Peptide de novo sequencing of mixture tandem mass spectra.

PubMed

Gorshkov, Vladimir; Hotta, Stéphanie Yuki Kolbeck; Verano-Braga, Thiago; Kjeldsen, Frank

2016-09-01

The impact of mixture spectra deconvolution on the performance of four popular de novo sequencing programs was tested using artificially constructed mixture spectra as well as experimental proteomics data. Mixture fragmentation spectra are recognized as a limitation in proteomics because they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co-isolation and thus prone to false identifications. The deconvolution approach matched complementary b-, y-ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co-isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced peptides. The improvement was in the range of 20-35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight candidate peptide score distribution and high sensitivity to small changes in the mass spectrum introduced by the employed deconvolution method could explain some of the missing peptide identifications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Peptide de novo sequencing of mixture tandem mass spectra

PubMed Central

Hotta, Stéphanie Yuki Kolbeck; Verano‐Braga, Thiago; Kjeldsen, Frank

2016-01-01

The impact of mixture spectra deconvolution on the performance of four popular de novo sequencing programs was tested using artificially constructed mixture spectra as well as experimental proteomics data. Mixture fragmentation spectra are recognized as a limitation in proteomics because they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co‐isolation and thus prone to false identifications. The deconvolution approach matched complementary b‐, y‐ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co‐isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced peptides. The improvement was in the range of 20–35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight candidate peptide score distribution and high sensitivity to small changes in the mass spectrum introduced by the employed deconvolution method could explain some of the missing peptide identifications. PMID:27329701

Similarity of High-Resolution Tandem Mass Spectrometry Spectra of Structurally Related Micropollutants and Transformation Products

NASA Astrophysics Data System (ADS)

Schollée, Jennifer E.; Schymanski, Emma L.; Stravs, Michael A.; Gulde, Rebekka; Thomaidis, Nikolaos S.; Hollender, Juliane

2017-12-01

High-resolution tandem mass spectrometry (HRMS2) with electrospray ionization is frequently applied to study polar organic molecules such as micropollutants. Fragmentation provides structural information to confirm structures of known compounds or propose structures of unknown compounds. Similarity of HRMS2 spectra between structurally related compounds has been suggested to facilitate identification of unknown compounds. To test this hypothesis, the similarity of reference standard HRMS2 spectra was calculated for 243 pairs of micropollutants and their structurally related transformation products (TPs); for comparison, spectral similarity was also calculated for 219 pairs of unrelated compounds. Spectra were measured on Orbitrap and QTOF mass spectrometers and similarity was calculated with the dot product. The influence of different factors on spectral similarity [e.g., normalized collision energy (NCE), merging fragments from all NCEs, and shifting fragments by the mass difference of the pair] was considered. Spectral similarity increased at higher NCEs and highest similarity scores for related pairs were obtained with merged spectra including measured fragments and shifted fragments. Removal of the monoisotopic peak was critical to reduce false positives. Using a spectral similarity score threshold of 0.52, 40% of related pairs and 0% of unrelated pairs were above this value. Structural similarity was estimated with the Tanimoto coefficient and pairs with higher structural similarity generally had higher spectral similarity. Pairs where one or both compounds contained heteroatoms such as sulfur often resulted in dissimilar spectra. This work demonstrates that HRMS2 spectral similarity may indicate structural similarity and that spectral similarity can be used in the future to screen complex samples for related compounds such as micropollutants and TPs, assisting in the prioritization of non-target compounds. [Figure not available: see fulltext.

Exploring Site-Specific N-Glycosylation Microheterogeneity of Haptoglobin using Glycopeptide CID Tandem Mass Spectra and Glycan Database Search

PubMed Central

Chandler, Kevin Brown; Pompach, Petr; Goldman, Radoslav

2013-01-01

Glycosylation is a common protein modification with a significant role in many vital cellular processes and human diseases, making the characterization of protein-attached glycan structures important for understanding cell biology and disease processes. Direct analysis of protein N-glycosylation by tandem mass spectrometry of glycopeptides promises site-specific elucidation of N-glycan microheterogeneity, something which detached N-glycan and de-glycosylated peptide analyses cannot provide. However, successful implementation of direct N-glycopeptide analysis by tandem mass spectrometry remains a challenge. In this work, we consider algorithmic techniques for the analysis of LC-MS/MS data acquired from glycopeptide-enriched fractions of enzymatic digests of purified proteins. We implement a computational strategy which takes advantage of the properties of CID fragmentation spectra of N-glycopeptides, matching the MS/MS spectra to peptide-glycan pairs from protein sequences and glycan structure databases. Significantly, we also propose a novel false-discovery-rate estimation technique to estimate and manage the number of false identifications. We use a human glycoprotein standard, haptoglobin, digested with trypsin and GluC, enriched for glycopeptides using HILIC chromatography, and analyzed by LC-MS/MS to demonstrate our algorithmic strategy and evaluate its performance. Our software, GlycoPeptideSearch (GPS), assigned glycopeptide identifications to 246 of the spectra at false-discovery-rate 5.58%, identifying 42 distinct haptoglobin peptide-glycan pairs at each of the four haptoglobin N-linked glycosylation sites. We further demonstrate the effectiveness of this approach by analyzing plasma-derived haptoglobin, identifying 136 N-linked glycopeptide spectra at false-discovery-rate 0.4%, representing 15 distinct glycopeptides on at least three of the four N-linked glycosylation sites. The software, GlycoPeptideSearch, is available for download from http

Tandem mass spectrometry data quality assessment by self-convolution.

PubMed

Choo, Keng Wah; Tham, Wai Mun

2007-09-20

Many algorithms have been developed for deciphering the tandem mass spectrometry (MS) data sets. They can be essentially clustered into two classes. The first performs searches on theoretical mass spectrum database, while the second based itself on de novo sequencing from raw mass spectrometry data. It was noted that the quality of mass spectra affects significantly the protein identification processes in both instances. This prompted the authors to explore ways to measure the quality of MS data sets before subjecting them to the protein identification algorithms, thus allowing for more meaningful searches and increased confidence level of proteins identified. The proposed method measures the qualities of MS data sets based on the symmetric property of b- and y-ion peaks present in a MS spectrum. Self-convolution on MS data and its time-reversal copy was employed. Due to the symmetric nature of b-ions and y-ions peaks, the self-convolution result of a good spectrum would produce a highest mid point intensity peak. To reduce processing time, self-convolution was achieved using Fast Fourier Transform and its inverse transform, followed by the removal of the "DC" (Direct Current) component and the normalisation of the data set. The quality score was defined as the ratio of the intensity at the mid point to the remaining peaks of the convolution result. The method was validated using both theoretical mass spectra, with various permutations, and several real MS data sets. The results were encouraging, revealing a high percentage of positive prediction rates for spectra with good quality scores. We have demonstrated in this work a method for determining the quality of tandem MS data set. By pre-determining the quality of tandem MS data before subjecting them to protein identification algorithms, spurious protein predictions due to poor tandem MS data are avoided, giving scientists greater confidence in the predicted results. We conclude that the algorithm performs well

Applying Tandem Mass Spectral Libraries for Solving the Critical Assessment of Small Molecule Identification (CASMI) LC/MS Challenge 2012

PubMed Central

Oberacher, Herbert

2013-01-01

The “Critical Assessment of Small Molecule Identification” (CASMI) contest was aimed in testing strategies for small molecule identification that are currently available in the experimental and computational mass spectrometry community. We have applied tandem mass spectral library search to solve Category 2 of the CASMI Challenge 2012 (best identification for high resolution LC/MS data). More than 230,000 tandem mass spectra part of four well established libraries (MassBank, the collection of tandem mass spectra of the “NIST/NIH/EPA Mass Spectral Library 2012”, METLIN, and the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’) were searched. The sample spectra acquired in positive ion mode were processed. Seven out of 12 challenges did not produce putative positive matches, simply because reference spectra were not available for the compounds searched. This suggests that to some extent the limited coverage of chemical space with high-quality reference spectra is still a problem encountered in tandem mass spectral library search. Solutions were submitted for five challenges. Three compounds were correctly identified (kanamycin A, benzyldiphenylphosphine oxide, and 1-isopropyl-5-methyl-1H-indole-2,3-dione). In the absence of any reference spectrum, a false positive identification was obtained for 1-aminoanthraquinone by matching the corresponding sample spectrum to the structurally related compounds N-phenylphthalimide and 2-aminoanthraquinone. Another false positive result was submitted for 1H-benz[g]indole; for the 1H-benz[g]indole-specific sample spectra provided, carbazole was listed as the best matching compound. In this case, the quality of the available 1H-benz[g]indole-specific reference spectra was found to hamper unequivocal identification. PMID:24957994

Dereplication of peptidic natural products through database search of mass spectra

PubMed Central

Mohimani, Hosein; Gurevich, Alexey; Mikheenko, Alla; Garg, Neha; Nothias, Louis-Felix; Ninomiya, Akihiro; Takada, Kentaro; Dorrestein, Pieter C.; Pevzner, Pavel A.

2016-01-01

Peptidic Natural Products (PNPs) are widely used compounds that include many antibiotics and a variety of other bioactive peptides. While recent breakthroughs in PNP discovery raised the challenge of developing new algorithms for their analysis, identification of PNPs via database search of tandem mass spectra remains an open problem. To address this problem, natural product researchers utilize dereplication strategies that identify known PNPs and lead to the discovery of new ones even in cases when the reference spectra are not present in existing spectral libraries. DEREPLICATOR is a new dereplication algorithm that enabled high-throughput PNP identification and that is compatible with large-scale mass spectrometry-based screening platforms for natural product discovery. After searching nearly one hundred million tandem mass spectra in the Global Natural Products Social (GNPS) molecular networking infrastructure, DEREPLICATOR identified an order of magnitude more PNPs (and their new variants) than any previous dereplication efforts. PMID:27820803

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

PubMed Central

2013-01-01

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com. PMID:24295440

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

PubMed

Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

2014-02-07

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

Reanalysis of Tyrannosaurus rex Mass Spectra.

PubMed

Bern, Marshall; Phinney, Brett S; Goldberg, David

2009-09-01

Asara et al. reported the detection of collagen peptides in a 68-million-year-old Tyrannosaurus rex bone by shotgun proteomics. This finding has been called into question as a possible statistical artifact. We reanalyze Asara et al.'s tandem mass spectra using a different search engine and different statistical tools. Our reanalysis shows a sample containing common laboratory contaminants, soil bacteria, and bird-like hemoglobin and collagen.

Reanalysis of Tyrannosaurus rex Mass Spectra

PubMed Central

Bern, Marshall; Phinney, Brett S.; Goldberg, David

2009-01-01

Asara et al. reported the detection of collagen peptides in a 68-million-year-old T. rex bone by shotgun proteomics. This finding has been called into question as a possible statistical artifact. We reanalyze Asara et al.'s tandem mass spectra using a different search engine and different statistical tools. Our reanalysis shows a sample containing common laboratory contaminants, soil bacteria, and bird-like hemoglobin and collagen. PMID:19603827

Evaluation of the performance of a tandem mass spectral library with mass spectral data extracted from literature.

PubMed

Würtinger, Philipp; Oberacher, Herbert

2012-01-01

MSforID represents a database of tandem mass spectral data obtained from (quasi-)molecular ions produced by atmospheric pressure ionization methods. At the current stage of development the library contains 12 122 spectra of 1208 small (bio-)organic molecules. The present work was aimed to evaluate the performance of the MSforID library in terms of accuracy and transferability with a collection of fragment ion mass spectra from various compounds acquired on multiple instruments. A literature survey was conducted to collect the set of sample spectra. A total number of 554 spectra covering 291 compounds were extracted from 109 publications. The majority of spectra originated from publications on applications of LC/MS/MS in drug monitoring, pharmacokinetics, environmental analysis, forensic analysis as well as food analysis. Almost all types of tandem mass spectrometric instruments distributed by the five most important instrument vendors were included in the study. The overall sensitivity of library search was found to be 96.4%, which clearly proves that the MSforID library can successfully handle data from a huge variety of mass spectrometric instruments to allow accurate compound identification. Only for spectra containing three or more fragment ions, however, the rate of classified matches (= matches with a relative average match probability (ramp) score > 40.0) was 95%. Ambiguous or unclassified results were mainly obtained for searches with single precursor-to-fragment ion transitions due to the insufficient specificity of such a low amount of structural information to unequivocally define a single compound. Copyright © 2011 John Wiley & Sons, Ltd.

Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra*

PubMed Central

Jeong, Kyowon; Kim, Sangtae; Bandeira, Nuno; Pevzner, Pavel A.

2011-01-01

Generating all plausible de novo interpretations of a peptide tandem mass (MS/MS) spectrum (Spectral Dictionary) and quickly matching them against the database represent a recently emerged alternative approach to peptide identification. However, the sizes of the Spectral Dictionaries quickly grow with the peptide length making their generation impractical for long peptides. We introduce Gapped Spectral Dictionaries (all plausible de novo interpretations with gaps) that can be easily generated for any peptide length thus addressing the limitation of the Spectral Dictionary approach. We show that Gapped Spectral Dictionaries are small thus opening a possibility of using them to speed-up MS/MS searches. Our MS-GappedDictionary algorithm (based on Gapped Spectral Dictionaries) enables proteogenomics applications (such as searches in the six-frame translation of the human genome) that are prohibitively time consuming with existing approaches. MS-GappedDictionary generates gapped peptides that occupy a niche between accurate but short peptide sequence tags and long but inaccurate full length peptide reconstructions. We show that, contrary to conventional wisdom, some high-quality spectra do not have good peptide sequence tags and introduce gapped tags that have advantages over the conventional peptide sequence tags in MS/MS database searches. PMID:21444829

Automated Lipid A Structure Assignment from Hierarchical Tandem Mass Spectrometry Data

NASA Astrophysics Data System (ADS)

Ting, Ying S.; Shaffer, Scott A.; Jones, Jace W.; Ng, Wailap V.; Ernst, Robert K.; Goodlett, David R.

2011-05-01

Infusion-based electrospray ionization (ESI) coupled to multiple-stage tandem mass spectrometry (MS n ) is a standard methodology for investigating lipid A structural diversity (Shaffer et al. J. Am. Soc. Mass. Spectrom. 18(6), 1080-1092, 2007). Annotation of these MS n spectra, however, has remained a manual, expert-driven process. In order to keep up with the data acquisition rates of modern instruments, we devised a computational method to annotate lipid A MS n spectra rapidly and automatically, which we refer to as hierarchical tandem mass spectrometry (HiTMS) algorithm. As a first-pass tool, HiTMS aids expert interpretation of lipid A MS n data by providing the analyst with a set of candidate structures that may then be confirmed or rejected. HiTMS deciphers the signature ions (e.g., A-, Y-, and Z-type ions) and neutral losses of MS n spectra using a species-specific library based on general prior structural knowledge of the given lipid A species under investigation. Candidates are selected by calculating the correlation between theoretical and acquired MS n spectra. At a false discovery rate of less than 0.01, HiTMS correctly assigned 85% of the structures in a library of 133 manually annotated Francisella tularensis subspecies novicida lipid A structures. Additionally, HiTMS correctly assigned 85% of the structures in a smaller library of lipid A species from Yersinia pestis demonstrating that it may be used across species.

Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Bathany, Katell; Owens, Neil W.; Guichard, Gilles; Schmitter, Jean-Marie

2013-03-01

This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N'H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.

Cloud parallel processing of tandem mass spectrometry based proteomics data.

PubMed

Mohammed, Yassene; Mostovenko, Ekaterina; Henneman, Alex A; Marissen, Rob J; Deelder, André M; Palmblad, Magnus

2012-10-05

Data analysis in mass spectrometry based proteomics struggles to keep pace with the advances in instrumentation and the increasing rate of data acquisition. Analyzing this data involves multiple steps requiring diverse software, using different algorithms and data formats. Speed and performance of the mass spectral search engines are continuously improving, although not necessarily as needed to face the challenges of acquired big data. Improving and parallelizing the search algorithms is one possibility; data decomposition presents another, simpler strategy for introducing parallelism. We describe a general method for parallelizing identification of tandem mass spectra using data decomposition that keeps the search engine intact and wraps the parallelization around it. We introduce two algorithms for decomposing mzXML files and recomposing resulting pepXML files. This makes the approach applicable to different search engines, including those relying on sequence databases and those searching spectral libraries. We use cloud computing to deliver the computational power and scientific workflow engines to interface and automate the different processing steps. We show how to leverage these technologies to achieve faster data analysis in proteomics and present three scientific workflows for parallel database as well as spectral library search using our data decomposition programs, X!Tandem and SpectraST.

Strategies for dereplication of natural compounds using high-resolution tandem mass spectrometry.

PubMed

Kind, Tobias; Fiehn, Oliver

2017-09-01

Complete structural elucidation of natural products is commonly performed by nuclear magnetic resonance spectroscopy (NMR), but annotating compounds to most likely structures using high-resolution tandem mass spectrometry is a faster and feasible first step. The CASMI contest 2016 (Critical Assessment of Small Molecule Identification) provided spectra of eighteen compounds for the best manual structure identification in the natural products category. High resolution precursor and tandem mass spectra (MS/MS) were available to characterize the compounds. We used the Seven Golden Rules, Sirius2 and MS-FINDER software for determination of molecular formulas, and then we queried the formulas in different natural product databases including DNP, UNPD, ChemSpider and REAXYS to obtain molecular structures. We used different in-silico fragmentation tools including CFM-ID, CSI:FingerID and MS-FINDER to rank these compounds. Additional neutral losses and product ion peaks were manually investigated. This manual and time consuming approach allowed for the correct dereplication of thirteen of the eighteen natural products.

Examination of segmental average mass spectra from liquid chromatography-tandem mass spectrometric (LC-MS/MS) data enables screening of multiple types of protein modifications.

PubMed

Liu, Nai-Yu; Lee, Hsiao-Hui; Chang, Zee-Fen; Tsay, Yeou-Guang

2015-09-10

It has been observed that a modified peptide and its non-modified counterpart, when analyzed with reverse phase liquid chromatography, usually share a very similar elution property [1-3]. Inasmuch as this property is common to many different types of protein modifications, we propose an informatics-based approach, featuring the generation of segmental average mass spectra ((sa)MS), that is capable of locating different types of modified peptides in two-dimensional liquid chromatography-mass spectrometric (LC-MS) data collected for regular protease digests from proteins in gels or solutions. To enable the localization of these peptides in the LC-MS map, we have implemented a set of computer programs, or the (sa)MS package, that perform the needed functions, including generating a complete set of segmental average mass spectra, compiling the peptide inventory from the Sequest/TurboSequest results, searching modified peptide candidates and annotating a tandem mass spectrum for final verification. Using ROCK2 as an example, our programs were applied to identify multiple types of modified peptides, such as phosphorylated and hexosylated ones, which particularly include those peptides that could have been ignored due to their peculiar fragmentation patterns and consequent low search scores. Hence, we demonstrate that, when complemented with peptide search algorithms, our approach and the entailed computer programs can add the sequence information needed for bolstering the confidence of data interpretation by the present analytical platforms and facilitate the mining of protein modification information out of complicated LC-MS/MS data. Copyright © 2015 Elsevier B.V. All rights reserved.

An Automated, High-Throughput Method for Interpreting the Tandem Mass Spectra of Glycosaminoglycans

NASA Astrophysics Data System (ADS)

Duan, Jiana; Jonathan Amster, I.

2018-05-01

The biological interactions between glycosaminoglycans (GAGs) and other biomolecules are heavily influenced by structural features of the glycan. The structure of GAGs can be assigned using tandem mass spectrometry (MS2), but analysis of these data, to date, requires manually interpretation, a slow process that presents a bottleneck to the broader deployment of this approach to solving biologically relevant problems. Automated interpretation remains a challenge, as GAG biosynthesis is not template-driven, and therefore, one cannot predict structures from genomic data, as is done with proteins. The lack of a structure database, a consequence of the non-template biosynthesis, requires a de novo approach to interpretation of the mass spectral data. We propose a model for rapid, high-throughput GAG analysis by using an approach in which candidate structures are scored for the likelihood that they would produce the features observed in the mass spectrum. To make this approach tractable, a genetic algorithm is used to greatly reduce the search-space of isomeric structures that are considered. The time required for analysis is significantly reduced compared to an approach in which every possible isomer is considered and scored. The model is coded in a software package using the MATLAB environment. This approach was tested on tandem mass spectrometry data for long-chain, moderately sulfated chondroitin sulfate oligomers that were derived from the proteoglycan bikunin. The bikunin data was previously interpreted manually. Our approach examines glycosidic fragments to localize SO3 modifications to specific residues and yields the same structures reported in literature, only much more quickly.

Tandem Mass Spectrum Sequencing: An Alternative to Database Search Engines in Shotgun Proteomics.

PubMed

Muth, Thilo; Rapp, Erdmann; Berven, Frode S; Barsnes, Harald; Vaudel, Marc

2016-01-01

Protein identification via database searches has become the gold standard in mass spectrometry based shotgun proteomics. However, as the quality of tandem mass spectra improves, direct mass spectrum sequencing gains interest as a database-independent alternative. In this chapter, the general principle of this so-called de novo sequencing is introduced along with pitfalls and challenges of the technique. The main tools available are presented with a focus on user friendly open source software which can be directly applied in everyday proteomic workflows.

Design and performance of an instrument for electron impact tandem mass spectrometry and action spectroscopy of mass/charge selected macromolecular ions stored in RF ion trap*

NASA Astrophysics Data System (ADS)

Ranković, Milos Lj.; Giuliani, Alexandre; Milosavljević, Aleksandar R.

2016-06-01

A new apparatus was designed, coupling an electron gun with a linear quadrupole ion trap mass spectrometer, to perform m/ z (mass over charge) selected ion activation by electron impact for tandem mass spectrometry and action spectroscopy. We present in detail electron tracing simulations of a 300 eV electron beam inside the ion trap, design of the mechanical parts, electron optics and electronic circuits used in the experiment. We also report examples of electron impact activation tandem mass spectra for Ubiquitin protein, Substance P and Melittin peptides, at incident electron energies in the range from 280 eV to 300 eV.

High-Speed Tandem Mass Spectrometric in Situ Imaging by Nanospray Desorption Electrospray Ionization Mass Spectrometry

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

Lanekoff, Ingela T.; Burnum-Johnson, Kristin E.; Thomas, Mathew

Nanospray desorption electrospray ionization (nano-DESI) combined with tandem mass spectrometry (MS/MS), high-resolution mass analysis (m/m=17,500 at m/z 200), and rapid spectral acquisition enabled simultaneous imaging and identification of more than 300 molecules from 92 selected m/z windows (± 1 Da) with a spatial resolution of better than 150 um. Uterine sections of implantation sites on day 6 of pregnancy were analyzed in the ambient environment without any sample pre-treatment. MS/MS imaging was performed by scanning the sample under the nano-DESI probe at 10 um/s while acquiring higher-energy collision-induced dissociation (HCD) spectra for a targeted inclusion list of 92 m/z valuesmore » at a rate of ~6.3 spectra/s. Molecular ions and their corresponding fragments, separated using high-resolution mass analysis, were assigned based on accurate mass measurement. Using this approach, we were able to identify and image both abundant and low-abundance isobaric species within each m/z window. MS/MS analysis enabled efficient separation and identification of isobaric sodium and potassium adducts of phospholipids. Furthermore, we identified several metabolites associated with early pregnancy and obtained the first 2D images of these molecules.« less

Evaluation of the sensitivity of the 'Wiley registry of tandem mass spectral data, MSforID' with MS/MS data of the 'NIST/NIH/EPA mass spectral library'.

PubMed

Oberacher, Herbert; Whitley, Graeme; Berger, Bernd

2013-04-01

Tandem mass spectral libraries are versatile tools for small molecular identification finding application in forensic science, doping control, drug monitoring, food and environmental analysis, as well as metabolomics. Two important libraries are the 'Wiley Registry of Tandem Mass Spectral Data, MSforID' (Wiley Registry MSMS) and the collection of MS/MS spectra part of the 2011 edition of the 'NIST/NIH/EPA Mass Spectral Library' (NIST 11 MSMS). Herein, the sensitivity and robustness of the Wiley Registry MSMS were evaluated using spectra extracted from the NIST 11 MSMS library. The sample set was found to be heterogeneous in terms of mass spectral resolution, type of CID, as well as applied collision energies. Nevertheless, sensitive compound identification with a true positive identification rate ≥95% was possible using either the MSforID Search program or the NIST MS Search program 2.0g for matching. To rate the performance of the Wiley Registry MSMS, cross-validation experiments were repeated using subcollections of NIST 11 MSMS as reference library and spectra extracted from the Wiley Registry MSMS as positive controls. Unexpectedly, with both search algorithms tested, correct results were obtained in less than 88% of cases. We examined possible causes for the results of the cross validation study. The large number of precursor ions represented by a single tandem mass spectrum only was identified as the basic cause for the comparably lower sensitivity of the NIST library. Copyright © 2013 John Wiley & Sons, Ltd.

Matrix effect on the determination of synthetic corticosteroids and diuretics by liquid chromatography-tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Dikunets, M. A.; Appolonova, S. A.; Rodchenkov, G. M.

2009-04-01

This work presents a high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) procedure for selective and reliable screening of corticosteroids and diuretics in human urine. Sample preparation included the extraction, evaporation of the organic extract under nitrogen, and solution of the dry residue. The extract was analyzed by HPLC combined with tandem mass spectrometry using electro-spraying ionization at atmospheric pressure with negative ion recording. The mass spectra of all compounds were recorded, and the characteristic ions, retention times, and detection limits were determined. The procedure was validated by evaluating the degree of the matrix suppression of ionization, extraction of analytes from human biological liquid, and the selectivity and specificity of determination.

Peptide Analysis Using Tandem Mass Spectrometry

DTIC Science & Technology

1989-06-01

to give pyroglutamic acid during storage, eliminating ammonia. It is almost absent in the spectrum of a freshly-prepared sample and is not seen in...USING TANDEM MASS SPECTROMETRY INTRODUCTION S The objective of the project was to determine the complete amino acid sequence of the large polypeptide...Ubiquitin by use of fast atom bombardment (FAB) ionization and tandem mass spectrometry. The peptide containing 76 amino acid residues was available

On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library: 2. Optimization and characterization of the search algorithm.

PubMed

Oberacher, Herbert; Pavlic, Marion; Libiseller, Kathrin; Schubert, Birthe; Sulyok, Michael; Schuhmacher, Rainer; Csaszar, Edina; Köfeler, Harald C

2009-04-01

A sophisticated matching algorithm developed for highly efficient identity search within tandem mass spectral libraries is presented. For the optimization of the search procedure a collection of 410 tandem mass spectra corresponding to 22 compounds was used. The spectra were acquired in three different laboratories on four different instruments. The following types of tandem mass spectrometric instruments were used: quadrupole-quadrupole-time-of-flight (QqTOF), quadrupole-quadrupole-linear ion trap (QqLIT), quadrupole-quadrupole-quadrupole (QqQ), and linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer (LIT-FTICR). The obtained spectra were matched to an established MS/MS-spectral library that contained 3759 MS/MS-spectra corresponding to 402 different reference compounds. All 22 test compounds were part of the library. A dynamic intensity cut-off, the search for neutral losses, and optimization of the formula used to calculate the match probability were shown to significantly enhance the performance of the presented library search approach. With the aid of these features the average number of correct assignments was increased to 98%. For statistical evaluation of the match reliability the set of fragment ion spectra was extended with 300 spectra corresponding to 100 compounds not included in the reference library. Performance was checked with the aid of receiver operating characteristic (ROC) curves. Using the magnitude of the match probability as well as the precursor ion mass as benchmarks to rate the obtained top hit, overall correct classification of a compound being included or not included in the mass spectrometric library, was obtained in more than 95% of cases clearly indicating a high predictive accuracy of the established matching procedure. Copyright (c) 2009 John Wiley & Sons, Ltd.

Binomial probability distribution model-based protein identification algorithm for tandem mass spectrometry utilizing peak intensity information.

PubMed

Xiao, Chuan-Le; Chen, Xiao-Zhou; Du, Yang-Li; Sun, Xuesong; Zhang, Gong; He, Qing-Yu

2013-01-04

Mass spectrometry has become one of the most important technologies in proteomic analysis. Tandem mass spectrometry (LC-MS/MS) is a major tool for the analysis of peptide mixtures from protein samples. The key step of MS data processing is the identification of peptides from experimental spectra by searching public sequence databases. Although a number of algorithms to identify peptides from MS/MS data have been already proposed, e.g. Sequest, OMSSA, X!Tandem, Mascot, etc., they are mainly based on statistical models considering only peak-matches between experimental and theoretical spectra, but not peak intensity information. Moreover, different algorithms gave different results from the same MS data, implying their probable incompleteness and questionable reproducibility. We developed a novel peptide identification algorithm, ProVerB, based on a binomial probability distribution model of protein tandem mass spectrometry combined with a new scoring function, making full use of peak intensity information and, thus, enhancing the ability of identification. Compared with Mascot, Sequest, and SQID, ProVerB identified significantly more peptides from LC-MS/MS data sets than the current algorithms at 1% False Discovery Rate (FDR) and provided more confident peptide identifications. ProVerB is also compatible with various platforms and experimental data sets, showing its robustness and versatility. The open-source program ProVerB is available at http://bioinformatics.jnu.edu.cn/software/proverb/ .

In Silico Identification Software (ISIS): A Machine Learning Approach to Tandem Mass Spectral Identification of Lipids

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

Kangas, Lars J.; Metz, Thomas O.; Isaac, Georgis

2012-05-15

Liquid chromatography-mass spectrometry-based metabolomics has gained importance in the life sciences, yet it is not supported by software tools for high throughput identification of metabolites based on their fragmentation spectra. An algorithm (ISIS: in silico identification software) and its implementation are presented and show great promise in generating in silico spectra of lipids for the purpose of structural identification. Instead of using chemical reaction rate equations or rules-based fragmentation libraries, the algorithm uses machine learning to find accurate bond cleavage rates in a mass spectrometer employing collision-induced dissocia-tion tandem mass spectrometry. A preliminary test of the algorithm with 45 lipidsmore » from a subset of lipid classes shows both high sensitivity and specificity.« less

Tandem mass spectrometric analysis of cyclophosphamide, ifosfamide and their metabolites.

PubMed

Liu, Zhongfa; Chan, Kenneth K; Wang, Jeffrey J

2005-01-01

A detailed multi-stage (MSn) fragmentation study of cyclophosphamide (CP), ifosfamide (IF) and their major metabolites, using an ion-trap mass spectrometer and a Q-TOF mass spectrometer, was performed with the aid of specifically deuterium-labeled analogs. The analytes showed good responses in positive-ion electrospray mass spectrometry as [MH]+ ions. Tandem mass spectra revealed a wealth of structurally specific ions, allowing characterization of the fragmentation pathways of these analytes. The major fragmentation pathways of the protonated CP and IF are elimination of ethylene from C5 and C6 of 1,3,2-oxazaphosphorine-2-oxide via a McLafferty rearrangement, and cleavage of the P-N bond. However, their activated 4-OOH and 4-OH metabolites primarily underwent hydrogen peroxide elimination and dehydration, respectively, followed by fragmentation pathways similar to those of CP and IF. These results should prove useful in structural elucidation of future analogs of CP and IF, and/or of their metabolites. Copyright (c) 2005 John Wiley & Sons, Ltd.

Atmospheric pressure ionization-tandem mass spectrometry of the phenicol drug family.

PubMed

Alechaga, Élida; Moyano, Encarnación; Galceran, M Teresa

2013-11-01

In this work, the mass spectrometry behaviour of the veterinary drug family of phenicols, including chloramphenicol (CAP) and its related compounds thiamphenicol (TAP), florfenicol (FF) and FF amine (FFA), was studied. Several atmospheric pressure ionization sources, electrospray (ESI), atmospheric pressure chemical ionization and atmospheric pressure photoionization were compared. In all atmospheric pressure ionization sources, CAP, TAP and FF were ionized in both positive and negative modes; while for the metabolite FFA, only positive ionization was possible. In general, in positive mode, [M + H](+) dominated the mass spectrum for FFA, while the other compounds, CAP, TAP and FF, with lower proton affinity showed intense adducts with species present in the mobile phase. In negative mode, ESI and atmospheric pressure photoionization showed the deprotonated molecule [M-H](-), while atmospheric pressure chemical ionization provided the radical molecular ion by electron capture. All these ions were characterized by tandem mass spectrometry using the combined information obtained by multistage mass spectrometry and high-resolution mass spectrometry in a quadrupole-Orbitrap instrument. In general, the fragmentation occurred via cyclization and losses or fragmentation of the N-(alkyl)acetamide group, and common fragmentation pathways were established for this family of compounds. A new chemical structure for the product ion at m/z 257 for CAP, on the basis of the MS(3) and MS(4) spectra is proposed. Thermally assisted ESI and selected reaction monitoring are proposed for the determination of these compounds by ultra high-performance liquid chromatography coupled to tandem mass spectrometry, achieving instrumental detection limits down to 0.1 pg. Copyright © 2013 John Wiley & Sons, Ltd.

Fast atom bombardment tandem mass spectrometry of carotenoids

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

van Breeman, R.B.; Schmitz, H.H.; Schwartz, S.J.

Positive ion fast atom bombardment (FAB) tandem mass spectrometry (MS-MS) using a double-focusing mass spectrometer with linked scanning at constant B/E and high-energy collisionally activated dissociation (CAD) was used to differentiate 17 different cartenoids, including {beta}-apo-8{prime}- carotenal, astaxanthin, {alpha}-carotene, {beta}-carotene, {gamma}-carotene, {zeta}-carotene, canthaxanthin, {beta}-cryptoxanthin, isozeaxanthin bis (pelargonate), neoxanthin, neurosporene, nonaprene, lutein, lycopene, phytoene, phytofluene, and zeaxanthin. The carotenoids were either synthetic or isolated from plant tissues. The use of FAB ionization minimized degradation or rearrangement of the carotenoid structures due to the inherent thermal instability generally ascribed to these compounds. Instead of protonated molecules, both polar xanthophylls and nonpolar carotenesmore » formed molecular ions, M{sup {center_dot}+}, during FAB ionization. Following collisionally activated dissociation, fragment ions of selected molecular ion precursors showed structural features indicative of the presence of hydroxyl groups, ring systems, ester groups, and aldehyde groups and the extent of aliphatic polyene conjugation. The fragmentation patterns observed in the mass spectra herein may be used as a reference for the structural determination of carotenoids isolated from plant and animal tissues. 18 refs., 4 figs.« less

Characterization of Wax Esters by Electrospray Ionization Tandem Mass Spectrometry: Double Bond Effect and Unusual Product Ions

PubMed Central

Chen, Jianzhong; Green, Kari B; Nichols, Kelly K

2015-01-01

A series of different types of wax esters (represented by RCOOR′) were systematically studied by using electrospray ionization (ESI) collision-induced dissociation tandem mass spectrometry (MS/MS) along with pseudo MS3 (in-source dissociation combined with MS/MS) on a quadrupole time-of-flight (Q-TOF) mass spectrometer. The tandem mass spectra patterns resulting from dissociation of ammonium/proton adducts of these wax esters were influenced by the wax ester type and the collision energy applied. The product ions [RCOOH2]+, [RCO]+ and [RCO – H2O]+ that have been reported previously were detected; however, different primary product ions were demonstrated for the three wax ester types including: 1) [RCOOH2]+ for saturated wax esters, 2) [RCOOH2]+, [RCO]+ and [RCO – H2O]+ for unsaturated wax esters containing only one double bond in the fatty acid moiety or with one additional double bond in the fatty alcohol moiety, and 3) [RCOOH2]+ and [RCO]+ for unsaturated wax esters containing a double bond in the fatty alcohol moiety alone. Other fragments included [R′]+ and several series of product ions for all types of wax esters. Interestingly, unusual product ions were detected, such as neutral molecule (including water, methanol and ammonia) adducts of [RCOOH2]+ ions for all types of wax esters and [R′ – 2H]+ ions for unsaturated fatty acyl-containing wax esters. The patterns of tandem mass spectra for different types of wax esters will inform future identification and quantification approaches of wax esters in biological samples as supported by a preliminary study of quantification of isomeric wax esters in human meibomian gland secretions. PMID:26178197

Characterization of Wax Esters by Electrospray Ionization Tandem Mass Spectrometry: Double Bond Effect and Unusual Product Ions.

PubMed

Chen, Jianzhong; Green, Kari B; Nichols, Kelly K

2015-08-01

A series of different types of wax esters (represented by RCOOR') were systematically studied by using electrospray ionization (ESI) collision-induced dissociation tandem mass spectrometry (MS/MS) along with pseudo MS(3) (in-source dissociation combined with MS/MS) on a quadrupole time-of-flight (Q-TOF) mass spectrometer. The tandem mass spectra patterns resulting from dissociation of ammonium/proton adducts of these wax esters were influenced by the wax ester type and the collision energy applied. The product ions [RCOOH2](+), [RCO](+) and [RCO-H2O](+) that have been reported previously were detected; however, different primary product ions were demonstrated for the three wax ester types including: (1) [RCOOH2](+) for saturated wax esters, (2) [RCOOH2](+), [RCO](+) and [RCO-H2O](+) for unsaturated wax esters containing only one double bond in the fatty acid moiety or with one additional double bond in the fatty alcohol moiety, and (3) [RCOOH2](+) and [RCO](+) for unsaturated wax esters containing a double bond in the fatty alcohol moiety alone. Other fragments included [R'](+) and several series of product ions for all types of wax esters. Interestingly, unusual product ions were detected, such as neutral molecule (including water, methanol and ammonia) adducts of [RCOOH2](+) ions for all types of wax esters and [R'-2H](+) ions for unsaturated fatty acyl-containing wax esters. The patterns of tandem mass spectra for different types of wax esters will inform future identification and quantification approaches of wax esters in biological samples as supported by a preliminary study of quantification of isomeric wax esters in human meibomian gland secretions.

Multifactorial Understanding of Ion Abundance in Tandem Mass Spectrometry Experiments.

