in loss modulus by 16.8%, the best anti-aging performance and the lowest degree of color fading. PMID:28772470

Radial Peripapillary Capillary Network Visualized Using Wide-Field Montage Optical Coherence Tomography Angiography.

PubMed

Mase, Tomoko; Ishibazawa, Akihiro; Nagaoka, Taiji; Yokota, Harumasa; Yoshida, Akitoshi

2016-07-01

We quantitatively analyzed the features of a radial peripapillary capillary (RPC) network visualized using wide-field montage optical coherence tomography (OCT) angiography in healthy human eyes. Twenty eyes of 20 healthy subjects were recruited. En face 3 × 3-mm OCT angiograms of multiple locations in the posterior pole were acquired using the RTVue XR Avanti, and wide-field montage images of the RPC were created. To evaluate the RPC density, the montage images were binarized and skeletonized. The correlation between the RPC density and the retinal nerve fiber layer (RNFL) thickness measured by an OCT circle scan was investigated. The RPC at the temporal retina was detected as far as 7.6 ± 0.7 mm from the edge of the optic disc but not around the perifoveal area within 0.9 ± 0.1 mm of the fovea. Capillary-free zones beside the first branches of the arterioles were significantly (P < 0.0001) narrower than those beside the second ones. The RPC densities at 0.5, 2.5, and 5 mm from the optic disc edge were 13.6 ± 0.8, 11.9 ± 0.9, and 10.4 ± 0.9 mm-1. The RPC density also was correlated significantly (r = 0.64, P < 0.0001) with the RNFL thickness, with the greatest density in the inferotemporal region. Montage OCT angiograms can visualize expansion of the RPC network. The RPC is present in the superficial peripapillary retina in proportion to the RNFL thickness, supporting the idea that the RPC may be the vascular network primarily responsible for RNFL nourishment.

Direct molecular mass determination of trehalose monomycolate from 11 species of mycobacteria by MALDI-TOF mass spectrometry.

PubMed

Fujita, Yukiko; Naka, Takashi; Doi, Takeshi; Yano, Ikuya

2005-05-01

Direct estimation of the molecular mass of single molecular species of trehalose 6-monomycolate (TMM), a ubiquitous cell-wall component of mycobacteria, was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. When less than 1 microg TMM was analysed by MALDI-TOF mass spectrometry, quasimolecular ions [M+Na]+ of each molecular species were demonstrated and the numbers of carbons and double bonds (or cyclopropane rings) were determined. Since the introduction of oxygen atoms such as carbonyl, methoxy and ester groups yielded the appropriate shift of mass ions, the major subclasses of mycolic acid (alpha, methoxy, keto and wax ester) were identified without resorting to hydrolytic procedures. The results showed a marked difference in the molecular species composition of TMM among mycobacterial species. Unexpectedly, differing from other mycoloyl glycolipids, TMM from Mycobacterium tuberculosis showed a distinctive mass pattern, with abundant odd-carbon-numbered monocyclopropanoic (or monoenoic) alpha-mycolates besides dicyclopropanoic mycolate, ranging from C75 to C85, odd- and even-carbon-numbered methoxymycolates ranging from C83 to C94 and even- and odd-carbon-numbered ketomycolates ranging from C83 to C90. In contrast, TMM from Mycobacterium bovis (wild strain and BCG substrains) possessed even-carbon-numbered dicyclopropanoic alpha-mycolates. BCG Connaught strain lacked methoxymycolates almost completely. These results were confirmed by MALDI-TOF mass analysis of mycolic acid methyl esters liberated by alkaline hydrolysis and methylation of the original TMM. Wax ester-mycoloyl TMM molecular species were demonstrated for the first time as an intact form in the Mycobacterium avium-intracellulare group, M. phlei and M. flavescens. The M. avium-intracellulare group possessed predominantly C85 and C87 wax ester-mycoloyl TMM, while M. phlei and the rapid growers tested contained C80, C81, C82 and C83 wax ester

Mayfly and fish species identification and sex determination in bleak (Alburnus alburnus) by MALDI-TOF mass spectrometry.

PubMed

Maasz, G; Takács, P; Boda, P; Varbiro, G; Pirger, Z

2017-12-01

Besides food quality control of fish or cephalopods, the novel mass spectrometry (MS) approaches could be effective and beneficial methods for the investigation of biodiversity in ecological research. Our aims were to verify the applicability of MALDI-TOF MS in the rapid identification of closely related species, and to further develop it for sex determination in phenotypically similar fish focusing on the low mass range. For MALDI-TOF MS spectra analysis, ClinProTools software was applied, but our observed classification was also confirmed by Self Organizing Map. For verifying the wide applicability of the method, brains from invertebrate and vertebrate species were used in order to detect the species related markers from two mayflies and eight fish as well as sex-related markers within bleak. Seven Ephemera larvae and sixty-one fish species related markers were observed and nineteen sex-related markers were identified in bleak. Similar patterns were observed between the individuals within one species. In contrast, there were markedly diverse patterns between the different species and sexes visualized by SOMs. Two different Ephemera species and male or female fish were identified with 100% accuracy. The various fish species were classified into 8 species with a high level of accuracy (96.2%). Based on MS data, dendrogram was generated from different fish species by using ClinProTools software. This MS-based dendrogram shows relatively high correspondence with the phylogenetic relationships of both the studied species and orders. In summary, MALDI-TOF MS provides a cheap, reliable, sensitive and fast identification tool for researchers in the case of closely related species using mass spectra acquired in a low mass range to define specific molecular profiles. Moreover, we presented evidence for the first time for determination of sex within one fish species by using this method. We conclude that it is a powerful tool that can revolutionize ecological and

Rapid Discrimination of Haemophilus influenzae, H. parainfluenzae, and H. haemolyticus by Fluorescence In Situ Hybridization (FISH) and Two Matrix-Assisted Laser-Desorption-Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS) Platforms

PubMed Central

Frickmann, Hagen; Christner, Martin; Donat, Martina; Berger, Anja; Essig, Andreas; Podbielski, Andreas; Hagen, Ralf Matthias; Poppert, Sven

2013-01-01

Background Due to considerable differences in pathogenicity, Haemophilus influenzae, H. parainfluenzae and H. haemolyticus have to be reliably discriminated in routine diagnostics. Retrospective analyses suggest frequent misidentifications of commensal H. haemolyticus as H. influenzae. In a multi-center approach, we assessed the suitability of fluorescence in situ hybridization (FISH) and matrix-assisted laser-desorption-ionization time-of-flight mass-spectrometry (MALDI-TOF-MS) for the identification of H. influenzae, H. parainfluenzae and H. haemolyticus to species level. Methodology A strain collection of 84 Haemophilus spp. comprising 50 H. influenzae, 25 H. parainfluenzae, 7 H. haemolyticus, and 2 H. parahaemolyticus including 77 clinical isolates was analyzed by FISH with newly designed DNA probes, and two different MALDI-TOF-MS systems (Bruker, Shimadzu) with and without prior formic acid extraction. Principal Findings Among the 84 Haemophilus strains analyzed, FISH led to 71 correct results (85%), 13 uninterpretable results (15%), and no misidentifications. Shimadzu MALDI-TOF-MS resulted in 59 correct identifications (70%), 19 uninterpretable results (23%), and 6 misidentifications (7%), using colony material applied directly. Bruker MALDI-TOF-MS with prior formic acid extraction led to 74 correct results (88%), 4 uninterpretable results (5%) and 6 misidentifications (7%). The Bruker MALDI-TOF-MS misidentifications could be resolved by the addition of a suitable H. haemolyticus reference spectrum to the system's database. In conclusion, no analyzed diagnostic procedure was free of errors. Diagnostic results have to be interpreted carefully and alternative tests should be applied in case of ambiguous test results on isolates from seriously ill patients. PMID:23646201

Ultra high performance liquid chromatography with ion-trap TOF-MS for the fast characterization of flavonoids in Citrus bergamia juice.

PubMed

Sommella, Eduardo; Pepe, Giacomo; Pagano, Francesco; Tenore, Gian Carlo; Dugo, Paola; Manfra, Michele; Campiglia, Pietro

2013-10-01

We have developed a fast ultra HPLC with ion-trap TOF-MS method for the analysis of flavonoids in Citrus bergamia juice. With respect to the typical methods for the analysis of these matrices based on conventional HPLC techniques, a tenfold faster separation was attained. The use of a core-shell particle column ensured high resolution within the fast analysis time of only 5 min. Unambiguous determination of flavonoid identity was obtained by the employment of a hybrid ion-trap TOF mass spectrometer with high mass accuracy (average error 1.69 ppm). The system showed good retention time and peak area repeatability, with maximum RSD% values of 0.36 and 3.86, respectively, as well as good linearity (R(2) ≥ 0.99). Our results show that ultra HPLC can be a useful tool for ultra fast qualitative/quantitative analysis of flavonoid compounds in citrus fruit juices. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Temporal variation of VOC fluxes measured with PTR-TOF above a boreal forest

NASA Astrophysics Data System (ADS)

Schallhart, Simon; Rantala, Pekka; Kajos, Maija K.; Aalto, Juho; Mammarella, Ivan; Ruuskanen, Taina M.; Kulmala, Markku

2018-01-01

Between April and June 2013 fluxes of volatile organic compounds (VOCs) were measured in a Scots pine and Norway spruce forest using the eddy covariance (EC) method with a proton transfer reaction time-of-flight (PTR-TOF) mass spectrometer. The observations were performed above a boreal forest at the SMEAR II site in southern Finland.We found a total of 25 different compounds with exchange and investigated their seasonal variations from spring to summer. The majority of the net VOC flux was comprised of methanol, monoterpenes, acetone and butene + butanol. The butene + butanol emissions were concluded to not originate from the forest and, therefore, be anthropogenic. The VOC exchange followed a seasonal trend and the emissions increased from spring to summer. Only three compounds were emitted during the snowmelt while in summer emissions of some 19 VOCs were observed. During the measurement period in April, the emissions were dominated by butene + butanol, while during the start of the growing season and in summer, methanol was the most emitted compound. The main source of methanol was likely the growth of new biomass. During a 21-day period in June, the net VOC flux was 2.1 nmol m-2 s-1. This is on the lower end of PTR-TOF flux measurements from other ecosystems, which range from 2 to 10 nmol m-2 s-1. The EC flux results were compared with surface layer profile measurements, using a proton transfer reaction quadrupole mass spectrometer, which is permanently installed at the SMEAR II site. For the major compounds, the fluxes measured with the two different methods agreed well.

MALDI-TOF MS versus VITEK 2 ANC card for identification of anaerobic bacteria.

PubMed

Li, Yang; Gu, Bing; Liu, Genyan; Xia, Wenying; Fan, Kun; Mei, Yaning; Huang, Peijun; Pan, Shiyang

2014-05-01

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is an accurate, rapid and inexpensive technique that has initiated a revolution in the clinical microbiology laboratory for identification of pathogens. The Vitek 2 anaerobe and Corynebacterium (ANC) identification card is a newly developed method for identification of corynebacteria and anaerobic species. The aim of this study was to evaluate the effectiveness of the ANC card and MALDI-TOF MS techniques for identification of clinical anaerobic isolates. Five reference strains and a total of 50 anaerobic bacteria clinical isolates comprising ten different genera and 14 species were identified and analyzed by the ANC card together with Vitek 2 identification system and Vitek MS together with version 2.0 database respectively. 16S rRNA gene sequencing was used as reference method for accuracy in the identification. Vitek 2 ANC card and Vitek MS provided comparable results at species level for the five reference strains. Of 50 clinical strains, the Vitek MS provided identification for 46 strains (92%) to the species level, 47 (94%) to genus level, one (2%) low discrimination, two (4%) no identification and one (2%) misidentification. The Vitek 2 ANC card provided identification for 43 strains (86%) correct to the species level, 47 (94%) correct to the genus level, three (6%) low discrimination, three (6%) no identification and one (2%) misidentification. Both Vitek MS and Vitek 2 ANC card can be used for accurate routine clinical anaerobe identification. Comparing to the Vitek 2 ANC card, Vitek MS is easier, faster and more economic for each test. The databases currently available for both systems should be updated and further developed to enhance performance.

Rapid screening of abused drugs by direct analysis in real time (DART) coupled to time-of-flight mass spectrometry (TOF-MS) combined with ion mobility spectrometry (IMS).