PubMed

Fazal, Zeeshan; Southey, Bruce R; Sweedler, Jonathan V; Rodriguez-Zas, Sandra L

2013-01-29

In a bottom-up shotgun approach, the proteins of a mixture are enzymatically digested, separated, and analyzed via tandem mass spectrometry. The mass spectra relating fragment ion intensities (abundance) to the mass-to-charge are used to deduce the amino acid sequence and identify the peptides and proteins. The variables that influence intensity were characterized using a multi-factorial mixed-effects model, a ten-fold cross-validation, and stepwise feature selection on 6,352,528 fragment ions from 61,543 peptide ions. Intensity was higher in fragment ions that did not have neutral mass loss relative to any mass loss or that had a +1 charge state. Peptide ions classified for proton mobility as non-mobile had lowest intensity of all mobility levels. Higher basic residue (arginine, lysine or histidine) counts in the peptide ion and low counts in the fragment ion were associated with lower fragment ion intensities. Higher counts of proline in peptide and fragment ions were associated with lower intensities. These results are consistent with the mobile proton theory. Opposite trends between peptide and fragment ion counts and intensity may be due to the different impact of factor under consideration at different stages of the MS/MS experiment or to the different distribution of observations across peptide and fragment ion levels. Presence of basic residues at all three positions next to the fragmentation site was associated with lower fragment ion intensity. The presence of proline proximal to the fragmentation site enhanced fragmentation and had the opposite trend when located distant from the site. A positive association between fragment ion intensity and presence of sulfur residues (cysteine and methionine) on the vicinity of the fragmentation site was identified. These results highlight the multi-factorial nature of fragment ion intensity and could improve the algorithms for peptide identification and the simulation in tandem mass spectrometry experiments.

Multifactorial Understanding of Ion Abundance in Tandem Mass Spectrometry Experiments

PubMed Central

Fazal, Zeeshan; Southey, Bruce R; Sweedler, Jonathan V.; Rodriguez-Zas, Sandra L.

2013-01-01

In a bottom-up shotgun approach, the proteins of a mixture are enzymatically digested, separated, and analyzed via tandem mass spectrometry. The mass spectra relating fragment ion intensities (abundance) to the mass-to-charge are used to deduce the amino acid sequence and identify the peptides and proteins. The variables that influence intensity were characterized using a multi-factorial mixed-effects model, a ten-fold cross-validation, and stepwise feature selection on 6,352,528 fragment ions from 61,543 peptide ions. Intensity was higher in fragment ions that did not have neutral mass loss relative to any mass loss or that had a +1 charge state. Peptide ions classified for proton mobility as non-mobile had lowest intensity of all mobility levels. Higher basic residue (arginine, lysine or histidine) counts in the peptide ion and low counts in the fragment ion were associated with lower fragment ion intensities. Higher counts of proline in peptide and fragment ions were associated with lower intensities. These results are consistent with the mobile proton theory. Opposite trends between peptide and fragment ion counts and intensity may be due to the different impact of factor under consideration at different stages of the MS/MS experiment or to the different distribution of observations across peptide and fragment ion levels. Presence of basic residues at all three positions next to the fragmentation site was associated with lower fragment ion intensity. The presence of proline proximal to the fragmentation site enhanced fragmentation and had the opposite trend when located distant from the site. A positive association between fragment ion intensity and presence of sulfur residues (cysteine and methionine) on the vicinity of the fragmentation site was identified. These results highlight the multi-factorial nature of fragment ion intensity and could improve the algorithms for peptide identification and the simulation in tandem mass spectrometry experiments. PMID

Tandem mass spectrometry characteristics of polyester anions and cations formed by electrospray ionization.

PubMed

Arnould, Mark A; Buehner, Rita W; Wesdemiotis, Chrys; Vargas, Rafael

2005-01-01

Electrospray ionization of polyesters composed of isophthalic acid and neopentyl glycol produces carboxylate anions in negative mode and mainly sodium ion adducts in positive mode. A tandem mass spectrometry (MS/MS) study of these ions in a quadrupole ion trap shows that the collisionally activated dissociation pathways of the anions are simpler than those of the corresponding cations. Charge-remote fragmentations predominate in both cases, but the spectra obtained in negative mode are devoid of the complicating cation exchange observed in positive mode. MS/MS of the Na(+) adducts gives rise to a greater number of fragments but not necessarily more structural information. In either positive or negative mode, polyester oligomers with different end groups fragment by similar mechanisms. The observed fragments are consistent with rearrangements initiated by the end groups. Single-stage ESI mass spectra also are more complex in positive mode because of extensive H/Na substitutions; this is also true for matrix-assisted laser desorption ionization (MALDI) mass spectra. Hence, formation and analysis of anions might be the method of choice for determining block length, end group structure and copolymer sequence, provided the polyester contains at least one carboxylic acid end group that is ionizable to anions.

DeMix Workflow for Efficient Identification of Cofragmented Peptides in High Resolution Data-dependent Tandem Mass Spectrometry*

PubMed Central

Zhang, Bo; Pirmoradian, Mohammad; Chernobrovkin, Alexey; Zubarev, Roman A.

2014-01-01

Based on conventional data-dependent acquisition strategy of shotgun proteomics, we present a new workflow DeMix, which significantly increases the efficiency of peptide identification for in-depth shotgun analysis of complex proteomes. Capitalizing on the high resolution and mass accuracy of Orbitrap-based tandem mass spectrometry, we developed a simple deconvolution method of “cloning” chimeric tandem spectra for cofragmented peptides. Additional to a database search, a simple rescoring scheme utilizes mass accuracy and converts the unwanted cofragmenting events into a surprising advantage of multiplexing. With the combination of cloning and rescoring, we obtained on average nine peptide-spectrum matches per second on a Q-Exactive workbench, whereas the actual MS/MS acquisition rate was close to seven spectra per second. This efficiency boost to 1.24 identified peptides per MS/MS spectrum enabled analysis of over 5000 human proteins in single-dimensional LC-MS/MS shotgun experiments with an only two-hour gradient. These findings suggest a change in the dominant “one MS/MS spectrum - one peptide” paradigm for data acquisition and analysis in shotgun data-dependent proteomics. DeMix also demonstrated higher robustness than conventional approaches in terms of lower variation among the results of consecutive LC-MS/MS runs. PMID:25100859

Formation of oligomeric alkenylperoxides during the oxidation of unsaturated fatty acids: an electrospray ionization tandem mass spectrometry study.

PubMed

Villaverde, Juan José; Santos, Sónia A O; Maciel, Elisabete; Simões, Mário M Q; Pascoal Neto, Carlos; Domingues, M Rosário M; Silvestre, Armando J D

2012-02-01

This study reports the identification of oligomeric alkenylperoxides by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (ESI-MS(2)), during the oxidation of oleic, linoleic and linolenic acids with Fenton's (Fe(2+)/H(2)O(2)) and Fe(2+)/O(2) systems. The reactions were followed by ferrous oxidation-xylenol orange method together with GC-MS and GC-FID, allowing to observe that both oxidation systems are different in terms of hydroperoxide evolution, probably due to the presence of different intermediate reactive species: perferryl ion and OH(·) radical responsible for the decomposition of lipid hydroperoxides and formation of new compounds. The analysis of ESI-MS in the negative mode, obtained after oxidation of each fatty acid, confirmed the presence of the monomeric oxidation products together with other compounds at high mass region above m/z 550. These new ions were attributed to oligomeric structures, identified by the fragmentation pathways observed in the tandem mass spectra. Copyright © 2012 John Wiley & Sons, Ltd.

MS/MS studies on the selective on-line detection of sesquiterpenes using a Flowing Afterglow-Tandem Mass Spectrometer (FA-TMS)

NASA Astrophysics Data System (ADS)

Rimetz-Planchon, J.; Dhooghe, F.; Schoon, N.; Vanhaecke, F.; Amelynck, C.

2011-04-01

A Flowing Afterglow-Tandem Mass Spectrometer (FA-TMS) was used to investigate the feasibility of selective on-line detection of a series of seven sesquiterpenes (SQTs). These SQTs were chemically ionized by either H3O+ or NO+ reagent ions in the FA, resulting among others in protonated SQT and SQT molecular ions, respectively. These and other Chemical Ionization (CI) product ions were subsequently subjected to dissociation by collisions with Ar atoms in the collision cell of the tandem mass spectrometer. The fragmentation spectra show similarities with mass spectra obtained for these compounds with other instruments such as a Proton Transfer Reaction-Linear Ion Trap (PTR-LIT), a Proton Transfer Reaction-Mass Spectrometer (PTR-MS), a Triple Quadrupole-Mass Spectrometer (QqQ-MS) and a Selected Ion Flow Tube-Mass Spectrometer (SIFT-MS). Fragmentation of protonated SQT is characterized by fragment ions at the same masses but with different intensities for the individual SQT. Distinction of SQTs is based on well-chosen intensity ratios and collision energies. The fragmentation patterns of SQT molecular ions show specific fragment ion tracers at m/z 119, m/z162, m/z 137 and m/z 131 for α-cedrene, δ-neoclovene, isolongifolene and α-humulene, respectively. Consequently, chemical ionization of SQT by NO+, followed by MS/MS of SQT+ seems to open a way for selective quantification of SQTs in mixtures.

Combinatorial Approach for Large-scale Identification of Linked Peptides from Tandem Mass Spectrometry Spectra*

PubMed Central

Wang, Jian; Anania, Veronica G.; Knott, Jeff; Rush, John; Lill, Jennie R.; Bourne, Philip E.; Bandeira, Nuno

2014-01-01

The combination of chemical cross-linking and mass spectrometry has recently been shown to constitute a powerful tool for studying protein–protein interactions and elucidating the structure of large protein complexes. However, computational methods for interpreting the complex MS/MS spectra from linked peptides are still in their infancy, making the high-throughput application of this approach largely impractical. Because of the lack of large annotated datasets, most current approaches do not capture the specific fragmentation patterns of linked peptides and therefore are not optimal for the identification of cross-linked peptides. Here we propose a generic approach to address this problem and demonstrate it using disulfide-bridged peptide libraries to (i) efficiently generate large mass spectral reference data for linked peptides at a low cost and (ii) automatically train an algorithm that can efficiently and accurately identify linked peptides from MS/MS spectra. We show that using this approach we were able to identify thousands of MS/MS spectra from disulfide-bridged peptides through comparison with proteome-scale sequence databases and significantly improve the sensitivity of cross-linked peptide identification. This allowed us to identify 60% more direct pairwise interactions between the protein subunits in the 20S proteasome complex than existing tools on cross-linking studies of the proteasome complexes. The basic framework of this approach and the MS/MS reference dataset generated should be valuable resources for the future development of new tools for the identification of linked peptides. PMID:24493012

Tandem Mass Spectrometry on a Miniaturized Laser Desorption Time-of-Flight Mass Spectrometer

NASA Technical Reports Server (NTRS)

Li, Xiang; Cornish, Timothy; Getty, Stephanie A.; Brinckerhoff, William B.

2016-01-01

Tandem mass spectrometry (MSMS) is a powerful and widely-used technique for identifying the molecular structure of organic constituents of a complex sample. Application of MSMS to the study of unknown planetary samples on a remote space mission would contribute to our understanding of the origin, evolution, and distribution of extraterrestrial organics in our solar system. Here we report on the realization of MSMS on a miniaturized laser desorption time-of-flight mass spectrometer (LD-TOF-MS), which is one of the most promising instrument types for future planetary missions. This achievement relies on two critical components: a curved-field reflectron and a pulsed-pin ion gate. These enable use of the complementary post-source decay (PSD) and laser-assisted collision induced dissociation (L-CID) MSMS methods on diverse measurement targets with only modest investment in instrument resources such as volume and weight. MSMS spectra of selected molecular targets in various organic standards exhibit excellent agreement when compared with results from a commercial, laboratory-scale TOF instrument, demonstrating the potential of this powerful technique in space and planetary environments.

Computational Prediction of Electron Ionization Mass Spectra to Assist in GC/MS Compound Identification.

PubMed

Allen, Felicity; Pon, Allison; Greiner, Russ; Wishart, David

2016-08-02

We describe a tool, competitive fragmentation modeling for electron ionization (CFM-EI) that, given a chemical structure (e.g., in SMILES or InChI format), computationally predicts an electron ionization mass spectrum (EI-MS) (i.e., the type of mass spectrum commonly generated by gas chromatography mass spectrometry). The predicted spectra produced by this tool can be used for putative compound identification, complementing measured spectra in reference databases by expanding the range of compounds able to be considered when availability of measured spectra is limited. The tool extends CFM-ESI, a recently developed method for computational prediction of electrospray tandem mass spectra (ESI-MS/MS), but unlike CFM-ESI, CFM-EI can handle odd-electron ions and isotopes and incorporates an artificial neural network. Tests on EI-MS data from the NIST database demonstrate that CFM-EI is able to model fragmentation likelihoods in low-resolution EI-MS data, producing predicted spectra whose dot product scores are significantly better than full enumeration "bar-code" spectra. CFM-EI also outperformed previously reported results for MetFrag, MOLGEN-MS, and Mass Frontier on one compound identification task. It also outperformed MetFrag in a range of other compound identification tasks involving a much larger data set, containing both derivatized and nonderivatized compounds. While replicate EI-MS measurements of chemical standards are still a more accurate point of comparison, CFM-EI's predictions provide a much-needed alternative when no reference standard is available for measurement. CFM-EI is available at https://sourceforge.net/projects/cfm-id/ for download and http://cfmid.wishartlab.com as a web service.

Mass spectrometry and tandem mass spectrometry of citrus limonoids.

PubMed

Tian, Qingguo; Schwartz, Steven J

2003-10-15

Methods for atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS/MS) of citrus limonoid aglycones and electrospray ionization tandem mass spectrometry (ESI-MS/MS) of limonoid glucosides are reported. The fragmentation patterns of four citrus limonoid aglycones (limonin, nomilin, obacunone, and deacetylnomilin) and six limonoid glucosides, that is, limonin 17-beta-D-glucopyranoside (LG), nomilin 17-beta-D-glucopyranoside (NG), nomilinic acid 17-beta-D-glucopyranoside (NAG), deacetyl nomilinic acid 17-beta-D-glucopyranoside (DNAG), obacunone 17-beta-D-glucopyranoside (OG), and obacunoic acid 17-beta-D-glucopyranoside (OAG) were investigated using a quadruple mass spectrometer in low-energy collisionally activated dissociation (CAD). The four limonoid aglycones and four limonoid glucosides (LG, OG, NAG, and DNAG) were purified from citrus seeds; the other two limonoid glucosides (NG and OAG) were tentatively identified in the crude extract of grapefruit seeds by ESI mass spectrometry in both positive and negative ion analysis. Ammonium hydroxide or acetic acid was added to the mobile phase to facilitate ionization. During positive ion APCI analysis of limonoid aglycones, protonated molecular ion, [M + H]+, or adduct ion, [M + NH3 + H]-, was formed as base peaks when ammonium hydroxide was added to the mobile phase. Molecular anions or adduct ions with acetic acid ([M + HOAc - H] and [M + HOAc]-) or a deprotonated molecular ion were produced during negative ion APCI analysis of limonoid aglycones, depending on the mobile-phase modifier used. Positive ion ESI-MS of limonoid glucosides produced adduct ions of [M + H + NH3]+, [M + Na]+, and [M + K]+ when ammonium hydroxide was added to the mobile phase. After collisionally activated dissociation (CAD) of the limonoid aglycone molecular ions in negative ion APCI analysis, fragment ions indicated structural information of the precursor ions, showing the presence of methyl, carboxyl, and oxygenated ring

Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.

PubMed

Nahnsen, Sven; Bertsch, Andreas; Rahnenführer, Jörg; Nordheim, Alfred; Kohlbacher, Oliver

2011-08-05

Database search is a standard technique for identifying peptides from their tandem mass spectra. To increase the number of correctly identified peptides, we suggest a probabilistic framework that allows the combination of scores from different search engines into a joint consensus score. Central to the approach is a novel method to estimate scores for peptides not found by an individual search engine. This approach allows the estimation of p-values for each candidate peptide and their combination across all search engines. The consensus approach works better than any single search engine across all different instrument types considered in this study. Improvements vary strongly from platform to platform and from search engine to search engine. Compared to the industry standard MASCOT, our approach can identify up to 60% more peptides. The software for consensus predictions is implemented in C++ as part of OpenMS, a software framework for mass spectrometry. The source code is available in the current development version of OpenMS and can easily be used as a command line application or via a graphical pipeline designer TOPPAS.

Mining Large Scale Tandem Mass Spectrometry Data for Protein Modifications Using Spectral Libraries.

PubMed

Horlacher, Oliver; Lisacek, Frederique; Müller, Markus

2016-03-04

Experimental improvements in post-translational modification (PTM) detection by tandem mass spectrometry (MS/MS) has allowed the identification of vast numbers of PTMs. Open modification searches (OMSs) of MS/MS data, which do not require prior knowledge of the modifications present in the sample, further increased the diversity of detected PTMs. Despite much effort, there is still a lack of functional annotation of PTMs. One possibility to narrow the annotation gap is to mine MS/MS data deposited in public repositories and to correlate the PTM presence with biological meta-information attached to the data. Since the data volume can be quite substantial and contain tens of millions of MS/MS spectra, the data mining tools must be able to cope with big data. Here, we present two tools, Liberator and MzMod, which are built using the MzJava class library and the Apache Spark large scale computing framework. Liberator builds large MS/MS spectrum libraries, and MzMod searches them in an OMS mode. We applied these tools to a recently published set of 25 million spectra from 30 human tissues and present tissue specific PTMs. We also compared the results to the ones obtained with the OMS tool MODa and the search engine X!Tandem.

Unassigned MS/MS Spectra: Who Am I?

PubMed

Pathan, Mohashin; Samuel, Monisha; Keerthikumar, Shivakumar; Mathivanan, Suresh

2017-01-01

Recent advances in high resolution tandem mass spectrometry (MS) has resulted in the accumulation of high quality data. Paralleled with these advances in instrumentation, bioinformatics software have been developed to analyze such quality datasets. In spite of these advances, data analysis in mass spectrometry still remains critical for protein identification. In addition, the complexity of the generated MS/MS spectra, unpredictable nature of peptide fragmentation, sequence annotation errors, and posttranslational modifications has impeded the protein identification process. In a typical MS data analysis, about 60 % of the MS/MS spectra remains unassigned. While some of these could attribute to the low quality of the MS/MS spectra, a proportion can be classified as high quality. Further analysis may reveal how much of the unassigned MS spectra attribute to search space, sequence annotation errors, mutations, and/or posttranslational modifications. In this chapter, the tools used to identify proteins and ways to assign unassigned tandem MS spectra are discussed.

DtaRefinery: a software tool for elimination of systematic errors from parent ion mass measurements in tandem mass spectra datasets

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

Petyuk, Vladislav A.; Mayampurath, Anoop M.; Monroe, Matthew E.

2009-12-16

Hybrid two-stage mass spectrometers capable of both highly accurate mass measurement and MS/MS fragmentation have become widely available in recent years and have allowed for sig-nificantly better discrimination between true and false MS/MS pep-tide identifications by applying relatively narrow windows for maxi-mum allowable deviations for parent ion mass measurements. To fully gain the advantage of highly accurate parent ion mass meas-urements, it is important to limit systematic mass measurement errors. The DtaRefinery software tool can correct systematic errors in parent ion masses by reading a set of fragmentation spectra, searching for MS/MS peptide identifications, then fitting a model that canmore » estimate systematic errors, and removing them. This results in a new fragmentation spectrum file with updated parent ion masses.« less

Non-Target Screening of Veterinary Drugs Using Tandem Mass Spectrometry on SmartMass

NASA Astrophysics Data System (ADS)

Xia, Bing; Liu, Xin; Gu, Yu-Cheng; Zhang, Zhao-Hui; Wang, Hai-Yan; Ding, Li-Sheng; Zhou, Yan

2013-05-01

Non-target screening of veterinary drugs using tandem mass spectrometric data was performed on the SmartMass platform. This newly developed software uses the characteristic fragmentation patterns (CFP) to identify chemicals, especially those containing particular substructures. A mixture of 17 sulfonamides was separated by ultra performance liquid chromatography (UPLC), and SmartMass was used to process the tandem mass spectrometry (MS/MS) data acquired on an Orbitrap mass spectrometer. The data were automatically extracted, and each sulfonamide was recognized and analyzed with a prebuilt analysis rule. By using this software, over 98 % of the false candidate structures were eliminated, and all the correct structures were found within the top 10 of the ranking lists. Furthermore, SmartMass could also be used to identify slightly modified contraband drugs and metabolites with simple prebuilt rules. [Figure not available: see fulltext.

Quantification of steroid hormones in human serum by liquid chromatography-high resolution tandem mass spectrometry.

PubMed

Matysik, Silke; Liebisch, Gerhard

2017-12-01

A limited specificity is inherent to immunoassays for steroid hormone analysis. To improve selectivity mass spectrometric analysis of steroid hormones by liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been introduced in the clinical laboratory over the past years usually with low mass resolution triple-quadrupole instruments or more recently by high resolution mass spectrometry (HR-MS). Here we introduce liquid chromatography-high resolution tandem mass spectrometry (LC-MS/HR-MS) to further increase selectivity of steroid hormone quantification. Application of HR-MS demonstrates an enhanced selectivity compared to low mass resolution. Separation of isobaric interferences reduces background noise and avoids overestimation. Samples were prepared by automated liquid-liquid extraction with MTBE. The LC-MS/HR-MS method using a quadrupole-Orbitrap analyzer includes eight steroid hormones i.e. androstenedione, corticosterone, cortisol, cortisone, 11-deoxycortisol, 17-hydroxyprogesterone, progesterone, and testosterone. It has a run-time of 5.3min and was validated according to the U.S. Food and Drug Administration (FDA) and the European Medicines Agency (EMA) guidelines. For most of the analytes coefficient of variation were 10% or lower and LOQs were determined significantly below 1ng/ml. Full product ion spectra including accurate masses substantiate compound identification by matching their masses and ratios with authentic standards. In summary, quantification of steroid hormones by LC-MS/HR-MS is applicable for clinical diagnostics and holds also promise for highly selective quantification of other small molecules. Copyright © 2017 Elsevier B.V. All rights reserved.

Qualitative analysis of seized synthetic cannabinoids and synthetic cathinones by gas chromatography triple quadrupole tandem mass spectrometry.

PubMed

Gwak, Seongshin; Arroyo-Mora, Luis E; Almirall, José R

2015-02-01

Designer drugs are analogues or derivatives of illicit drugs with a modification of their chemical structure in order to circumvent current legislation for controlled substances. Designer drugs of abuse have increased dramatically in popularity all over the world for the past couple of years. Currently, the qualitative seized-drug analysis is mainly performed by gas chromatography-electron ionization-mass spectrometry (GC-EI-MS) in which most of these emerging designer drug derivatives are extensively fragmented not presenting a molecular ion in their mass spectra. The absence of molecular ion and/or similar fragmentation pattern among these derivatives may cause the equivocal identification of unknown seized-substances. In this study, the qualitative identification of 34 designer drugs, mainly synthetic cannabinoids and synthetic cathinones, were performed by gas chromatography-triple quadrupole-tandem mass spectrometry with two different ionization techniques, including electron ionization (EI) and chemical ionization (CI) only focusing on qualitative seized-drug analysis, not from the toxicological point of view. The implementation of CI source facilitates the determination of molecular mass and the identification of seized designer drugs. Developed multiple reaction monitoring (MRM) mode may increase sensitivity and selectivity in the analysis of seized designer drugs. In addition, CI mass spectra and MRM mass spectra of these designer drug derivatives can be used as a potential supplemental database along with EI mass spectral database. Copyright © 2014 John Wiley & Sons, Ltd.

Searching molecular structure databases with tandem mass spectra using CSI:FingerID

PubMed Central

Dührkop, Kai; Shen, Huibin; Meusel, Marvin; Rousu, Juho; Böcker, Sebastian

2015-01-01

Metabolites provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually rely on tandem MS to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. We present a method for searching molecular structure databases using tandem MS data of small molecules. Our method computes a fragmentation tree that best explains the fragmentation spectrum of an unknown molecule. We use the fragmentation tree to predict the molecular structure fingerprint of the unknown compound using machine learning. This fingerprint is then used to search a molecular structure database such as PubChem. Our method is shown to improve on the competing methods for computational metabolite identification by a considerable margin. PMID:26392543

Direct Analysis in Real Time (DART) of an Organothiophosphate at Ultrahigh Resolution by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Tandem Mass Spectrometry

PubMed Central

Prokai, Laszlo; Stevens, Stanley M.

2016-01-01

Direct analysis in real time (DART) is a recently developed ambient ionization technique for mass spectrometry to enable rapid and sensitive analyses with little or no sample preparation. After swab-based field sampling, the organothiophosphate malathion was analyzed using DART-Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Mass resolution was documented to be over 800,000 in full-scan MS mode and over 1,000,000 for an MS/MS product ion produced by collision-induced dissociation of the protonated analyte. Mass measurement accuracy below 1 ppm was obtained for all DART-generated ions that belonged to the test compound in the mass spectra acquired using only external mass calibration. This high mass measurement accuracy, achievable at present only through FTMS, was required for unequivocal identification of the corresponding molecular formulae. PMID:26784186

Direct Analysis in Real Time (DART) of an Organothiophosphate at Ultrahigh Resolution by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry and Tandem Mass Spectrometry.

PubMed

Prokai, Laszlo; Stevens, Stanley M

2016-01-16

Direct analysis in real time (DART) is a recently developed ambient ionization technique for mass spectrometry to enable rapid and sensitive analyses with little or no sample preparation. After swab-based field sampling, the organothiophosphate malathion was analyzed using DART-Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Mass resolution was documented to be over 800,000 in full-scan MS mode and over 1,000,000 for an MS/MS product ion produced by collision-induced dissociation of the protonated analyte. Mass measurement accuracy below 1 ppm was obtained for all DART-generated ions that belonged to the test compound in the mass spectra acquired using only external mass calibration. This high mass measurement accuracy, achievable at present only through FTMS, was required for unequivocal identification of the corresponding molecular formulae.

High energy collisions on tandem time-of-flight mass spectrometers†

PubMed Central

Cotter, Robert J.

2013-01-01

Long before the introduction of matrix-assisted laser desorption (MALDI), electrospray ionization (ESI), Orbitraps and any of the other tools that are now used ubiquitously for proteomics and metabolomics, the highest performance mass spectrometers were sector instruments, providing high resolution mass measurements by combining an electrostatic energy analyzer (E) with a high field magnet (B). In its heyday, the four sector mass spectrometer (or EBEB) was the crown jewel, providing the highest performance tandem mass spectrometry using single, high energy collisions to induce fragmentation. During a time in which quadrupole and tandem triple quadrupole instruments were also enjoying increased usage and popularity, there were nonetheless some clear advantages for sectors over their low collision energy counterparts. Time-of-flight mass spectrometers are high voltage, high vacuum instruments that have much in common with sectors and have inspired the development of tandem instruments exploiting single high energy collisions. In this retrospective we recount our own journey to produce high performance time-of-flights and tandems, describing the basic theory, problems and the advantages for such instruments. An experiment testing impulse collision theory (ICT) underscores the similarities with sector mass spectrometers where this concept was first developed. Applications provide examples of more extensive fragmentation, side chain cleavages and charge-remote fragmentation, also characteristic of high energy sector mass spectrometers. Moreover, the so-called curved-field reflectron has enabled the design of instruments that are simpler, collect and focus all of the ions, and may provide the future technology for the clinic, for tissue imaging and the characterization of microorganisms. PMID:23519928

Analysis of lignans in Magnoliae Flos by turbulent flow chromatography with online solid-phase extraction and high-performance liquid chromatography with tandem mass spectrometry.

PubMed

Zhou, Xuan; Chen, Cen; Ye, Xiaolan; Song, Fenyun; Fan, Guorong; Wu, Fuhai

2016-04-01

In this study, a method coupling turbulent flow chromatography with online solid-phase extraction and high-performance liquid chromatography with tandem mass spectrometry was developed for analyzing the lignans in Magnoliae Flos. By the online pretreatment of turbulent flow chromatography solid-phase extraction, the impurities removal and analytes concentration were automatically processed, and the lignans were separated rapidly and well. Seven lignans of Magnoliae Flos including epieudesmin, magnolin, 1-irioresinol-B-dimethyl ether, epi-magnolin, fargesin aschantin, and demethoxyaschantin were identified by comparing their retention behavior, UV spectra, and mass spectra with those of reference substances or literature data. The developed method was validated, and the good results showed that the method was not only automatic and rapid, but also accurate and reliable. The turbulent flow chromatography with online solid-phase extraction and high-performance liquid chromatography with tandem mass spectrometry method holds a high potential to become an effective method for the quality control of lignans in Magnoliae Flos and a useful tool for the analysis of other complex mixtures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Portable Tandem Mass Spectrometer Analyzer

DTIC Science & Technology

1991-07-01

The planned instrument was to be small enough to be portable in small vehicles and was to be able to use either an atmospheric pressure ion source or a...conventional electron impact/chemical ionization ion source. In order to accomplish these developments an atmospheric pressure ionization source was...developed for a compact, commercially available tandem quadrupole mass spectrometer. This ion source could be readily exchanged with the conventional

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

PubMed

Mo, Fan; Hong, Xu; Gao, Feng; Du, Lin; Wang, Jun; Omenn, Gilbert S; Lin, Biaoyang

2008-12-16

Alternative splicing is an important gene regulation mechanism. It is estimated that about 74% of multi-exon human genes have alternative splicing. High throughput tandem (MS/MS) mass spectrometry provides valuable information for rapidly identifying potentially novel alternatively-spliced protein products from experimental datasets. However, the ability to identify alternative splicing events through tandem mass spectrometry depends on the database against which the spectra are searched. We wrote scripts in perl, Bioperl, mysql and Ensembl API and built a theoretical exon-exon junction protein database to account for all possible combinations of exons for a gene while keeping the frame of translation (i.e., keeping only in-phase exon-exon combinations) from the Ensembl Core Database. Using our liver cancer MS/MS dataset, we identified a total of 488 non-redundant peptides that represent putative exon skipping events. Our exon-exon junction database provides the scientific community with an efficient means to identify novel alternatively spliced (exon skipping) protein isoforms using mass spectrometry data. This database will be useful in annotating genome structures using rapidly accumulating proteomics data.

Simulation of Two Dimensional Electrophoresis and Tandem Mass Spectrometry for Teaching Proteomics

ERIC Educational Resources Information Center

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations--2D electrophoresis and tandem mass spectrometry.…

Optimizing Algorithm Choice for Metaproteomics: Comparing X!Tandem and Proteome Discoverer for Soil Proteomes

NASA Astrophysics Data System (ADS)

Diaz, K. S.; Kim, E. H.; Jones, R. M.; de Leon, K. C.; Woodcroft, B. J.; Tyson, G. W.; Rich, V. I.

2014-12-01

The growing field of metaproteomics links microbial communities to their expressed functions by using mass spectrometry methods to characterize community proteins. Comparison of mass spectrometry protein search algorithms and their biases is crucial for maximizing the quality and amount of protein identifications in mass spectral data. Available algorithms employ different approaches when mapping mass spectra to peptides against a database. We compared mass spectra from four microbial proteomes derived from high-organic content soils searched with two search algorithms: 1) Sequest HT as packaged within Proteome Discoverer (v.1.4) and 2) X!Tandem as packaged in TransProteomicPipeline (v.4.7.1). Searches used matched metagenomes, and results were filtered to allow identification of high probability proteins. There was little overlap in proteins identified by both algorithms, on average just ~24% of the total. However, when adjusted for spectral abundance, the overlap improved to ~70%. Proteome Discoverer generally outperformed X!Tandem, identifying an average of 12.5% more proteins than X!Tandem, with X!Tandem identifying more proteins only in the first two proteomes. For spectrally-adjusted results, the algorithms were similar, with X!Tandem marginally outperforming Proteome Discoverer by an average of ~4%. We then assessed differences in heat shock proteins (HSP) identification by the two algorithms by BLASTing identified proteins against the Heat Shock Protein Information Resource, because HSP hits typically account for the majority signal in proteomes, due to extraction protocols. Total HSP identifications for each of the 4 proteomes were approximately ~15%, ~11%, ~17%, and ~19%, with ~14% for total HSPs with redundancies removed. Of the ~15% average of proteins from the 4 proteomes identified as HSPs, ~10% of proteins and spectra were identified by both algorithms. On average, Proteome Discoverer identified ~9% more HSPs than X!Tandem.

Context-Sensitive Markov Models for Peptide Scoring and Identification from Tandem Mass Spectrometry

PubMed Central

Grover, Himanshu; Wallstrom, Garrick; Wu, Christine C.

2013-01-01

Abstract Peptide and protein identification via tandem mass spectrometry (MS/MS) lies at the heart of proteomic characterization of biological samples. Several algorithms are able to search, score, and assign peptides to large MS/MS datasets. Most popular methods, however, underutilize the intensity information available in the tandem mass spectrum due to the complex nature of the peptide fragmentation process, thus contributing to loss of potential identifications. We present a novel probabilistic scoring algorithm called Context-Sensitive Peptide Identification (CSPI) based on highly flexible Input-Output Hidden Markov Models (IO-HMM) that capture the influence of peptide physicochemical properties on their observed MS/MS spectra. We use several local and global properties of peptides and their fragment ions from literature. Comparison with two popular algorithms, Crux (re-implementation of SEQUEST) and X!Tandem, on multiple datasets of varying complexity, shows that peptide identification scores from our models are able to achieve greater discrimination between true and false peptides, identifying up to ∼25% more peptides at a False Discovery Rate (FDR) of 1%. We evaluated two alternative normalization schemes for fragment ion-intensities, a global rank-based and a local window-based. Our results indicate the importance of appropriate normalization methods for learning superior models. Further, combining our scores with Crux using a state-of-the-art procedure, Percolator, we demonstrate the utility of using scoring features from intensity-based models, identifying ∼4-8 % additional identifications over Percolator at 1% FDR. IO-HMMs offer a scalable and flexible framework with several modeling choices to learn complex patterns embedded in MS/MS data. PMID:23289783

Discrimination Between Peptide O-Sulfo- and O-Phosphotyrosine Residues by Negative Ion Mode Electrospray Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Edelson-Averbukh, Marina; Shevchenko, Andrej; Pipkorn, Rüdiger; Lehmann, Wolf D.

2011-12-01

Unambiguous differentiation between isobaric sulfated and phosphorylated tyrosine residues (sTyr and pTyr) of proteins by mass spectrometry is challenging, even using high resolution mass spectrometers. Here we show that upon negative ion mode collision-induced dissociation (CID), pTyr- and sTyr-containing peptides exhibit entirely different modification-specific fragmentation patterns leading to a rapid discrimination between the isobaric covalent modifications using the tandem mass spectral data. This study reveals that the ratio between the relative abundances of [M-H-80]- and [M-H-98]- fragment ions in ion-trap CID and higher energy collision dissociation (HCD) spectra of singly deprotonated +80 Da Tyr-peptides can be used as a reliable indication of the Tyr modification group nature. For multiply deprotonated +80 Da Tyr-peptides, CID spectra of sTyr- and pTyr-containing sequences can be readily distinguished based on the presence/absence of the [M-nH-79](n-1)- and [M-nH-79-NL]( n-1)- ( n = 2, 3) fragment ions (NL = neutral loss).

PECAN: library-free peptide detection for data-independent acquisition tandem mass spectrometry data

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

Ting, Ying S.; Egertson, Jarrett D.; Bollinger, James G.

Data-independent acquisition (DIA) is an emerging mass spectrometry (MS)-based technique for unbiased and reproducible measurement of protein mixtures. DIA tandem mass spectrometry spectra are often highly multiplexed, containing product ions from multiple cofragmenting precursors. Detecting peptides directly from DIA data is therefore challenging; most DIA data analyses require spectral libraries. Here we present PECECAN (http://pecan.maccosslab.org), a library-free, peptide-centric tool that robustly and accurately detects peptides directly from DIA data. PECECAN reports evidence of detection based on product ion scoring, which enables detection of low-abundance analytes with poor precursor ion signal. We demonstrate the chromatographic peak picking accuracy and peptide detectionmore » capability of PECECAN, and we further validate its detection with data-dependent acquisition and targeted analyses. Lastly, we used PECECAN to build a plasma proteome library from DIA data and to query known sequence variants.« less

Ariadne: a database search engine for identification and chemical analysis of RNA using tandem mass spectrometry data.

PubMed

Nakayama, Hiroshi; Akiyama, Misaki; Taoka, Masato; Yamauchi, Yoshio; Nobe, Yuko; Ishikawa, Hideaki; Takahashi, Nobuhiro; Isobe, Toshiaki

2009-04-01

We present here a method to correlate tandem mass spectra of sample RNA nucleolytic fragments with an RNA nucleotide sequence in a DNA/RNA sequence database, thereby allowing tandem mass spectrometry (MS/MS)-based identification of RNA in biological samples. Ariadne, a unique web-based database search engine, identifies RNA by two probability-based evaluation steps of MS/MS data. In the first step, the software evaluates the matches between the masses of product ions generated by MS/MS of an RNase digest of sample RNA and those calculated from a candidate nucleotide sequence in a DNA/RNA sequence database, which then predicts the nucleotide sequences of these RNase fragments. In the second step, the candidate sequences are mapped for all RNA entries in the database, and each entry is scored for a function of occurrences of the candidate sequences to identify a particular RNA. Ariadne can also predict post-transcriptional modifications of RNA, such as methylation of nucleotide bases and/or ribose, by estimating mass shifts from the theoretical mass values. The method was validated with MS/MS data of RNase T1 digests of in vitro transcripts. It was applied successfully to identify an unknown RNA component in a tRNA mixture and to analyze post-transcriptional modification in yeast tRNA(Phe-1).

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

NASA Astrophysics Data System (ADS)

Liang, Zhidan; McGuinness, Kenneth N.; Crespo, Alejandro; Zhong, Wendy

2018-05-01

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. [Figure not available: see fulltext.

Characterization of Disulfide-Linked Peptides Using Tandem Mass Spectrometry Coupled with Automated Data Analysis Software

NASA Astrophysics Data System (ADS)

Liang, Zhidan; McGuinness, Kenneth N.; Crespo, Alejandro; Zhong, Wendy

2018-01-01

Disulfide bond formation is critical for maintaining structure stability and function of many peptides and proteins. Mass spectrometry has become an important tool for the elucidation of molecular connectivity. However, the interpretation of the tandem mass spectral data of disulfide-linked peptides has been a major challenge due to the lack of appropriate tools. Developing proper data analysis software is essential to quickly characterize disulfide-linked peptides. A thorough and in-depth understanding of how disulfide-linked peptides fragment in mass spectrometer is a key in developing software to interpret the tandem mass spectra of these peptides. Two model peptides with inter- and intra-chain disulfide linkages were used to study fragmentation behavior in both collisional-activated dissociation (CAD) and electron-based dissociation (ExD) experiments. Fragments generated from CAD and ExD can be categorized into three major types, which result from different S-S and C-S bond cleavage patterns. DiSulFinder is a computer algorithm that was newly developed based on the fragmentation observed in these peptides. The software is vendor neutral and capable of quickly and accurately identifying a variety of fragments generated from disulfide-linked peptides. DiSulFinder identifies peptide backbone fragments with S-S and C-S bond cleavages and, more importantly, can also identify fragments with the S-S bond still intact to aid disulfide linkage determination. With the assistance of this software, more comprehensive disulfide connectivity characterization can be achieved. [Figure not available: see fulltext.

Simultaneous detection of low and high molecular weight carbonylated compounds derived from lipid peroxidation by electrospray ionization-tandem mass spectrometry.

PubMed

Milic, Ivana; Hoffmann, Ralf; Fedorova, Maria

2013-01-02

Reactive oxygen species (ROS) and other oxidative agents such as free radicals can oxidize polyunsaturated fatty acids (PUFA) as well as PUFA in lipids. The oxidation products can undergo consecutive reactions including oxidative cleavages to yield a chemically diverse group of products, such as lipid peroxidation products (LPP). Among them are aldehydes and ketones ("reactive carbonyls") that are strong electrophiles and thus can readily react with nucleophilic side chains of proteins, which can alter the protein structure, function, cellular distribution, and antigenicity. Here, we report a novel technique to specifically derivatize both low molecular and high molecular weight carbonylated LPP with 7-(diethylamino)coumarin-3-carbohydrazide (CHH) and analyze all compounds by electrospray ionization-mass spectrometry (ESI-MS) in positive ion mode. CHH-derivatized compounds were identified by specific neutral losses or fragment ions. The fragment ion spectra displayed additional signals that allowed unambiguous identification of the lipid, fatty acids, cleavage sites, and oxidative modifications. Oxidation of docosahexaenoic (DHA, 22:6), arachidonic (AA, 20:4), linoleic (LA, 18:2), and oleic acids (OA, 18:1) yielded 69 aliphatic carbonyls, whose structures were all deduced from the tandem mass spectra. When four phosphatidylcholine (PC) vesicles containing the aforementioned unsaturated fatty acids were oxidized, we were able to deduce the structures of 122 carbonylated compounds from the tandem mass spectra of a single shotgun analysis acquired within 15 min. The high sensitivity (LOD ∼ 1 nmol/L for 4-hydroxy-2-nonenal, HNE) and a linear range of more than 3 orders of magnitude (10 nmol/L to 10 μmol/L for HNE) will allow further studies on complex biological samples including plasma.

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

PubMed Central

2015-01-01

Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit (http://cruxtoolkit.sourceforge.net) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. PMID:25182276

Separation of ion types in tandem mass spectrometry data interpretation -- a graph-theoretic approach.

PubMed

Yan, Bo; Pan, Chongle; Olman, Victor N; Hettich, Robert L; Xu, Ying

2004-01-01

Mass spectrometry is one of the most popular analytical techniques for identification of individual proteins in a protein mixture, one of the basic problems in proteomics. It identifies a protein through identifying its unique mass spectral pattern. While the problem is theoretically solvable, it remains a challenging problem computationally. One of the key challenges comes from the difficulty in distinguishing the N- and C-terminus ions, mostly b- and y-ions respectively. In this paper, we present a graph algorithm for solving the problem of separating bfrom y-ions in a set of mass spectra. We represent each spectral peak as a node and consider two types of edges: a type-1 edge connects two peaks possibly of the same ion types and a type-2 edge connects two peaks possibly of different ion types, predicted based on local information. The ion-separation problem is then formulated and solved as a graph partition problem, which is to partition the graph into three subgraphs, namely b-, y-ions and others respectively, so to maximize the total weight of type-1 edges while minimizing the total weight of type-2 edges within each subgraph. We have developed a dynamic programming algorithm for rigorously solving this graph partition problem and implemented it as a computer program PRIME. We have tested PRIME on 18 data sets of high accurate FT-ICR tandem mass spectra and found that it achieved ~90% accuracy for separation of b- and y- ions.

Mass Spectra-Based Framework for Automated Structural Elucidation of Metabolome Data to Explore Phytochemical Diversity

PubMed Central

Matsuda, Fumio; Nakabayashi, Ryo; Sawada, Yuji; Suzuki, Makoto; Hirai, Masami Y.; Kanaya, Shigehiko; Saito, Kazuki

2011-01-01

A novel framework for automated elucidation of metabolite structures in liquid chromatography–mass spectrometer metabolome data was constructed by integrating databases. High-resolution tandem mass spectra data automatically acquired from each metabolite signal were used for database searches. Three distinct databases, KNApSAcK, ReSpect, and the PRIMe standard compound database, were employed for the structural elucidation. The outputs were retrieved using the CAS metabolite identifier for identification and putative annotation. A simple metabolite ontology system was also introduced to attain putative characterization of the metabolite signals. The automated method was applied for the metabolome data sets obtained from the rosette leaves of 20 Arabidopsis accessions. Phenotypic variations in novel Arabidopsis metabolites among these accessions could be investigated using this method. PMID:22645535

Isotopologue Distributions of Peptide Product Ions by Tandem Mass Spectrometry: Quantitation of Low Levels of Deuterium Incorporation1

PubMed Central

Wang, Benlian; Sun, Gang; Anderson, David R.; Jia, Minghong; Previs, Stephen; Anderson, Vernon E.

2007-01-01

Protonated molecular peptide ions and their product ions generated by tandem mass spectrometry appear as isotopologue clusters due to the natural isotopic variations of carbon, hydrogen, nitrogen, oxygen and sulfur. Quantitation of the isotopic composition of peptides can be employed in experiments involving isotope effects, isotope exchange, isotopic labeling by chemical reactions, and studies of metabolism by stable isotope incorporation. Both ion trap and quadrupole-time of flight mass spectrometry are shown to be capable of determining the isotopic composition of peptide product ions obtained by tandem mass spectrometry with both precision and accuracy. Tandem mass spectra obtained in profile-mode of clusters of isotopologue ions are fit by non-linear least squares to a series of Gaussian peaks (described in the accompanying manuscript) which quantify the Mn/M0 values which define the isotopologue distribution (ID). To determine the isotopic composition of product ions from their ID, a new algorithm that predicts the Mn/M0 ratios is developed which obviates the need to determine the intensity of all of the ions of an ID. Consequently a precise and accurate determination of the isotopic composition a product ion may be obtained from only the initial values of the ID, however the entire isotopologue cluster must be isolated prior to fragmentation. Following optimization of the molecular ion isolation width, fragmentation energy and detector sensitivity, the presence of isotopic excess (2H, 13C, 15N, 18O) is readily determined within 1%. The ability to determine the isotopic composition of sequential product ions permits the isotopic composition of individual amino acid residues in the precursor ion to be determined. PMID:17559791

Simulation of two dimensional electrophoresis and tandem mass spectrometry for teaching proteomics.

PubMed

Fisher, Amanda; Sekera, Emily; Payne, Jill; Craig, Paul

2012-01-01

In proteomics, complex mixtures of proteins are separated (usually by chromatography or electrophoresis) and identified by mass spectrometry. We have created 2DE Tandem MS, a computer program designed for use in the biochemistry, proteomics, or bioinformatics classroom. It contains two simulations-2D electrophoresis and tandem mass spectrometry. The two simulations are integrated together and are designed to teach the concept of proteome analysis of prokaryotic and eukaryotic organisms. 2DE-Tandem MS can be used as a freestanding simulation, or in conjunction with a wet lab, to introduce proteomics in the undergraduate classroom. 2DE Tandem MS is a free program available on Sourceforge at https://sourceforge.net/projects/jbf/. It was developed using Java Swing and functions in Mac OSX, Windows, and Linux, ensuring that every student sees a consistent and informative graphical user interface no matter the computer platform they choose. Java must be installed on the host computer to run 2DE Tandem MS. Example classroom exercises are provided in the Supporting Information. Copyright © 2012 Wiley Periodicals, Inc.

Development of an advanced spacecraft tandem mass spectrometer

NASA Astrophysics Data System (ADS)

Drew, Russell C.

1992-03-01

The purpose of this research was to apply current advanced technology in electronics and materials to the development of a miniaturized Tandem Mass Spectrometer that would have the potential for future development into a package suitable for spacecraft use. The mass spectrometer to be used as a basis for the tandem instrument would be a magnetic sector instrument, of Nier-Johnson configuration, as used on the Viking Mars Lander mission. This instrument configuration would then be matched with a suitable second stage MS to provide the benefits of tandem MS operation for rapid identification of unknown organic compounds. This tandem instrument is configured with a newly designed GC system to aid in separation of complex mixtures prior to MS analysis. A number of important results were achieved in the course of this project. Among them were the development of a miniaturized GC subsystem, with a unique desorber-injector, fully temperature feedback controlled oven with powered cooling for rapid reset to ambient conditions, a unique combination inlet system to the MS that provides for both membrane sampling and direct capillary column sample transfer, a compact and ruggedized alignment configuration for the MS, an improved ion source design for increased sensitivity, and a simple, rugged tandem MS configuration that is particularly adaptable to spacecraft use because of its low power and low vacuum pumping requirements. The potential applications of this research include use in manned spacecraft like the space station as a real-time detection and warning device for the presence of potentially harmful trace contaminants of the spacecraft atmosphere, use as an analytical device for evaluating samples collected on the Moon or a planetary surface, or even use in connection with monitoring potentially hazardous conditions that may exist in terrestrial locations such as launch pads, environmental test chambers or other sensitive areas. Commercial development of the technology

Development of an advanced spacecraft tandem mass spectrometer

NASA Technical Reports Server (NTRS)

Drew, Russell C.

1992-01-01

The purpose of this research was to apply current advanced technology in electronics and materials to the development of a miniaturized Tandem Mass Spectrometer that would have the potential for future development into a package suitable for spacecraft use. The mass spectrometer to be used as a basis for the tandem instrument would be a magnetic sector instrument, of Nier-Johnson configuration, as used on the Viking Mars Lander mission. This instrument configuration would then be matched with a suitable second stage MS to provide the benefits of tandem MS operation for rapid identification of unknown organic compounds. This tandem instrument is configured with a newly designed GC system to aid in separation of complex mixtures prior to MS analysis. A number of important results were achieved in the course of this project. Among them were the development of a miniaturized GC subsystem, with a unique desorber-injector, fully temperature feedback controlled oven with powered cooling for rapid reset to ambient conditions, a unique combination inlet system to the MS that provides for both membrane sampling and direct capillary column sample transfer, a compact and ruggedized alignment configuration for the MS, an improved ion source design for increased sensitivity, and a simple, rugged tandem MS configuration that is particularly adaptable to spacecraft use because of its low power and low vacuum pumping requirements. The potential applications of this research include use in manned spacecraft like the space station as a real-time detection and warning device for the presence of potentially harmful trace contaminants of the spacecraft atmosphere, use as an analytical device for evaluating samples collected on the Moon or a planetary surface, or even use in connection with monitoring potentially hazardous conditions that may exist in terrestrial locations such as launch pads, environmental test chambers or other sensitive areas. Commercial development of the technology

EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra*

PubMed Central

Yuan, Zuo-Fei; Lin, Shu; Molden, Rosalynn C.; Cao, Xing-Jun; Bhanu, Natarajan V.; Wang, Xiaoshi; Sidoli, Simone; Liu, Shichong; Garcia, Benjamin A.

2015-01-01

Histone post-translational modifications contribute to chromatin function through their chemical properties which influence chromatin structure and their ability to recruit chromatin interacting proteins. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry (nanoLC-MS/MS) has emerged as the most suitable technology for global histone modification analysis because of the high sensitivity and the high mass accuracy of this approach that provides confident identification. However, analysis of histones with this method is even more challenging because of the large number and variety of isobaric histone peptides and the high dynamic range of histone peptide abundances. Here, we introduce EpiProfile, a software tool that discriminates isobaric histone peptides using the distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. The accuracy of EpiProfile was evaluated by analysis of mixtures containing different ratios of synthetic histone peptides. In addition to label-free quantification of histone peptides, EpiProfile is flexible and can quantify different types of isotopically labeled histone peptides. EpiProfile is unique in generating layouts (i.e. relative retention time) of histone peptides when compared with manual quantification of the data and other programs (such as Skyline), filling the need of an automatic and freely available tool to quantify labeled and non-labeled modified histone peptides. In summary, EpiProfile is a valuable nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. PMID:25805797

ANALYSIS OF POLYCYCLIC AROMATIC HYDROCARBONS BY ION TRAP TANDEM MASS SPECTROMETRY

EPA Science Inventory

An ion-trap mass spectrometer with a wave board and tandem mass spectrometry software was used to analyze gas chromatographically separated polycyclic aromatic hydrocarbons (PAHs) by using collision-induced dissociation (CID). The nonresonant (multiple collision) mode was used to...

Multivariate Analysis of Electron Detachment Dissociation and Infrared Multiphoton Dissociation Mass Spectra of Heparan Sulfate Tetrasaccharides Differing Only in Hexuronic acid Stereochemistry

NASA Astrophysics Data System (ADS)

Oh, Han Bin; Leach, Franklin E.; Arungundram, Sailaja; Al-Mafraji, Kanar; Venot, Andre; Boons, Geert-Jan; Amster, I. Jonathan

2011-03-01

The structural characterization of glycosaminoglycan (GAG) carbohydrates by mass spectrometry has been a long-standing analytical challenge due to the inherent heterogeneity of these biomolecules, specifically polydispersity, variability in sulfation, and hexuronic acid stereochemistry. Recent advances in tandem mass spectrometry methods employing threshold and electron-based ion activation have resulted in the ability to determine the location of the labile sulfate modification as well as assign the stereochemistry of hexuronic acid residues. To facilitate the analysis of complex electron detachment dissociation (EDD) spectra, principal component analysis (PCA) is employed to differentiate the hexuronic acid stereochemistry of four synthetic GAG epimers whose EDD spectra are nearly identical upon visual inspection. For comparison, PCA is also applied to infrared multiphoton dissociation spectra (IRMPD) of the examined epimers. To assess the applicability of multivariate methods in GAG mixture analysis, PCA is utilized to identify the relative content of two epimers in a binary mixture.

Identification of Phase II Metabolites of Thiol-conjugated [6]-Shogaol in Mouse Urine Using High-Performance Liquid Chromatography Tandem Mass Spectrometry

PubMed Central

Chen, Huadong; Sang, Shengmin

2012-01-01

Ginger is frequently consumed as a spice and has numerous medicinal properties. Extensive research has characterized the anti-inflammatory, antioxidant, and antitumor activities of ginger. Previously, we reported the mercapturic acid pathway as a major metabolic route of [6]-shogaol in mice and the thiol conjugates of [6]-shogaol existed in the glucuronidated and sulfated forms in mouse urine. However, their structures are still unknown. In the present study, we further investigated the phase II metabolism of thiol-conjugated [6]-shogaol in mouse urine, in which we identified sixteen phase II metabolites of thiol-conjugated [6]-shogaol: 5-cysteinyl-[6]-shogaol glucuronide (9), 5-N-acetylcysteinyl-[6]-shogaol glucuronide (10), 5-cysteinylglycinyl-[6]-shogaol glucuronide (11), 5-methylthio-[6]-shogaol glucuronide (12), 5-cysteinyl-M6 glucuronide (13 and 14), 5-cysteinyl-M6 sulfate (15 and 16), 5-N-acetylcysteinyl-M6 glucuronide (17 and 18), 5-cysteinylglycinyl-M6 glucuronide (19 and 20), 5-cysteinylglycinyl-M6 sulfate (21 and 22), and 5-methylthio-M6 glucuronide (23 and 24) using liquid chromatography/electrospray ionization tandem mass spectrometry. The structures of these metabolites were confirmed by analyzing their MSn (n =1! 4) spectra as well as comparing with the tandem mass spectra of authentic standards. To our knowledge, this is the first report involving identification of phase II urinary metabolites of [6]-shogaol in mice. PMID:23031413

Use of electrospray ionization ion-trap tandem mass spectrometry and principal component analysis to directly distinguish monosaccharides.

PubMed

Xia, Bing; Zhou, Yan; Liu, Xin; Xiao, Juan; Liu, Qing; Gu, Yucheng; Ding, Lisheng

2012-06-15

Carbohydrates are good source of drugs and play important roles in metabolism processes and cellular interactions in organisms. Distinguishing monosaccharide isomers in saccharide derivates is an important and elementary work in investigating saccharides. It is important to develop a fast, simple and direct method for this purpose, which is described in this study. Stock solutions of monosaccharide with a concentration of 400 μM and sodium chloride at a concentration of 10 μM were made in water/methanol (50:50, v/v). The samples were subjected to electrospray ionization ion-trap tandem mass spectrometry (ESI-MS) and the detected [2M + Na - H(2)O](+) ions were further investigated by tandem mass spectrometry (MS/MS), followed by applying principal component analysis (PCA) on the obtained MS/MS data sets. The MS/MS spectra of the [2M + Na - H(2)O](+) ions at m/z 365 for hexoses and m/z 305 for pentoses yielded unambiguous fragment patterns, while rhamnose can be directly identified by its ESI-MS [M + Na](+) ion at m/z 187. PCA showed clustering of MS/MS data of identical monosaccharide samples obtained from different experiments. By using this method, the monosaccharide in daucosterol hydrolysate was successfully identified. A new strategy was developed for differentiation of the monosaccharides using ESI-MS/MS and PCA. In MS/MS spectra, the [2M + Na - H(2)O](+) ions yielded unambiguous distinction. PCA of the archived MS/MS data sets was applied to demonstrate the spatial resolution of the studied samples. This method presented a simple and reliable way for distinguishing monosaccharides by ESI-MS/MS. Copyright © 2012 John Wiley & Sons, Ltd.

Tandem mass spectrometry of human tryptic blood peptides calculated by a statistical algorithm and captured by a relational database with exploration by a general statistical analysis system.

PubMed

Bowden, Peter; Beavis, Ron; Marshall, John

2009-11-02

A goodness of fit test may be used to assign tandem mass spectra of peptides to amino acid sequences and to directly calculate the expected probability of mis-identification. The product of the peptide expectation values directly yields the probability that the parent protein has been mis-identified. A relational database could capture the mass spectral data, the best fit results, and permit subsequent calculations by a general statistical analysis system. The many files of the Hupo blood protein data correlated by X!TANDEM against the proteins of ENSEMBL were collected into a relational database. A redundant set of 247,077 proteins and peptides were correlated by X!TANDEM, and that was collapsed to a set of 34,956 peptides from 13,379 distinct proteins. About 6875 distinct proteins were only represented by a single distinct peptide, 2866 proteins showed 2 distinct peptides, and 3454 proteins showed at least three distinct peptides by X!TANDEM. More than 99% of the peptides were associated with proteins that had cumulative expectation values, i.e. probability of false positive identification, of one in one hundred or less. The distribution of peptides per protein from X!TANDEM was significantly different than those expected from random assignment of peptides.

Development of a dedicated peptide tandem mass spectral library for conservation science.

PubMed

Fremout, Wim; Dhaenens, Maarten; Saverwyns, Steven; Sanyova, Jana; Vandenabeele, Peter; Deforce, Dieter; Moens, Luc

2012-05-30

In recent years, the use of liquid chromatography tandem mass spectrometry (LC-MS/MS) on tryptic digests of cultural heritage objects has attracted much attention. It allows for unambiguous identification of peptides and proteins, and even in complex mixtures species-specific identification becomes feasible with minimal sample consumption. Determination of the peptides is commonly based on theoretical cleavage of known protein sequences and on comparison of the expected peptide fragments with those found in the MS/MS spectra. In this approach, complex computer programs, such as Mascot, perform well identifying known proteins, but fail when protein sequences are unknown or incomplete. Often, when trying to distinguish evolutionarily well preserved collagens of different species, Mascot lacks the required specificity. Complementary and often more accurate information on the proteins can be obtained using a reference library of MS/MS spectra of species-specific peptides. Therefore, a library dedicated to various sources of proteins in works of art was set up, with an initial focus on collagen rich materials. This paper discusses the construction and the advantages of this spectral library for conservation science, and its application on a number of samples from historical works of art. Copyright © 2012 Elsevier B.V. All rights reserved.

Automated tandem mass spectrometry by orthogonal acceleration TOF data acquisition and simultaneous magnet scanning for the characterization of petroleum mixtures.

PubMed

Roussis, S G

2001-08-01

The automated acquisition of the product ion spectra of all precursor ions in a selected mass range by using a magnetic sector/orthogonal acceleration time-of-flight (oa-TOF) tandem mass spectrometer for the characterization of complex petroleum mixtures is reported. Product ion spectra are obtained by rapid oa-TOF data acquisition and simultaneous scanning of the magnet. An analog signal generator is used for the scanning of the magnet. Slow magnet scanning rates permit the accurate profiling of precursor ion peaks and the acquisition of product ion spectra for all isobaric ion species. The ability of the instrument to perform both high- and low-energy collisional activation experiments provides access to a large number of dissociation pathways useful for the characterization of precursor ions. Examples are given that illustrate the capability of the method for the characterization of representative petroleum mixtures. The structural information obtained by the automated MS/MS experiment is used in combination with high-resolution accurate mass measurement results to characterize unknown components in a polar extract of a refinery product. The exhaustive mapping of all precursor ions in representative naphtha and middle-distillate fractions is presented. Sets of isobaric ion species are separated and their structures are identified by interpretation from first principles or by comparison with standard 70-eV EI libraries of spectra. The utility of the method increases with the complexity of the samples.

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.

Towards a full reference library of MS(n) spectra. Testing of a library containing 3126 MS2 spectra of 1743 compounds.

PubMed

Milman, Boris L

2005-01-01

A library consisting of 3766 MS(n) spectra of 1743 compounds, including 3126 MS2 spectra acquired mainly using ion trap (IT) and triple-quadrupole (QqQ) instruments, was composed of numerous collections/sources. Ionization techniques were mainly electrospray ionization and also atmospheric pressure chemical ionization and chemical ionization. The library was tested for the performance in identification of unknowns, and in this context this work is believed to be the largest of all known tests of product-ion mass spectral libraries. The MS2 spectra of the same compounds from different collections were in turn divided into spectra of 'unknown' and reference compounds. For each particular compound, library searches were performed resulting in selection by taking into account the best matches for each spectral collection/source. Within each collection/source, replicate MS2 spectra differed in the collision energy used. Overall, there were up to 950 search results giving the best match factors and their ranks in corresponding hit lists. In general, the correct answers were obtained as the 1st rank in up to 60% of the search results when retrieved with (on average) 2.2 'unknown' and 6.2 reference replicates per compound. With two or more replicates of both 'unknown' and reference spectra (the average numbers of replicates were 4.0 and 7.8, respectively), the fraction of correct answers in the 1st rank increased to 77%. This value is close to the performance of established electron ionization mass spectra libraries (up to 79%) found by other workers. The hypothesis that MS2 spectra better match reference spectra acquired using the same type of tandem mass spectrometer (IT or QqQ) was neither strongly proved nor rejected here. The present work shows that MS2 spectral libraries containing sufficiently numerous different entries for each compound are sufficiently efficient for identification of unknowns and suitable for use with different tandem mass spectrometers. 2005 John

Electrospray ionization tandem mass spectrometry differentiation of N-phosphoryl-[alpha]-, [beta]- and [gamma]-amino acids

NASA Astrophysics Data System (ADS)

Qiang, Liming; Cao, Shuxia; Zhao, Xiaoyang; Mao, Xiangju; Guo, Yanchun; Liao, Xincheng; Zhao, Yufen

2007-10-01

The fragmentation patterns of N-diisopropyloxyphosphoryl-l-[alpha]-Ala (DIPP-l-[alpha]-Ala), N-diisopropyloxyphosphoryl-d-[alpha]-Ala (DIPP-d-[alpha]-Ala), N-diisopropyloxyphosphoryl-[beta]-Ala (DIPP-[beta]-Ala) and N-diisopropyloxyphosphoryl-[gamma]-amino butyric acid (DIPP-[gamma]-Aba) were investigated by electrospray ionization tandem mass spectrometry (ESI-MS/MS). DIPP-d-[alpha]-Ala showed the same fragmentation pathways as DIPP-l-[alpha]-Ala. In the fragmentation of protonated DIPP-[beta]-Ala, the characteristic fragment ion [M + H - 2C3H6 - H2O - CH2CO]+ appeared and could be used to distinguish [beta]-Ala from l-[alpha]-Ala and d-[alpha]-Ala through tandem mass spectra, even though they possess the same molecular weight. In the fragmentation of protonated DIPP-[gamma]-Aba, the break of PN bond occurred and an interesting protonated lactam ion with five-membered ring was generated. Furthermore, in the MS3 spectrum of [M + Na - 2C3H6]+ ion of DIPP-[gamma]-Aba, a strong intensity of unique fragment ion, namely lactam-sodium adduct with five-membered ring, was observed, which could be considered as a mark for [gamma]-amino acids. The stepwise fragmentations of their [M + Na]+ ions and [M - H]- ions showed that they all underwent a PN to PO bond migration through a five-membered or six-membered or even seven-membered ring transition state, respectively, which supported the great affinity of hydroxyl for phosphoryl group.

Simultaneous quantification of protein phosphorylation sites using liquid chromatography-tandem mass spectrometry-based targeted proteomics: a linear algebra approach for isobaric phosphopeptides.

PubMed

Xu, Feifei; Yang, Ting; Sheng, Yuan; Zhong, Ting; Yang, Mi; Chen, Yun

2014-12-05

As one of the most studied post-translational modifications (PTM), protein phosphorylation plays an essential role in almost all cellular processes. Current methods are able to predict and determine thousands of phosphorylation sites, whereas stoichiometric quantification of these sites is still challenging. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)-based targeted proteomics is emerging as a promising technique for site-specific quantification of protein phosphorylation using proteolytic peptides as surrogates of proteins. However, several issues may limit its application, one of which relates to the phosphopeptides with different phosphorylation sites and the same mass (i.e., isobaric phosphopeptides). While employment of site-specific product ions allows for these isobaric phosphopeptides to be distinguished and quantified, site-specific product ions are often absent or weak in tandem mass spectra. In this study, linear algebra algorithms were employed as an add-on to targeted proteomics to retrieve information on individual phosphopeptides from their common spectra. To achieve this simultaneous quantification, a LC-MS/MS-based targeted proteomics assay was first developed and validated for each phosphopeptide. Given the slope and intercept of calibration curves of phosphopeptides in each transition, linear algebraic equations were developed. Using a series of mock mixtures prepared with varying concentrations of each phosphopeptide, the reliability of the approach to quantify isobaric phosphopeptides containing multiple phosphorylation sites (≥ 2) was discussed. Finally, we applied this approach to determine the phosphorylation stoichiometry of heat shock protein 27 (HSP27) at Ser78 and Ser82 in breast cancer cells and tissue samples.

Dissociation reactions of protonated anthracycline antibiotics following electrospray ionization-tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Sleno, Lekha; Campagna-Slater, Valerie; Volmer, Dietrich A.

2006-09-01

Fragmentation pathways of doxorubicin, a common cancer therapy agent, and three closely related analogs (epirubicin, daunorubicin, idarubicin) were compared using electrospray ionization with tandem mass spectrometry. This class of antibiotics with anti-tumour activity has important structural features, with a tetracyclic aromatic, polyketide portion, which is glycosylated with an amino sugar in order to exhibit its biological activity. Collision-induced dissociation spectra revealed very similar product ions for each analog, however, important differences were seen in the relative abundances and the ease at which certain fragments were formed. Fragment ions observed included those from cleavage of the glycosidic bond, loss of the side chain from the aglycone moiety, water losses and loss of a methyl radical. Following cleavage of the glycosidic bond, the charge can either reside on the aglycone portion or the sugar moiety, and each of these primary fragments undergoes several secondary dissociation pathways, depending on the collision energy. By ramping the collision voltage, we were able to correlate the changes in fragmentation behavior with small alterations in the structure of the precursor ion. The detailed study of the fragmentation behavior of doxorubicin was supported by accurate mass measurements, using an electrospray-time of flight instrument, as well as MS3 data from a quadrupole-linear ion trap mass spectrometer. Computational studies were also performed to help explain the role of certain functional groups in the fragmentation reactions.

Analytical Utility of Mass Spectral Binning in Proteomic Experiments by SPectral Immonium Ion Detection (SPIID)*

PubMed Central

Kelstrup, Christian D.; Frese, Christian; Heck, Albert J. R.; Olsen, Jesper V.; Nielsen, Michael L.

2014-01-01

Unambiguous identification of tandem mass spectra is a cornerstone in mass-spectrometry-based proteomics. As the study of post-translational modifications (PTMs) by means of shotgun proteomics progresses in depth and coverage, the ability to correctly identify PTM-bearing peptides is essential, increasing the demand for advanced data interpretation. Several PTMs are known to generate unique fragment ions during tandem mass spectrometry, the so-called diagnostic ions, which unequivocally identify a given mass spectrum as related to a specific PTM. Although such ions offer tremendous analytical advantages, algorithms to decipher MS/MS spectra for the presence of diagnostic ions in an unbiased manner are currently lacking. Here, we present a systematic spectral-pattern-based approach for the discovery of diagnostic ions and new fragmentation mechanisms in shotgun proteomics datasets. The developed software tool is designed to analyze large sets of high-resolution peptide fragmentation spectra independent of the fragmentation method, instrument type, or protease employed. To benchmark the software tool, we analyzed large higher-energy collisional activation dissociation datasets of samples containing phosphorylation, ubiquitylation, SUMOylation, formylation, and lysine acetylation. Using the developed software tool, we were able to identify known diagnostic ions by comparing histograms of modified and unmodified peptide spectra. Because the investigated tandem mass spectra data were acquired with high mass accuracy, unambiguous interpretation and determination of the chemical composition for the majority of detected fragment ions was feasible. Collectively we present a freely available software tool that allows for comprehensive and automatic analysis of analogous product ions in tandem mass spectra and systematic mapping of fragmentation mechanisms related to common amino acids. PMID:24895383

Identification of phase II metabolites of thiol-conjugated [6]-shogaol in mouse urine using high-performance liquid chromatography tandem mass spectrometry.

PubMed

Chen, Huadong; Sang, Shengmin

2012-10-15

Ginger is frequently consumed as a spice and has numerous medicinal properties. Extensive research has characterized the anti-inflammatory, antioxidant, and antitumor activities of ginger. Previously, we reported the mercapturic acid pathway as a major metabolic route of [6]-shogaol in mice and the thiol conjugates of [6]-shogaol existed in the glucuronidated and sulfated forms in mouse urine. However, their structures are still unknown. In the present study, we further investigated the phase II metabolism of thiol-conjugated [6]-shogaol in mouse urine, in which we identified sixteen phase II metabolites of thiol-conjugated [6]-shogaol: 5-cysteinyl-[6]-shogaol glucuronide (9), 5-N-acetylcysteinyl-[6]-shogaol glucuronide (10), 5-cysteinylglycinyl-[6]-shogaol glucuronide (11), 5-methylthio-[6]-shogaol glucuronide (12), 5-cysteinyl-M6 glucuronide (13 and 14), 5-cysteinyl-M6 sulfate (15 and 16), 5-N-acetylcysteinyl-M6 glucuronide (17 and 18), 5-cysteinylglycinyl-M6 glucuronide (19 and 20), 5-cysteinylglycinyl-M6 sulfate (21 and 22), and 5-methylthio-M6 glucuronide (23 and 24) using liquid chromatography/electrospray ionization tandem mass spectrometry. The structures of these metabolites were confirmed by analyzing their MS(n) (n=1-4) spectra as well as comparing with the tandem mass spectra of authentic standards. To the best of our knowledge, this is the first report involving identification of phase II urinary metabolites of [6]-shogaol in mice. Copyright © 2012 Elsevier B.V. All rights reserved.

Fragmentation pathways and structural characterization of organophosphorus compounds related to the Chemical Weapons Convention by electron ionization and electrospray ionization tandem mass spectrometry.

PubMed

Hosseini, Seyed Esmaeil; Saeidian, Hamid; Amozadeh, Ali; Naseri, Mohammad Taghi; Babri, Mehran

2016-12-30

For unambiguous identification of Chemical Weapons Convention (CWC)-related chemicals in environmental samples, the availability of mass spectra, interpretation skills and rapid microsynthesis of suspected chemicals are essential requirements. For the first time, the electron ionization single quadrupole and electrospray ionization tandem mass spectra of a series of O-alkyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidates (Scheme 1, cpd 4) were studied for CWC verification purposes. O-Alkyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidates were prepared through a microsynthetic method and were analyzed using electron ionization and electrospray ionization mass spectrometry with gas and liquid chromatography, respectively, as MS-inlet systems. General EI and ESI fragmentation pathways were proposed and discussed, and collision-induced dissociation studies of the protonated derivatives of these compounds were performed to confirm proposed fragment ion structures by analyzing mass spectra of deuterated analogs. Mass spectrometric studies revealed some interesting fragmentation pathways during the ionization process, such as McLafferty rearrangement, hydrogen rearrangement and a previously unknown intramolecular electrophilic aromatic substitution reaction. The EI and ESI fragmentation routes of the synthesized compounds 4 were investigated with the aim of detecting and identifying CWC-related chemicals during on-site inspection and/or off-site analysis and toxic chemical destruction monitoring. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Successful adaption of a forensic toxicological screening workflow employing nontargeted liquid chromatography-tandem mass spectrometry to water analysis.

PubMed

Steger, Julia; Arnhard, Kathrin; Haslacher, Sandra; Geiger, Klemens; Singer, Klaus; Schlapp, Michael; Pitterl, Florian; Oberacher, Herbert

2016-04-01

Forensic toxicology and environmental water analysis share the common interest and responsibility in ensuring comprehensive and reliable confirmation of drugs and pharmaceutical compounds in samples analyzed. Dealing with similar analytes, detection and identification techniques should be exchangeable between scientific disciplines. Herein, we demonstrate the successful adaption of a forensic toxicological screening workflow employing nontargeted LC/MS/MS under data-dependent acquisition control and subsequent database search to water analysis. The main modification involved processing of an increased sample volume with SPE (500 mL vs. 1-10 mL) to reach LODs in the low ng/L range. Tandem mass spectra acquired with a qTOF instrument were submitted to database search. The targeted data mining strategy was found to be sensitive and specific; automated search produced hardly any false results. To demonstrate the applicability of the adapted workflow to complex samples, 14 wastewater effluent samples collected on seven consecutive days at the local wastewater-treatment plant were analyzed. Of the 88,970 fragment ion mass spectra produced, 8.8% of spectra were successfully assigned to one of the 1040 reference compounds included in the database, and this enabled the identification of 51 compounds representing important illegal drugs, members of various pharmaceutical compound classes, and metabolites thereof. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry and tandem mass spectrometry for peptide de novo amino acid sequencing for a seven-protein mixture by paired single-residue transposed Lys-N and Lys-C digestion.

PubMed

Guan, Xiaoyan; Brownstein, Naomi C; Young, Nicolas L; Marshall, Alan G

2017-01-30

Bottom-up tandem mass spectrometry (MS/MS) is regularly used in proteomics to identify proteins from a sequence database. De novo sequencing is also available for sequencing peptides with relatively short sequence lengths. We recently showed that paired Lys-C and Lys-N proteases produce peptides of identical mass and similar retention time, but different tandem mass spectra. Such parallel experiments provide complementary information, and allow for up to 100% MS/MS sequence coverage. Here, we report digestion by paired Lys-C and Lys-N proteases of a seven-protein mixture: human hemoglobin alpha, bovine carbonic anhydrase 2, horse skeletal muscle myoglobin, hen egg white lysozyme, bovine pancreatic ribonuclease, bovine rhodanese, and bovine serum albumin, followed by reversed-phase nanoflow liquid chromatography, collision-induced dissociation, and 14.5 T Fourier transform ion cyclotron resonance mass spectrometry. Matched pairs of product peptide ions of equal precursor mass and similar retention times from each digestion are compared, leveraging single-residue transposed information with independent interferences to confidently identify fragment ion types, residues, and peptides. Selected pairs of product ion mass spectra for de novo sequenced protein segments from each member of the mixture are presented. Pairs of the transposed product ions as well as complementary information from the parallel experiments allow for both high MS/MS coverage for long peptide sequences and high confidence in the amino acid identification. Moreover, the parallel experiments in the de novo sequencing reduce false-positive matches of product ions from the single-residue transposed peptides from the same segment, and thereby further improve the confidence in protein identification. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Protein Sequencing with Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Ziady, Assem G.; Kinter, Michael

The recent introduction of electrospray ionization techniques that are suitable for peptides and whole proteins has allowed for the design of mass spectrometric protocols that provide accurate sequence information for proteins. The advantages gained by these approaches over traditional Edman Degradation sequencing include faster analysis and femtomole, sometimes attomole, sensitivity. The ability to efficiently identify proteins has allowed investigators to conduct studies on their differential expression or modification in response to various treatments or disease states. In this chapter, we discuss the use of electrospray tandem mass spectrometry, a technique whereby protein-derived peptides are subjected to fragmentation in the gas phase, revealing sequence information for the protein. This powerful technique has been instrumental for the study of proteins and markers associated with various disorders, including heart disease, cancer, and cystic fibrosis. We use the study of protein expression in cystic fibrosis as an example.