PubMed

Lian, Ru; Wu, Zhongping; Lv, Xiaobao; Rao, Yulan; Li, Haiyang; Li, Jinghua; Wang, Rong; Ni, Chunfang; Zhang, Yurong

2017-10-01

Increasing in cases involving drugs of abuse leads to heavy burden for law enforcement agencies, exacerbating demand for rapid screening technique. In this study, atmospheric pressure ionization technologies including direct analysis in real time (DART) ion source coupled to a time-of-flight mass spectrometer (DART-TOF-MS)as well asdopant-assisted positive photoionization ion mobility spectrometry (DAPP-IMS) without radioactivity were utilized together as the powerful analytical tool for the rapid screening and identification of 53 abused drugs.The limits of detection (LOD) were 0.05-2μg/mL when using DART-TOF-MS and 0.02-2μg when using DAPP-IMS which could satisfy the actual requirement in forensic science laboratory. The advantages of this method included fast response, high-throughput potential, high specificity, and minimal sample preparation. A screening library of reduced mobility (K 0 ), accurate mass of informative precursor ion ([M+H] + ) and fragment ions was established respectively by employing a bench-top DAPP-IMS and TOF-MS in-source collision induced dissociation (CID) mode. Then the standardized screening procedure was developed with criteria for the confirmation of positive result. A total of 50 seized drug samples provided by local forensic laboratory we reanalyzed to testify the utility of the method. This study suggests that a method combing DART-TOF-MS and DAPP-IMS is promising for the rapid screening and identification of abused drugs with minimal sample preparation and absence of chromatography. Copyright © 2017 Elsevier B.V. All rights reserved.

Comprehensive analysis of proteins of pH fractionated samples using monolithic LC/MS/MS, intact MW measurement and MALDI-QIT-TOF MS

PubMed Central

Yoo, Chul; Patwa, Tasneem H.; Kreunin, Paweena; Miller, Fred R.; Huber, Christian G.; Nesvizhskii, Alexey I.; Lubman, David M.

2012-01-01

A comprehensive platform that integrates information from the protein and peptide levels by combining various MS techniques has been employed for the analysis of proteins in fully malignant human breast cancer cells. The cell lysates were subjected to chromatofocusing fractionation, followed by tryptic digestion of pH fractions for on-line monolithic RP-HPLC interfaced with linear ion trap MS analysis for rapid protein identification. This unique approach of direct analysis of pH fractions resulted in the identification of large numbers of proteins from several selected pH fractions, in which approximately 1.5 μg of each of the pH fraction digests was consumed for an analysis time of ca 50 min. In order to combine valuable information retained at the protein level with the protein identifications obtained from the peptide level information, the same pH fraction was analyzed using nonporous (NPS)-RP-HPLC/ESI-TOF MS to obtain intact protein MW measurements. In order to further validate the protein identification procedures from the fraction digest analysis, NPS-RP-HPLC separation was performed for off-line protein collection to closely examine each protein using MALDI-TOF MS and MALDI-quadrupole ion trap (QIT)-TOF MS, and excellent agreement of protein identifications was consistently observed. It was also observed that the comparison to intact MW and other MS information was particularly useful for analyzing proteins whose identifications were suggested by one sequenced peptide from fraction digest analysis. PMID:17206599

Novel approaches for the taxonomic and metabolic characterization of lactobacilli: Integration of 16S rRNA gene sequencing with MALDI-TOF MS and 1H-NMR

PubMed Central

Parolin, Carola; Giordani, Barbara; Compri, Monica; Cevenini, Roberto; Vitali, Beatrice

2017-01-01

Lactobacilli represent a wide range of bacterial species with several implications for the human host. They play a crucial role in maintaining the ecological equilibrium of different biological niches and are essential for fermented food production and probiotic formulation. Despite the consensus about the ‘health-promoting’ significance of Lactobacillus genus, its genotypic and phenotypic characterization still poses several difficulties. The aim of this study was to assess the integration of different approaches, genotypic (16S rRNA gene sequencing), proteomic (MALDI-TOF MS) and metabolomic (1H-NMR), for the taxonomic and metabolic characterization of Lactobacillus species. For this purpose we analyzed 40 strains of various origin (intestinal, vaginal, food, probiotics), belonging to different species. The high discriminatory power of MALDI-TOF for species identification was underlined by the excellent agreement with the genotypic analysis. Indeed, MALDI-TOF allowed to correctly identify 39 out of 40 Lactobacillus strains at the species level, with an overall concordance of 97.5%. In the perspective to simplify the MALDI TOF sample preparation, especially for routine practice, we demonstrated the perfect agreement of the colony-picking from agar plates with the protein extraction protocol. 1H-NMR analysis, applied to both culture supernatants and bacterial lysates, identified a panel of metabolites whose variations in concentration were associated with the taxonomy, but also revealed a high intra-species variability that did not allow a species-level identification. Therefore, despite not suitable for mere taxonomic purposes, metabolomics can be useful to correlate particular biological activities with taxonomy and to understand the mechanisms related to the antimicrobial effect shown by some Lactobacillus species. PMID:28207855

Ni62(n,γ) and Ni63(n,γ) cross sections measured at the n_TOF facility at CERN

NASA Astrophysics Data System (ADS)

Lederer, C.; Massimi, C.; Berthoumieux, E.; Colonna, N.; Dressler, R.; Guerrero, C.; Gunsing, F.; Käppeler, F.; Kivel, N.; Pignatari, M.; Reifarth, R.; Schumann, D.; Wallner, A.; Altstadt, S.; Andriamonje, S.; Andrzejewski, J.; Audouin, L.; Barbagallo, M.; Bécares, V.; Bečvář, F.; Belloni, F.; Berthier, B.; Billowes, J.; Boccone, V.; Bosnar, D.; Brugger, M.; Calviani, M.; Calviño, F.; Cano-Ott, D.; Carrapiço, C.; Cerutti, F.; Chiaveri, E.; Chin, M.; Cortés, G.; Cortés-Giraldo, M. A.; Dillmann, I.; Domingo-Pardo, C.; Duran, I.; Dzysiuk, N.; Eleftheriadis, C.; Fernández-Ordóñez, M.; Ferrari, A.; Fraval, K.; Ganesan, S.; García, A. R.; Giubrone, G.; Gómez-Hornillos, M. B.; Gonçalves, I. F.; González-Romero, E.; Gramegna, F.; Griesmayer, E.; Gurusamy, P.; Harrisopulos, S.; Heil, M.; Ioannides, K.; Jenkins, D. G.; Jericha, E.; Kadi, Y.; Karadimos, D.; Korschinek, G.; Krtička, M.; Kroll, J.; Langer, C.; Lebbos, E.; Leeb, H.; Leong, L. S.; Losito, R.; Lozano, M.; Manousos, A.; Marganiec, J.; Marrone, S.; Martinez, T.; Mastinu, P. F.; Mastromarco, M.; Meaze, M.; Mendoza, E.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Mirea, M.; Mondalaers, W.; Paradela, C.; Pavlik, A.; Perkowski, J.; Plag, R.; Plompen, A.; Praena, J.; Quesada, J. M.; Rauscher, T.; Riego, A.; Roman, F.; Rubbia, C.; Sarmento, R.; Schillebeeckx, P.; Schmidt, S.; Tagliente, G.; Tain, J. L.; Tarrío, D.; Tassan-Got, L.; Tsinganis, A.; Tlustos, L.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vermeulen, M. J.; Versaci, R.; Vlachoudis, V.; Vlastou, R.; Ware, T.; Weigand, M.; Weiß, C.; Wright, T. J.; Žugec, P.; n TOF Collaboration