Fragmentation study of iridoid glucosides through positive and negative electrospray ionization, collision-induced dissociation and tandem mass spectrometry.

PubMed

Es-Safi, Nour-Eddine; Kerhoas, Lucien; Ducrot, Paul-Henri

2007-01-01

Mass spectrometric methodology based on the combined use of positive and negative electrospray ionization, collision-induced dissociation (CID) and tandem mass spectrometry (MS/MS) has been applied to the mass spectral study of a series of six naturally occurring iridoids through in-source fragmentation of the protonated [M+H]+, deprotonated [M--H]- and sodiated [M+Na]+ ions. This led to the unambiguous determination of the molecular masses of the studied compounds and allowed CID spectra of the molecular ions to be obtained. Valuable structural information regarding the nature of both the glycoside and the aglycone moiety was thus obtained. Glycosidic cleavage and ring cleavages of both aglycone and sugar moieties were the major fragmentation pathways observed during CID, where the losses of small molecules, the cinnamoyl and the cinnamate parts were also observed. The formation of the ionized aglycones, sugars and their product ions was thus obtained giving information on their basic skeleton. The protonated, i.e. [M+H]+ and deprotonated [M--H]-, ions were found to fragment mainly by glycosidic cleavages. MS/MS spectra of the [M+Na]+ ions gave complementary information for the structural characterization of the studied compounds. Unlike the dissociation of protonated molecular ions, that of sodiated molecules also provided sodiated sugar fragments where the C0+ fragment corresponding to the glucose ion was obtained as base peak for all the studied compounds. Copyright (c) 2007 John Wiley & Sons, Ltd.

Characterization of crude oil biomarkers using comprehensive two-dimensional gas chromatography coupled to tandem mass spectrometry.

PubMed

Mogollón, Noroska Gabriela Salazar; Prata, Paloma Santana; Dos Reis, Jadson Zeni; Neto, Eugênio Vaz Dos Santos; Augusto, Fabio

2016-09-01

Oil samples from Recôncavo basin (NE Brazil), previously analyzed by traditional techniques such as gas chromatography coupled to tandem mass spectrometry, were evaluated using comprehensive two-dimensional gas chromatography coupled to quadrupole mass spectrometry and comprehensive two-dimensional gas chromatography coupled to tandem mass spectrometry along with simplified methods of samples preparation to evaluate the differences and advantages of these analytical techniques to better understand the development of the organic matter in this basin without altering the normal distribution of the compounds in the samples. As a result, the geochemical parameters calculated by comprehensive two-dimensional gas chromatography coupled to tandem mass spectrometry described better the origin, maturity, and biodegradation of both samples probably by increased selectivity, resolution, and sensitivity inherent of the multidimensional technique. Additionally, the detection of the compounds such as, the C(14α-) homo-26-nor-17α-hopane series, diamoretanes, nor-spergulanes, C19 -C26 A-nor-steranes and 4α-methylsteranes resolved and detected by comprehensive two-dimensional gas chromatography coupled to tandem mass spectrometry were key to classify and differentiate these lacustrine samples according to their maturity and deposition conditions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectra library assisted de novo peptide sequencing for HCD and ETD spectra pairs.

PubMed

Yan, Yan; Zhang, Kaizhong

2016-12-23

De novo peptide sequencing via tandem mass spectrometry (MS/MS) has been developed rapidly in recent years. With the use of spectra pairs from the same peptide under different fragmentation modes, performance of de novo sequencing is greatly improved. Currently, with large amount of spectra sequenced everyday, spectra libraries containing tens of thousands of annotated experimental MS/MS spectra become available. These libraries provide information of the spectra properties, thus have the potential to be used with de novo sequencing to improve its performance. In this study, an improved de novo sequencing method assisted with spectra library is proposed. It uses spectra libraries as training datasets and introduces significant scores of the features used in our previous de novo sequencing method for HCD and ETD spectra pairs. Two pairs of HCD and ETD spectral datasets were used to test the performance of the proposed method and our previous method. The results show that this proposed method achieves better sequencing accuracy with higher ranked correct sequences and less computational time. This paper proposed an advanced de novo sequencing method for HCD and ETD spectra pair and used information from spectra libraries and significant improved previous similar methods.

The Fundamental Flaws of Immunoassays and Potential Solutions Using Tandem Mass Spectrometry

PubMed Central

Hoofnagle, Andrew N.; Wener, Mark H.

2009-01-01

Immunoassays have made it possible to measure dozens of individual proteins and other analytes in human samples for help in establishing the diagnosis and prognosis of disease. In too many cases the results of those measurements are misleading and can lead to unnecessary treatment or missed opportunities for therapeutic interventions. These cases stem from problems inherent to immunoassays performed with human samples, which include a lack of concordance across platforms, autoantibodies, anti-reagent antibodies, and the high-dose hook effect. Tandem mass spectrometry may represent a detection method capable of alleviating many of the flaws inherent to immunoassays. We review our understanding of the problems associated with immunoassays on human specimens and describe methodologies using tandem mass spectrometry that could solve some of those problems. We also provide a critical discussion of the potential pitfalls of novel mass spectrometric approaches in the clinical laboratory. PMID:19538965

Estimating the Efficiency of Phosphopeptide Identification by Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Hsu, Chuan-Chih; Xue, Liang; Arrington, Justine V.; Wang, Pengcheng; Paez Paez, Juan Sebastian; Zhou, Yuan; Zhu, Jian-Kang; Tao, W. Andy

2017-06-01

Mass spectrometry has played a significant role in the identification of unknown phosphoproteins and sites of phosphorylation in biological samples. Analyses of protein phosphorylation, particularly large scale phosphoproteomic experiments, have recently been enhanced by efficient enrichment, fast and accurate instrumentation, and better software, but challenges remain because of the low stoichiometry of phosphorylation and poor phosphopeptide ionization efficiency and fragmentation due to neutral loss. Phosphoproteomics has become an important dimension in systems biology studies, and it is essential to have efficient analytical tools to cover a broad range of signaling events. To evaluate current mass spectrometric performance, we present here a novel method to estimate the efficiency of phosphopeptide identification by tandem mass spectrometry. Phosphopeptides were directly isolated from whole plant cell extracts, dephosphorylated, and then incubated with one of three purified kinases—casein kinase II, mitogen-activated protein kinase 6, and SNF-related protein kinase 2.6—along with 16O4- and 18O4-ATP separately for in vitro kinase reactions. Phosphopeptides were enriched and analyzed by LC-MS. The phosphopeptide identification rate was estimated by comparing phosphopeptides identified by tandem mass spectrometry with phosphopeptide pairs generated by stable isotope labeled kinase reactions. Overall, we found that current high speed and high accuracy mass spectrometers can only identify 20%-40% of total phosphopeptides primarily due to relatively poor fragmentation, additional modifications, and low abundance, highlighting the urgent need for continuous efforts to improve phosphopeptide identification efficiency. [Figure not available: see fulltext.

Tandem Laser Induced Breakdown Spectroscopy (LIBS), Laser Ablation Inductively Coupled Plasma Mass Spectroscopy (LA-ICP-MS) and/or Laser Ablation Inductively Coupled Plasma Optical Emission Spectroscopy (LA-ICP-OES) for the analysis of samples of geological interest

NASA Astrophysics Data System (ADS)

Oropeza, D.

2016-12-01

A highly innovative laser ablation sampling instrument (J200 Tandem LA - LIBS) that combines the capabilities and analytical benefits of LIBS, LA-ICP-MS and LA-ICP-OES was used for micrometer-scale, spatially-resolved, elemental analysis of a wide variety of samples of geological interest. Data collected using ablation systems consisted of nanosecond (Nd:YAG operated 266nm) and femtosecond lasers (1030 and 343nm). An ICCD LIBS detector and Quadrupole based mass spectrometer were selected for LIBS and ICP-MS detection, respectively. This tandem instrument allows simultaneous determination of major and minor elements (for example, Si, Ca, Na, and Al, and trace elements such as Li, Ce, Cr, Sr, Y, Zn, Zr among others). The research also focused on elemental mapping and calibration strategies, specifically the use of emission and mass spectra for multivariate data analysis. Partial Least Square Regression (PLSR) is shown to minimize and compensate for matrix effects in the emission and mass spectra improving quantitative analysis by LIBS and LA-ICP-MS, respectively. The study provides a benchmark to evaluate analytical results for more complex geological sample matrices.

Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins.

PubMed

Bandeira, Nuno; Clauser, Karl R; Pevzner, Pavel A

2007-07-01

Despite significant advances in the identification of known proteins, the analysis of unknown proteins by MS/MS still remains a challenging open problem. Although Klaus Biemann recognized the potential of MS/MS for sequencing of unknown proteins in the 1980s, low throughput Edman degradation followed by cloning still remains the main method to sequence unknown proteins. The automated interpretation of MS/MS spectra has been limited by a focus on individual spectra and has not capitalized on the information contained in spectra of overlapping peptides. Indeed the powerful shotgun DNA sequencing strategies have not been extended to automated protein sequencing. We demonstrate, for the first time, the feasibility of automated shotgun protein sequencing of protein mixtures by utilizing MS/MS spectra of overlapping and possibly modified peptides generated via multiple proteases of different specificities. We validate this approach by generating highly accurate de novo reconstructions of multiple regions of various proteins in western diamondback rattlesnake venom. We further argue that shotgun protein sequencing has the potential to overcome the limitations of current protein sequencing approaches and thus catalyze the otherwise impractical applications of proteomics methodologies in studies of unknown proteins.

Libraries of Peptide Fragmentation Mass Spectra Database

National Institute of Standards and Technology Data Gateway

SRD 1C NIST Libraries of Peptide Fragmentation Mass Spectra Database (Web, free access)   The purpose of the library is to provide peptide reference data for laboratories employing mass spectrometry-based proteomics methods for protein analysis. Mass spectral libraries identify these compounds in a more sensitive and robust manner than alternative methods. These databases are freely available for testing and development of new applications.

Quantitative thin-layer chromatography/mass spectrometry analysis of caffeine using a surface sampling probe electrospray ionization tandem mass spectrometry system.

PubMed

Ford, Michael J; Deibel, Michael A; Tomkins, Bruce A; Van Berkel, Gary J

2005-07-15

Quantitative determination of caffeine on reversed-phase C8 thin-layer chromatography plates using a surface sampling electrospray ionization system with tandem mass spectrometry detection is reported. The thin-layer chromatography/electrospray tandem mass spectrometry method employed a deuterium-labeled caffeine internal standard and selected reaction monitoring detection. Up to nine parallel caffeine bands on a single plate were sampled in a single surface scanning experiment requiring 35 min at a surface scan rate of 44 mum/s. A reversed-phase HPLC/UV caffeine assay was developed in parallel to assess the mass spectrometry method performance. Limits of detection for the HPLC/UV and thin-layer chromatography/electrospray tandem mass spectrometry methods determined from the calibration curve statistics were 0.20 ng injected (0.50 muL) and 1.0 ng spotted on the plate, respectively. Spike recoveries with standards and real samples ranged between 97 and 106% for both methods. The caffeine content of three diet soft drinks (Diet Coke, Diet Cherry Coke, Diet Pepsi) and three diet sport drinks (Diet Turbo Tea, Speed Stack Grape, Speed Stack Fruit Punch) was measured. The HPLC/UV and mass spectrometry determinations were in general agreement, and these values were consistent with the quoted values for two of the three diet colas. In the case of Diet Cherry Coke and the diet sports drinks, the determined caffeine amounts using both methods were consistently higher (by approximately 8% or more) than the literature values.

Quantitative Thin-Layer Chromatography/Mass Spectrometry Analysis of Caffeine Using a Surface Sampling Probe Electrospray Ionization Tandem Mass Spectrometry System

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

Ford, Michael J; Deibel, Michael A.; Tomkins, Bruce A

Quantitative determination of caffeine on reversed-phase C8 thin-layer chromatography plates using a surface sampling electrospray ionization system with tandem mass spectrometry detection is reported. The thin-layer chromatography/electrospray tandem mass spectrometry method employed a deuterium-labeled caffeine internal standard and selected reaction monitoring detection. Up to nine parallel caffeine bands on a single plate were sampled in a single surface scanning experiment requiring 35 min at a surface scan rate of 44 {mu}m/s. A reversed-phase HPLC/UV caffeine assay was developed in parallel to assess the mass spectrometry method performance. Limits of detection for the HPLC/UV and thin-layer chromatography/electrospray tandem mass spectrometry methodsmore » determined from the calibration curve statistics were 0.20 ng injected (0.50 {mu}L) and 1.0 ng spotted on the plate, respectively. Spike recoveries with standards and real samples ranged between 97 and 106% for both methods. The caffeine content of three diet soft drinks (Diet Coke, Diet Cherry Coke, Diet Pepsi) and three diet sport drinks (Diet Turbo Tea, Speed Stack Grape, Speed Stack Fruit Punch) was measured. The HPLC/UV and mass spectrometry determinations were in general agreement, and these values were consistent with the quoted values for two of the three diet colas. In the case of Diet Cherry Coke and the diet sports drinks, the determined caffeine amounts using both methods were consistently higher (by 8% or more) than the literature values.« less

Derivatization reagents in liquid chromatography/electrospray ionization tandem mass spectrometry.

PubMed

Santa, Tomofumi

2011-01-01

Liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) is one of the most prominent analytical techniques owing to its inherent selectivity and sensitivity. In LC/ESI-MS/MS, chemical derivatization is often used to enhance the detection sensitivity. Derivatization improves the chromatographic separation, and enhances the mass spectrometric ionization efficiency and MS/MS detectability. In this review, an overview of the derivatization reagents which have been applied to LC/ESI-MS/MS is presented, focusing on the applications to low molecular weight compounds. 2010 John Wiley & Sons, Ltd.

[Separation and identification of 5 glycosidic flavor precursors in tobacco by ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry].

PubMed

Wu, Xinhua; Zhu, Ruizhi; Ren, Zhuoying; Wang, Kai; Mou, Dingrong; Wei, Wanzhi; Miao, Mingming

2009-11-01

A qualitative method for the identification of 5 main glycosidic flavor precursors in tobacco was developed by using ultra performance liquid chromatography-electrospray ionization tandem mass spectrometry (UPLC-ESI MS/MS) and gas chromatography-mass spectrometry (GC-MS). The glycosidic flavor precursors in tobacco were extracted with methanol, cleaned up with an XAD-2 column. The aglycones were later released by enzyme-mediated hydrolysis under the condition of pH 5. The 5 volatile aglycone moieties were identified by GC-MS standard spectra library. The precursor ions of glycosides were determined by using electrospray ionization mass spectrometry in negative ion mode, then the 5 glycosidic flavor precursors were identified by using product ion scan (MS2) finally, using UPLC-ESI MS/MS, separation and identification of 5 glycosidic flavor precursors were accomplished on an RP-C,8 column in the multiple reaction monitoring (MRM) mode by using methanol and acetic acid-ammonium acetate aqueous solution as eluent. This work lays a foundation for the analysis of glycosidic flavor precursors without the standards by using liquid chromatography-mass spectrometry.

Quantitative Caffeine Analysis Using a Surface Sampling Probe Electrospray Ionization Tandem Mass Spectrometry System

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

Ford, Michael J; Deibel, Michael A.; Tomkins, Bruce A

Quantitative determination of caffeine on reversed-phase C8 thin-layer chromatography plates using a surface sampling electrospray ionization system with tandem mass spectrometry detection is reported. The thin-layer chromatography/electrospray tandem mass spectrometry method employed a deuterium-labeled caffeine internal standard and selected reaction monitoring detection. Up to nine parallel caffeine bands on a single plate were sampled in a single surface scanning experiment requiring 35 min at a surface scan rate of 44 {mu}m/s. A reversed-phase HPLC/UV caffeine assay was developed in parallel to assess the mass spectrometry method performance. Limits of detection for the HPLC/UV and thin-layer chromatography/electrospray tandem mass spectrometry methodsmore » determined from the calibration curve statistics were 0.20 ng injected (0.50 {mu}L) and 1.0 ng spotted on the plate, respectively. Spike recoveries with standards and real samples ranged between 97 and 106% for both methods. The caffeine content of three diet soft drinks (Diet Coke, Diet Cherry Coke, Diet Pepsi) and three diet sport drinks (Diet Turbo Tea, Speed Stack Grape, Speed Stack Fruit Punch) was measured. The HPLC/UV and mass spectrometry determinations were in general agreement, and these values were consistent with the quoted values for two of the three diet colas. In the case of Diet Cherry Coke and the diet sports drinks, the determined caffeine amounts using both methods were consistently higher (by 8% or more) than the literature values.« less

Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library.

PubMed

Lee, Hyeyoung; Cuthbertson, Daniel J; Otter, Don E; Barile, Daniela

2016-08-17

A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching.

Rapid Screening of Bovine Milk Oligosaccharides in a Whey Permeate Product and Domestic Animal Milks by Accurate Mass Database and Tandem Mass Spectral Library

PubMed Central

Lee, Hyeyoung; Cuthbertson, Daniel J.; Otter, Don E.; Barile, Daniela

2018-01-01

A bovine milk oligosaccharide (BMO) library, prepared from cow colostrum, with 34 structures was generated and used to rapidly screen oligosaccharides in domestic animal milks and a whey permeate powder. The novel library was entered into a custom Personal Compound Database and Library (PCDL) and included accurate mass, retention time, and tandem mass spectra. Oligosaccharides in minute-sized samples were separated using nanoliquid chromatography (nanoLC) coupled to a high resolution and sensitive quadrupole-Time of Flight (Q-ToF) MS system. Using the PCDL, 18 oligosaccharides were found in a BMO-enriched product obtained from whey permeate processing. The usefulness of the analytical system and BMO library was further validated using milks from domestic sheep and buffaloes. Through BMO PCDL searching, 15 and 13 oligosaccharides in the BMO library were assigned in sheep and buffalo milks, respectively, thus demonstrating significant overlap between oligosaccharides in bovine (cow and buffalo) and ovine (sheep) milks. This method was shown to be an efficient, reliable, and rapid tool to identify oligosaccharide structures using automated spectral matching. PMID:27428379

Mechanism of Formation of the Major Estradiol Product Ions Following Collisional Activation of the Molecular Anion in a Tandem Quadrupole Mass Spectrometer

NASA Astrophysics Data System (ADS)

Wooding, Kerry M.; Barkley, Robert M.; Hankin, Joseph A.; Johnson, Christopher A.; Bradford, Andrew P.; Santoro, Nanette; Murphy, Robert C.

2013-10-01

The importance of the mass spectral product ion structure is highlighted in quantitative assays, which typically use multiple reaction monitoring (MRM), and in the discovery of novel metabolites. Estradiol is an important sex steroid whose quantitation and metabolite identification using tandem mass spectrometry has been widely employed in numerous clinical studies. Negative electrospray ionization tandem mass spectrometry of estradiol (E2) results in several product ions, including the abundant m/z 183 and 169. Although m/z 183 is one of the most abundant product ions used in many quantitative assays, the structure of m/z 183 has not been rigorously examined. We suggest a structure for m/z 183 and a mechanism of formation consistent with collision induced dissociation (CID) of E2 and several stable isotopes ([D4]-E2, [13C6]-E2, and [D1]-E2). An additional product ion from E2, namely m/z 169, has also been examined. MS3 experiments indicated that both m/z 183 and m/z 169 originate from only E2 [M - H]- m/z 271. These ions, m/z 183 and m/z 169, were also present in the collision induced decomposition mass spectra of other prominent estrogens, estrone (E1) and estriol (E3), indicating that these two product ions could be used to elucidate the estrogenic origin of novel metabolites. We propose two fragmentation schemes to explain the CID data and suggest a structure of m/z 183 and m/z 169 consistent with several isotopic variants and high resolution mass spectrometric measurements.

Ultraperformance convergence chromatography-high resolution tandem mass spectrometry for lipid biomarker profiling and identification.

PubMed

Jones, Jace W; Carter, Claire L; Li, Fei; Yu, Jianshi; Pierzchalski, Keely; Jackson, Isabel L; Vujaskovic, Zeljko; Kane, Maureen A

2017-03-01

Lipids represent biologically ubiquitous and highly dynamic molecules in terms of abundance and structural diversity. Whereas the potential for lipids to inform on disease/injury is promising, their unique characteristics make detection and identification of lipids from biological samples analytically demanding. We report the use of ultraperformance convergence chromatography (UPC 2 ), a variant of supercritical fluid chromatography, coupled to high-resolution, data-independent tandem mass spectrometry for characterization of total lipid extracts from mouse lung tissue. The UPC 2 platform resulted in lipid class separation and when combined with orthogonal column chemistries yielded chromatographic separation of intra-class species based on acyl chain hydrophobicity. Moreover, the combined approach of using UPC 2 with orthogonal column chemistries, accurate mass measurements, time-aligned low- and high-collision energy total ion chromatograms, and positive and negative ion mode product ion spectra correlation allowed for confident lipid identification. Of great interest was the identification of differentially expressed ceramides that were elevated 24 h post whole thorax lung irradiation. The identification of lipids that were elevated 24 h post-irradiation signifies a unique opportunity to investigate early mechanisms of action prior to the onset of clinical symptoms in the whole thorax lung irradiation mouse model. Copyright © 2016 John Wiley & Sons, Ltd.

Discovery of Neuropeptides in the Nematode Ascaris suum by Database Mining and Tandem Mass Spectrometry

PubMed Central

Jarecki, Jessica L.; Frey, Brian L.; Smith, Lloyd M.; Stretton, Antony O.

2011-01-01

Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used to discover peptides in extracts of the large parasitic nematode Ascaris suum. This required the assembly of a new database of known and predicted peptides. In addition to those already sequenced, peptides were either previously predicted to be processed from precursor proteins identified in an A. suum library of expressed sequence tags (ESTs), or newly predicted from a library of A. suum genome survey sequences (GSSs). The predicted MS/MS fragmentation patterns of this collection of real and putative peptides were compared with the actual fragmentation patterns found in the MS/MS spectra of peptides fractionated by MS; this enabled individual peptides to be sequenced. Many previously identified peptides were found, and 21 novel peptides were discovered. Thus, this approach is very useful, despite the fact that the available GSS database is still preliminary, having only 1X coverage. PMID:21524146

Rapid separation and identification of phenolics in crude red grape skin extracts by high performance liquid chromatography coupled to diode array detection and tandem mass spectrometry.

PubMed

Ji, Mei; Li, Chen; Li, Qiang

2015-10-02

A rapid and efficient method was established for the simultaneous determination of structures and configurations for 45 phenolics isolated from crude red grape skin extracts without extensive sample preparation. Separation and compound assignments were achieved using high performance liquid chromatography coupled to diode array detection and tandem mass spectrometry (HPLC-DAD-MS(2)). A Poroshell 120 EC-C18 (100mm×3.0mm, 2.7μm) column was employed to separate the phenolics, which were eluted using a gradient of acetonitrile and water acidified with 0.2% formic acid. Phenolics were identified by comparison of their UV-vis spectra, mass spectra and MS(2) data with those in the literature. Using this procedure, five compounds were detected for the first time in Vitis amurensis. Good separation of most phenolics was achieved in 26min. The methods described here can be used for the characterization of phenolics in a variety of grapes and grape products. Copyright © 2015 Elsevier B.V. All rights reserved.

Structure of [M + H - H(2)O](+) from protonated tetraglycine revealed by tandem mass spectrometry and IRMPD spectroscopy.

PubMed

Bythell, Benjamin J; Dain, Ryan P; Curtice, Stephanie S; Oomens, Jos; Steill, Jeffrey D; Groenewold, Gary S; Paizs, Béla; Van Stipdonk, Michael J

2010-04-22

Multiple-stage tandem mass spectrometry and collision-induced dissociation were used to investigate loss of H(2)O or CH(3)OH from protonated versions of GGGX (where X = G, A, and V), GGGGG, and the methyl esters of these peptides. In addition, wavelength-selective infrared multiple photon dissociation was used to characterize the [M + H - H(2)O](+) product derived from protonated GGGG and the major MS(3) fragment, [M + H - H(2)O - 29](+) of this peak. Consistent with the earlier work [ Ballard , K. D. ; Gaskell , S. J. J. Am. Soc. Mass Spectrom. 1993 , 4 , 477 - 481 ; Reid , G. E. ; Simpson , R. J. ; O'Hair , R. A. J. Int. J. Mass Spectrom. 1999 , 190/191 , 209 -230 ], CID experiments show that [M + H - H(2)O](+) is the dominant peak generated from both protonated GGGG and protonated GGGG-OMe. This strongly suggests that the loss of the H(2)O molecule occurs from a position other than the C-terminal free acid and that the product does not correspond to formation of the b(4) ion. Subsequent CID of [M + H - H(2)O](+) supports this proposal by resulting in a major product that is 29 mass units less than the precursor ion. This is consistent with loss of HN horizontal lineCH(2) rather than loss of carbon monoxide (28 mass units), which is characteristic of oxazolone-type b(n) ions. Comparison between experimental and theoretical infrared spectra for a group of possible structures confirms that the [M + H - H(2)O](+) peak is not a substituted oxazolone but instead suggests formation of an ion that features a five-membered ring along the peptide backbone, close to the amino terminus. Additionally, transition structure calculations and comparison of theoretical and experimental spectra of the [M + H - H(2)O - 29](+) peak also support this proposal.

Characterization of solution-phase and gas-phase reactions in on-line electrochemistry-thermospray tandem mass spectrometry.

PubMed

Volk, K J; Yost, R A; Brajter-Toth, A

1989-07-14

Electrochemistry was used on-line with high-performance liquid chromatography-thermospray tandem mass spectrometry to provide insight into the solution-phase decomposition reactions of electrochemically generated oxidation products. Products formed during electrooxidation were monitored as the electrode potential was varied. The solution reactions which follow the initial electron transfer at the electrode are affected by the vaporizer tip temperature of the thermospray probe and the composition of the thermospray buffer. Either hydrolysis or ammonolysis reactions of the initial electrochemical oxidation products can occur with pH 7 ammonium acetate buffer. Both the electrochemically generated and the synthesized disulfide of 6-thiopurine decompose under thermospray conditions to produce 6-thiopurine and purine-6-sulfinate. Solution-phase studies indicate that nucleophilic and electrophilic substitution reactions with purine-6-sulfinate result in the formation of purine, adenine, and hypoxanthine. Products were identified and characterized by tandem mass spectrometry. This work shows the first example of high-performance liquid chromatography used on-line with electrochemistry to separate stable oxidation products prior to analysis by thermospray tandem mass spectrometry. In addition, solution-phase and gas-phase studies with methylamine show that the site of the nucleophilic and electrophilic reactions is probably inside the thermospray probe. Most importantly, these results also show that the on-line combination of electrochemistry with thermospray tandem mass spectrometry provides valuable information about redox and associated chemical reactions of biological molecules such as the structures of intermediates or products as well as providing insight into reaction pathways.

Doubling down on peptide phosphorylation as a variable mass modification

USDA-ARS?s Scientific Manuscript database

Some mass spectrometrists believe that searching for variable post-translational modifications like phosphorylation of serine or threonine when using database-search algorithms to interpret peptide tandem mass spectra will increase false positive rates. The basis for this is the premise that the al...

Tandem mass spectrometry for the detection of plant pathogenic fungi and the effects of database composition on protein inferences.

PubMed

Padliya, Neerav D; Garrett, Wesley M; Campbell, Kimberly B; Tabb, David L; Cooper, Bret

2007-11-01

LC-MS/MS has demonstrated potential for detecting plant pathogens. Unlike PCR or ELISA, LC-MS/MS does not require pathogen-specific reagents for the detection of pathogen-specific proteins and peptides. However, the MS/MS approach we and others have explored does require a protein sequence reference database and database-search software to interpret tandem mass spectra. To evaluate the limitations of database composition on pathogen identification, we analyzed proteins from cultured Ustilago maydis, Phytophthora sojae, Fusarium graminearum, and Rhizoctonia solani by LC-MS/MS. When the search database did not contain sequences for a target pathogen, or contained sequences to related pathogens, target pathogen spectra were reliably matched to protein sequences from nontarget organisms, giving an illusion that proteins from nontarget organisms were identified. Our analysis demonstrates that when database-search software is used as part of the identification process, a paradox exists whereby additional sequences needed to detect a wide variety of possible organisms may lead to more cross-species protein matches and misidentification of pathogens.

Odor Impression Prediction from Mass Spectra.

PubMed

Nozaki, Yuji; Nakamoto, Takamichi

2016-01-01

The sense of smell arises from the perception of odors from chemicals. However, the relationship between the impression of odor and the numerous physicochemical parameters has yet to be understood owing to its complexity. As such, there is no established general method for predicting the impression of odor of a chemical only from its physicochemical properties. In this study, we designed a novel predictive model based on an artificial neural network with a deep structure for predicting odor impression utilizing the mass spectra of chemicals, and we conducted a series of computational analyses to evaluate its performance. Feature vectors extracted from the original high-dimensional space using two autoencoders equipped with both input and output layers in the model are used to build a mapping function from the feature space of mass spectra to the feature space of sensory data. The results of predictions obtained by the proposed new method have notable accuracy (R≅0.76) in comparison with a conventional method (R≅0.61).

Tandem Mass Spectrometry Imaging and in Situ Characterization of Bioactive Wood Metabolites in Amazonian Tree Species Sextonia rubra.

PubMed

Fu, Tingting; Touboul, David; Della-Negra, Serge; Houël, Emeline; Amusant, Nadine; Duplais, Christophe; Fisher, Gregory L; Brunelle, Alain

2018-06-19

Driven by a necessity for confident molecular identification at high spatial resolution, a new time-of-flight secondary ion mass spectrometry (TOF-SIMS) tandem mass spectrometry (tandem MS) imaging instrument has been recently developed. In this paper, the superior MS/MS spectrometry and imaging capability of this new tool is shown for natural product study. For the first time, via in situ analysis of the bioactive metabolites rubrynolide and rubrenolide in Amazonian tree species Sextonia rubra (Lauraceae), we were able both to analyze and to image by tandem MS the molecular products of natural biosynthesis. Despite the low abundance of the metabolites in the wood sample(s), efficient MS/MS analysis of these γ-lactone compounds was achieved, providing high confidence in the identification and localization. In addition, tandem MS imaging minimized the mass interferences and revealed specific localization of these metabolites primarily in the ray parenchyma cells but also in certain oil cells and, further, revealed the presence of previously unidentified γ-lactone, paving the way for future studies in biosynthesis.

A new technique for high performance tandem time-of- flight mass spectrometry

NASA Astrophysics Data System (ADS)

Katz, Daniel Louis

2001-08-01

The main result of this written dissertation is a mathematical solution to the problem of multiplex recording for high performance tandem time-of-flight mass spectrometry. The prescription is to use a time-lag accelerator in the second stage to match the ion optical properties of the decay fragments to the requirements of the electrostatic ion mirror. With this technique the ion mirror is able to focus the full mass range of fragment ions at a single voltage setting, permitting acquisition of the entire mass spectrum from a single ionization event. This work was performed in support of a joint project carried out by researchers at Oregon State University and The University of Uppsala, Sweden, to design, build and test a tandem instrument featuring precision selection of the precursor species in the first stage of the spectrometer, a means of fragmenting the precursor species, and multiplex recording of the resulting fragment spectrum in the second stage. A patent application has been filed on the complete instrument with the United States Patent Office, a copy of which has been included as an appendix, and a prototype of that instrument has been constructed and awaits testing at Oregon State University.

Determination of phospholipid regiochemistry by Ag(I) adduction and tandem mass spectrometry.

PubMed

Yoo, Hyun Ju; Håkansson, Kristina

2011-02-15

Collision-activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD) of Ag-adducted phospholipids were investigated as structural tools. Previously, determination of the acyl chains at the two phospholipid esterification sites has been performed based on the R(1)COO(-)/R(2)COO(-) ratio in negative ion mode CAD tandem mass spectrometry. However, the observed product ion ratio is dependent on the extent of unsaturation of the fatty acyl group at sn-2 as well as on the total chain length. Similarly, in positive ion mode CAD with/without alkaline or alkaline earth metal adduction, the ratio of product ions resulting from either R(1)COOH or R(2)COOH neutral losses is dependent on the nature of the phospholipid polar headgroup. Ag(+) ion chromatography, in which silver ions are part of the stationary phase, can provide information on double bond number/distribution as well as double bond configuration (cis/trans) because of interaction between Ag(+) ions and olefinic π electrons of fatty acids and lipids. We hypothesized that interactions between double bonds and Ag(+) may be utilized to also reveal phospholipid esterification site information in tandem mass spectrometry. CAD and IRMPD of Ag-adducted phospholipids with unsaturated fatty acids (R(x)COOH, x = 1 or 2) provided characteristic product ions, [R(x)COOH + Ag](+), and their neutral losses. The characteristic product ions and their abundances do not depend on the type of polar headgroup or the number of double bonds of unsaturated acyl chains. Tandem mass spectrometry of Cu-adducted phospholipids was also performed for comparison based on the Lewis acid and base properties of Cu(+) and phospholipid double bonds, respectively.

Characterization of vitamin D3 metabolites using continuous-flow fast atom bombardment tandem mass spectrometry and high-performance liquid chromatography.

PubMed

Yeung, B; Vouros, P; Reddy, G S

1993-08-13

A mass spectrometric method for the detection of vitamin D3 metabolites is described. This method involves the derivatization of the metabolites by cycloaddition with 4-phenyl-1,2,4-triazoline-3,5-dione, followed by their characterization by continuous-flow fast atom bombardment (CF-FAB) tandem mass spectrometry (MS-MS) and high-performance liquid chromatography (HPLC). Using HPLC, this derivatization has been shown to increase the UV detectability of 25-hydroxyvitamin D3 by about 5-fold. The FAB spectra of the adducts are dominated by peaks corresponding to a protonated molecule and a fragment ion derived in part from the loss of the side chain. Multiple reaction monitoring (MRM) of this transition by MS-MS may be utilized for trace level analysis of vitamin D metabolites. Sample introduction by flow injection yields detection limits in the low nanogram to high picogram range, whereas the use of on-line capillary LC has been found to decrease the detection limits to the low picogram level.

Random and independent sampling of endogenous tryptic peptides from normal human EDTA plasma by liquid chromatography micro electrospray ionization and tandem mass spectrometry.

PubMed

Dufresne, Jaimie; Florentinus-Mefailoski, Angelique; Ajambo, Juliet; Ferwa, Ammara; Bowden, Peter; Marshall, John

2017-01-01

Normal human EDTA plasma samples were collected on ice, processed ice cold, and stored in a freezer at - 80 °C prior to experiments. Plasma test samples from the - 80 °C freezer were thawed on ice or intentionally warmed to room temperature. Protein content was measured by CBBR binding and the release of alcohol soluble amines by the Cd ninhydrin assay. Plasma peptides released over time were collected over C18 for random and independent sampling by liquid chromatography micro electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) and correlated with X!TANDEM. Fully tryptic peptides by X!TANDEM returned a similar set of proteins, but was more computationally efficient, than "no enzyme" correlations. Plasma samples maintained on ice, or ice with a cocktail of protease inhibitors, showed lower background amounts of plasma peptides compared to samples incubated at room temperature. Regression analysis indicated that warming plasma to room temperature, versus ice cold, resulted in a ~ twofold increase in the frequency of peptide identification over hours-days of incubation at room temperature. The type I error rate of the protein identification from the X!TANDEM algorithm combined was estimated to be low compared to a null model of computer generated random MS/MS spectra. The peptides of human plasma were identified and quantified with low error rates by random and independent sampling that revealed 1000s of peptides from hundreds of human plasma proteins from endogenous tryptic peptides.

Stable Isotope Labeling Strategy for Curcumin Metabolite Study in Human Liver Microsomes by Liquid Chromatography-Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Gao, Dan; Chen, Xiaowu; Yang, Xiaomei; Wu, Qin; Jin, Feng; Wen, Hongliang; Jiang, Yuyang; Liu, Hongxia

2015-04-01

The identification of drug metabolites is very important in drug development. Nowadays, the most widely used methods are isotopes and mass spectrometry. However, the commercial isotopic labeled reagents are usually very expensive, and the rapid and convenient identification of metabolites is still difficult. In this paper, an 18O isotope labeling strategy was developed and the isotopes were used as a tool to identify drug metabolites using mass spectrometry. Curcumin was selected as a model drug to evaluate the established method, and the 18O labeled curcumin was successfully synthesized. The non-labeled and 18O labeled curcumin were simultaneously metabolized in human liver microsomes (HLMs) and analyzed by liquid chromatography/mass spectrometry (LC-MS). The two groups of chromatograms obtained from metabolic reaction mixture with and without cofactors were compared and analyzed using Metabolynx software (Waters Corp., Milford, MA, USA). The mass spectra of the newly appearing chromatographic peaks in the experimental sample were further analyzed to find the metabolite candidates. Their chemical structures were confirmed by tandem mass spectrometry. Three metabolites, including two reduction products and a glucuronide conjugate, were successfully detected under their specific HLMs metabolic conditions, which were in accordance with the literature reported results. The results demonstrated that the developed isotope labeling method, together with post-acquisition data processing using Metabolynx software, could be used for fast identification of new drug metabolites.

Half-life of Si-32 from tandem-accelerator mass spectrometry

NASA Technical Reports Server (NTRS)

Elmore, D.; Anantaraman, N.; Fulbright, H. W.; Gove, H. E.; Nishiizumi, K.; Murrell, M. T.; Honda, M.; Hans, H. S.

1980-01-01

A newly developed mass-spectrometry technique employing a tandem Van de Graaff accelerator together with a special beam-transport system and heavy-ion detector has been used to determine the half-life of Si-32. The result obtained, 108 plus or minus 18 yr, disagrees with the accepted value of 330 plus or minus 40 yr. The implications of the new half-life of Si-32, which is used for dating studies, are discussed.