2014-02-01

The cross section of the Ni62(n,γ) reaction was measured with the time-of-flight technique at the neutron time-of-flight facility n_TOF at CERN. Capture kernels of 42 resonances were analyzed up to 200 keV neutron energy and Maxwellian averaged cross sections (MACS) from kT = 5-100 keV were calculated. With a total uncertainty of 4.5%, the stellar cross section is in excellent agreement with the the KADoNiS compilation at kT=30 keV, while being systematically lower up to a factor of 1.6 at higher stellar temperatures. The cross section of the Ni63(n ,γ) reaction was measured for the first time at n_TOF. We determined unresolved cross sections from 10 to 270 keV with a systematic uncertainty of 17%. These results provide fundamental constraints on s-process production of heavier species, especially the production of Cu in massive stars, which serve as the dominant source of Cu in the solar system.

Linearly scaling and almost Hamiltonian dielectric continuum molecular dynamics simulations through fast multipole expansions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de

2015-11-14

Hamiltonian Dielectric Solvent (HADES) is a recent method [S. Bauer et al., J. Chem. Phys. 140, 104103 (2014)] which enables atomistic Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric solvent continua. Such simulations become rapidly impractical for large proteins, because the computational effort of HADES scales quadratically with the number N of atoms. If one tries to achieve linear scaling by applying a fast multipole method (FMM) to the computation of the HADES electrostatics, the Hamiltonian character (conservation of total energy, linear, and angular momenta) may get lost. Here, we show that the Hamiltonian character of HADESmore » can be almost completely preserved, if the structure-adapted fast multipole method (SAMM) as recently redesigned by Lorenzen et al. [J. Chem. Theory Comput. 10, 3244-3259 (2014)] is suitably extended and is chosen as the FMM module. By this extension, the HADES/SAMM forces become exact gradients of the HADES/SAMM energy. Their translational and rotational invariance then guarantees (within the limits of numerical accuracy) the exact conservation of the linear and angular momenta. Also, the total energy is essentially conserved—up to residual algorithmic noise, which is caused by the periodically repeated SAMM interaction list updates. These updates entail very small temporal discontinuities of the force description, because the employed SAMM approximations represent deliberately balanced compromises between accuracy and efficiency. The energy-gradient corrected version of SAMM can also be applied, of course, to MD simulations of all-atom solvent-solute systems enclosed by periodic boundary conditions. However, as we demonstrate in passing, this choice does not offer any serious advantages.« less

Plasma protein absolute quantification by nano-LC Q-TOF UDMSE for clinical biomarker verification

PubMed Central

ILIES, MARIA; IUGA, CRISTINA ADELA; LOGHIN, FELICIA; DHOPLE, VISHNU MUKUND; HAMMER, ELKE

2017-01-01

Background and aims Proteome-based biomarker studies are targeting proteins that could serve as diagnostic, prognosis, and prediction molecules. In the clinical routine, immunoassays are currently used for the absolute quantification of such biomarkers, with the major limitation that only one molecule can be targeted per assay. The aim of our study was to test a mass spectrometry based absolute quantification method for the verification of plasma protein sets which might serve as reliable biomarker panels for the clinical practice. Methods Six EDTA plasma samples were analyzed after tryptic digestion using a high throughput data independent acquisition nano-LC Q-TOF UDMSE proteomics approach. Synthetic Escherichia coli standard peptides were spiked in each sample for the absolute quantification. Data analysis was performed using ProgenesisQI v2.0 software (Waters Corporation). Results Our method ensured absolute quantification of 242 non redundant plasma proteins in a single run analysis. The dynamic range covered was 105. 86% were represented by classical plasma proteins. The overall median coefficient of variation was 0.36, while a set of 63 proteins was found to be highly stable. Absolute protein concentrations strongly correlated with values reviewed in the literature. Conclusions Nano-LC Q-TOF UDMSE proteomic analysis can be used for a simple and rapid determination of absolute amounts of plasma proteins. A large number of plasma proteins could be analyzed, while a wide dynamic range was covered with low coefficient of variation at protein level. The method proved to be a reliable tool for the quantification of protein panel for biomarker verification in the clinical practice. PMID:29151793

Optimized light sharing for high-resolution TOF PET detector based on digital silicon photomultipliers.

PubMed

Marcinkowski, R; España, S; Van Holen, R; Vandenberghe, S

2014-12-07

The majority of current whole-body PET scanners are based on pixelated scintillator arrays with a transverse pixel size of 4 mm. However, recent studies have shown that decreasing the pixel size to 2 mm can significantly improve image spatial resolution. In this study, the performance of Digital Photon Counter (DPC) from Philips Digital Photon Counting (PDPC) was evaluated to determine their potential for high-resolution whole-body time of flight (TOF) PET scanners. Two detector configurations were evaluated. First, the DPC3200-44-22 DPC array was coupled to a LYSO block of 15 × 15 2 × 2 × 22 mm(3) pixels through a 1 mm thick light guide. Due to light sharing among the dies neighbour logic of the DPC was used. In a second setup the same DPC was coupled directly to a scalable 4 × 4 LYSO matrix of 1.9 × 1.9 × 22 mm(3) crystals with a dedicated reflector arrangement allowing for controlled light sharing patterns inside the matrix. With the first approach an average energy resolution of 14.5% and an average CRT of 376 ps were achieved. For the second configuration an average energy resolution of 11% and an average CRT of 295 ps were achieved. Our studies show that the DPC is a suitable photosensor for a high-resolution TOF-PET detector. The dedicated reflector arrangement allows one to achieve better performances than the light guide approach. The count loss, caused by dark counts, is overcome by fitting the matrix size to the size of DPC single die.

Discrimination of Aspergillus lentulus from Aspergillus fumigatus by Raman spectroscopy and MALDI-TOF MS.

PubMed

Verwer, P E B; van Leeuwen, W B; Girard, V; Monnin, V; van Belkum, A; Staab, J F; Verbrugh, H A; Bakker-Woudenberg, I A J M; van de Sande, W W J

2014-02-01

In 2005, a new sibling species of Aspergillus fumigatus was discovered: Aspergillus lentulus. Both species can cause invasive fungal disease in immune-compromised patients. The species are morphologically very similar. Current techniques for identification are PCR-based or morphology-based. These techniques are labour-intense and not sufficiently discriminatory. Since A. lentulus is less susceptible to several antifungal agents, it is important to correctly identify the causative infectious agent in order to optimize antifungal therapy. In this study we determined whether Raman spectroscopy and/or MALDI-TOF MS were able to differentiate between A. lentulus and A. fumigatus. For 16 isolates of A. lentulus and 16 isolates of A. fumigatus, Raman spectra and peptide profiles were obtained using the Spectracell and MALDI-TOF MS (VITEK MS RUO, bioMérieux) respectively. In order to obtain reliable Raman spectra for A. fumigatus and A. lentulus, the culture medium needed to be adjusted to obtain colourless conidia. Only Raman spectra obtained from colourless conidia were reproducible and correctly identified 25 out of 32 (78 %) of the Aspergillus strains. For VITEK MS RUO, no medium adjustments were necessary. Pigmented conidia resulted in reproducible peptide profiles as well in this case. VITEK MS RUO correctly identified 100 % of the Aspergillus isolates, within a timeframe of approximately 54 h including culture. Of the two techniques studied here, VITEK MS RUO was superior to Raman spectroscopy in the discrimination of A. lentulus from A. fumigatus. VITEK MS RUO seems to be a successful technique in the daily identification of Aspergillus spp. within a limited timeframe.

MALDI-TOF mass spectrometry for the monitoring of she-donkey's milk contamination or adulteration.

PubMed

Cunsolo, Vincenzo; Muccilli, Vera; Saletti, Rosaria; Foti, Salvatore

2013-02-01

Donkey's milk (DM), representing a safe and alternative food in both IgE-mediated and non-IgE-mediated cow's milk protein allergy, can be categorized as precious pharma-food. Moreover, an economically relevant interest for the use of DM in cosmetology is also developing. The detection of adulterations and contaminations of DM is a matter of fundamental importance from both an economic and allergenic standpoint, and, to this aim, fast and efficient analytical approaches to assess the authenticity of this precious nutrient are desirable. Here, a rapid matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS)-based method aimed to the detection of bovine or caprine milk in raw DM is reported. The presence of the extraneous milks was revealed by monitoring the protein profiles of the most abundant whey proteins, α-lactalbumin (α-LA) and β-lactoglobulin, used as molecular markers. The possibility of obtaining a quantitative analysis of the level of cow or goat milk in DM based on the MALDI-TOF peak areas of α-LAs was also explored. The results showed that the experimental quantitative values were in good agreement with the real composition of each mixture. As pretreatment of the milk samples is not required, and owing to the speed and the high sensitivity of MALDI-MS, the protocol here reported could represent a reliable method for routine analyses aimed to assess the absence of contamination in raw fresh DM samples. Copyright © 2013 John Wiley & Sons, Ltd.

Magnetic graphene composites as both an adsorbent for sample enrichment and a MALDI-TOF MS matrix for the detection of nitropolycyclic aromatic hydrocarbons in PM2.5.

PubMed

Zhang, Jiangang; Zhang, Li; Li, Ruijin; Hu, Di; Ma, Nengxuan; Shuang, Shaomin; Cai, Zongwei; Dong, Chuan

2015-03-07

A simple and rapid method that uses synthesized magnetic graphene composites as both an adsorbent for enrichment and as a matrix in MALDI-TOF MS analysis was developed for the detection of nitropolycyclic hydrocarbons (nitro-PAHs) in PM2.5 samples. Three nitro-PAHs were detected down to sub pg μL(-1) levels based on calculations from an instrumental signal-to-noise better than 3, which shows the feasibility of using the new materials in MALDI-TOF MS as a potential powerful analytical approach for the analysis of nitro-PAHs in PM2.5 samples.

Effect of nano-titanium dioxide on mechanical and electrical properties and microstructure of reactive powder concrete

NASA Astrophysics Data System (ADS)

Li, Zhen; Han, Baoguo; Yu, Xun; Dong, Sufen; Zhang, Liqing; Dong, Xufeng; Ou, Jinping

2017-09-01

Nano-titanium dioxide (NT) was introduced into reactive powder concrete (RPC) to prepare NT reinforced RPC (NTRRPC) in this study. The mechanical and electrical properties and microstructure of NTRRPC were investigated. Research results indicate that NT can accelerate the hydration of RPC at early ages due to its nucleation effect. Cement hydration degree is free from the inclusion of NT at the curing age of 28 d. However, x-ray powder diffraction (XRD) analysis and scanning electron microscope (SEM) observation confirm that the nucleation effect of NT not only can reduce the orientation degree of calcium hydroxide (CH), but also can restrict the size of CH. Hence, NT may also benefit to enhance the strength at late age. The flexural and compressive strengths of NTRRPC at age of 28 d achieve increases of 47.07% (relative increase rate)/3.62 MPa (the absolute increase) and 18.05%/18.42 MPa with respect to the control RPC, respectively. The compactedness model demonstrates that NT can improve the compactedness of RPC and reduce the porosity of RPC from 9.04% to 6.96%. SEM observations suggest that the NT can refine the pores and micro cracks of the RPC by its filling effect, which is in accordance with the result of compactedness model. In addition, the addition of NT can improve the electrically conductivity property of RPC and make a 13.61% decrease in the electrical resistivity of RPC.