Fast quantitative detection of cocaine in beverages using nanoextractive electrospray ionization tandem mass spectrometry.

PubMed

Hu, Bin; Peng, Xuejiao; Yang, Shuiping; Gu, Haiwei; Chen, Huanwen; Huan, Yanfu; Zhang, Tingting; Qiao, Xiaolin

2010-02-01

Without any sample pretreatment, effervescent beverage fluids were manually sprayed into the primary ion plume created by using a nanoelectrospray ionization source for direct ionization, and the analyte ions of interest were guided into an ion trap mass spectrometer for tandem mass analysis. Functional ingredients (e.g., vitamins, taurine, and caffeine, etc.) and spiked impurity (e.g., cocaine) in various beverages, such as Red Bull energy drink, Coco-cola, and Pepsi samples were rapidly identified within 1.5 s. The limit of detection was found to be 7-15 fg (S/N = 3) for cocaine in different samples using the characteristic fragment (m/z 150) observed in the MS(3) experiments. Typical relative standard deviation and recovery of this method were 6.9%-8.6% and 104%-108% for direct analysis of three actual samples, showing that nanoextractive electrospray ionization tandem mass spectrometry is a useful technique for fast screening cocaine presence in beverages. 2010. Published by Elsevier Inc.

Systematization of the mass spectra for speciation of inorganic salts with static secondary ion mass spectrometry.

PubMed

Van Ham, Rita; Van Vaeck, Luc; Adams, Freddy C; Adriaens, Annemie

2004-05-01

The analytical use of mass spectra from static secondary ion mass spectrometry for the molecular identification of inorganic analytes in real life surface layers and microobjects requires an empirical insight in the signals to be expected from a given compound. A comprehensive database comprising over 50 salts has been assembled to complement prior data on oxides. The present study allows the systematic trends in the relationship between the detected signals and molecular composition of the analyte to be delineated. The mass spectra provide diagnostic information by means of atomic ions, structural fragments, molecular ions, and adduct ions of the analyte neutrals. The prediction of mass spectra from a given analyte must account for the charge state of the ions in the salt, the formation of oxide-type neutrals from oxy salts, and the occurrence of oxidation-reduction processes.

Structural derivation of lipid A from Cronobacter sakazakii using tandem mass spectrometry.

PubMed

Li, Yanyan; Yoon, Sung Hwan; Wang, Xiaoyuan; Ernst, Robert K; Goodlett, David R

2016-10-30

Cronobacter sakazakii is a Gram-negative opportunistic pathogen that can cause necrotizing enterocolitis, bacteremia, and meningitis. Lipid A, the glycolipid membrane anchor of lipopolysaccharide (LPS), is a potential virulence factor for C. sakazakii. Given the potential importance of this molecule in infection and virulence, structural characterization of lipid A was carried out. The structural characterization of lipid A extracted from C. sakazakii was performed using electrospray ionization and collision-induced dissociation in a linear ion trap mass spectrometer. Specifically, for detailed structural characterization, hierarchical tandem mass spectrometry was performed on the dominant ions present in the precursor ion mass spectra. By comparing the C. sakazakii fragmentation pathways to those of the known structure of E. coli lipid A, a structure of C. sakazakii lipid A was derived. The precursor ion at m/z 1796 from C. sakazakii is produced from a lipid A molecule where the acyl chains between the 2'b (C14) and 3'b (C12) positions are reversed as compared to E. coli lipid A. Additionally, the precursor ion at m/z 1824 from C. sakazakii corresponds to an E. coli structure with the same acyl chain at the 2'b position (C14), but a longer acyl chain (C14) at the 3'b position versus m/z 1796. Two lipid A structures were derived for the C. sakazakii ions at m/z 1796 and 1824. They differed in composition at the 2'b and 3'b acyl chain substituents, which may be a result of differences in substrate specificity of the two lipid A acyl chain transferases: LpxL and LpxM. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

De novo peptide sequencing using CID and HCD spectra pairs.

PubMed

Yan, Yan; Kusalik, Anthony J; Wu, Fang-Xiang

2016-10-01

In tandem mass spectrometry (MS/MS), there are several different fragmentation techniques possible, including, collision-induced dissociation (CID) higher energy collisional dissociation (HCD), electron-capture dissociation (ECD), and electron transfer dissociation (ETD). When using pairs of spectra for de novo peptide sequencing, the most popular methods are designed for CID (or HCD) and ECD (or ETD) spectra because of the complementarity between them. Less attention has been paid to the use of CID and HCD spectra pairs. In this study, a new de novo peptide sequencing method is proposed for these spectra pairs. This method includes a CID and HCD spectra merging criterion and a parent mass correction step, along with improvements to our previously proposed algorithm for sequencing merged spectra. Three pairs of spectral datasets were used to investigate and compare the performance of the proposed method with other existing methods designed for single spectrum (HCD or CID) sequencing. Experimental results showed that full-length peptide sequencing accuracy was increased significantly by using spectra pairs in the proposed method, with the highest accuracy reaching 81.31%. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Urinary free cortisol assessment by liquid chromatography tandem mass spectrometry: a case study of ion suppression due to unacquainted administration of piperacillin

PubMed Central

Danese, Elisa; Salvagno, Gian Luca; Guzzo, Alessandra; Scurati, Samuele; Fava, Cristiano; Lippi, Giuseppe

2017-01-01

Introduction Liquid chromatography coupled to atmospheric pressure ionization tandem mass spectrometry (LC-ESI-MS/MS) is currently considered the reference method for quantitative determination of urinary free cortisol (UFC). One of the major drawbacks of this measurement is a particular form of matrix effect, conventionally known as ion suppression. Materials and methods We describe here the case of a 66-year-old-patient referred to the daily service of general medicine for intravenous antibiotic administration due to a generalized Staphylococcus aureus infection and for routine 24 hours UFC monitoring in the setting of glucocorticoid replacement therapy. Results The observation of 10-fold decrease of internal standard of cortisol signal led us to hypothesize the presence of an ion suppression effect due to a co-eluting endogenous compound. Screening analysis of tandem mass spectrometry (MS/MS) spectra of the interfering molecule, along with in vitro confirmation analyses, were suggestive of the presence of high concentration of piperacillin. The problem was then easily solved with minor modifications of the chromatographic technique. Conclusions According to our findings, antibiotic therapy with piperacillin/tazobactam should be regarded as an important interference in UFC assessment, which may potentially affect detection capability, precision and accuracy of this measurement. This case report emphasizes that accurate anamnesis and standardization of all phases of urine collection are essential aspects for preventing potential interference in laboratory testing. PMID:29180920

Multiresidue analysis of pesticides in straw roughage by liquid chromatography - tandem mass spectrometry

USDA-ARS?s Scientific Manuscript database

A multiresidue analytical method using a modification of the “quick, easy, cheap, effective, rugged, and safe” (QuEChERS) sample preparation approach combined with liquid chromatography–tandem mass spectrometry (LC-MS/MS) analysis was established and validated for the rapid determination of 69 pesti...

Ion Mobility Separation of Isomeric Carbohydrate Precursor Ions and Acquisition of their Independent Tandem Mass Spectra

PubMed Central

Zhu, Maolei; Bendiak, Brad; Clowers, Brian; Hill, Herbert H.

2010-01-01

The rapid separation of isomeric precursor ions of oligosaccharides prior to their analysis by MSn was demonstrated using an ambient pressure ion mobility spectrometer (IMS) interfaced with a quadrupole ion trap. Separations were not limited to specific types of isomers; representative isomers differing solely in the stereochemistry of sugars, in their anomeric configurations, and in their overall branching patterns and linkage positions could be resolved in the millisecond time frame. Physical separation of precursor ions permitted independent mass spectra of individual oligosaccharide isomers to be acquired to at least MS3, the number of stages of dissociation limited only practically by the abundance of specific product ions. IMS-MSn analysis was particularly valuable in the evaluation of isomeric oligosaccharides that yielded identical sets of product ions in MS/MS experiments, revealing pairs of isomers that would otherwise not be known to be present in a mixture if evaluated solely by MS dissociation methods alone. A practical example of IMS-MSn analysis of a set of isomers included within a single HPLC fraction of oligosaccharides released from bovine submaxillary mucin is described. PMID:19562326

Ultra-high-pressure liquid chromatography-tandem mass spectrometry method for the determination of alkylphenols in soil.

PubMed

Wang, Jing; Pan, Hefang; Liu, Zhengzheng; Ge, Fei

2009-03-20

A novel method has been developed for the determination of alkylphenols in soil by ultra-high-pressure liquid chromatography employing small particle sizes, combined with tandem mass spectrometry. Soil samples were extracted with pressurized liquid extraction (PLE) and then cleaned with solid-phase extraction (SPE). The extracts were separated on C18 column (1.7 microm, 50 mm x 2.1mm) with a gradient elution and a mobile phase consisting of water and acetonitrile, and then detected by an electrospray ionization tandem mass spectrometry in negative ion mode with multiple reaction monitoring (MRM). Compared with traditional liquid chromatography, it took ultra-high-pressure liquid chromatography much less time to analyze alkylphenols. Additionally, the ultra-high-pressure liquid chromatography/tandem mass spectrometry method produces satisfactory reliability, sensitivity, and accuracy. The average recoveries of the three target analytes were 74.0-103.4%, with the RSD<15%. The calibration curves for alkylphenols were linear within the range of 0.01-0.4 microg/ml, with the correlation coefficients greater than 0.99. When 10 g soil sample was used for analysis, the limits of quantification (LOQs) of the three alkylphenols were all 1.0 microg/kg.

Determination of tiropramide in human plasma by liquid chromatography-tandem mass spectrometry.

PubMed

Lee, Hye Won; Ji, Hye Young; Kim, Hee Hyun; Cho, Hea-Young; Lee, Yong-Bok; Lee, Hye Suk

2003-11-05

A rapid, sensitive and selective liquid chromatography-tandem mass spectrometric (LC/MS/MS) method for the determination of tiropramide in human plasma was developed. Tiropramide and internal standard, cisapride were extracted from human plasma by liquid-liquid extraction and analyzed on a Luna C8 column with the mobile phase of acetonitrile-ammonium formate (10mM, pH 4.5) (50:50, v/v). The analytes was detected using an electrospray ionization tandem mass spectrometry in the multiple-reaction-monitoring mode. The standard curve was linear (r=0.998) over the concentration range of 2.0-200 ng/ml. The intra- and inter-assay coefficients of variation ranged from 2.8 to 7.8 and 6.7 to 8.9%, respectively. The recoveries of tiropramide ranged from 50.2 to 53.1%, with that of cisapride (internal standard) being 60.9+/-5.3%. The lower limit of quantification for tiropramide was 2.0 ng/ml using 100 microl plasma sample. This method was applied to the pharmacokinetic study of tiropramide in human.

Structural characterization of trace stilbene glycosides in Lysidice brevicalyx Wei using liquid chromatography/diode-array detection/electrospray ionization tandem mass spectrometry.

PubMed

Hu, Youcai; Qu, Jing; Liu, Yuanyan; Yu, Shishan; Li, Jianbei; Zhang, Jinlan; Du, Dan

2010-01-01

The mass fragmentation patterns of stilbene glycosides isolated from the genus Lysidice were investigated by negative ion electrospray ionization tandem mass spectrometry, and the influence of collision energy on their fragmentation behavior is discussed. It is found that the presence of the Y(0)(-) and B(0)(-) ions in the MS(2) spectra is characteristic for 1-->6 linked diglycosyl stilbenes, while the Y(0)(-), Y(1)(-), and Z(1)(-) ions are representative ions of 1-->2 linked diglycosyl stilbenes. These results indicate that ESI-MS(n) in the negative ion mode can be used to differentiate 1-->6 and 1-->2 linked diglycosyl stilbenes. Based on the fragmentation rules, 9 new trace constituents were identified or tentatively characterized in a fraction of Lysidice brevicalyx by using HPLC/HRMS and HPLC-DAD/ESI-MS(n). The results of the present study can assist in on-line structural identification of analogous constituents and targeted isolation of novel compounds from crude plant extracts.

Determination of endocrine-disrupting compounds in drinking waters by fast liquid chromatography-tandem mass spectrometry.

PubMed

Magi, Emanuele; Scapolla, Carlo; Di Carro, Marina; Liscio, Camilla

2010-09-01

Growing attention has been recently paid to safety of food and drinking water, making necessary the adoption of policies for water sources protection and the development of sensitive and rapid analytical methods to identify micropollutants. Endocrine-disrupting compounds (EDCs) have emerged as a major issue as they alter the functioning of the endocrine system. Since ingestion of EDCs via food is considered the major exposure route, there is a growing interest in understanding EDC fate during drinking water treatment and in monitoring potential contamination of surface waters and groundwaters. In this work, a fast liquid chromatography-electrospray ionization-tandem mass spectrometry method was developed for the determination of 4-n-nonylphenol (NP), bisphenol A (BPA), estrone (E1), 17β-estradiol (E2) and 17α-ethinylestradiol (EE2) in drinking waters. In the literature analytical articles seldom provide details regarding fragmentation pathways. In this paper spectra of the five EDCs in negative ESI were interpreted with the support of accurate mass spectra acquired by a quadrupole time-of-flight instrument; fragmentation pathways were also proposed. The chromatographic separation of EDCs was optimized on a Pinnacle DB Biphenylic column with a water-acetonitrile gradient. Quantitative analysis was performed in multiple reaction monitoring (MRM) mode using bisphenol A-d(16) (BPA-d(16)) as internal standard; calibration curves showed good correlation coefficients (0.9989-0.9997). All figures of merit of the method were satisfactory; limits of detection were in the range 0.2-0.4 ng/ml. The method was applied to the determination of the analytes in waters sampled by polar organic chemical integrative samplers in a drinking water treatment plant. Rather low concentration of BPA, NP and E1 were measured in the inlet, while none of the considered EDCs was detected in the outlet. 2010 John Wiley & Sons, Ltd.

Multi-matrix, dual polarity, tandem mass spectrometry imaging strategy applied to a germinated maize seed: toward mass spectrometry imaging of an untargeted metabolome

DOE PAGES

Feenstra, Adam D.; Hansen, Rebecca L.; Lee, Young Jin

2015-08-27

Mass spectrometry imaging (MSI) provides high spatial resolution information that is unprecedented in traditional metabolomics analyses; however, the molecular coverage is often limited to a handful of compounds and is insufficient to understand overall metabolomic changes of a biological system. Here, we propose an MSI methodology to increase the diversity of chemical compounds that can be imaged and identified, in order to eventually perform untargeted metabolomic analysis using MSI. We use the desorption/ionization bias of various matrixes for different metabolite classes along with dual polarities and a tandem MSI strategy. The use of multiple matrixes and dual polarities allows usmore » to visualize various classes of compounds, while data-dependent MS/MS spectra acquired in the same MSI scans allow us to identify the compounds directly on the tissue. In a proof of concept application to a germinated corn seed, a total of 166 unique ions were determined to have high-quality MS/MS spectra, without counting structural isomers, of which 52 were identified as unique compounds. According to an estimation based on precursor MSI datasets, we expect over five hundred metabolites could be potentially identified and visualized once all experimental conditions are optimized and an MS/MS library is available. Finally, metabolites involved in the glycolysis pathway and tricarboxylic acid cycle were imaged to demonstrate the potential of this technology to better understand metabolic biology.« less

Biological Matrix Effects in Quantitative Tandem Mass Spectrometry-Based Analytical Methods: Advancing Biomonitoring

PubMed Central

Panuwet, Parinya; Hunter, Ronald E.; D’Souza, Priya E.; Chen, Xianyu; Radford, Samantha A.; Cohen, Jordan R.; Marder, M. Elizabeth; Kartavenka, Kostya; Ryan, P. Barry; Barr, Dana Boyd

2015-01-01

The ability to quantify levels of target analytes in biological samples accurately and precisely, in biomonitoring, involves the use of highly sensitive and selective instrumentation such as tandem mass spectrometers and a thorough understanding of highly variable matrix effects. Typically, matrix effects are caused by co-eluting matrix components that alter the ionization of target analytes as well as the chromatographic response of target analytes, leading to reduced or increased sensitivity of the analysis. Thus, before the desired accuracy and precision standards of laboratory data are achieved, these effects must be characterized and controlled. Here we present our review and observations of matrix effects encountered during the validation and implementation of tandem mass spectrometry-based analytical methods. We also provide systematic, comprehensive laboratory strategies needed to control challenges posed by matrix effects in order to ensure delivery of the most accurate data for biomonitoring studies assessing exposure to environmental toxicants. PMID:25562585

[Determination of four bisphenolic compounds in drinking water by liquid chromatography-tandem mass spectrometry].

PubMed

Hu, Xiaojian; Zhang, Haijing; Wang, Xiaohong; Ding, Changming; Lin, Shaobin

2015-05-01

To simultaneously determine the four bisphenolic compounds (bisphenol F, bisphenol A, tetrachlorobisphenol A and tetrabromobisphenol A) in drinking water by liquid chromatography tandem mass spectrometry. 200 ml water sample was extracted by solid-phase extraction, eluted with methanol and analyzed by liquid chromatography tandem mass spectrometry under the MRM mode. The separation was carried out on a T3 column (2.1 mm x 150 mm, 3 μm). The limits of detection for the four bisphenolic compounds were in the range of 0.20 - 5.5 ng/L. The mean recoveries at the two spiked levels were 87.1% - 109.0% with the intra-day precision between 6.3% - 12.4% and inter-day precision between 4.5% - 15.4%. The method was applied for determination of 15 water samples. The method was sensitive, precise and accurate.

Identification of a tryptanthrin metabolite in rat liver microsomes by liquid chromatography/electrospray ionization-tandem mass spectrometry.

PubMed

Lee, Sang Kyu; Kim, Ghee Hwan; Kim, Dong Hyeon; Kim, Dong Hyun; Jahng, Yurngdong; Jeong, Tae Cheon

2007-10-01

Tryptanthrin originally isolated from Isatis tinctoria L. has been characterized to have anti-inflammatory activities through the dual inhibition of cyclooxygenase-2 and 5-lipoxygenase mediated prostaglandin and leukotriene syntheses. To characterize phase I metabolite(s), tryptanthrin was incubated with rat liver microsomes in the presence of NADPH-generating system. One metabolite was identified by liquid chromatography/electrospray ionization-tandem mass spectrometry. M1 could be identified as a metabolite mono-hydroxylated on the aromatic ring of indole moiety from the MS(2) spectra of protonated tryptanthrin and M1. The structure of metabolite was confirmed as 8-hydroxytryptanthrin with a chemically synthesized authentic standard. The formation of M1 was NADPH-dependent and was inhibited by SKF-525A, a general CYP-inhibitor, indicating the cytochrome P450 (CYP)-mediated reaction. In addition, it was proposed that M1 might be formed by CYP 1A in rat liver microsomes from the experiments with enriched rat liver microsomes.

Detection, characterization and quantification of salicylic acid conjugates in plant extracts by ESI tandem mass spectrometric techniques.

PubMed

Pastor, Victoria; Vicent, Cristian; Cerezo, Miguel; Mauch-Mani, Brigitte; Dean, John; Flors, Victor

2012-04-01

An approach for the detection and characterization of SA derivatives in plant samples is presented based on liquid chromatography coupled to electrospray ionization (ESI) tandem mass spectrometric techniques. Precursor ion scan methods using an ESI triple quadrupole spectrometer for samples from plants challenged with the virulent Pseudomonas syringae pv tomato DC3000 allowed us to detect two potential SA derivatives. The criterion used to consider a potential SA derivative is based on the detection of analytes in the precursor ion scan chromatogram upon selecting m/z 137 and m/z 93 that correspond to the salicylate and its main product ion, respectively. Product ion spectra of the newly-detected analytes as well as accurate m/z determinations using an ESI Q-time-of-flight instrument were registered as means of characterization and strongly suggest that glucosylated forms of SA at the carboxylic and at the phenol functional groups are present in plant samples. The specific synthesis and subsequent chromatography of salicylic glucosyl ester (SGE) and glucosyl salicylate (SAG) standards confirmed the chemical identity of both peaks that were obtained applying different tandem mass spectrometric techniques and accurate m/z determinations. A multiple reaction monitoring method has been developed and applied to plant samples. The advantages of this LC-ESI-MS/MS methods with respect to the traditional analysis of glucosyl conjugates are also discussed. Preliminary results revealed that SA and the glucosyl conjugates are accumulated in Arabidopsis thaliana in a time dependent manner, accordingly to the up-regulation of SA-dependent defenses following P. syringae infection. This technique applied to plant hormones or fragment ions may be useful to obtain chemical family members of plant metabolites and help identify their contribution in the signaling of plant defenses. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Tandem Mass Spectrometry for Structural Identification of Sesquiterpene Alkaloids from the Stems of Dendrobium nobile Using LC-QToF.

PubMed

Wang, Yan-Hong; Avula, Bharathi; Abe, Naohito; Wei, Feng; Wang, Mei; Ma, Shuang-Cheng; Ali, Zulfiqar; Elsohly, Mahmoud A; Khan, Ikhlas A

2016-05-01

Dendrobium nobile is one of the fundamental herbs in traditional Chinese medicine. Sesquiterpene alkaloids are the main active components in this plant. Due to weak ultraviolet absorption and low content in D. nobile, these sesquiterpene alkaloids have not been extensively studied using chromatographic methods. Herein, tandem mass spectrometry combined with liquid chromatography separation provides a tool for the identification and characterization of the alkaloids from D. nobile. A total of nine sesquiterpene alkaloids were characterized by ultrahigh-performance liquid chromatography tandem mass spectrometry. These alkaloids can be classified into two subgroups that are represented by dendrobine and nobilonine. Tandem mass spectrometric studies revealed the fragmentation pathways of these two subgroup alkaloids that were used for the identification and characterization of other alkaloids in D. nobile. Characterization of these alkaloids using accurate mass and diagnostic fragments provided a reliable methodology for the analysis of D. nobile by ultrahigh-performance liquid chromatography tandem mass spectrometry. The limit of detection was defined as the signal-to-noise ratio equal to 3 : 1. Limits of detection of dendrobine and nobilonine were less than 30 ng/mL. The developed method was applied for the analysis of various Dendrobium species and related dietary supplements. Alkaloids were identified from D. nobile, but not detected from commercial samples including 13 other Dendrobium species and the 7 dietary supplements. Georg Thieme Verlag KG Stuttgart · New York.

Origin of Disagreements in Tandem Mass Spectra Interpretation by Search Engines.

PubMed

Tessier, Dominique; Lollier, Virginie; Larré, Colette; Rogniaux, Hélène

2016-10-07

Several proteomic database search engines that interpret LC-MS/MS data do not identify the same set of peptides. These disagreements occur even when the scores of the peptide-to-spectrum matches suggest good confidence in the interpretation. Our study shows that these disagreements observed for the interpretations of a given spectrum are almost exclusively due to the variation of what we call the "peptide space", i.e., the set of peptides that are actually compared to the experimental spectra. We discuss the potential difficulties of precisely defining the "peptide space." Indeed, although several parameters that are generally reported in publications can easily be set to the same values, many additional parameters-with much less straightforward user access-might impact the "peptide space" used by each program. Moreover, in a configuration where each search engine identifies the same candidates for each spectrum, the inference of the proteins may remain quite different depending on the false discovery rate selected.

High Resolution Mass Spectra Analysis with a Programmable Calculator.

ERIC Educational Resources Information Center

Holdsworth, David K.

1980-01-01

Highlighted are characteristics of programs written for a pocket-sized programmable calculator to analyze mass spectra data (such as displaying high resolution masses for formulas, predicting whether formulas are stable molecules or molecular ions, determining formulas by isotopic abundance measurement) in a laboratory or classroom. (CS)

MEASUREMENT OF OXIDATIVE STRESS PARAMETERS USING LIQUID CHROMATOGRAPHY - TANDEM MASS SPECTROSCOPY (LC-MS/MS)

EPA Science Inventory

What is the study?
An invited review article. Measurement of oxidative stress parameters using liquid chromatography-tandem mass spectroscopy (LC-MS/MS)
Why was it done?
Although oxidative stress is frequently cited as a cause of various adverse biological eff...

The current role of high-resolution mass spectrometry in food analysis.

PubMed

Kaufmann, Anton

2012-05-01

High-resolution mass spectrometry (HRMS), which is used for residue analysis in food, has gained wider acceptance in the last few years. This development is due to the availability of more rugged, sensitive, and selective instrumentation. The benefits provided by HRMS over classical unit-mass-resolution tandem mass spectrometry are considerable. These benefits include the collection of full-scan spectra, which provides greater insight into the composition of a sample. Consequently, the analyst has the freedom to measure compounds without previous compound-specific tuning, the possibility of retrospective data analysis, and the capability of performing structural elucidations of unknown or suspected compounds. HRMS strongly competes with classical tandem mass spectrometry in the field of quantitative multiresidue methods (e.g., pesticides and veterinary drugs). It is one of the most promising tools when moving towards nontargeted approaches. Certain hardware and software issues still have to be addressed by the instrument manufacturers for it to dislodge tandem mass spectrometry from its position as the standard trace analysis tool.

Automatic Preocessing of Impact Ionization Mass Spectra Obtained by Cassini CDA

NASA Astrophysics Data System (ADS)

Villeneuve, M.

2015-12-01

Since Cassini's arrival at Saturn in 2004, the Comic Dust Analyzer (CDA) has recorded nearly 200,000 mass spectra of dust particles. A majority of this data has been collected in Saturn's diffuse E ring where sodium salts embedded in water ice particles indicate that many particles are in fact frozen droplets from Enceladus' subsurface ocean that have been expelled from cracks in the icy crust. So far only a small fraction of the obtained spectra have been processed because the steps in processing the spectra require human manipulation. We developed an automatic processing pipeline for CDA mass spectra which will consistently analyze this data. The preprocessing steps are to de-noise the spectra, determine and remove the baseline, calculate the correct stretch parameter, and finally to identify elements and compounds in the spectra. With the E ring constantly evolving due to embedded active moons, this data will provide valuable information about the source of the E ring, the subsurface of Saturn's ice moon Enceladus, as well as about the dynamics of the ring itself.

Product ion tandem mass spectrometric differentiation of regioisomeric side-chain groups in cathinone derivatives.

PubMed

Abiedalla, Younis; DeRuiter, Jack; Clark, C Randall

2016-07-30

Precursor materials are available to prepare aminoketone drugs containing regioisomeric propyl and isopropyl side-chain groups related to the drug alpha-pyrrovalerone (Flakka) and MDPV (3,4-methylenedioxypyrrovalerone). These compounds yield equivalent regioisomeric iminium cation base peaks in electron ionization mass spectrometry (EI-MS). The propyl and isopropyl side-chain groups related to alpha-pyrrovalerone and MDPV were prepared and evaluated in EI-MS and tandem mass spectrometry (MS/MS) product ion experiments. Deuterium labeling in both the pyrrolidine and alkyl side-chain groups allowed for the confirmation of the structures for the major product ions formed from the regioisomeric EI-MS iminium cation base peaks. These iminium cation base peaks show characteristic product ion spectra which allow differentiation of the side-chain propyl and isopropyl groups in the structure. The n-propyl side chain containing iminium cation base peak (m/z 126) in the EI-MS spectrum yields a major product ion at m/z 84 while the regioisomeric m/z 126 base peak for the isopropyl side chain yields a characteristic product ion at m/z 70. Deuterium labeling in both the pyrrolidine ring and the alkyl side chain confirmed the process for the formation of these major product ions. Product ion fragmentation provides useful data for differentiation of n-propyl and isopropyl side-chain iminium cations from cathinone derivative drugs of abuse. Regioisomeric n-propyl and isopropyl iminium cations of equal mass yield characteristic product ions identifying the alkyl side-chain regioisomers in the pyrrolidine cathinone derivatives. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Affinity purification and mass spectrometry: an attractive choice to investigate protein-protein interactions in plant immunity

USDA-ARS?s Scientific Manuscript database

Affinity purification of protein complexes from biological tissues, followed by liquid chromatography- tandem mass spectrometry (AP-MS/MS), has ballooned in recent years due to sizeable increases in nucleic acid sequence data essential for interpreting mass spectra, improvements in affinity purifica...

Identification of di(ethylhexyl) phthalate as impurity in the analysis by using chromatography gas tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Pusfitasari, Eka Dian; Hendarsyah, Hendris; Salahuddin, Ariani, Novita

2017-01-01

Di(ethylhexyl) phthalate (DEHP) is a plasticizer commonly used in plastics. Physically DEHP has a low vapor pressure. DEHP can seep into the liquid in direct contact with the plastic wrapping materials, and typically can occur rapidly if extractable into food or non-polar solvents, such as oil, once the food is packaged in PVC packaging materials. DEHP has been analyzed by using gas chromatography which has a high sensitivity level. If the equipment used for the analysis is made from plastic containing DEHP, then it may be possible that DEHP can be extracted and appear on the outcome of the injection. It can interfere with the process of analysis, especially for the analysis of food samples. This study has identified the present of DEHP in the blank injection performed by Gas Chromatography tandem Mass Spectrometry with Selected Ion Monitoring mode (SIM). Researchers are required to verify whether the gas chromatographic system used is ready for the analysis process. In addition, the comparison and calculation of the intensity of the ion fragmentation spectra generated by mass spectrometry detector can be used for the qualitative determination to ensure the presence of the target compound. In this study is also discussed the differences between the high-intensity fragmentation of DEHP and dioctyl phthalate (DOP).

Novel product ions of 2-aminoanilide and benzimidazole Ag(I) complexes using electrospray ionization with multi-stage tandem mass spectrometry.

PubMed

Johnson, Byron S; Burinsky, David J; Burova, Svetlana A; Davis, Roman; Fitzgerald, Russ N; Matsuoka, Richard T

2012-05-15

The 2-aminoaniline scaffold is of significant value to the pharmaceutical industry and is embedded in a number of pharmacophores including 2-aminoanilides and benzimidazoles. A novel application of coordination ion spray mass spectrometry (CIS-MS) for interrogating the silver ion (Ag(+)) complexes of a homologous series of these compounds using multi-stage tandem mass spectrometry is described. Unlike the ubiquitous alkali metal ion complexes, Ag(+) complexes of 2-aminoanilides and benzimidazoles were found to yield [M - H](+) ions in significant abundance via gas-phase elimination of the metal hydride (AgH) resulting in unique product ion cascades. Sample introduction was by liquid chromatography with mass spectrometry analysis performed on a hybrid linear ion trap/orbitrap instrument capable of high-resolution measurements. Rigorous structural characterization by multi-stage tandem mass spectrometry using [M +  H](+), [M - H](-) and [M - H](+) precursor ions derived from ESI and CIS experiments was performed for the homologous series of 2-aminoanilide and benzimidazole compounds. A full tabular comparison of structural information resulting from these product ion cascades was produced. Multi-stage tandem mass spectrometry of [M - H](+) ions resulting from Ag(+) complexes of 2-aminoanilides and benzimidazoles in CIS-MS experiments produced unique product ion cascades that exhibited complementary structural information to that obtained from tandem mass spectrometry of [M  +  H](+) and [M - H](-) ions by electrospray ionization (ESI). These observations may be broadly applicable to other compounds that are observed to form Ag(+) complexes and eliminate AgH. Copyright © 2012 John Wiley & Sons, Ltd.

Gas Chromatography-Tandem Mass Spectrometry of Lignin Pyrolyzates with Dopant-Assisted Atmospheric Pressure Chemical Ionization and Molecular Structure Search with CSI:FingerID

NASA Astrophysics Data System (ADS)

Larson, Evan A.; Hutchinson, Carolyn P.; Lee, Young Jin

2018-06-01

Dopant-assisted atmospheric pressure chemical ionization (dAPCI) is a soft ionization method rarely used for gas chromatography-mass spectrometry (GC-MS). The current study combines GC-dAPCI with tandem mass spectrometry (MS/MS) for analysis of a complex mixture such as lignin pyrolysis analysis. To identify the structures of volatile lignin pyrolysis products, collision-induced dissociation (CID) MS/MS using a quadrupole time-of-flight mass spectrometer (QTOFMS) and pseudo MS/MS through in-source collision-induced dissociation (ISCID) using a single stage TOFMS are utilized. To overcome the lack of MS/MS database, Compound Structure Identification (CSI):FingerID is used to interpret CID spectra and predict best matched structures from PubChem library. With this approach, a total of 59 compounds were positively identified in comparison to only 22 in NIST database search of GC-EI-MS dataset. This study demonstrates the effectiveness of GC-dAPCI-MS/MS to overcome the limitations of traditional GC-EI-MS analysis when EI-MS database is not sufficient. [Figure not available: see fulltext.

Multispectra CWT-based algorithm (MCWT) in mass spectra for peak extraction.

PubMed

Hsueh, Huey-Miin; Kuo, Hsun-Chih; Tsai, Chen-An

2008-01-01

An important objective in mass spectrometry (MS) is to identify a set of biomarkers that can be used to potentially distinguish patients between distinct treatments (or conditions) from tens or hundreds of spectra. A common two-step approach involving peak extraction and quantification is employed to identify the features of scientific interest. The selected features are then used for further investigation to understand underlying biological mechanism of individual protein or for development of genomic biomarkers to early diagnosis. However, the use of inadequate or ineffective peak detection and peak alignment algorithms in peak extraction step may lead to a high rate of false positives. Also, it is crucial to reduce the false positive rate in detecting biomarkers from ten or hundreds of spectra. Here a new procedure is introduced for feature extraction in mass spectrometry data that extends the continuous wavelet transform-based (CWT-based) algorithm to multiple spectra. The proposed multispectra CWT-based algorithm (MCWT) not only can perform peak detection for multiple spectra but also carry out peak alignment at the same time. The author' MCWT algorithm constructs a reference, which integrates information of multiple raw spectra, for feature extraction. The algorithm is applied to a SELDI-TOF mass spectra data set provided by CAMDA 2006 with known polypeptide m/z positions. This new approach is easy to implement and it outperforms the existing peak extraction method from the Bioconductor PROcess package.

The application of new software tools to quantitative protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry: I. Statistically annotated datasets for peptide sequences and proteins identified via the application of ICAT and tandem mass spectrometry to proteins copurifying with T cell lipid rafts.

PubMed

von Haller, Priska D; Yi, Eugene; Donohoe, Samuel; Vaughn, Kelly; Keller, Andrew; Nesvizhskii, Alexey I; Eng, Jimmy; Li, Xiao-jun; Goodlett, David R; Aebersold, Ruedi; Watts, Julian D

2003-07-01

Lipid rafts were prepared according to standard protocols from Jurkat T cells stimulated via T cell receptor/CD28 cross-linking and from control (unstimulated) cells. Co-isolating proteins from the control and stimulated cell preparations were labeled with isotopically normal (d0) and heavy (d8) versions of the same isotope-coded affinity tag (ICAT) reagent, respectively. Samples were combined, proteolyzed, and resultant peptides fractionated via cation exchange chromatography. Cysteine-containing (ICAT-labeled) peptides were recovered via the biotin tag component of the ICAT reagents by avidin-affinity chromatography. On-line micro-capillary liquid chromatography tandem mass spectrometry was performed on both avidin-affinity (ICAT-labeled) and flow-through (unlabeled) fractions. Initial peptide sequence identification was by searching recorded tandem mass spectrometry spectra against a human sequence data base using SEQUEST software. New statistical data modeling algorithms were then applied to the SEQUEST search results. These allowed for discrimination between likely "correct" and "incorrect" peptide assignments, and from these the inferred proteins that they collectively represented, by calculating estimated probabilities that each peptide assignment and subsequent protein identification was a member of the "correct" population. For convenience, the resultant lists of peptide sequences assigned and the proteins to which they corresponded were filtered at an arbitrarily set cut-off of 0.5 (i.e. 50% likely to be "correct") and above and compiled into two separate datasets. In total, these data sets contained 7667 individual peptide identifications, which represented 2669 unique peptide sequences, corresponding to 685 proteins and related protein groups.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets

PubMed Central

Griss, Johannes; Perez-Riverol, Yasset; Lewis, Steve; Tabb, David L.; Dianes, José A.; del-Toro, Noemi; Rurik, Marc; Walzer, Mathias W.; Kohlbacher, Oliver; Hermjakob, Henning; Wang, Rui; Vizcaíno, Juan Antonio

2016-01-01

Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average 75% of spectra analysed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large-scale to shed a light on these unidentified spectra. PRoteomics IDEntifications database (PRIDE) Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in PRIDE Archive, coming from hundreds of datasets, we were able to consistently characterize three distinct groups of spectra: 1) incorrectly identified spectra, 2) spectra correctly identified but below the set scoring threshold, and 3) truly unidentified spectra. Using a multitude of complementary analysis approaches, we were able to identify less than 20% of the consistently unidentified spectra. The complete spectrum clustering results are available through the new version of the PRIDE Cluster resource (http://www.ebi.ac.uk/pride/cluster). This resource is intended, among other aims, to encourage and simplify further investigation into these unidentified spectra. PMID:27493588

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

PubMed

Griss, Johannes; Perez-Riverol, Yasset; Lewis, Steve; Tabb, David L; Dianes, José A; Del-Toro, Noemi; Rurik, Marc; Walzer, Mathias W; Kohlbacher, Oliver; Hermjakob, Henning; Wang, Rui; Vizcaíno, Juan Antonio

2016-08-01

Mass spectrometry (MS) is the main technology used in proteomics approaches. However, on average 75% of spectra analysed in an MS experiment remain unidentified. We propose to use spectrum clustering at a large-scale to shed a light on these unidentified spectra. PRoteomics IDEntifications database (PRIDE) Archive is one of the largest MS proteomics public data repositories worldwide. By clustering all tandem MS spectra publicly available in PRIDE Archive, coming from hundreds of datasets, we were able to consistently characterize three distinct groups of spectra: 1) incorrectly identified spectra, 2) spectra correctly identified but below the set scoring threshold, and 3) truly unidentified spectra. Using a multitude of complementary analysis approaches, we were able to identify less than 20% of the consistently unidentified spectra. The complete spectrum clustering results are available through the new version of the PRIDE Cluster resource (http://www.ebi.ac.uk/pride/cluster). This resource is intended, among other aims, to encourage and simplify further investigation into these unidentified spectra.