Practises to identify and prevent adverse aircraft-and-rotorcraft-pilot couplings-A ground simulator perspective

NASA Astrophysics Data System (ADS)

Pavel, Marilena D.; Jump, Michael; Masarati, Pierangelo; Zaichik, Larisa; Dang-Vu, Binh; Smaili, Hafid; Quaranta, Giuseppe; Stroosma, Olaf; Yilmaz, Deniz; Johnes, Michael; Gennaretti, Massimmo; Ionita, Achim

2015-08-01

The aviation community relies heavily on flight simulators as a fundamental tool for research, pilot training and development of any new aircraft design. The goal of the present paper is to provide a review on how effective ground simulation is as an assessment tool for unmasking adverse Aircraft-and-Rotorcraft Pilot Couplings (APC/RPC). Although it is generally believed that simulators are not reliable in revealing the existence of A/RPC tendencies, the paper demonstrates that a proper selection of high-gain tasks combined with appropriate motion and visual cueing can reveal negative features of a particular aircraft that may lead to A/RPC. The paper discusses new methods for real-time A/RPC detection that can be used as a tool for unmasking adverse A/RPC. Although flight simulators will not achieve the level of reality of in-flight testing, exposing A/RPC tendencies in the simulator may be the only convenient safe place to evaluate the wide range of conditions that could produce hazardous A/RPC events.

Application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in Alzheimer's disease.

PubMed

Grela, Agatha; Turek, Agata; Piekoszewski, Wojciech

2012-02-11

Alzheimer's disease is becoming an increasing problem in our aging society. According to our knowledge, so far, no effective pharmacotherapy to cure the cause of the disease has been developed. Therefore, early diagnosis is needed, which will result in implementation of a drug therapy aimed at decreasing and/or inhibiting disease development. Mass spectrometry techniques (MS) have a wide range of applications in proteomics and the search for biomarkers of neurodegenerative disorders, opening new possibilities in diagnostics. Identification of proteins in body fluids (like cerebrospinal fluid or blood) is possible due to MS spectra analysis. The detected changes in protein concentrations are connected with pathological states in an organism and, therefore, can be regarded as biomarkers. Developing procedures for proteome analysis might result in fast diagnosis, as well as creating better suited pharmaceuticals. This paper reviews the search of biomarkers in cerebrospinal fluid and blood. Later on, the use of matrix-assisted-laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in proteomics, focusing on blood-related biomarkers, is discussed. The aim of the work is also to highlight the advantages and disadvantages of MALDI-TOF-based analyses.

Measurement and analysis of the 241Am neutron capture cross section at the n_TOF facility at CERN

NASA Astrophysics Data System (ADS)

Mendoza, E.; Cano-Ott, D.; Altstadt, S.; Andriamonje, S.; Andrzejewski, J.; Audouin, L.; Balibrea, J.; Bécares, V.; Barbagallo, M.; Bečvář, F.; Belloni, F.; Berthier, B.; Berthoumieux, E.; Billowes, J.; Bosnar, D.; Brugger, M.; Calviño, F.; Calviani, M.; Carrapiço, C.; Cerutti, F.; Chiaveri, E.; Chin, M.; Colonna, N.; Cortés, G.; Cortés-Giraldo, M. A.; Diakaki, M.; Dillmann, I.; Domingo-Pardo, C.; Durán, I.; Dzysiuk, N.; Eleftheriadis, C.; Ferrari, A.; Fraval, K.; Furman, V.; Gómez-Hornillos, M. B.; Ganesan, S.; García, A. R.; Giubrone, G.; Gonçalves, I. F.; González, E.; Goverdovski, A.; Gramegna, F.; Griesmayer, E.; Guerrero, C.; Gunsing, F.; Gurusamy, P.; Heftrich, T.; Heinitz, S.; Hernández-Prieto, A.; Heyse, J.; Jenkins, D. G.; Jericha, E.; Käppeler, F.; Kadi, Y.; Karadimos, D.; Katabuchi, T.; Ketlerov, V.; Khryachkov, V.; Koehler, P.; Kokkoris, M.; Kroll, J.; Krtička, M.; Lampoudis, C.; Langer, C.; Leal-Cidoncha, E.; Lederer, C.; Leeb, H.; Leong, L. S.; Lerendegui-Marco, J.; Licata, M.; López, D.; Losito, R.; Manousos, A.; Marganiec, J.; Martínez, T.; Massimi, C.; Mastinu, P.; Mastromarco, M.; Mengoni, A.; Milazzo, P. M.; Mingrone, F.; Mirea, M.; Mondelaers, W.; Paradela, C.; Pavlik, A.; Perkowski, J.; Plompen, A. J. M.; Praena, J.; Quesada, J. M.; Rauscher, T.; Reifarth, R.; Riego-Perez, A.; Robles, M.; Roman, F.; Rubbia, C.; Ryan, J. A.; Sabaté-Gilarte, M.; Sarmento, R.; Saxena, A.; Schillebeeckx, P.; Schmidt, S.; Schumann, D.; Sedyshev, P.; Tagliente, G.; Tain, J. L.; Tarifeño-Saldivia, A.; Tarrío, D.; Tassan-Got, L.; Tsinganis, A.; Valenta, S.; Vannini, G.; Variale, V.; Vaz, P.; Ventura, A.; Vermeulen, M. J.; Versaci, R.; Vlachoudis, V.; Vlastou, R.; Wallner, A.; Ware, T.; Weigand, M.; Weiss, C.; Wright, T.; Žugec, P.; n TOF Collaboration

2018-05-01

The 241Am(n ,γ ) cross section has been measured at the n_TOF facility at CERN with the n_TOF BaF2 Total Absorption Calorimeter in the energy range between 0.2 eV and 10 keV. Our results are analyzed as resolved resonances up to 700 eV, allowing a more detailed description of the cross section than in the current evaluations, which contain resolved resonances only up to 150-160 eV. The cross section in the unresolved resonance region is perfectly consistent with the predictions based on the average resonance parameters deduced from the resolved resonances, thus obtaining a consistent description of the cross section in the full neutron energy range under study. Below 20 eV, our results are in reasonable agreement with JEFF-3.2 as well as with the most recent direct measurements of the resonance integral, and differ up to 20-30% with other experimental data. Between 20 eV and 1 keV, the disagreement with other experimental data and evaluations gradually decreases, in general, with the neutron energy. Above 1 keV, we find compatible results with previously existing values.

Global relative quantification with liquid chromatography-matrix-assisted laser desorption ionization time-of-flight (LC-MALDI-TOF)--cross-validation with LTQ-Orbitrap proves reliability and reveals complementary ionization preferences.

PubMed

Hessling, Bernd; Büttner, Knut; Hecker, Michael; Becher, Dörte

2013-10-01

Quantitative LC-MALDI is an underrepresented method, especially in large-scale experiments. The additional fractionation step that is needed for most MALDI-TOF-TOF instruments, the comparatively long analysis time, and the very limited number of established software tools for the data analysis render LC-MALDI a niche application for large quantitative analyses beside the widespread LC-electrospray ionization workflows. Here, we used LC-MALDI in a relative quantification analysis of Staphylococcus aureus for the first time on a proteome-wide scale. Samples were analyzed in parallel with an LTQ-Orbitrap, which allowed cross-validation with a well-established workflow. With nearly 850 proteins identified in the cytosolic fraction and quantitative data for more than 550 proteins obtained with the MASCOT Distiller software, we were able to prove that LC-MALDI is able to process highly complex samples. The good correlation of quantities determined via this method and the LTQ-Orbitrap workflow confirmed the high reliability of our LC-MALDI approach for global quantification analysis. Because the existing literature reports differences for MALDI and electrospray ionization preferences and the respective experimental work was limited by technical or methodological constraints, we systematically compared biochemical attributes of peptides identified with either instrument. This genome-wide, comprehensive study revealed biases toward certain peptide properties for both MALDI-TOF-TOF- and LTQ-Orbitrap-based approaches. These biases are based on almost 13,000 peptides and result in a general complementarity of the two approaches that should be exploited in future experiments.

Molecular imaging of enhanced Na + expression in the liver of total sleep deprived rats by TOF-SIMS

NASA Astrophysics Data System (ADS)

Chang, Hung-Ming; Chen, Bo-Jung; Wu, Un-In; Huang, Yi-Lun; Mai, Fu-Der

2008-12-01

Sleep disorder is associated with metabolic disturbances, which was related to oxidative stress and subsequently sodium overload. Since liver plays important roles in metabolic regulation, present study is aimed to determine whether hepatic sodium, together with oxidative stress, would significantly alter after total sleep deprivation (TSD). Sodium ion was investigated by time-of-flight secondary ion mass spectrometry (TOF-SIMS). Parameter for oxidative stress was examined by heat shock protein-25 (HSP-25) immunohistochemistry. TOF-SIMS spectrum indicated that hepatic Na +/K + ratio counting as 82.41 ± 9.5 was obtained in normal rats. Sodium ions were distributed in hepatocytes with several aggregations. However, following TSD, the intensity for Na +/K + ratio was relatively increased (101.94 ± 6.9) and signals for sodium image were strongly expressed throughout hepatocytes without spatial localization. Quantitative analysis revealed that HSP-25 staining intensity is 1.78 ± 0.27 in TSD rats, which was significantly higher than that of normal ones (0.68 ± 0.15). HSP-25 augmentation suggests that hepatocytes suffer from oxidative stress following TSD. Concerning oxidative stress induced sodium overload would impair metabolic function; enhanced hepatic sodium expression after TSD may be a major cause of TSD relevant metabolic diseases.

[Dynamic variation of components in exocarp of Juglans mandshurica with browning based on UPLC-Q-TOF/MS].

PubMed

Sun, Guo-Dong; Huo, Jin-Hai; Xie, Rong-Juan; Wang, Wei-Ming

2017-08-01

To analyze the dynamic changes in components in exocarp of Juglans mandshurica at different browning periods. Twenty-six batches of exocarp of J. mandshurica samples from thirteen browning periods were assessed by UPLC-Q-TOF-MS/MS. The formula of different compounds were determined by accurate mass and isotopic abundance ratio from target screening function of Peakview 2.0/masterview1.0 software. Then their structures were determined by analysis of MS/MS fragment or comparison with standard substances and references. The contents of chemical components were changed significantly in different browning periods and twenty five compounds were identified or inferred. Of the 13 naphthoquinone compounds, the contents of 6 compounds with similar parent nucleus as juglone and 3 naphthoquinone glycosides compounds were decreased significantly, and 4 naphthoquinone derivatives such as regiolone were produced; the contents of four flavones and two phenolic acids compounds were decreased significantly; and the contents of 6 diarylheptanoids compounds were increased significantly. UPLC-Q-TOF/MS method can be used to identify and analyze the chemical constituents from exocarp of J. mandshurica rapidly and accurately, and analyze the rules of dynamic changes, to reveal the browning of Chinese medicinal materials and its effects on compositions of fruits and vegetables. Copyright© by the Chinese Pharmaceutical Association.

Rapid MALDI-TOF Mass Spectrometry Strain Typing during a Large Outbreak of Shiga-Toxigenic Escherichia coli

PubMed Central

Christner, Martin; Trusch, Maria; Rohde, Holger; Kwiatkowski, Marcel; Schlüter, Hartmut; Wolters, Manuel; Aepfelbacher, Martin; Hentschke, Moritz

2014-01-01

Background In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Methods Specific peaks in the outbreak strain’s spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Results Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. Conclusions MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow. PMID:25003758

UPLC-MS-IT-TOF Identification of Circumdatins Produced by Aspergillus ochraceus.

PubMed

González-Jartı N, Jesús M; Alfonso, Amparo; Sainz, María J; Vieytes, Mercedes R; Botana, Luis M

2017-06-14

A method based on the combined use of ultraperformance liquid chromatography coupled to mass spectrometry-ion trap-time-of-flight (UPLC-MS-IT-TOF) detection was employed to identify the metabolite production of Aspergillus ochraceus, which is the major cause of food and feed contamination due to ochratoxin A. Under the proposed chromatographic conditions, seven metabolites belonging to the family of circumdatins were separated and identified. Their initial identification was performed through the exact molecular formula, as a function of their accurate mass. Collision-induced dissociation was applied to predict precursor and product ions, and the elemental composition of each compound was obtained. The elimination of nitrogenous groups followed by successive losses of carbonyl groups is the common fragmentation pathway of circumdatins. With the fragmentation data obtained, an UPLC-MS/MS method was created and optimized to detect circumdatins in corn samples.

Unravelling the complex venom landscapes of lethal Australian funnel-web spiders (Hexathelidae: Atracinae) using LC-MALDI-TOF mass spectrometry.