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra

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

Kou, Qiang; Wu, Si; Tolić, Nikola

Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a “bird’s eye view” of intact proteoforms. The combinatorial explosion of various alterations on a protein may result inmore » billions of possible proteoforms, making proteoform identification a challenging computational problem. Results: We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry data sets showed that TopMG outperformed existing methods in identifying complex proteoforms.« less

Identification of the chemical constituents of Chinese medicine Yi-Xin-Shu capsule by molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation.

PubMed

Wang, Hong-ping; Chen, Chang; Liu, Yan; Yang, Hong-Jun; Wu, Hong-Wei; Xiao, Hong-Bin

2015-11-01

The incomplete identification of the chemical components of traditional Chinese medicinal formula has been one of the bottlenecks in the modernization of traditional Chinese medicine. Tandem mass spectrometry has been widely used for the identification of chemical substances. Current automatic tandem mass spectrometry acquisition, where precursor ions were selected according to their signal intensity, encounters a drawback in chemical substances identification when samples contain many overlapping signals. Compounds in minor or trace amounts could not be identified because most tandem mass spectrometry information was lost. Herein, a molecular feature orientated precursor ion selection and tandem mass spectrometry structure elucidation method for complex Chinese medicine chemical constituent analysis was developed. The precursor ions were selected according to their two-dimensional characteristics of retention times and mass-to-charge ratio ranges from herbal compounds, so that all precursor ions from herbal compounds were included and more minor chemical constituents in Chinese medicine were identified. Compared to the conventional automatic tandem mass spectrometry setups, the approach is novel and can overcome the drawback for chemical substances identification. As an example, 276 compounds from the Chinese Medicine of Yi-Xin-Shu capsule were identified. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electrospray ionization tandem mass spectrometry of ammonium cationized polyethers.

PubMed

Nasioudis, Andreas; Heeren, Ron M A; van Doormalen, Irene; de Wijs-Rot, Nicolette; van den Brink, Oscar F

2011-05-01

Quaternary ammonium salts (Quats) and amines are known to facilitate the MS analysis of high molar mass polyethers by forming low charge state adduct ions. The formation, stability, and behavior upon collision-induced dissociation (CID) of adduct ions of polyethers with a variety of Quats and amines were studied by electrospray ionization quadrupole time-of-flight, quadrupole ion trap, and linear ion trap tandem mass spectrometry (MS/MS). The linear ion trap instrument was part of an Orbitrap hybrid mass spectrometer that allowed accurate mass MS/MS measurements. The Quats and amines studied were of different degree of substitution, structure, and size. The stability of the adduct ions was related to the structure of the cation, especially the amine's degree of substitution. CID of singly/doubly charged primary and tertiary ammonium cationized polymers resulted in the neutral loss of the amine followed by fragmentation of the protonated product ions. The latter reveals information about the monomer unit, polymer sequence, and endgroup structure. In addition, the detection of product ions retaining the ammonium ion was observed. The predominant process in the CID of singly charged quaternary ammonium cationized polymers was cation detachment, whereas their doubly charged adduct ions provided the same information as the primary and tertiary ammonium cationized adduct ions. This study shows the potential of specific amines as tools for the structural elucidation of high molar mass polyethers. © American Society for Mass Spectrometry, 2011

High-performance liquid chromatography–tandem mass spectrometry in the identification and determination of phase I and phase II drug metabolites

PubMed Central

Kolářová, L.; Nobilis, M.

2008-01-01

Applications of tandem mass spectrometry (MS/MS) techniques coupled with high-performance liquid chromatography (HPLC) in the identification and determination of phase I and phase II drug metabolites are reviewed with an emphasis on recent papers published predominantly within the last 6 years (2002–2007) reporting the employment of atmospheric pressure ionization techniques as the most promising approach for a sensitive detection, positive identification and quantitation of metabolites in complex biological matrices. This review is devoted to in vitro and in vivo drug biotransformation in humans and animals. The first step preceding an HPLC-MS bioanalysis consists in the choice of suitable sample preparation procedures (biomatrix sampling, homogenization, internal standard addition, deproteination, centrifugation, extraction). The subsequent step is the right optimization of chromatographic conditions providing the required separation selectivity, analysis time and also good compatibility with the MS detection. This is usually not accessible without the employment of the parent drug and synthesized or isolated chemical standards of expected phase I and sometimes also phase II metabolites. The incorporation of additional detectors (photodiode-array UV, fluorescence, polarimetric and others) between the HPLC and MS instruments can result in valuable analytical information supplementing MS results. The relation among the structural changes caused by metabolic reactions and corresponding shifts in the retention behavior in reversed-phase systems is discussed as supporting information for identification of the metabolite. The first and basic step in the interpretation of mass spectra is always the molecular weight (MW) determination based on the presence of protonated molecules [M+H]+ and sometimes adducts with ammonium or alkali-metal ions, observed in the positive-ion full-scan mass spectra. The MW determination can be confirmed by the [M-H]- ion for metabolites

Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry.

PubMed

Yao, Jingwen; Utsunomiya, Shin-Ichi; Kajihara, Shigeki; Tabata, Tsuyoshi; Aoshima, Ken; Oda, Yoshiya; Tanaka, Koichi

2014-01-01

A new peak detection method has been developed for rapid selection of peptide and its fragment ion peaks for protein identification using tandem mass spectrometry. The algorithm applies classification of peak intensities present in the defined mass range to determine the noise level. A threshold is then given to select ion peaks according to the determined noise level in each mass range. This algorithm was initially designed for the peak detection of low resolution peptide mass spectra, such as matrix-assisted laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectra. But it can also be applied to other type of mass spectra. This method has demonstrated obtaining a good rate of number of real ions to noises for even poorly fragmented peptide spectra. The effect of using peak lists generated from this method produces improved protein scores in database search results. The reliability of the protein identifications is increased by finding more peptide identifications. This software tool is freely available at the Mass++ home page (http://www.first-ms3d.jp/english/achievement/software/).

Peptide Peak Detection for Low Resolution MALDI-TOF Mass Spectrometry

PubMed Central

Yao, Jingwen; Utsunomiya, Shin-ichi; Kajihara, Shigeki; Tabata, Tsuyoshi; Aoshima, Ken; Oda, Yoshiya; Tanaka, Koichi

2014-01-01

A new peak detection method has been developed for rapid selection of peptide and its fragment ion peaks for protein identification using tandem mass spectrometry. The algorithm applies classification of peak intensities present in the defined mass range to determine the noise level. A threshold is then given to select ion peaks according to the determined noise level in each mass range. This algorithm was initially designed for the peak detection of low resolution peptide mass spectra, such as matrix-assisted laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectra. But it can also be applied to other type of mass spectra. This method has demonstrated obtaining a good rate of number of real ions to noises for even poorly fragmented peptide spectra. The effect of using peak lists generated from this method produces improved protein scores in database search results. The reliability of the protein identifications is increased by finding more peptide identifications. This software tool is freely available at the Mass++ home page (http://www.first-ms3d.jp/english/achievement/software/). PMID:26819872

An efficient approach to identify different chemical markers between fibrous root and rhizome of Anemarrhena asphodeloides by ultra high-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry with multivariate statistical analysis.

PubMed

Wang, Fang-Xu; Yuan, Jian-Chao; Kang, Li-Ping; Pang, Xu; Yan, Ren-Yi; Zhao, Yang; Zhang, Jie; Sun, Xin-Guang; Ma, Bai-Ping

2016-09-10

An ultra high-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry approach coupled with multivariate statistical analysis was established and applied to rapidly distinguish the chemical differences between fibrous root and rhizome of Anemarrhena asphodeloides. The datasets of tR-m/z pairs, ion intensity and sample code were processed by principal component analysis and orthogonal partial least squares discriminant analysis. Chemical markers could be identified based on their exact mass data, fragmentation characteristics, and retention times. And the new compounds among chemical markers could be isolated rapidly guided by the ultra high-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometry and their definitive structures would be further elucidated by NMR spectra. Using this approach, twenty-four markers were identified on line including nine new saponins and five new steroidal saponins of them were obtained in pure form. The study validated this proposed approach as a suitable method for identification of the chemical differences between various medicinal parts in order to expand medicinal parts and increase the utilization rate of resources. Copyright © 2016 Elsevier B.V. All rights reserved.

The laser desorption/laser ionization mass spectra of some anti-inflammatory drugs

NASA Astrophysics Data System (ADS)

Milnes, John; Rogers, Kevin; Jones, Sian; Gormally, John

1994-03-01

The IR laser desorption/ultraviolet laser ionization time-of-flight mass spectra are reported for the anti-inflammatory drugs indomethacin, acemetacin, ibuprofen, flurbiprofen, diflunisal and mefenamic acid. It is found that the six compounds can be readily ionized by two photon absorption at a fixed wavelength of 266 nm. Mass spectra have been obtained under conditions of high ionizing irradiance and the observed fragmentation behaviour is discussed.

A mass graph-based approach for the identification of modified proteoforms using top-down tandem mass spectra.

PubMed

Kou, Qiang; Wu, Si; Tolic, Nikola; Paša-Tolic, Ljiljana; Liu, Yunlong; Liu, Xiaowen

2017-05-01

Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions. Top-down mass spectrometry is the method of choice for identifying complex proteoforms because it provides a 'bird's eye view' of intact proteoforms. The combinatorial explosion of various alterations on a protein may result in billions of possible proteoforms, making proteoform identification a challenging computational problem. We propose a new data structure, called the mass graph, for efficient representation of proteoforms and design mass graph alignment algorithms. We developed TopMG, a mass graph-based software tool for proteoform identification by top-down mass spectrometry. Experiments on top-down mass spectrometry datasets showed that TopMG outperformed existing methods in identifying complex proteoforms. http://proteomics.informatics.iupui.edu/software/topmg/. xwliu@iupui.edu. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Making the Case for Objective Performance Metrics in Newborn Screening by Tandem Mass Spectrometry

ERIC Educational Resources Information Center

Rinaldo, Piero; Zafari, Saba; Tortorelli, Silvia; Matern, Dietrich

2006-01-01

The expansion of newborn screening programs to include multiplex testing by tandem mass spectrometry requires understanding and close monitoring of performance metrics. This is not done consistently because of lack of defined targets, and interlaboratory comparison is almost nonexistent. Between July 2004 and April 2006 (N = 176,185 cases), the…

Assessment of Dimeric Metal-Glycan Adducts via Isotopic Labeling and Ion Mobility-Mass Spectrometry.

PubMed

Morrison, Kelsey A; Bendiak, Brad K; Clowers, Brian H

2018-05-25

Adduction of multivalent metal ions to glycans has been shown in recent years to produce altered tandem mass spectra with collision-induced dissociation, electron transfer techniques, and photon-based fragmentation approaches. However, these approaches assume the presence of a well-characterized precursor ion population and do not fully account for the possibility of multimeric species for select glycan-metal complexes. With the use of ion mobility separations prior to mass analysis, doubly charged dimers are not necessarily problematic for tandem MS experiments given that monomer and dimer drift times are sufficiently different. However, multistage mass spectrometric experiments performed on glycans adducted to multivalent metals without mobility separation can yield chimeric fragmentation spectra that are essentially a superposition of the fragments from both the monomeric and dimeric adducts. For homodimeric adducts, where the dimer contains two of the same glycan species, this is less of a concern but if heterodimers can form, there exists the potential for erroneous and misleading fragment ions to appear if a heterodimer containing two different isomers is fragmented along with a targeted monomer. We present an assessment of heterodimer formation between a series of six tetrasaccharides, of which three are isomers, adducted with cobalt(II) and a monodeuterated tetrasaccharide. Using ion mobility separations prior to single-stage and tandem mass analysis, the data shown demonstrate that heterodimeric species can indeed form, and that ion mobility separations are highly necessary prior to using tandem techniques on metal-glycan adducts. Graphical Abstract ᅟ.

Assessment of Dimeric Metal-Glycan Adducts via Isotopic Labeling and Ion Mobility-Mass Spectrometry

NASA Astrophysics Data System (ADS)

Morrison, Kelsey A.; Bendiak, Brad K.; Clowers, Brian H.

2018-05-01

Adduction of multivalent metal ions to glycans has been shown in recent years to produce altered tandem mass spectra with collision-induced dissociation, electron transfer techniques, and photon-based fragmentation approaches. However, these approaches assume the presence of a well-characterized precursor ion population and do not fully account for the possibility of multimeric species for select glycan-metal complexes. With the use of ion mobility separations prior to mass analysis, doubly charged dimers are not necessarily problematic for tandem MS experiments given that monomer and dimer drift times are sufficiently different. However, multistage mass spectrometric experiments performed on glycans adducted to multivalent metals without mobility separation can yield chimeric fragmentation spectra that are essentially a superposition of the fragments from both the monomeric and dimeric adducts. For homodimeric adducts, where the dimer contains two of the same glycan species, this is less of a concern but if heterodimers can form, there exists the potential for erroneous and misleading fragment ions to appear if a heterodimer containing two different isomers is fragmented along with a targeted monomer. We present an assessment of heterodimer formation between a series of six tetrasaccharides, of which three are isomers, adducted with cobalt(II) and a monodeuterated tetrasaccharide. Using ion mobility separations prior to single-stage and tandem mass analysis, the data shown demonstrate that heterodimeric species can indeed form, and that ion mobility separations are highly necessary prior to using tandem techniques on metal-glycan adducts.

Reproducing impact ionization mass spectra of E and F ring ice grains at different impact speeds

NASA Astrophysics Data System (ADS)

Klenner, F.; Reviol, R.; Postberg, F.

2017-09-01

As impact speeds of E and F ring ice grains impinging onto the target of impact ionization mass spectrometers in space can vary greatly, the resulting cationic or anionic mass spectra can have very different appearances. The mass spectra can be accurately reproduced with an analog experimental setup IR-FL-MALDI-ToF-MS (Infrared Free Liquid Matrix Assisted Laser Desorption and Ionization Time of Flight Mass Spectrometry). We compare mass spectra of E and F ring ice grains taken by the Cosmic Dust Analyzer (CDA) onboard Cassini recorded at different impact speeds with our analog spectra and prove the capability of the analog experiment.

Liquid Chromatography-Tandem Mass Spectrometry: An Emerging Technology in the Toxicology Laboratory.

PubMed

Zhang, Yan Victoria; Wei, Bin; Zhu, Yu; Zhang, Yanhua; Bluth, Martin H

2016-12-01

In the last decade, liquid chromatography-tandem mass spectrometry (LC-MS/MS) has seen enormous growth in routine toxicology laboratories. LC-MS/MS offers significant advantages over other traditional testing, such as immunoassay and gas chromatography-mass spectrometry methodologies. Major strengths of LC-MS/MS include improvement in specificity, flexibility, and sample throughput when compared with other technologies. Here, the basic principles of LC-MS/MS technology are reviewed, followed by advantages and disadvantages of this technology compared with other traditional techniques. In addition, toxicology applications of LC-MS/MS for simultaneous detection of large panels of analytes are presented. Copyright © 2016 Elsevier Inc. All rights reserved.

Covalently Linked Tandem Lesions in DNA

PubMed Central

Patrzyc, Helen B.; Dawidzik, Jean B.; Budzinski, Edwin E.; Freund, Harold G.; Wilton, John H.; Box, Harold C.

2013-01-01

Reactive oxygen species (ROS) generate a type of DNA damage called tandem lesions, two adjacent nucleotides both modified. A subcategory of tandem lesions consists of adjacent nucleotides linked by a covalent bond. Covalently linked tandem lesions generate highly characteristic liquid chromotography-tandem mass spectrometry (LC-MS/MS) elution profiles. We have used this property to comprehensively survey X-irradiated DNA for covalently linked tandem lesions. A total of 15 tandem lesions were detected in DNA irradiated in deoxygenated aqueous solution, five tandem lesions were detected in DNA that was irradiated in oxygenated solution. PMID:23106212

Xylose Migration During Tandem Mass Spectrometry of N-Linked Glycans

NASA Astrophysics Data System (ADS)

Hecht, Elizabeth S.; Loziuk, Philip L.; Muddiman, David C.

2017-04-01

Understanding the rearrangement of gas-phase ions via tandem mass spectrometry is critical to improving manual and automated interpretation of complex datasets. N-glycan analysis may be carried out under collision induced (CID) or higher energy collision dissociation (HCD), which favors cleavage at the glycosidic bond. However, fucose migration has been observed in tandem MS, leading to the formation of new bonds over four saccharide units away. In the following work, we report the second instance of saccharide migration ever to occur for N-glycans. Using horseradish peroxidase as a standard, the beta-1,2 xylose was observed to migrate from a hexose to a glucosamine residue on the (Xyl)Man3GlcNac2 glycan. This investigation was followed up in a complex N-linked glycan mixture derived from stem differentiating xylem tissue, and the rearranged product ion was observed for 75% of the glycans. Rearrangement was not favored in isomeric glycans with a core or antennae fucose and unobserved in glycans predicted to have a permanent core-fucose modification. As the first empirical observation of this rearrangement, this work warrants dissemination so it may be searched in de novo sequencing glycan workflows.

Occurrence of C-Terminal Residue Exclusion in Peptide Fragmentation by ESI and MALDI Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Dupré, Mathieu; Cantel, Sonia; Martinez, Jean; Enjalbal, Christine

2012-02-01

By screening a data set of 392 synthetic peptides MS/MS spectra, we found that a known C-terminal rearrangement was unexpectedly frequently occurring from monoprotonated molecular ions in both ESI and MALDI tandem mass spectrometry upon low and high energy collision activated dissociations with QqTOF and TOF/TOF mass analyzer configuration, respectively. Any residue localized at the C-terminal carboxylic acid end, even a basic one, was lost, provided that a basic amino acid such arginine and to a lesser extent histidine and lysine was present in the sequence leading to a fragment ion, usually depicted as (bn-1 + H2O) ion, corresponding to a shortened non-scrambled peptide chain. Far from being an epiphenomenon, such a residue exclusion from the peptide chain C-terminal extremity gave a fragment ion that was the base peak of the MS/MS spectrum in certain cases. Within the frame of the mobile proton model, the ionizing proton being sequestered onto the basic amino acid side chain, it is known that the charge directed fragmentation mechanism involved the C-terminal carboxylic acid function forming an anhydride intermediate structure. The same mechanism was also demonstrated from cationized peptides. To confirm such assessment, we have prepared some of the peptides that displayed such C-terminal residue exclusion as a C-terminal backbone amide. As expected in this peptide amide series, the production of truncated chains was completely suppressed. Besides, multiply charged molecular ions of all peptides recorded in ESI mass spectrometry did not undergo such fragmentation validating that any mobile ionizing proton will prevent such a competitive C-terminal backbone rearrangement. Among all well-known nondirect sequence fragment ions issued from non specific loss of neutral molecules (mainly H2O and NH3) and multiple backbone amide ruptures (b-type internal ions), the described C-terminal residue exclusion is highly identifiable giving raise to a single fragment ion in

Mass spectra and decay properties of the c\\bar{c} meson

NASA Astrophysics Data System (ADS)

Chaturvedi, Raghav; Kumar Rai, Ajay

2018-06-01

In this article we present the result of c\\bar{c} meson mass calculation by solving the Schrödinger equation numerically considering the Coulomb plus linear potential. The spin-hyperfine, spin-orbit and tensor components of one-gluon-exchange interactions are employed to obtain the mass spectra of c\\bar{c} meson. The calculated mass spectra are compared with the latest results of PDG and are found to be in good accordance. The Regge trajectories of the calculated mass spectra have also been constructed. The values of the wave function are extracted and employed to calculate the leptonic decay constant, γγ, gg, e+e-, light hadron (LH) and γγγ decay widths of S-wave 0^{-+} and 1^{- -} states of c\\bar{c} meson, the widths have been calculated by Van Royen-Weisskopf formula and by NRQCD mechanism incorporating relativistic corrections of order ν2. The γγ and gg decay widths of χ0 and χ2 states of c\\bar{c} meson have also been calculated. The calculated decay constants and widths have been compared with the experimental results.

reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

PubMed Central

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

2016-01-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contributes to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), that enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the following iterations. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. PMID:26419769

reSpect: Software for Identification of High and Low Abundance Ion Species in Chimeric Tandem Mass Spectra

NASA Astrophysics Data System (ADS)

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R.; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W.; Moritz, Robert L.

2015-11-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website.

NIST Libraries of Peptide Fragmentation Mass Spectra Databass

National Institute of Standards and Technology Data Gateway

SRD 4 NIST Libraries of Peptide Fragmentation Mass Spectra Databass (PC database for purchase)   Interactive computer program for predicting thermodynamic and transport properties of pure fluids and fluid mixtures containing up to 20 components. The components are selected from a database of 196 components, mostly hydrocarbons.

A comparison of flavonoid glycosides by electrospray tandem mass spectrometry

NASA Astrophysics Data System (ADS)

March, Raymond E.; Lewars, Errol G.; Stadey, Christopher J.; Miao, Xiu-Sheng; Zhao, Xiaoming; Metcalfe, Chris D.

2006-01-01

A comparison is presented of product ion mass spectra of protonated and deprotonated molecules of kaempferol-3-O-glucoside, quercitin-3-O-glucoside (isoquercitrin), quercitin-3-O-galactoside (hyperoin), apigenin-7-O-glucoside, luteolin-7-O-glucoside, genistein-7-O-glucoside, naringenin-7-O-glucoside (prunin), luteolin-4'-O-glucoside, luteolin-6-C-glucoside (homoorientin, known also as isoorientin), apigenin-8-C-glucoside (vitexin), and luteolin-8-C-glucoside (orientin) together with the product ion mass spectrum of deprotonated kaempferol-7-O-glucoside. All isomeric ions were distinguishable on the basis of their product ion mass spectra. For protonated 3-O-, 7-O-, and 4'-O-glycosides at a collision energy of 46-47 eV, homolytic cleavage of the O-glycosidic bond yielded aglycon Y+ ions, whereas in deprotonated 3-O-, 7-O-, and 4'-O-glycosides, heterolytic and homolytic cleavage of the O-glycosidic bond yielded radical aglycon (Y-H)- and aglycon (Y-) ions. In each case, fragmentation of either the glycan or the aglycon or both was observed. For 6-C- and 8-C-glycosides at a collision energy of 46-47 eV, fragmentation was restricted almost exclusively to the glycan. For luteolin-6-C-glucoside, the integrity of the aglycon structure is preserved at the expense of the glycan for which some 30 fragmentations were observed. Breakdown curves were determined as a function of collision energy for protonated and deprotonated luteolin-6-C-glucoside. An attempt has been made to rationalize the product ion mass spectra derived from C-O- and C-C-luteolin glucosides in terms of computed structures that indicate significant intramolecular hydrogen bonding and rotation of the B-ring to form a coplanar luteolin structure. It is proposed that protonated and deprotonated luteolin-6-C-glucoside may afford examples of cooperative interactive bonding that plays a major role in directing fragmentation.

Zwitterionic-hydrophilic interaction capillary liquid chromatography coupled to tandem mass spectrometry for the characterization of human alpha-acid-glycoprotein N-glycan isomers.

PubMed

Mancera-Arteu, Montserrat; Giménez, Estela; Barbosa, José; Peracaula, Rosa; Sanz-Nebot, Victòria

2017-10-23

In this work, a μZIC-HILIC-MS/MS methodology was established in negative ion mode for the characterization of glycan isomers. The possibility to separate the glycan isomers by the μZIC-HILIC strategy coupled to a high resolution tandem mass spectrometry detection permitted us to obtain valuable information about each glycan structure. The most important diagnostic ion fragments previously described to characterize structural features of glycans, were evaluated in this study using hAGP as model glycoprotein. The assignation of hAGP glycan isomers performed in our previous work using the GRIL strategy in combination with exoglycosidase digestion [1] was used in this paper to confirm or discard some ion fragments reported in the literature and delve into the structural characterization of glycan isomers. Sialic acid as well as fucose linkage-type glycan isomers were assigned using this approach and daughter ions with higher diagnostic value were determined. The location of α2-3/α2-6 sialic acids on antennas and a deeper characterization of several highly sialylated tri- and tetraantennary glycans was also possible using the established MS/MS method. Moreover, relying on the characterization performed in Ref. [1], core and antenna fucosylation were differentiated in this work using specific ion fragments obtained in the tandem mass spectra. This methodology was also applied to hAGP purified from control and pathological serum samples, which corroborated its robustness and its potential for finding novel glycan-based biomarkers in patho-glycomic studies. Copyright © 2017 Elsevier B.V. All rights reserved.

STRAPS v1.0: Evaluating a methodology for predicting electron impact ionisation mass spectra for the aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Topping, David; Allan, James; Alfarra, Rami; Aumont, Bernard

2017-04-01

Our ability to model the chemical and thermodynamic processes that lead to secondary organic aerosol (SOA) formation is thought to be hampered by the complexity of the system. While there are fundamental models now available that can simulate the tens of thousands of reactions thought to take place, validation against experiments is highly challenging. Techniques capable of identifying individual molecules such as chromatography are generally only capable of quantifying a subset of the material present, making it unsuitable for a carbon budget analysis. Integrative analytical methods such as the Aerosol Mass Spectrometer (AMS) are capable of quantifying all mass, but because of their inability to isolate individual molecules, comparisons have been limited to simple data products such as total organic mass and O:C ratio. More detailed comparisons could be made if more of the mass spectral information could be used, but because a discrete inversion of AMS data is not possible, this activity requires a system of predicting mass spectra based on molecular composition. In this proof of concept study, the ability to train supervised methods to predict electron impact ionisation (EI) mass spectra for the AMS is evaluated. Supervised Training Regression for the Arbitrary Prediction of Spectra (STRAPS), is not built from first principles. A methodology is constructed whereby the presence of specific mass-to-charge ratio (m/z) channels are fit as a function of molecular structure before the relative peak height for each channel is similarly fit using a range of regression methods. The widely-used AMS mass spectral database is used as a basis for this, using unit mass resolution spectra of laboratory standards. Key to the fitting process is choice of structural information, or molecular fingerprint. Initial results suggest the generic public 'MACCS' fingerprints provide the most accurate trained model when combined with both decision trees and random forests with median

Analysis of small carbohydrates in several bioactive botanicals by gas chromatography with mass spectrometry and liquid chromatography with tandem mass spectrometry.

PubMed

Moldoveanu, Serban; Scott, Wayne; Zhu, Jeff

2015-11-01

Bioactive botanicals contain natural compounds with specific biological activity, such as antibacterial, antioxidant, immune stimulating, and taste improving. A full characterization of the chemical composition of these botanicals is frequently necessary. A study of small carbohydrates from the plant materials of 18 bioactive botanicals is further described. The study presents the identification of the carbohydrate using a gas chromatographic-mass spectrometric analysis that allows detection of molecules as large as maltotetraose, after changing them into trimethylsilyl derivatives. A number of carbohydrates in the plant (fructose, glucose, mannose, sucrose, maltose, xylose, sorbitol, and myo-, chiro-, and scyllo-inositols) were quantitated using a novel liquid chromatography with tandem mass spectrometric technique. Both techniques involved new method developments. The gas chromatography with mass spectrometric analysis involved derivatization and separation on a Rxi(®)-5Sil MS column with H2 as a carrier gas. The liquid chromatographic separation was obtained using a hydrophilic interaction type column, YMC-PAC Polyamine II. The tandem mass spectrometer used an electrospray ionization source in multiple reaction monitoring positive ion mode with the detection of the adducts of the carbohydrates with Cs(+) ions. The validated quantitative procedure showed excellent precision and accuracy allowing the analysis in a wide range of concentrations of the analytes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lipid Identification by Untargeted Tandem Mass Spectrometry Coupled with Ultra-High-Pressure Liquid Chromatography.

PubMed

Gugiu, Gabriel B

2017-01-01

Lipidomics refers to the large-scale study of lipids in biological systems (Wenk, Nat Rev Drug Discov 4(7):594-610, 2005; Rolim et al., Gene 554(2):131-139, 2015). From a mass spectrometric point of view, by lipidomics we understand targeted or untargeted mass spectrometric analysis of lipids using either liquid chromatography (LC) (Castro-Perez et al., J Proteome Res 9(5):2377-2389, 2010) or shotgun (Han and Gross, Mass Spectrom Rev 24(3):367-412, 2005) approaches coupled with tandem mass spectrometry. This chapter describes the former methodology, which is becoming rapidly the preferred method for lipid identification owing to similarities with established omics workflows, such as proteomics (Washburn et al., Nat Biotechnol 19(3):242-247, 2001) or genomics (Yadav, J Biomol Tech: JBT 18(5):277, 2007). The workflow described consists in lipid extraction using a modified Bligh and Dyer method (Bligh and Dyer, Can J Biochem Physiol 37(8):911-917, 1959), ultra high pressure liquid chromatography fractionation of lipid samples on a reverse phase C18 column, followed by tandem mass spectrometric analysis and in silico database search for lipid identification based on MSMS spectrum matching (Kind et al., Nat Methods 10(8):755-758, 2013; Yamada et al., J Chromatogr A 1292:211-218, 2013; Taguchi and Ishikawa, J Chromatogr A 1217(25):4229-4239, 2010; Peake et al., Thermoscientifices 1-3, 2015) and accurate mass of parent ion (Sud et al., Nucleic Acids Res 35(database issue):D527-D532, 2007; Wishart et al., Nucleic Acids Res 35(database):D521-D526, 2007).

Simultaneous determination of estrogens and progestogens in honey using high performance liquid chromatography-tandem mass spectrometry

USDA-ARS?s Scientific Manuscript database

This work describes the development and validation of a method for the simultaneous determination of 13 estrogens and progestogens in honey by high performance liquid chromatography-tandem mass spectrometry. The target compounds were preconcentrated by solid phase extraction. Pretreatment variables ...

How to Compute Electron Ionization Mass Spectra from First Principles.

PubMed

Bauer, Christoph Alexander; Grimme, Stefan

2016-06-02

The prediction of electron ionization (EI) mass spectra (MS) from first principles has been a major challenge for quantum chemistry (QC). The unimolecular reaction space grows rapidly with increasing molecular size. On the one hand, statistical models like Eyring's quasi-equilibrium theory and Rice-Ramsperger-Kassel-Marcus theory have provided valuable insight, and some predictions and quantitative results can be obtained from such calculations. On the other hand, molecular dynamics-based methods are able to explore automatically the energetically available regions of phase space and thus yield reaction paths in an unbiased way. We describe in this feature article the status of both methodologies in relation to mass spectrometry for small to medium sized molecules. We further present results obtained with the QCEIMS program developed in our laboratory. Our method, which incorporates stochastic and dynamic elements, has been a significant step toward the reliable routine calculation of EI mass spectra.

reSpect: software for identification of high and low abundance ion species in chimeric tandem mass spectra.

PubMed

Shteynberg, David; Mendoza, Luis; Hoopmann, Michael R; Sun, Zhi; Schmidt, Frank; Deutsch, Eric W; Moritz, Robert L

2015-11-01

Most shotgun proteomics data analysis workflows are based on the assumption that each fragment ion spectrum is explained by a single species of peptide ion isolated by the mass spectrometer; however, in reality mass spectrometers often isolate more than one peptide ion within the window of isolation that contribute to additional peptide fragment peaks in many spectra. We present a new tool called reSpect, implemented in the Trans-Proteomic Pipeline (TPP), which enables an iterative workflow whereby fragment ion peaks explained by a peptide ion identified in one round of sequence searching or spectral library search are attenuated based on the confidence of the identification, and then the altered spectrum is subjected to further rounds of searching. The reSpect tool is not implemented as a search engine, but rather as a post-search engine processing step where only fragment ion intensities are altered. This enables the application of any search engine combination in the iterations that follow. Thus, reSpect is compatible with all other protein sequence database search engines as well as peptide spectral library search engines that are supported by the TPP. We show that while some datasets are highly amenable to chimeric spectrum identification and lead to additional peptide identification boosts of over 30% with as many as four different peptide ions identified per spectrum, datasets with narrow precursor ion selection only benefit from such processing at the level of a few percent. We demonstrate a technique that facilitates the determination of the degree to which a dataset would benefit from chimeric spectrum analysis. The reSpect tool is free and open source, provided within the TPP and available at the TPP website. Graphical Abstract ᅟ.

Structural analysis of isomeric chondroitin sulfate oligosaccharides using regioselective 6-O-desulfation method and tandem mass spectrometry.

PubMed

Chen, Shu-Ting; Her, Guor-Rong

2014-09-16

A strategy based on a regioselective 6-O-desulfation reaction and negative ion electrospray ionization tandem mass spectrometry (ESI-MS(n)) was developed for the structural delineation of isomeric chondroitin sulfate oligosaccharides. Product ions resulting from the glycosidic cleavage provided information about the number of sulfate groups in each sugar residue. After the regioselective 6-O-desulfation reaction, the number of sulfate groups on each residue was obtained using a tandem mass spectrometry analysis of the reaction product. The sulfation pattern could be obtained based on the product ions of analytes before and after the desulfation reaction. The strategy was demonstrated using a series of tetrasaccharides prepared from shark cartilage chondroitin sulfate D. Among the 12 identified tetrasaccharides, six structures had not been reported before. Copyright © 2014 Elsevier B.V. All rights reserved.

Recent developments and new applications of tandem mass spectrometry in newborn screening.

PubMed

Rinaldo, Piero; Tortorelli, Silvia; Matern, Dietrich

2004-08-01

To summarize recent developments in the field of newborn screening related to the use of tandem mass spectrometry as an analytic platform. Novel inborn errors of metabolism with informative amino acid and/or acylcarnitine profiles have been characterized, increasing the complexity of the differential diagnosis of abnormal results. In addition, methods have been developed for the analysis in dried blood spots of steroids and lysosomal enzymes. Previously unrecognized genotype/phenotype correlations have been found among cohorts of patients whose conditions were diagnosed by screening rather than clinically. Several government entities and professional organizations have issued position statements on newborn screening, and worldwide outcome studies continue to underscore the clinical and financial benefits of expanded newborn screening. Although it is done inconsistently, newborn screening in the United States is undergoing a rapid expansion driven by the introduction of tandem mass spectrometry in at least 34 state programs. This technology is also used to detect disease markers beyond acylcarnitines and amino acids, as both primary and second-tier tests. In addition to analytic improvements, there is a trend toward the development of joint programs not limited to contiguous geographic areas, often based upon public-private partnerships. This review will summarize several new developments in the field that have occurred since early 2003 and will mention others likely to occur in the near future.

Online extraction-high performance liquid chromatography-diode array detector-quadrupole time-of-flight tandem mass spectrometry for rapid flavonoid profiling of Fructus aurantii immaturus.

PubMed

Tong, Runna; Peng, Mijun; Tong, Chaoying; Guo, Keke; Shi, Shuyun

2018-03-01

Chemical profiling of natural products by high performance liquid chromatography (HPLC) was critical for understanding of their clinical bioactivities, and sample pretreatment steps have been considered as a bottleneck for analysis. Currently, concerted efforts have been made to develop sample pretreatment methods with high efficiency, low solvent and time consumptions. Here, a simple and efficient online extraction (OLE) strategy coupled with HPLC-diode array detector-quadrupole time-of-flight tandem mass spectrometry (HPLC-DAD-QTOF-MS/MS) was developed for rapid chemical profiling. For OLE strategy, guard column inserted with ground sample (2 mg) instead of sample loop was connected with manual injection valve, in which components were directly extracted and transferred to HPLC-DAD-QTOF-MS/MS system only by mobile phase without any extra time, solvent, instrument and operation. By comparison with offline heat-reflux extraction for Fructus aurantii immaturus (Zhishi), OLE strategy presented higher extraction efficiency perhaps because of the high pressure and gradient elution mode. A total of eighteen flavonoids were detected according to their retention times, UV spectra, exact mass, and fragmentation ions in MS/MS spectra, and compound 9, natsudaidain-3-O-glucoside, was discovered in Zhishi for the first time. It is concluded that the developed OLE-HPLC-DAD-QTOF-MS/MS system offers new perspectives for rapid chemical profiling of natural products. Copyright © 2018. Published by Elsevier B.V.

Automated protein identification by the combination of MALDI MS and MS/MS spectra from different instruments.

PubMed

Levander, Fredrik; James, Peter

2005-01-01

The identification of proteins separated on two-dimensional gels is most commonly performed by trypsin digestion and subsequent matrix-assisted laser desorption ionization (MALDI) with time-of-flight (TOF). Recently, atmospheric pressure (AP) MALDI coupled to an ion trap (IT) has emerged as a convenient method to obtain tandem mass spectra (MS/MS) from samples on MALDI target plates. In the present work, we investigated the feasibility of using the two methodologies in line as a standard method for protein identification. In this setup, the high mass accuracy MALDI-TOF spectra are used to calibrate the peptide precursor masses in the lower mass accuracy AP-MALDI-IT MS/MS spectra. Several software tools were developed to automate the analysis process. Two sets of MALDI samples, consisting of 142 and 421 gel spots, respectively, were analyzed in a highly automated manner. In the first set, the protein identification rate increased from 61% for MALDI-TOF only to 85% for MALDI-TOF combined with AP-MALDI-IT. In the second data set the increase in protein identification rate was from 44% to 58%. AP-MALDI-IT MS/MS spectra were in general less effective than the MALDI-TOF spectra for protein identification, but the combination of the two methods clearly enhanced the confidence in protein identification.

Re-investigation of the fragmentation of protonated carotenoids by electrospray ionization and nanospray tandem mass spectrometry.