PubMed

Palagi, Alexandre; Koh, Jennifer M S; Leblanc, Mathieu; Wilson, David; Dutertre, Sébastien; King, Glenn F; Nicholson, Graham M; Escoubas, Pierre

2013-03-27

Spider venoms represent vast sources of bioactive molecules whose diversity remains largely unknown. Indeed, only a small subset of species have been studied out of the ~43,000 extant spider species. The present study investigated inter- and intra-species venom complexity in 18 samples collected from a variety of lethal Australian funnel-web spiders (Mygalomorphae: Hexathelidae: Atracinae) using C4 reversed-phase separation coupled to offline MALDI-TOF mass spectrometry (LC-MALDI-TOF MS). An in-depth investigation focusing on four atracine venoms (male Illawarra wisharti, male and female Hadronyche cerberea, and female Hadronyche infensa Toowoomba) revealed, on average, ~800 peptides in female venoms while male venoms contained ~400 peptides, distributed across most HPLC fractions. This is significantly higher than previous estimates of peptide expression in mygalomorph venoms. These venoms also showed distinct intersexual as well as intra- and inter-species variation in peptide masses. Construction of both 3D and 2D contour plots revealed that peptide mass distributions in all 18 venoms were centered around the 3200-5400m/z range and to a lesser extent the 6600-8200m/z range, consistent with previously described hexatoxins. These findings highlight the extensive diversity of peptide toxins in Australian funnel-web spider venoms that that can be exploited as novel therapeutic and biopesticide lead molecules. In the present study we describe the complexity of 18 venoms from lethal Australian funnel-web spiders using LC-MALDI-TOF MS. The study includes an in-depth investigation, focusing on four venoms, that revealed the presence of ~800 peptides in female venoms and ~400 peptides in male venoms. This is significantly higher than previous estimates of peptide expression in spider venoms. By constructing both 3D and 2D contour plots we were also able to reveal the distinct intersexual as well as intra- and inter-species variation in venom peptide masses. We show that

Revealing the glycation sites in synthetic neoglycoconjugates formed by conjugation of the antigenic monosaccharide hapten of Vibrio cholerae O1, serotype Ogawa with the BSA protein carrier using LC-ESI-QqTOF-MS/MS

PubMed Central

Jahouh, Farid; Saksena, Rina; Kováč, Pavol; Banoub, Joseph

2012-01-01

In this manuscript, we present the determination of glycation sites in synthetic neoglycoconjugates formed by conjugation of the antigenic monosaccharide hapten of Vibrio cholerae O1 serotype Ogawa to BSA using nano- liquid chromatography electrospray ionization quadrupole time-of-flight tandem mass spectroscopy (LC-ESI-QqTOF-MS/MS). The matrix-assisted laser desorption/ionization-TOF/TOF-MS/MS analyses of the tryptic digests of the glycoconjugates having a hapten:BSA ratio of 4.3:1, 6.6:1 and 13.2:1 revealed only three glycation sites, on the following lysine residues: Lys 235, Lys 437 and Lys 455. Digestion of the neoglycoconjugates with the proteases trypsin and GluC V8 gave complementary structural information and was shown to maximize the number of recognized glycation sites. Here, we report identification of 20, 27 and 33 glycation sites using LC-ESI-QqTOF-MS/MS analysis of a series of synthetic neoglycoconjugates with a hapten:BSA ratio of, respectively, 4.3:1, 6.6:1 and 13.2:1. We also tentatively propose that all the glycated lysine residues are located mainly near the outer surface of the protein. PMID:22791257

Differentiation of clinically relevant Mucorales Rhizopus microsporus and R. arrhizus by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

PubMed

Dolatabadi, Somayeh; Kolecka, Anna; Versteeg, Matthijs; de Hoog, Sybren G; Boekhout, Teun

2015-07-01

This study addresses the usefulness of matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS for reliable identification of the two most frequently occurring clinical species of Rhizopus, namely Rhizopus arrhizus with its two varieties, arrhizus and delemar, and Rhizopus microsporus. The test-set comprised 38 isolates of clinical and environmental origin previously identified by internal transcribed spacer (ITS) sequencing of rDNA. Multi-locus sequence data targeting three gene markers (ITS, ACT, TEF ) showed two monophylic clades for Rhizopus arrhizus and Rhizopus microsporus (bootstrap values of 99 %). Cluster analysis confirmed the presence of two distinct clades within Rhizopus arrhizus representing its varieties arrhizus and delemar. The MALDI Biotyper 3.0 Microflex LT platform (Bruker Daltonics) was used to confirm the distinction between Rhizopus arrhizus and Rhizopus microsporus and the presence of two varieties within the species Rhizopus arrhizus. An in-house database of 30 reference main spectra (MSPs) was initially tested for correctness using commercially available databases of Bruker Daltonics. By challenging the database with the same strains of which an in-house database was created, automatic identification runs confirmed that MALDI-TOF MS is able to recognize the strains at the variety level. Based on principal component analysis, two MSP dendrograms were created and showed concordance with the multi-locus tree; thus, MALDI-TOF MS is a useful tool for diagnostics of mucoralean species.

Next-generation technologies for spatial proteomics: Integrating ultra-high speed MALDI-TOF and high mass resolution MALDI FTICR imaging mass spectrometry for protein analysis.

PubMed

Spraggins, Jeffrey M; Rizzo, David G; Moore, Jessica L; Noto, Michael J; Skaar, Eric P; Caprioli, Richard M

2016-06-01

MALDI imaging mass spectrometry is a powerful analytical tool enabling the visualization of biomolecules in tissue. However, there are unique challenges associated with protein imaging experiments including the need for higher spatial resolution capabilities, improved image acquisition rates, and better molecular specificity. Here we demonstrate the capabilities of ultra-high speed MALDI-TOF and high mass resolution MALDI FTICR IMS platforms as they relate to these challenges. High spatial resolution MALDI-TOF protein images of rat brain tissue and cystic fibrosis lung tissue were acquired at image acquisition rates >25 pixels/s. Structures as small as 50 μm were spatially resolved and proteins associated with host immune response were observed in cystic fibrosis lung tissue. Ultra-high speed MALDI-TOF enables unique applications including megapixel molecular imaging as demonstrated for lipid analysis of cystic fibrosis lung tissue. Additionally, imaging experiments using MALDI FTICR IMS were shown to produce data with high mass accuracy (<5 ppm) and resolving power (∼75 000 at m/z 5000) for proteins up to ∼20 kDa. Analysis of clear cell renal cell carcinoma using MALDI FTICR IMS identified specific proteins localized to healthy tissue regions, within the tumor, and also in areas of increased vascularization around the tumor. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.