PubMed

Neto, Fausto Carnevale; Guaratini, Thais; Costa-Lotufo, Letícia; Colepicolo, Pio; Gates, Paul J; Lopes, Norberto Peporine

2016-07-15

Carotenoids are polyene isoprenoids with an important role in photosynthesis and photoprotection. Their characterization in biological matrices is a crucial subject for biochemical research. In this work we report the full fragmentation of 16 polyenes (carotenes and xanthophylls) by electrospray ionization tandem mass spectrometry (ESI-CID-MS/MS) and nanospray tandem mass spectrometry (nanoESI-CID-MS/MS). Analyses were carried out on a quadrupole time-of-flight (QTOF) mass spectrometer coupled with a nanoESI source and on a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer with an ESI source. The formulae of the product ions were determined by accurate-mass measurements. It is demonstrated that the fragmentation routes observed for the protonated carotenoids derive essentially from charge-remote fragmentations and pericyclic rearrangements, such as electrocyclic and retro-ene eliminations (assisted or not by a sigmatropic hydrogen shift). All mechanisms are dependent on cis-trans isomerization through the formation of several conjugated polyene carbocation intermediates. Some specific ions for the carotenoid epoxides were justified through formation of cyclic oxonium ions. Complete fragmentation pathways of protonated carotenoids by ESI- and nanoESI-CID-MS/MS provided structural information about functional groups, polyene chain and double bonds, and contribute to identification of carotenoids based on MS/MS fragmentation patterns. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A novel liquid chromatography-tandem mass spectrometry method for determination of menadione in human plasma after derivatization with 3-mercaptopropionic acid.

PubMed

Liu, Ruijuan; Wang, Mengmeng; Ding, Li

2014-10-01

Menadione (VK3), an essential fat-soluble naphthoquinone, takes very important physiological and pathological roles, but its detection and quantification is challenging. Herein, a new method was developed for quantification of VK3 in human plasma by liquid chromatography-tandem mass spectrometry (LC-MS/MS) after derivatization with 3-mercaptopropionic acid via Michael addition reaction. The derivative had been identified by the mass spectra and the derivatization conditions were optimized by considering different parameters. The method was demonstrated with high sensitivity and a low limit of quantification of 0.03 ng mL(-1) for VK3, which is about 33-fold better than that for the direct analysis of the underivatized compound. The method also had good precision and reproducibility. It was applied in the determination of basal VK3 in human plasma and a clinical pharmacokinetic study of menadiol sodium diphosphate. Furthermore, the method for the quantification of VK3 using LC-MS/MS was reported in this paper for the first time, and it will provide an important strategy for the further research on VK3 and menadione analogs. Copyright © 2014 Elsevier B.V. All rights reserved.

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

PubMed

Vaudel, Marc; Barsnes, Harald; Berven, Frode S; Sickmann, Albert; Martens, Lennart

2011-03-01

The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user-friendly, lightweight and open-source graphical user interface called SearchGUI (http://searchgui.googlecode.com), for configuring and running the freely available OMSSA (open mass spectrometry search algorithm) and X!Tandem search engines simultaneously. Freely available under the permissible Apache2 license, SearchGUI is supported on Windows, Linux and OSX. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simultaneous determination of four alkaloids in Lindera aggregata by ultra-high-pressure liquid chromatography-tandem mass spectrometry.

PubMed

Han, Zheng; Zheng, Yunliang; Chen, Na; Luan, Lianjun; Zhou, Changxin; Gan, Lishe; Wu, Yongjiang

2008-11-28

A new separation and quantification method using liquid chromatography under ultra-high-pressure in combination with tandem mass spectrometry (MS/MS) was developed for simultaneous determination of four alkaloids in Lindera aggregata. The analysis was performed on an Acquity UPLC BEH C(18) column (50mmx2.1mm, 1.7microm particle size; Waters, Milford, MA, USA) utilizing a gradient elution profile and a mobile phase consisting of (A) water containing 10mM ammonium acetate adjusted to pH 3 with acetic acid and (B) acetonitrile. An electrospray ionization (ESI)-tandem interface in the positive mode was employed prior to mass spectrometric detection. The calibration curve was linear over the range of 17.1-856ng for boldine, 42.4-2652ng for norboldine, 6.1-304ng for reticuline and 0.5-50ng for linderegatine, respectively. The average recoveries ranged from 99.2 to 101.4% with RSDs< or =2.7%. Then, four L. aggregata samples from different batches were analyzed using the established method. The results indicated that ultra-high-pressure liquid chromatography-tandem mass spectrometry provided improved chromatographic parameters resulting in significantly increased sample throughput including lower solvent consumption and lower limits of quantitation (LOQs) for most of target analytes compared to previous method employing conventional high-performance liquid chromatography (HPLC) separation. So, the established method was validated, sensitive and reliable for the determination of four alkaloids in L. aggregata.

A Robust Two-Dimensional Separation for Top-Down Tandem Mass Spectrometry of the Low-Mass Proteome

PubMed Central

Lee, Ji Eun; Kellie, John F.; Tran, John C.; Tipton, Jeremiah D.; Catherman, Adam D.; Thomas, Haylee M.; Ahlf, Dorothy R.; Durbin, Kenneth R.; Vellaichamy, Adaikkalam; Ntai, Ioanna; Marshall, Alan G.; Kelleher, Neil L.

2010-01-01

For fractionation of intact proteins by molecular weight (MW), a sharply improved two-dimensional (2D) separation is presented to drive reproducible and robust fractionation before top-down mass spectrometry of complex mixtures. The “GELFrEE” (i.e., gel-eluted liquid fraction entrapment electrophoresis) approach is implemented by use of Tris-glycine and Tris-tricine gel systems applied to human cytosolic and nuclear extracts from HeLa S3 cells, to achieve a MW-based fractionation of proteins from 5 to >100 kDa in 1 h. For top-down tandem mass spectroscopy (MS/MS) of the low-mass proteome (5–25 kDa), between 5 and 8 gel-elution (GE) fractions are sampled by nanocapillary-LC-MS/MS with 12 or 14.5 tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers. Single injections give about 40 detectable proteins, about half of which yield automated ProSight identifications. Reproducibility metrics of the system are presented, along with comparative analysis of protein targets in mitotic versus asynchronous cells. We forward this basic 2D approach to facilitate wider implementation of top-down mass spectrometry and a variety of other protein separation and/or characterization approaches. PMID:19747844

Profiling N-glycans of the egg jelly coat of the sea urchin Paracentrotus lividus by MALDI-TOF mass spectrometry and capillary liquid chromatography electrospray ionization-ion trap tandem mass spectrometry systems.

PubMed

Şahar, Umut; Deveci, Remziye

2017-05-01

Sea urchin eggs are surrounded by a carbohydrate-rich layer, termed the jelly coat, that consists of polysaccharides and glycoproteins. In the present study, we describe two mass spectrometric strategies to characterize the N-glycosylation of the Paracentrotus lividus egg jelly coat, which has an alecithal-type extracellular matrix like mammalian eggs. Egg jelly was isolated, lyophilized, and dialyzed, followed by peptide N-glycosidase F (PNGase-F) treatment to release N-glycans from their protein chain. These N-glycans were then derivatized by permethylation reaction, and analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and capillary liquid chromatography electrospray ionization-ion trap tandem mass spectroscopy (CapLC ESI-Ion trap-MS/MS). N-glycans in the egg jelly coat glycoproteins were indicated by sodiated molecules at m/z 1579.8, 1783.9, 1988.0, 2192.0, and 2397.1 for permethylated oligosaccharides on MALDI-TOF MS. Fragmentation and structural characterization of these oligosaccharides were performed by ESI-Ion trap MS/MS. Then, MALDI-TOF-MS and ESI-Ion trap-MS/MS spectra were interpreted using the GlycoWorkbench software suite, a tool for building, displaying, and profiling glycan masses, to identify the original oligosaccharide structures. The oligosaccharides of the isolated egg jelly coat were mainly of the high mannose type. © 2017 Wiley Periodicals, Inc.

Identification of Microorganisms by High Resolution Tandem Mass Spectrometry with Accurate Statistical Significance

NASA Astrophysics Data System (ADS)

Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y.; Drake, Steven K.; Gucek, Marjan; Suffredini, Anthony F.; Sacks, David B.; Yu, Yi-Kuo

2016-02-01

Correct and rapid identification of microorganisms is the key to the success of many important applications in health and safety, including, but not limited to, infection treatment, food safety, and biodefense. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is challenging correct microbial identification because of the large number of choices present. To properly disentangle candidate microbes, one needs to go beyond apparent morphology or simple `fingerprinting'; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptidome profiles of microbes to better separate them and by designing an analysis method that yields accurate statistical significance. Here, we present an analysis pipeline that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms. The proposed analysis pipeline has been implemented in MiCId, a freely available software for Microorganism Classification and Identification. MiCId is available for download at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

Advances in structure elucidation of small molecules using mass spectrometry

PubMed Central

Fiehn, Oliver

2010-01-01

The structural elucidation of small molecules using mass spectrometry plays an important role in modern life sciences and bioanalytical approaches. This review covers different soft and hard ionization techniques and figures of merit for modern mass spectrometers, such as mass resolving power, mass accuracy, isotopic abundance accuracy, accurate mass multiple-stage MS(n) capability, as well as hybrid mass spectrometric and orthogonal chromatographic approaches. The latter part discusses mass spectral data handling strategies, which includes background and noise subtraction, adduct formation and detection, charge state determination, accurate mass measurements, elemental composition determinations, and complex data-dependent setups with ion maps and ion trees. The importance of mass spectral library search algorithms for tandem mass spectra and multiple-stage MS(n) mass spectra as well as mass spectral tree libraries that combine multiple-stage mass spectra are outlined. The successive chapter discusses mass spectral fragmentation pathways, biotransformation reactions and drug metabolism studies, the mass spectral simulation and generation of in silico mass spectra, expert systems for mass spectral interpretation, and the use of computational chemistry to explain gas-phase phenomena. A single chapter discusses data handling for hyphenated approaches including mass spectral deconvolution for clean mass spectra, cheminformatics approaches and structure retention relationships, and retention index predictions for gas and liquid chromatography. The last section reviews the current state of electronic data sharing of mass spectra and discusses the importance of software development for the advancement of structure elucidation of small molecules. Electronic supplementary material The online version of this article (doi:10.1007/s12566-010-0015-9) contains supplementary material, which is available to authorized users. PMID:21289855

Direct determination of trace phthalate esters in alcoholic spirits by spray-inlet microwave plasma torch ionization tandem mass spectrometry.

PubMed

Miao, Meng; Zhao, Gaosheng; Xu, Li; Dong, Junguo; Cheng, Ping

2018-03-01

A direct analytical method based on spray-inlet microwave plasma torch tandem mass spectrometry was applied to simultaneously determine 4 phthalate esters (PAEs), namely, benzyl butyl phthalate, diethyl phthalate, dipentyl phthalate, and dodecyl phthalate with extremely high sensitivity in spirits without sample treatment. Among the 4 brands of spirit products, 3 kinds of PAE compounds were directly determined at very low concentrations from 1.30 to 114 ng·g -1 . Compared with other online and off-line methods, the spray-inlet microwave plasma torch tandem mass spectrometry technique is extremely simple, rapid, sensitive, and high efficient, providing an ideal screening tool for PAEs in spirits. Copyright © 2017 John Wiley & Sons, Ltd.

High-throughput quantification for a drug mixture in rat plasma-a comparison of Ultra Performance liquid chromatography/tandem mass spectrometry with high-performance liquid chromatography/tandem mass spectrometry.

PubMed

Yu, Kate; Little, David; Plumb, Rob; Smith, Brian

2006-01-01

A quantitative Ultra Performance liquid chromatography/tandem mass spectrometry (UPL/MS/MS) protocol was developed for a five-compound mixture in rat plasma. A similar high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) quantification protocol was developed for comparison purposes. Among the five test compounds, three preferred positive electrospray ionization (ESI) and two preferred negative ESI. As a result, both UPLC/MS/MS and HPLC/MS/MS analyses were performed by having the mass spectrometer collecting ESI multiple reaction monitoring (MRM) data in both positive and negative ion modes during a single injection. Peak widths for most standards were 4.8 s for the HPLC analysis and 2.4 s for the UPLC analysis. There were 17 to 20 data points obtained for each of the LC peaks. Compared with the HPLC/MS/MS method, the UPLC/MS/MS method offered 3-fold decrease in retention time, up to 10-fold increase in detected peak height, with 2-fold decrease in peak width. Limits of quantification (LOQs) for both HPLC and UPLC methods were evaluated. For UPLC/MS/MS analysis, a linear range up to four orders of magnitude was obtained with r2 values ranging from 0.991 to 0.998. The LOQs for the five analytes ranged from 0.08 to 9.85 ng/mL. Three levels of quality control (QC) samples were analyzed. For the UPLC/MS/MS protocol, the percent relative standard deviation (RSD%) for low QC (2 ng/mL) ranged from 3.42 to 8.67% (N = 18). The carryover of the UPLC/MS/MS protocol was negligible and the robustness of the UPLC/MS/MS system was evaluated with up to 963 QC injections. Copyright 2006 John Wiley & Sons, Ltd.

Determination of parabens in serum by liquid chromatography-tandem mass spectrometry: Correlation with lipstick use.

PubMed

Tahan, Gabriella Padovani; Santos, Nayara de Kássia Souza; Albuquerque, Ana Carolina; Martins, Isarita

2016-08-01

Parabens are the most widely used preservative and are considered to be relatively safe compounds. However, studies have demonstrated that they may have estrogenic activity, and there is ongoing debate regarding the safety and potential cancer risk of using products containing these compounds. In the present work, liquid chromatography-tandem mass spectrometry was applied to determine methylparaben and propylparaben concentrations in serum, and the results were correlated with lipstick application. Samples were analyzed using liquid-liquid extraction, followed by liquid chromatography-tandem mass spectrometry. The validation results demonstrated the linearity of the method over a range of 1-20 ng/mL, in addition to the method's precision and accuracy. A statistically significant difference was demonstrated between serum parabens in women who used lipstick containing these substances compared with those not using this cosmetic (p = 0.0005 and 0.0016, respectively), and a strong association was observed between serum parabens and lipstick use (Spearman correlation = 0.7202). Copyright © 2016 Elsevier Inc. All rights reserved.

Characterization of alkaloids in Sophora flavescens Ait. by high-performance liquid chromatography-electrospray ionization tandem mass spectrometry.

PubMed

Liu, Guoqiang; Dong, Jing; Wang, Hong; Hashi, Yuki; Chen, Shizhong

2011-04-05

Sophora flavescens Ait., a well-known Chinese herbal medicine, is widely used in clinical practice for the treatment of viral hepatitis, cancer, gastrointestinal hemorrhage, and skin diseases. This paper is the first report on a method based on the combined use of high-performance liquid chromatography, photodiode array detection, and electrospray ionization tandem mass spectrometry for the comprehensive and systematic separation and characterization of bioactive alkaloids in Sophora flavescens Ait. A total of 22 constituents were identified on the basis of the extracted ion chromatograms for different [M+H](+) ions of the alkaloids present in S. flavescens Ait. Among these, 5 constituents were unambiguously identified by comparing the experimental data on their retention times and MS(n) spectra with those of the authentic compounds, and 17 other constituents were tentatively identified on the basis of their MS(n) fragmentation behaviors and/or molecular weight information from literatures. Furthermore, some characteristic fragmentation pathways of the alkaloids in S. flavescens Ait. were detected and examined. This information may be useful for characterizing the bioactive alkaloids present in S. flavescens Ait. and for possible applications in formulations. Copyright © 2010 Elsevier B.V. All rights reserved.

Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y.; Drake, Steven K.; Gucek, Marjan; Sacks, David B.; Yu, Yi-Kuo

2018-06-01

Rapid and accurate identification and classification of microorganisms is of paramount importance to public health and safety. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is complicating correct microbial identification even in a simple sample due to the large number of candidates present. To properly untwine candidate microbes in samples containing one or more microbes, one needs to go beyond apparent morphology or simple "fingerprinting"; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptide-centric representations of microbes to better separate them and by augmenting our earlier analysis method that yields accurate statistical significance. Here, we present an updated analysis workflow that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using 226 MS/MS publicly available data files (each containing from 2500 to nearly 100,000 MS/MS spectra) and 4000 additional MS/MS data files, that the updated workflow can correctly identify multiple microbes at the genus and often the species level for samples containing more than one microbe. We have also shown that the proposed workflow computes accurate statistical significances, i.e., E values for identified peptides and unified E values for identified microbes. Our updated analysis workflow MiCId, a freely available software for Microorganism Classification and Identification, is available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html.

Rapid Classification and Identification of Multiple Microorganisms with Accurate Statistical Significance via High-Resolution Tandem Mass Spectrometry.

PubMed

Alves, Gelio; Wang, Guanghui; Ogurtsov, Aleksey Y; Drake, Steven K; Gucek, Marjan; Sacks, David B; Yu, Yi-Kuo

2018-06-05

Rapid and accurate identification and classification of microorganisms is of paramount importance to public health and safety. With the advance of mass spectrometry (MS) technology, the speed of identification can be greatly improved. However, the increasing number of microbes sequenced is complicating correct microbial identification even in a simple sample due to the large number of candidates present. To properly untwine candidate microbes in samples containing one or more microbes, one needs to go beyond apparent morphology or simple "fingerprinting"; to correctly prioritize the candidate microbes, one needs to have accurate statistical significance in microbial identification. We meet these challenges by using peptide-centric representations of microbes to better separate them and by augmenting our earlier analysis method that yields accurate statistical significance. Here, we present an updated analysis workflow that uses tandem MS (MS/MS) spectra for microbial identification or classification. We have demonstrated, using 226 MS/MS publicly available data files (each containing from 2500 to nearly 100,000 MS/MS spectra) and 4000 additional MS/MS data files, that the updated workflow can correctly identify multiple microbes at the genus and often the species level for samples containing more than one microbe. We have also shown that the proposed workflow computes accurate statistical significances, i.e., E values for identified peptides and unified E values for identified microbes. Our updated analysis workflow MiCId, a freely available software for Microorganism Classification and Identification, is available for download at https://www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads.html . Graphical Abstract ᅟ.

Advanced Laser Architecture for Two-Step Laser Tandem Mass Spectrometer

NASA Technical Reports Server (NTRS)

Fahey, Molly E.; Li, Steven X.; Yu, Anthony W.; Getty, Stephanie A.

2016-01-01

Future astrobiology missions will focus on planets with significant astrochemical or potential astrobiological features, such as small, primitive bodies and the icy moons of the outer planets that may host diverse organic compounds. These missions require advanced instrument techniques to fully and unambiguously characterize the composition of surface and dust materials. Laser desorptionionization mass spectrometry (LDMS) is an emerging instrument technology for in situ mass analysis of non-volatile sample composition. A recent Goddard LDMS advancement is the two-step laser tandem mass spectrometer (L2MS) instrument to address the need for future flight instrumentation to deconvolve complex organic signatures. The L2MS prototype uses a resonance enhanced multi-photon laser ionization mechanism to selectively detect aromatic species from a more complex sample. By neglecting the aliphatic and inorganic mineral signatures in the two-step mass spectrum, the L2MS approach can provide both mass assignments and clues to structural information for an in situ investigation of non-volatile sample composition. In this paper we will describe our development effort on a new laser architecture that is based on the previously flown Lunar Orbiter Laser Altimeter (LOLA) laser transmitter for the L2MS instrument. The laser provides two discrete midinfrared wavelengths (2.8 m and 3.4 m) using monolithic optical parametric oscillators and ultraviolet (UV) wavelength (266 nm) on a single laser bench with a straightforward development path toward flight readiness.

Comprehensive and accurate tracking of carbon origin of LC-tandem mass spectrometry collisional fragments for 13C-MFA.

PubMed

Kappelmann, Jannick; Klein, Bianca; Geilenkirchen, Petra; Noack, Stephan

2017-03-01

In recent years the benefit of measuring positionally resolved 13 C-labeling enrichment from tandem mass spectrometry (MS/MS) collisional fragments for improved precision of 13 C-Metabolic Flux Analysis ( 13 C-MFA) has become evident. However, the usage of positional labeling information for 13 C-MFA faces two challenges: (1) The mass spectrometric acquisition of a large number of potentially interfering mass transitions may hamper accuracy and sensitivity. (2) The positional identity of carbon atoms of product ions needs to be known. The present contribution addresses the latter challenge by deducing the maximal positional labeling information contained in LC-ESI-MS/MS spectra of product anions of central metabolism as well as product cations of amino acids. For this purpose, we draw on accurate mass spectrometry, selectively labeled standards, and published fragmentation pathways to structurally annotate all dominant mass peaks of a large collection of metabolites, some of which with a complete fragmentation pathway. Compiling all available information, we arrive at the most detailed map of carbon atom fate of LC-ESI-MS/MS collisional fragments yet, comprising 170 intense and structurally annotated product ions with unique carbon origin from 76 precursor ions of 72 metabolites. Our 13 C-data proof that heuristic fragmentation rules often fail to yield correct fragment structures and we expose common pitfalls in the structural annotation of product ions. We show that the positionally resolved 13 C-label information contained in the product ions that we structurally annotated allows to infer the entire isotopomer distribution of several central metabolism intermediates, which is experimentally demonstrated for malate using quadrupole-time-of-flight MS technology. Finally, the inclusion of the label information from a subset of these fragments improves flux precision in a Corynebacterium glutamicum model of the central carbon metabolism.

N-Linked Glycan Profiling of Mature Human Milk by High Performance Microfluidic Chip Liquid Chromatography Time-of-Flight Tandem Mass Spectrometry

PubMed Central

Dallas, David C.; Martin, William F.; Strum, John S.; Zivkovic, Angela M.; Smilowitz, Jennifer T.; Underwood, Mark A.; Affolter, Michael; Lebrilla, Carlito B.; German, J. Bruce

2015-01-01

N-linked glycans of skim human milk proteins were determined for three mothers. N-linked glycans are linked to immune defense, cell growth, and cell-cell adhesion, but their functions in human milk are undetermined. Protein-bound N-linked glycans were released with Peptidyl N-glycosidase F (PNGase F), enriched by graphitized carbon chromatography and analyzed with Chip-TOF MS. To be defined as N-glycans, compounds were required, in all three procedural replicates, to match, within 6 ppm, against a theoretical human N-glycan library, be at least two-fold higher in abundance in PNGase F-treated than in control samples. Fifty-two N-linked glycan compositions were identified and 24 were confirmed via tandem mass spectra analysis. Twenty-seven compositions have been found previously in human milk and 25 are novel compositions. By abundance, 84% of N-glycans were fucosylated and 47% were sialylated. The majority (70%) of total N-glycan abundance was comprised of N-glycans found in all three milk samples. PMID:21384928

Analysis of Human Plasma Metabolites across Different Liquid Chromatography - Mass Spectrometry Platforms: Cross-platform Transferable Chemical Signatures

PubMed Central

Telu, Kelly H.; Yan, Xinjian; Wallace, William E.; Stein, Stephen E.; Simón-Manso, Yamil

2016-01-01

RATIONALE The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different LC-MS platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. METHODS Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC-MS platforms using reversed phase chromatography and different chromatographic scales (nano, conventional and UHPLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). RESULTS Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (RSD < 2%); however, substantial differences were found in the LC-MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. CONLUSIONS Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable. PMID:26842580

Investigation of the neuroleptic drug haloperidol and its metabolites using tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Fang, Jian; Gorrod, John W.; Kajbaf, Mahmud; Lamb, John H.; Naylor, Stephen

1992-12-01

The in vitro metabolism of haloperidol, a clinically utilized neuroleptic drug, was investigated using guinea pig derived hepatic microsomal incubates. By employing a combination of reversed phase HPLC and tandem mass spectrometry, it was revealed that haloperidol was metabolized to at least eight different compounds, including the proposed dopaminergic toxin 4-(4-chlorophenyl)-1-[4-(4-fluorophenyl)-4- oxobutyl]-pyridinium species and an intermediate metabolite 4-(4-chlorophenyl)-1-[4-(4-fluorophenyl)-4- oxobutyl]- 1,2,3,6-tetrahydropyridine.

Analysis of human plasma metabolites across different liquid chromatography/mass spectrometry platforms: Cross-platform transferable chemical signatures.

PubMed

Telu, Kelly H; Yan, Xinjian; Wallace, William E; Stein, Stephen E; Simón-Manso, Yamil

2016-03-15

The metabolite profiling of a NIST plasma Standard Reference Material (SRM 1950) on different liquid chromatography/mass spectrometry (LC/MS) platforms showed significant differences. Although these findings suggest caution when interpreting metabolomics results, the degree of overlap of both profiles allowed us to use tandem mass spectral libraries of recurrent spectra to evaluate to what extent these results are transferable across platforms and to develop cross-platform chemical signatures. Non-targeted global metabolite profiles of SRM 1950 were obtained on different LC/MS platforms using reversed-phase chromatography and different chromatographic scales (conventional HPLC, UHPLC and nanoLC). The data processing and the metabolite differential analysis were carried out using publically available (XCMS), proprietary (Mass Profiler Professional) and in-house software (NIST pipeline). Repeatability and intermediate precision showed that the non-targeted SRM 1950 profiling was highly reproducible when working on the same platform (relative standard deviation (RSD) <2%); however, substantial differences were found in the LC/MS patterns originating on different platforms or even using different chromatographic scales (conventional HPLC, UHPLC and nanoLC) on the same platform. A substantial degree of overlap (common molecular features) was also found. A procedure to generate consistent chemical signatures using tandem mass spectral libraries of recurrent spectra is proposed. Different platforms rendered significantly different metabolite profiles, but the results were highly reproducible when working within one platform. Tandem mass spectral libraries of recurrent spectra are proposed to evaluate the degree of transferability of chemical signatures generated on different platforms. Chemical signatures based on our procedure are most likely cross-platform transferable. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA.

A Distonic Radical-Ion for Detection of Traces of Adventitious Molecular Oxygen (O2) in Collision Gases Used in Tandem Mass Spectrometers

NASA Astrophysics Data System (ADS)

Jariwala, Freneil B.; Hibbs, John A.; Weisbecker, Carl S.; Ressler, John; Khade, Rahul L.; Zhang, Yong; Attygalle, Athula B.

2014-09-01

We describe a diagnostic ion that enables rapid semiquantitative evaluation of the degree of oxygen contamination in the collision gases used in tandem mass spectrometers. Upon collision-induced dissociation (CID), the m/z 359 positive ion generated from the analgesic etoricoxib undergoes a facile loss of a methyl sulfone radical [•SO2(CH3); 79-Da] to produce a distonic radical cation of m/z 280. The product-ion spectrum of this m/z 280 ion, recorded under low-energy activation on tandem-in-space QqQ or QqTof mass spectrometers using nitrogen from a generator as the collision gas, or tandem-in-time ion-trap (LCQ, LTQ) mass spectrometers using purified helium as the buffer gas, showed two unexpected peaks at m/z 312 and 295. This enigmatic m/z 312 ion, which bears a mass-to-charge ratio higher than that of the precursor ion, represented an addition of molecular oxygen (O2) to the precursor ion. The exceptional affinity of the m/z 280 radical cation towards oxygen was deployed to develop a method to determine the oxygen content in collision gases.

Expert system for computer-assisted annotation of MS/MS spectra.

PubMed

Neuhauser, Nadin; Michalski, Annette; Cox, Jürgen; Mann, Matthias

2012-11-01

An important step in mass spectrometry (MS)-based proteomics is the identification of peptides by their fragment spectra. Regardless of the identification score achieved, almost all tandem-MS (MS/MS) spectra contain remaining peaks that are not assigned by the search engine. These peaks may be explainable by human experts but the scale of modern proteomics experiments makes this impractical. In computer science, Expert Systems are a mature technology to implement a list of rules generated by interviews with practitioners. We here develop such an Expert System, making use of literature knowledge as well as a large body of high mass accuracy and pure fragmentation spectra. Interestingly, we find that even with high mass accuracy data, rule sets can quickly become too complex, leading to over-annotation. Therefore we establish a rigorous false discovery rate, calculated by random insertion of peaks from a large collection of other MS/MS spectra, and use it to develop an optimized knowledge base. This rule set correctly annotates almost all peaks of medium or high abundance. For high resolution HCD data, median intensity coverage of fragment peaks in MS/MS spectra increases from 58% by search engine annotation alone to 86%. The resulting annotation performance surpasses a human expert, especially on complex spectra such as those of larger phosphorylated peptides. Our system is also applicable to high resolution collision-induced dissociation data. It is available both as a part of MaxQuant and via a webserver that only requires an MS/MS spectrum and the corresponding peptides sequence, and which outputs publication quality, annotated MS/MS spectra (www.biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions.

Expert System for Computer-assisted Annotation of MS/MS Spectra*

PubMed Central

Neuhauser, Nadin; Michalski, Annette; Cox, Jürgen; Mann, Matthias

2012-01-01

An important step in mass spectrometry (MS)-based proteomics is the identification of peptides by their fragment spectra. Regardless of the identification score achieved, almost all tandem-MS (MS/MS) spectra contain remaining peaks that are not assigned by the search engine. These peaks may be explainable by human experts but the scale of modern proteomics experiments makes this impractical. In computer science, Expert Systems are a mature technology to implement a list of rules generated by interviews with practitioners. We here develop such an Expert System, making use of literature knowledge as well as a large body of high mass accuracy and pure fragmentation spectra. Interestingly, we find that even with high mass accuracy data, rule sets can quickly become too complex, leading to over-annotation. Therefore we establish a rigorous false discovery rate, calculated by random insertion of peaks from a large collection of other MS/MS spectra, and use it to develop an optimized knowledge base. This rule set correctly annotates almost all peaks of medium or high abundance. For high resolution HCD data, median intensity coverage of fragment peaks in MS/MS spectra increases from 58% by search engine annotation alone to 86%. The resulting annotation performance surpasses a human expert, especially on complex spectra such as those of larger phosphorylated peptides. Our system is also applicable to high resolution collision-induced dissociation data. It is available both as a part of MaxQuant and via a webserver that only requires an MS/MS spectrum and the corresponding peptides sequence, and which outputs publication quality, annotated MS/MS spectra (www.biochem.mpg.de/mann/tools/). It provides expert knowledge to beginners in the field of MS-based proteomics and helps advanced users to focus on unusual and possibly novel types of fragment ions. PMID:22888147

Structure revision of hupehensis saponin F and G and characterization of new trace triterpenoid saponins from Anemone hupehensis by tandem electrospray ionization mass spectrometry.

PubMed

Li, Fu; Liu, Xin; Tang, Minghai; Chen, Bin; Ding, Lisheng; Chen, Lijuan; Wang, Mingkui

2012-05-15

Electrospray ionization ion-trap tandem mass spectrometry (ESI-MS(n)) was first employed for reinvestigating the structures of hupehensis saponin F and G previously isolated from Anemone hupehensis in our lab. Hupehensis saponin G was determined to contain one more trisaccharide unit (Rha-(1→4)-Glc-(1→6)-Glc-), not a glucose residue, than saponin F based on their molecular weights deduced from their [M+Na](+) ions in ESI-MS spectra. The (2,4)A(4α)-ion at m/z 551.3 formed by retro-Diels-Alder (RDA) rearrangement in positive mode illustrated that the C-28 sugar chains of the two saponins were composed of trisaccharide repeating moieties with (1→4) linkages rather than (1→3) linkages. The interpretation of 2D-NMR spectra of the two compounds also confirmed the results obtained by ESI-MS(n). Moreover, from the water soluble part of A. hupehensis, two novel triterpene saponins were tentatively characterized to contain 4 and 5 (1→4)-linked above trisaccharide repeating moieties at C-28 position according to their ESI-MS(n) behaviors, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

Tandem mass spectrometry in combination with product ion mobility for the identification of phospholipids

DOE PAGES

Berry, Karin A. Zemski; Barkley, Robert M.; Berry, Joseph J.; ...

2016-11-29

Concerted tandem and traveling wave ion mobility mass spectrometry (CTS analysis) is a unique method that results in a four-dimensional data set including nominal precursor ion mass, product ion mobility, accurate mass of product ion, and ion abundance. This nontargeted lipidomics CTS approach was applied in both positive- and negative-ion mode to phospholipids present in human serum, and the data set was used to evaluate the value of product ion mobility in identifying lipids in a complex mixture. As a result, it was determined that the combination of diagnostic product ions and unique collisional cross-section values of product ions ismore » a powerful tool in the structural identification of lipids in a complex biological sample.« less

Tandem mass spectrometry in combination with product ion mobility for the identification of phospholipids

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

Berry, Karin A. Zemski; Barkley, Robert M.; Berry, Joseph J.

Concerted tandem and traveling wave ion mobility mass spectrometry (CTS analysis) is a unique method that results in a four-dimensional data set including nominal precursor ion mass, product ion mobility, accurate mass of product ion, and ion abundance. This nontargeted lipidomics CTS approach was applied in both positive- and negative-ion mode to phospholipids present in human serum, and the data set was used to evaluate the value of product ion mobility in identifying lipids in a complex mixture. As a result, it was determined that the combination of diagnostic product ions and unique collisional cross-section values of product ions ismore » a powerful tool in the structural identification of lipids in a complex biological sample.« less

Optical and Near-infrared Spectra of σ Orionis Isolated Planetary-mass Objects

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

Zapatero Osorio, M. R.; Béjar, V. J. S.; Ramírez, K. Peña, E-mail: mosorio@cab.inta-csic.es, E-mail: vbejar@iac.es, E-mail: karla.pena@uantof.cl

We have obtained low-resolution optical (0.7–0.98 μ m) and near-infrared (1.11–1.34 μ m and 0.8–2.5 μ m) spectra of 12 isolated planetary-mass candidates ( J = 18.2–19.9 mag) of the 3 Myr σ Orionis star cluster with the aim of determining the spectroscopic properties of very young, substellar dwarfs and assembling a complete cluster mass function. We have classified our targets by visual comparison with high- and low-gravity standards and by measuring newly defined spectroscopic indices. We derived L0–L4.5 and M9–L2.5 using high- and low-gravity standards, respectively. Our targets reveal clear signposts of youth, thus corroborating their cluster membership andmore » planetary masses (6–13 M {sub Jup}). These observations complete the σ Orionis mass function by spectroscopically confirming the planetary-mass domain to a confidence level of ∼75%. The comparison of our spectra with BT-Settl solar metallicity model atmospheres yields a temperature scale of 2350–1800 K and a low surface gravity of log g ≈ 4.0 [cm s{sup −2}], as would be expected for young planetary-mass objects. We discuss the properties of the cluster’s least-massive population as a function of spectral type. We have also obtained the first optical spectrum of S Ori 70, a T dwarf in the direction of σ Orionis. Our data provide reference optical and near-infrared spectra of very young L dwarfs and a mass function that may be used as templates for future studies of low-mass substellar objects and exoplanets. The extrapolation of the σ Orionis mass function to the solar neighborhood may indicate that isolated planetary-mass objects with temperatures of ∼200–300 K and masses in the interval 6–13 M {sub Jup} may be as numerous as very low-mass stars.« less

Determination of the location of positive charges in gas-phase polypeptide polycations by tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Kjeldsen, Frank; Savitski, Mikhail M.; Adams, Christopher M.; Zubarev, Roman A.

2006-06-01

Location of protonated sites in electrospray-ionized gas-phase peptides and proteins was performed with tandem mass spectrometry using ion activation by both electron capture dissociation (ECD) and collisional activation dissociation (CAD). Charge-carrying sites were assigned based on the increment in the charge state of fragment ions compared to that of the previous fragment in the same series. The property of ECD to neutralize preferentially the least basic site was confirmed by the analysis of three thousand ECD mass spectra of doubly charged tryptic peptides. Multiply charged cations of bradykinin, neurotensin and melittin were studied in detail. For n+ precursors, ECD revealed the positions of (n - 1) most basic sites, while CAD could in principle locate alln charges. However, ECD introduced minimal proton mobilization and produced more conclusive data than CAD, for which N- and C-terminal data often disagreed. Consistent with the dominance of one charge conformer and its preservation in ECD, the average charge states of complementary fragments of n+ ions almost always added up to (n - 1)+, while the similar figure in CAD often deviated from n+, indicating extensive charge isomerization under collisional excitation. For bradykinin and neurotensin, the charge assignments were largely in agreement with the intrinsic gas-phase basicity of the respective amino acid residues. For melittin ions in higher charge states, ECD revealed the charging at both intrinsically basic as well as at less basic residues, which was attributed to charge sharing with other groups due to the presence of secondary and higher order structures in this larger polypeptide.

Measuring masses of large biomolecules and bioparticles using mass spectrometric techniques.

PubMed

Peng, Wen-Ping; Chou, Szu-Wei; Patil, Avinash A

2014-07-21

Large biomolecules and bioparticles play a vital role in biology, chemistry, biomedical science and physics. Mass is a critical parameter for the characterization of large biomolecules and bioparticles. To achieve mass analysis, choosing a suitable ion source is the first step and the instruments for detecting ions, mass analyzers and detectors should also be considered. Abundant mass spectrometric techniques have been proposed to determine the masses of large biomolecules and bioparticles and these techniques can be divided into two categories. The first category measures the mass (or size) of intact particles, including single particle quadrupole ion trap mass spectrometry, cell mass spectrometry, charge detection mass spectrometry and differential mobility mass analysis; the second category aims to measure the mass and tandem mass of biomolecular ions, including quadrupole ion trap mass spectrometry, time-of-flight mass spectrometry, quadrupole orthogonal time-of-flight mass spectrometry and orbitrap mass spectrometry. Moreover, algorithms for the mass and stoichiometry assignment of electrospray mass spectra are developed to obtain accurate structure information and subunit combinations.

Stable isotope labeling tandem mass spectrometry (SILT) to quantify protein production and clearance rates

PubMed Central

Bateman, Randall J.; Munsell, Ling Y.; Chen, Xianghong; Holtzman, David M.; Yarasheski, Kevin E.

2007-01-01

In all biological systems, protein amount is a function of the rate of production and clearance. The speed of a response to a disturbance in protein homeostasis is determined by turnover rate. Quantifying alterations in protein synthesis and clearance rates is vital to understanding disease pathogenesis (e.g., aging, inflammation). No methods exist for quantifying production and clearance rates of low abundance (femtomole) proteins in vivo. We describe a novel, mass spectrometry-based method for quantitating low abundance protein synthesis and clearance rates in vitro and in vivo in animals and humans. The utility of this method is demonstrated with amyloid-beta (Aß), an important low abundance protein involved in Alzheimer's disease pathogenesis. We used in vivo stable isotope labeling, immunoprecipitation of Aß from cerebrospinal fluid, and quantitative liquid chromatography electrospray-ionization tandem mass spectrometry (LC-ESI-tandem MS) to quantify human Aß protein production and clearance rates. The method is sensitive and specific for stable isotope labeled amino acid incorporation into CNS (± 1% accuracy). This in vivo method can be used to identify pathophysiologic changes in protein metabolism; and may serve as a biomarker for monitoring disease risk, progression, or response to novel therapeutic agents. The technique is adaptable to other macromolecules, such as carbohydrates or lipids. PMID:17383190

Correction to: Top Down Tandem Mass Spectrometric Analysis of a Chemically Modified Rough-Type Lipopolysaccharide Vaccine Candidate

NASA Astrophysics Data System (ADS)

Oyler, Benjamin L.; Khan, Mohd M.; Smith, Donald F.; Harberts, Erin M.; Kilgour, David P. A.; Ernst, Robert K.; Cross, Alan S.; Goodlett, David R.

2018-04-01

In the preceding article "Top Down Tandem Mass Spectrometric Analysis of a Chemically Modified Rough-Type Lipopolysaccharide Vaccine Candidate" by Oyler et al., an error in the J5 E. coli LPS chemical structure (Figs. 2 and 4) was introduced and propagated into the final revision.

Capillary-HPLC with tandem mass spectrometry in analysis of alkaloid dyestuffs - a new approach.

PubMed

Dąbrowski, Damian; Lech, Katarzyna; Jarosz, Maciej

2018-05-01

Development of the identification method of alkaloid compounds in Amur cork tree as well as not examined so far Oregon grape and European Barberry shrubs are presented. The novel approach to separation of alkaloids was applied and the capillary-high-performance liquid chromatography (capillary-HPLC) system was used, which has never previously been reported for alkaloid-based dyestuffs analysis. Its optimization was conducted with three different stationary phases (unmodified octadecylsilane-bonded silica, octadecylsilane modified with polar groups and silica-bonded pentaflourophenyls) as well as with different solvent buffers. Detection of the isolated compounds was carried out using diode-array detector (DAD) and tandem mass spectrometer with electrospray ionization (ESI MS/MS). The working parameters of ESI were optimized, whereas the multiple reactions monitoring (MRM) parameters of MS/MS detection were chosen based on the product ion spectra of the quasi-molecular ions. Calibration curve of berberine has been estimated (y = 1712091x + 4785.03 with the correlation coefficient 0.9999). Limit of detection and limit of quantification were calculated to be 3.2 and 9.7 ng/mL, respectively. Numerous alkaloids (i.e., berberine, jatrorrhizine and magnoflorine, as well as phellodendrine, menisperine and berbamine) were identified in the extracts from alkaloid plants and silk and wool fibers dyed with these dyestuffs, among them their markers. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Compound annotation in liquid chromatography/high-resolution mass spectrometry based metabolomics: robust adduct ion determination as a prerequisite to structure prediction in electrospray ionization mass spectra.

PubMed

Jaeger, Carsten; Méret, Michaël; Schmitt, Clemens A; Lisec, Jan

2017-08-15

A bottleneck in metabolic profiling of complex biological extracts is confident, non-supervised annotation of ideally all contained, chemically highly diverse small molecules. Recent computational strategies combining sum formula prediction with in silico fragmentation achieve confident de novo annotation, once the correct neutral mass of a compound is known. Current software solutions for automated adduct ion assignment, however, are either publicly unavailable or have been validated against only few experimental electrospray ionization (ESI) mass spectra. We here present findMAIN (find Main Adduct IoN), a new heuristic approach for interpreting ESI mass spectra. findMAIN scores MS 1 spectra based on explained intensity, mass accuracy and isotope charge agreement of adducts and related ionization products and annotates peaks of the (de)protonated molecule and adduct ions. The approach was validated against 1141 ESI positive mode spectra of chemically diverse standard compounds acquired on different high-resolution mass spectrometric instruments (Orbitrap and time-of-flight). Robustness against impure spectra was evaluated. Correct adduct ion assignment was achieved for up to 83% of the spectra. Performance was independent of compound class and mass spectrometric platform. The algorithm proved highly tolerant against spectral contamination as demonstrated exemplarily for co-eluting compounds as well as systematically by pairwise mixing of spectra. When used in conjunction with MS-FINDER, a state-of-the-art sum formula tool, correct sum formulas were obtained for 77% of spectra. It outperformed both 'brute force' approaches and current state-of-the-art annotation packages tested as potential alternatives. Limitations of the heuristic pertained to poorly ionizing compounds and cationic compounds forming [M] + ions. A new, validated approach for interpreting ESI mass spectra is presented, filling a gap in the nontargeted metabolomics workflow. It is freely available

Characterization of the components of meleumycin by liquid chromatography with photo-diode array detection and electrospray ionization tandem mass spectrometry.

PubMed

Wang, Ming-Juan; Li, Ya-Ping; Wang, Yan; Li, Jin; Hu, Chang-Qin; Hoogmartens, Jos; Van Schepdael, Ann; Adams, Erwin

2013-10-01

Reversed-phase liquid chromatography coupled with photo-diode array (PDA) detection and electrospray ionization tandem mass spectrometry (ESI-MS/MS) was used to characterize the components of meleumycin, a 16-membered macrolide antibiotic produced by fermentation. In total 31 components were characterized in commercial samples, including 12 impurities that had never been reported before and 12 others that were partially characterized. The structures of these unknown compounds were deduced by comparison of their fragmentation patterns with those of known components. Their ultraviolet spectra and chromatographic behavior were used to confirm the proposed structures: e.g. λmax shift from 232 nm to 282 nm would indicate the presence of an α-, β-, γ-, δ-unsaturated ketone instead of a normal α-, β-, γ-, δ-unsaturated alcohol in the 16-membered ring of the examined components. Compared to other methods, this LC/MS(n) method is particularly advantageous to characterize minor components at trace levels in multi-components antibiotics, in terms of sensitivity and efficiency. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes.

PubMed

Lu, Jonathan; Trnka, Michael J; Roh, Soung-Hun; Robinson, Philip J J; Shiau, Carrie; Fujimori, Danica Galonic; Chiu, Wah; Burlingame, Alma L; Guan, Shenheng

2015-12-01

Native electrospray-ionization mass spectrometry (native MS) measures biomolecules under conditions that preserve most aspects of protein tertiary and quaternary structure, enabling direct characterization of large intact protein assemblies. However, native spectra derived from these assemblies are often partially obscured by low signal-to-noise as well as broad peak shapes because of residual solvation and adduction after the electrospray process. The wide peak widths together with the fact that sequential charge state series from highly charged ions are closely spaced means that native spectra containing multiple species often suffer from high degrees of peak overlap or else contain highly interleaved charge envelopes. This situation presents a challenge for peak detection, correct charge state and charge envelope assignment, and ultimately extraction of the relevant underlying mass values of the noncovalent assemblages being investigated. In this report, we describe a comprehensive algorithm developed for addressing peak detection, peak overlap, and charge state assignment in native mass spectra, called PeakSeeker. Overlapped peaks are detected by examination of the second derivative of the raw mass spectrum. Charge state distributions of the molecular species are determined by fitting linear combinations of charge envelopes to the overall experimental mass spectrum. This software is capable of deconvoluting heterogeneous, complex, and noisy native mass spectra of large protein assemblies as demonstrated by analysis of (1) synthetic mononucleosomes containing severely overlapping peaks, (2) an RNA polymerase II/α-amanitin complex with many closely interleaved ion signals, and (3) human TriC complex containing high levels of background noise. Graphical Abstract ᅟ.

MetaUniDec: High-Throughput Deconvolution of Native Mass Spectra

NASA Astrophysics Data System (ADS)

Reid, Deseree J.; Diesing, Jessica M.; Miller, Matthew A.; Perry, Scott M.; Wales, Jessica A.; Montfort, William R.; Marty, Michael T.

2018-04-01

The expansion of native mass spectrometry (MS) methods for both academic and industrial applications has created a substantial need for analysis of large native MS datasets. Existing software tools are poorly suited for high-throughput deconvolution of native electrospray mass spectra from intact proteins and protein complexes. The UniDec Bayesian deconvolution algorithm is uniquely well suited for high-throughput analysis due to its speed and robustness but was previously tailored towards individual spectra. Here, we optimized UniDec for deconvolution, analysis, and visualization of large data sets. This new module, MetaUniDec, centers around a hierarchical data format 5 (HDF5) format for storing datasets that significantly improves speed, portability, and file size. It also includes code optimizations to improve speed and a new graphical user interface for visualization, interaction, and analysis of data. To demonstrate the utility of MetaUniDec, we applied the software to analyze automated collision voltage ramps with a small bacterial heme protein and large lipoprotein nanodiscs. Upon increasing collisional activation, bacterial heme-nitric oxide/oxygen binding (H-NOX) protein shows a discrete loss of bound heme, and nanodiscs show a continuous loss of lipids and charge. By using MetaUniDec to track changes in peak area or mass as a function of collision voltage, we explore the energetic profile of collisional activation in an ultra-high mass range Orbitrap mass spectrometer. [Figure not available: see fulltext.

A tandem mass spectrometric method for singlet oxygen measurement.

PubMed

Karonen, Maarit; Mattila, Heta; Huang, Ping; Mamedov, Fikret; Styring, Stenbjörn; Tyystjärvi, Esa

2014-01-01

Singlet oxygen, a harmful reactive oxygen species, can be quantified with the substance 2,2,6,6-tetramethylpiperidine (TEMP) that reacts with singlet oxygen, forming a stable nitroxyl radical (TEMPO). TEMPO has earlier been quantified with electron paramagnetic resonance (EPR) spectroscopy. In this study, we designed an ultra-high-performance liquid chromatographic-tandem mass spectrometric (UHPLC-ESI-MS/MS) quantification method for TEMPO and showed that the method based on multiple reaction monitoring (MRM) can be used for the measurements of singlet oxygen from both nonbiological and biological samples. Results obtained with both UHPLC-ESI-MS/MS and EPR methods suggest that plant thylakoid membranes produce 3.7 × 10(-7) molecules of singlet oxygen per chlorophyll molecule in a second when illuminated with the photosynthetic photon flux density of 2000 μmol m(-2 ) s(-1). © 2014 The American Society of Photobiology.

Screening and analysis of the multiple absorbed bioactive components and metabolites in rat plasma after oral administration of Jitai tablets by high-performance liquid chromatography/diode-array detection coupled with electrospray ionization tandem mass spectrometry.

PubMed

Wang, Shu-Ping; Liu, Lei; Wang, Ling-Ling; Jiang, Peng; Zhang, Ji-Quan; Zhang, Wei-Dong; Liu, Run-Hui

2010-06-15

Based on the serum pharmacochemistry technique and high-performance liquid chromatography/diode-array detection (HPLC/DAD) coupled with electrospray tandem mass spectrometry (HPLC/ESI-MS/MS), a method for screening and analysis of the multiple absorbed bioactive components and metabolites of Jitai tablets (JTT) in orally dosed rat plasma was developed. Plasma was treated by methanol precipitation prior to liquid chromatography, and the separation was carried out on a Symmetry C(18) column, with a linear gradient (0.1% formic acid/water/acetonitrile). Mass spectra were acquired in negative and positive ion modes, respectively. As a result, 26 bioactive components originated from JTT and 5 metabolites were tentatively identified in orally dosed rat plasma by comparing their retention times and MS spectra with those of authentic standards and literature data. It is concluded that an effective and reliable analytical method was set up for screening the bioactive components of Chinese herbal medicine, which provided a meaningful basis for further pharmacology and active mechanism research of JTT. Copyright (c) 2010 John Wiley & Sons, Ltd.

Simultaneous quantification of GM1 and GM2 gangliosides by isotope dilution tandem mass spectrometry.

PubMed

Gu, Jianghong; Tifft, Cynthia J; Soldin, Steven J

2008-04-01

Gangliosides (GGs) are considered as diagnostic biomarkers and therapeutic targets and agents. The goal of this study was to develop a tandem mass spectrometry (MS/MS) method for the simultaneous measurement of both GM1 and GM2 gangliosides in human cerebrospinal fluid (CSF) samples in order to be able to determine their concentrations in patients with Tay-Sachs and Sandhoff disease and assess whether drugs or transplantation affect their concentrations. An API-4000 tandem mass spectrometer equipped with TurboIonSpray source and Shimadzu HPLC system was employed to perform the analysis using isotope dilution with deuterium labeled internal standards. To a 1.5 mL conical plastic Eppendorf centrifuge tube, 40 microL of human CSF sample was added and mixed with 400 microL of internal standard solution for deproteinization. After centrifugation, 100 microL of supernatant was injected onto a C-18 column. After a 2.5 min wash, the switching valve was activated and the analytes were eluted from the column with a water/methanol gradient into the MS/MS system. Quantification by multiple reaction-monitoring (MRM) analysis was performed in the negative mode. The within-day coefficients of variation were <3% for GM1 and <2% for GM2 and the between-day coefficients of variation were <5% for both GM1 and GM2 at all concentrations tested. Accuracy ranged between 98% and 102% for both analytes. Good linearity was also obtained within the concentration range of 10-200 ng/mL (6.5-129.3 nmol/L) for GM1 and 5-100 ng/mL (3.6-72.3 nmol/L) for GM2 (r> or =0.995). A new simple, accurate, and fast isotope dilution tandem mass spectrometry method was developed for the simultaneous quantification of GM1 and GM2 gangliosides in a small amount of human CSF. Concentrations were measured in "normal" CSF and in CSF from patients with Tay-Sachs disease.

Determination of nitroaromatic explosives and their degradation products in unsaturated-zone water samples by high-performance liquid chromatography with photodiode-array, mass spectrometric, and tandem mass spectrometric detection

USGS Publications Warehouse

Gates, Paul M.; Furlong, E.T.; Dorsey, T.F.; Burkhardt, M.R.

1996-01-01

Mass spectrometry and tandem mass spectrometry, coupled by a thermospray interface to a high-performance liguid chromatography system and equipped with a photodiode array detector, were used to determine the presence of nitroaromatic explosives and their degradation products in USA unsaturated-zone water samples. Using this approach, the lower limits of quantitation for explosives determined by mass spectrometry in this study typically ranged from 10 to 100 ng/l.

Determination of effective mass of heavy hole from phonon-assisted excitonic luminescence spectra in ZnO

NASA Astrophysics Data System (ADS)

Shi, S. L.; Xu, S. J.

2011-03-01

Longitudinal optical (LO) phonon-assisted luminescence spectra of free excitons in high-quality ZnO crystal were investigated both experimentally and theoretically. By using the rigorous Segall-Mahan model based on the Green's function, good agreement between the experimental emission spectra involving one or two LO phonons and theoretical spectra can be achieved when only one adjustable parameter (effective mass of heavy hole) was adopted. This leads to determination of the heavy-hole effective mass mh⊥ = (0.8 m0 and mh∥ = 5.0 m0) in ZnO. Influence of anisotropic effective masses of heavy holes on the phonon sidebands is also discussed.

Pre-processing liquid chromatography/high-resolution mass spectrometry data: extracting pure mass spectra by deconvolution from the invariance of isotopic distribution.

PubMed

Krishnan, Shaji; Verheij, Elwin E R; Bas, Richard C; Hendriks, Margriet W B; Hankemeier, Thomas; Thissen, Uwe; Coulier, Leon

2013-05-15

Mass spectra obtained by deconvolution of liquid chromatography/high-resolution mass spectrometry (LC/HRMS) data can be impaired by non-informative mass-over-charge (m/z) channels. This impairment of mass spectra can have significant negative influence on further post-processing, like quantification and identification. A metric derived from the knowledge of errors in isotopic distribution patterns, and quality of the signal within a pre-defined mass chromatogram block, has been developed to pre-select all informative m/z channels. This procedure results in the clean-up of deconvoluted mass spectra by maintaining the intensity counts from m/z channels that originate from a specific compound/molecular ion, for example, molecular ion, adducts, (13) C-isotopes, multiply charged ions and removing all m/z channels that are not related to the specific peak. The methodology has been successfully demonstrated for two sets of high-resolution LC/MS data. The approach described is therefore thought to be a useful tool in the automatic processing of LC/HRMS data. It clearly shows the advantages compared to other approaches like peak picking and de-isotoping in the sense that all information is retained while non-informative data is removed automatically. Copyright © 2013 John Wiley & Sons, Ltd.

Detailed phenolic composition of Vidal grape pomace by ultrahigh-performance liquid chromatography-tandem mass spectrometry.

PubMed

Luo, Lanxin; Cui, Yan; Zhang, Shuting; Li, Lingxi; Suo, Hao; Sun, Baoshan

2017-11-15

Vidal Blanc grape (Vitis vinifera cv.) is the predominant white grape variety used for the production of icewine in China's Liaoning province. In this paper, the development and validation of the method by ultrahigh-performance liquid chromatography-tandem mass spectrometry has been performed for determination of the detailed phenolic composition in the skin, seed and stem of Vidal grapes. The validation of the method was realized by calculating the linearity, repeatability, precision, stability and the limits of detection (LOD) and quantification (LOQ) of standard solutions. All the curves exhibited good linearity (r 2 >0.9997) and the LOD and LOQ were in the range of 0.002-0.025 and 0.006-0.086μg/ml, respectively. Good repeatability (RSD<4.3%) and stability (RSD<3.7%) were also found. Results confirmed that the developed method was more effective and sensitive for simultaneous determination of the major phenolic compounds in Vidal grape pomace. The optimized and validated method of ultrahigh-performance liquid chromatography tandem two complementary techniques, fourier transform ion cyclotron resonance mass spectrometry and triple-quadrupole mass spectrometry, allowed to identify and quantify up to 35 phenolic compounds in Vidal grape pomace, which has, as far as we know, been reported this grapevine variety for the first time. Seeds, skins and stems exhibited different qualitative and quantitative phenolic profiles. These results provided useful information for recovery of phenolic antioxidants from different parts of icewine pomace. Copyright © 2017. Published by Elsevier B.V.

Mass spectra features of biomass burning boiler and coal burning boiler emitted particles by single particle aerosol mass spectrometer.

PubMed

Xu, Jiao; Li, Mei; Shi, Guoliang; Wang, Haiting; Ma, Xian; Wu, Jianhui; Shi, Xurong; Feng, Yinchang

2017-11-15

In this study, single particle mass spectra signatures of both coal burning boiler and biomass burning boiler emitted particles were studied. Particle samples were suspended in clean Resuspension Chamber, and analyzed by ELPI and SPAMS simultaneously. The size distribution of BBB (biomass burning boiler sample) and CBB (coal burning boiler sample) are different, as BBB peaks at smaller size, and CBB peaks at larger size. Mass spectra signatures of two samples were studied by analyzing the average mass spectrum of each particle cluster extracted by ART-2a in different size ranges. In conclusion, BBB sample mostly consists of OC and EC containing particles, and a small fraction of K-rich particles in the size range of 0.2-0.5μm. In 0.5-1.0μm, BBB sample consists of EC, OC, K-rich and Al_Silicate containing particles; CBB sample consists of EC, ECOC containing particles, while Al_Silicate (including Al_Ca_Ti_Silicate, Al_Ti_Silicate, Al_Silicate) containing particles got higher fractions as size increase. The similarity of single particle mass spectrum signatures between two samples were studied by analyzing the dot product, results indicated that part of the single particle mass spectra of two samples in the same size range are similar, which bring challenge to the future source apportionment activity by using single particle aerosol mass spectrometer. Results of this study will provide physicochemical information of important sources which contribute to particle pollution, and will support source apportionment activities. Copyright © 2017. Published by Elsevier B.V.

STRAPS v1.0: evaluating a methodology for predicting electron impact ionisation mass spectra for the aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Topping, David O.; Allan, James; Rami Alfarra, M.; Aumont, Bernard

2017-06-01

Our ability to model the chemical and thermodynamic processes that lead to secondary organic aerosol (SOA) formation is thought to be hampered by the complexity of the system. While there are fundamental models now available that can simulate the tens of thousands of reactions thought to take place, validation against experiments is highly challenging. Techniques capable of identifying individual molecules such as chromatography are generally only capable of quantifying a subset of the material present, making it unsuitable for a carbon budget analysis. Integrative analytical methods such as the Aerosol Mass Spectrometer (AMS) are capable of quantifying all mass, but because of their inability to isolate individual molecules, comparisons have been limited to simple data products such as total organic mass and the O : C ratio. More detailed comparisons could be made if more of the mass spectral information could be used, but because a discrete inversion of AMS data is not possible, this activity requires a system of predicting mass spectra based on molecular composition. In this proof-of-concept study, the ability to train supervised methods to predict electron impact ionisation (EI) mass spectra for the AMS is evaluated. Supervised Training Regression for the Arbitrary Prediction of Spectra (STRAPS) is not built from first principles. A methodology is constructed whereby the presence of specific mass-to-charge ratio (m/z) channels is fitted as a function of molecular structure before the relative peak height for each channel is similarly fitted using a range of regression methods. The widely used AMS mass spectral database is used as a basis for this, using unit mass resolution spectra of laboratory standards. Key to the fitting process is choice of structural information, or molecular fingerprint. Our approach relies on using supervised methods to automatically optimise the relationship between spectral characteristics and these molecular fingerprints. Therefore

[Determination of biurea in flour and its products by liquid chromatography-tandem mass spectrometry].

PubMed

Wang, Ya; Wang, Junsu; Xiang, Lu; Xi, Cunxian; Chen, Dongdong; Peng, Tao; Wang, Guomin; Mu, Zhaode

2014-05-01

A novel method was established for the determination and identification of biurea in flour and its products using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The biurea was extracted with water and oxidized to azodicarbonamide by potassium permanganate. The azodicarbonamide was then derivatized using sodium p-toluene sulfinate solution. The separation was performed on a Shimpak XR-ODS II column (150 mm x 2.0 mm, 2.2 microm) using the mobile phase composed of acetonitrile and 2 mmol/L ammonium acetate aqueous solution (containing 0.2% (v/v) formic acid) with a gradient elution program. Tandem mass spectrometric detection was performed in multiple reaction monitoring (MRM) scan mode with a positive electrospray ionization (ESI(+)) source. The method used stable isotope internal standard quantitation. The calibration curve showed good linearity over the range of 1-20 000 microg/kg (R2 = 0.999 9). The limit of quantification was 5 microg/kg for biurea spiked in flour and its products. At the spiking levels of 5.0, 10.0 and 50.0 microg/kg in different matrices, the average recovery o biurea was 78.3%-108.0% with the relative standard deviations (RSDs) < or = 5.73%. The method developed is novel, reliable and sensitive with wide linear range, and can be used to determine the biurea in flour and its products.

Determination of formetanate hydrochloride in fruit samples using liquid chromatography-mass selective detection or -tandem mass spectrometry.

PubMed

Podhorniak, Lynda V; Kamel, Alaa; Rains, Diane M

2010-05-26

A rapid multiresidue method that captures residues of the insecticide formetanate hydrochloride (FHCl) in selected fruits is described. The method was used to provide residue data for dietary exposure determinations of FHCl. Using an acetonitrile extraction with a dispersive cleanup based on AOAC International method 2007.01, also known as QuEChERS, which was further modified and streamlined, thousands of samples were successfully analyzed for FHCl residues. FHCl levels were determined both by liquid chromatography-single-stage mass spectrometry (LC-MS) and ultraperformance liquid chromatography (UPLC)-tandem mass spectrometry (LC-MS/MS). The target limit of detection (LOD) and the limit of quantitation (LOQ) achieved for FHCl were 3.33 and 10 ng/g, respectively, with LC-MS and 0.1 and 0.3 ng/g, respectively, with LC-MS/MS. Recoveries at these previously unpublished levels ranged from 95 to 109%. A set of 20-40 samples can be prepared in one working day by two chemists.

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning.

PubMed

Zhou, Xie-Xuan; Zeng, Wen-Feng; Chi, Hao; Luo, Chunjie; Liu, Chao; Zhan, Jianfeng; He, Si-Min; Zhang, Zhifei

2017-12-05

In tandem mass spectrometry (MS/MS)-based proteomics, search engines rely on comparison between an experimental MS/MS spectrum and the theoretical spectra of the candidate peptides. Hence, accurate prediction of the theoretical spectra of peptides appears to be particularly important. Here, we present pDeep, a deep neural network-based model for the spectrum prediction of peptides. Using the bidirectional long short-term memory (BiLSTM), pDeep can predict higher-energy collisional dissociation, electron-transfer dissociation, and electron-transfer and higher-energy collision dissociation MS/MS spectra of peptides with >0.9 median Pearson correlation coefficients. Further, we showed that intermediate layer of the neural network could reveal physicochemical properties of amino acids, for example the similarities of fragmentation behaviors between amino acids. We also showed the potential of pDeep to distinguish extremely similar peptides (peptides that contain isobaric amino acids, for example, GG = N, AG = Q, or even I = L), which were very difficult to distinguish using traditional search engines.

Mono-isotope Prediction for Mass Spectra Using Bayes Network.

PubMed

Li, Hui; Liu, Chunmei; Rwebangira, Mugizi Robert; Burge, Legand

2014-12-01

Mass spectrometry is one of the widely utilized important methods to study protein functions and components. The challenge of mono-isotope pattern recognition from large scale protein mass spectral data needs computational algorithms and tools to speed up the analysis and improve the analytic results. We utilized naïve Bayes network as the classifier with the assumption that the selected features are independent to predict mono-isotope pattern from mass spectrometry. Mono-isotopes detected from validated theoretical spectra were used as prior information in the Bayes method. Three main features extracted from the dataset were employed as independent variables in our model. The application of the proposed algorithm to publicMo dataset demonstrates that our naïve Bayes classifier is advantageous over existing methods in both accuracy and sensitivity.

SpecOMS: A Full Open Modification Search Method Performing All-to-All Spectra Comparisons within Minutes.

PubMed

David, Matthieu; Fertin, Guillaume; Rogniaux, Hélène; Tessier, Dominique

2017-08-04

The analysis of discovery proteomics experiments relies on algorithms that identify peptides from their tandem mass spectra. The almost exhaustive interpretation of these spectra remains an unresolved issue. At present, an important number of missing interpretations is probably due to peptides displaying post-translational modifications and variants that yield spectra that are particularly difficult to interpret. However, the emergence of a new generation of mass spectrometers that provide high fragment ion accuracy has paved the way for more efficient algorithms. We present a new software, SpecOMS, that can handle the computational complexity of pairwise comparisons of spectra in the context of large volumes. SpecOMS can compare a whole set of experimental spectra generated by a discovery proteomics experiment to a whole set of theoretical spectra deduced from a protein database in a few minutes on a standard workstation. SpecOMS can ingeniously exploit those capabilities to improve the peptide identification process, allowing strong competition between all possible peptides for spectrum interpretation. Remarkably, this software resolves the drawbacks (i.e., efficiency problems and decreased sensitivity) that usually accompany open modification searches. We highlight this promising approach using results obtained from the analysis of a public human data set downloaded from the PRIDE (PRoteomics IDEntification) database.

[Determination of antibiotics in oral hygiene products by high performance liquid chromatography-tandem mass spectrometry].

PubMed

Zhou, Weijun; Xie, Zhengfu; Shao, Linzhi

2012-07-01

A high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/ MS) method was developed for simultaneous determination of 13 antibiotics in oral hygiene products, including five tetracyclines, three macrolides, two quinolones, one beta-lactam and two lincosamides. The sample was extracted with 0.1% (volume percentage, same hereinafter) formic acid-acetonitrile (95:5, v/v), then centrifuged, filtered and diluted. The target compounds were separated on a C18 column (150 mm x 2.1 mm, 5 microm) with a gradient elution of 0. 1% formic acid and acetonitrile as the mobile phases, and detected by tandem mass spectrometry in positive electrospray ionization and multiple reaction monitoring (MRM) mode. The quantification of 13 antibiotics was performed by the external standard method. The calibration curves showed good linearity in the range of 5.0-50.0 microg/L with detection limits of 10.0 mg/kg. The recoveries of antibiotics in mouthwash and toothpaste samples at the three spiked levels of 10, 20 and 100 mg/kg were in the range of 80.1%-115% with the relative standard deviations in the range of 0.94%-8.69%. This method is accurate, reliable, simple, and suitable for the analysis of antibiotics in oral hygiene products.

Characterization and identification of iridoid glucosides, flavonoids and anthraquinones in Hedyotis diffusa by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry.

PubMed

Liu, E-Hu; Zhou, Ting; Li, Guo-Bin; Li, Jing; Huang, Xiu-Ning; Pan, Feng; Gao, Ning

2012-01-01

The multiple bioactive constituents in Hedyotis diffusa Willd. (H. diffusa) were extracted and characterized by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC-ESI-MS(n)). The optimized separation condition was obtained using an Agilent ZorBax SB-C18 column (4.6×150 mm, 5 μm) and gradient elution with water (containing 0.1% formic acid) and acetonitrile (containing 0.1% formic acid), under which baseline separation for the majority of compounds was achieved. Among the compounds detected, 14 iridoid glucosides, 10 flavonoids, 7 anthraquinones, 1 coumarin and 1 triterpene were unambiguously identified or tentatively characterized based on their retention times and mass spectra in comparison with the data from standards or references. The fragmentation behavior for different types of constituents was also investigated, which could contribute to the elucidation of these constituents in H. diffusa. The present study reveals that even more iridoid glycosides were found in H. diffusa than hitherto assumed. The occurrence of two iridoid glucosides and five flavonoids in particular has not yet been described. This paper marks the first report on the structural characterization of chemical compounds in H. diffusa by a developed HPLC-ESI-MS(n) method. Copyright © 2012 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.

Multiple analyte adduct formation in liquid chromatography-tandem mass spectrometry - Advantages and limitations in the analysis of biologically-related samples.

PubMed

Dziadosz, Marek

2018-05-01

Multiple analyte adduct formation was examined and discussed in the context of reproducible signal detection in liquid chromatography-tandem mass spectrometry applied in the analysis of biologically-related samples. Appropriate infusion solutions were prepared in H 2 O/methanol (3/97, v/v) with 1 mM sodium acetate and 10 mM acetic acid. An API 4000 QTrap tandem mass spectrometer was used for experiments performed in the negative scan mode (-Q1 MS) and the negative enhanced product ion mode (-EPI). γ‑Hydroxybutyrate and its deuterated form were used as model compounds to highlight both the complexity of adduct formation in popular mobile phases used and the effective signal compensation by the application of isotope-labelled analytes as internal standards. Copyright © 2018 Elsevier B.V. All rights reserved.

Use of an online extraction liquid chromatography quadrupole time-of-flight tandem mass spectrometry method for the characterization of polyphenols in Citrus paradisi cv. Changshanhuyu peel.

PubMed

Tong, Chaoying; Peng, Mijun; Tong, Runna; Ma, Ruyi; Guo, Keke; Shi, Shuyun

2018-01-19

Chemical profiling of natural products by high performance liquid chromatography (HPLC) was critical for understanding of their clinical bioactivities, and sample pretreatment steps have been considered as a bottleneck for analysis. Currently, concerted efforts have been made to develop sample pretreatment methods with high efficiency, low solvent and time consumptions. Here, a simple and efficient online extraction (OLE) strategy coupled with HPLC-diode array detector-quadrupole time-of-flight tandem mass spectrometry (HPLC-DAD-QTOF-MS/MS) was developed for rapid chemical profiling. For OLE strategy, guard column inserted with ground sample (2 mg) instead of sample loop was connected with manual injection valve, in which components were directly extracted and transferred to HPLC-DAD-QTOF-MS/MS system only by mobile phase without any extra time, solvent, instrument and operation. By comparison with offline heat-reflux extraction of Citrus paradisi cv. Changshanhuyu (Changshanhuyu) peel, OLE strategy presented higher extraction efficiency perhaps because of the high pressure and gradient elution mode. A total of twenty-two secondary metabolites were detected according to their retention times, UV spectra, exact mass, and fragmentation ions in MS/MS spectra, and nine of them were discovered in Changshanhuyu peel for the first time to our knowledge. It is concluded that the developed OLE-HPLC-DAD-QTOF-MS/MS system offers new perspectives for rapid chemical profiling of natural products. Copyright © 2017 Elsevier B.V. All rights reserved.

Atmospheric Pressure Photoionization Tandem Mass Spectrometry of Androgens in Prostate Cancer

PubMed Central

Lih, Fred Bjørn; Titus, Mark A.; Mohler, James L.; Tomer, Kenneth B.

2010-01-01

Androgen deprivation therapy is the most common treatment option for advanced prostate cancer. Almost all prostate cancers recur during androgen deprivation therapy, and new evidence suggests that androgen receptor activation persists despite castrate levels of circulating androgens. Quantitation of tissue levels of androgens is critical to understanding the mechanism of recurrence of prostate cancer during androgen deprivation therapy. A liquid chromatography atmospheric pressure photoionization tandem mass spectrometric method was developed for quantitation of tissue levels of androgens. Quantitation of the saturated keto-steroids dihydrotestosterone and 5-α-androstanedione required detection of a novel parent ion, [M + 15]+. The nature of this parent ion was explored and the method applied to prostate tissue and cell culture with comparison to results achieved using electrospray ionization. PMID:20560527

An Undergraduate Experiment for the Measurement of Perfluorinated Surfactants in Fish Liver by Liquid Chromatography-Tandem Mass Spectrometry

ERIC Educational Resources Information Center

Stock, Naomi L.; Martin, Jonathan W.; Ye, Yun; Mabury, Scott A.

2007-01-01

A laboratory experiment that provides students a hands-on introduction to the specific techniques of liquid chromatography-tandem mass spectrometry (LC-MS/MS) and electrospray ionization is presented. The students can thus practice the analytical principles of sample extraction, detection, quantification, and quality control using a fresh fish…

A new HF-resistant tandem spray chamber for improved determination of trace elements and Pb isotopes using inductively coupled plasma-mass spectrometry

NASA Astrophysics Data System (ADS)

Krachler, Michael; Rausch, Nicole; Feuerbacher, Helmut; Klemens, Patrick

2005-07-01

The use of a new HF-resistant tandem spray chamber arrangement consisting of a cyclonic spray chamber and a Scott-type spray chamber made from PFA and PEEK provides a straightforward approach for improving the performance of inductively coupled-mass spectrometry (ICP-MS). The characteristics of the tandem spray chamber were critically evaluated against a PEEK cyclonic and a PFA Scott-type spray chamber, respectively. Sensitivity across the entire mass range was increased by about three times compared to the conventional setup utilizing only one spray chamber. Precision of the results, especially at low signal intensities, improved by 160% and 31% compared to the cyclonic and Scott-type spray chamber, respectively. Using the tandem spray chamber, the oxide formation rate was lowered by about 50%. Signals as low as 30 counts could be determined under routine measurement conditions with a RSD of 2.4% thus allowing to precisely quantify small concentration differences at the ng l - 1 concentration level. The excellent precision (0.02-0.07%) of 206Pb / 207Pb and 206Pb / 208Pb ratios determined in pore water samples was rather limited by the instrumental capabilities of the single collector ICP-MS instrument than by the performance of the tandem spray chamber.

[Measurement of free urinary cortisol and cortisone using liquid chromatography associated with tandem mass spectrometry method].

PubMed

Vieira, José Gilberto H; Nakamura, Odete H; Carvalho, Valdemir M

2005-04-01

Free urinary cortisol (UFF) measurement is one of the most useful screening tests for Cushing's syndrome. Immunoassays employed today by most clinical laboratories present limitations, specially concerning specificity. These limitations restrain a widespread application of the method, as well as the comparison of results obtained by the use of different methods. We present the development and characterization of a UFF and cortisone method based on liquid chromatography and tandem mass spectrometry (LC-MS/MS). A 200 microL aliquot from a 24 h urine sample is mixed with a solution containing a known quantity of deuterated cortisol and on-line extracted in solid phase (C18). The eluate is transferred to a second C18 column (Phenomenex Luna, 3 micro, 50 x 2 mm) and the isocratic mode elution profile is directly applied to a tandem mass spectrometer model Quattro Micro operating in positive mode atmospheric pressure chemical ionization (APCI). All process is automated and the quantification is performed by isotopic dilution, based on the analyte and the deuterated internal standard peak area ratios. The specificity study showed that all the steroids tested presented cross reactivity of <1% for cortisol and cortisone. Functional sensitivity is <1 microg/L for both steroids, and the interassay CV <8%. Recovery and linearity studies were satisfactory and comparison of results obtained using a RIA for UFF and the present method in 98 routine samples showed a correlation of r= 0.838, with the results obtained with LC-MS/MS significantly lower (medians of 22.0 vs. 49.4 microg/24 h for RIA) (P<0.0001). Reference values for cortisol were defined as values between 11 and 43 microg/24 h, compatible to those recently described for similar methods. The concomitant measurement of UF cortisone allows the study of the activity of the enzyme 11beta-HSD2 and the diagnosis of the apparent mineralocorticoid excess syndrome. The method represents the first steroid assay of a new generation

Structural Characterization of New Peptide Variants Produced by Cyanobacteria from the Brazilian Atlantic Coastal Forest Using Liquid Chromatography Coupled to Quadrupole Time-of-Flight Tandem Mass Spectrometry

PubMed Central

Sanz, Miriam; Andreote, Ana Paula Dini; Fiore, Marli Fatima; Dörr, Felipe Augusto; Pinto, Ernani

2015-01-01

Cyanobacteria from underexplored and extreme habitats are attracting increasing attention in the search for new bioactive substances. However, cyanobacterial communities from tropical and subtropical regions are still largely unknown, especially with respect to metabolite production. Among the structurally diverse secondary metabolites produced by these organisms, peptides are by far the most frequently described structures. In this work, liquid chromatography/electrospray ionization coupled to high resolution quadrupole time-of-flight tandem mass spectrometry with positive ion detection was applied to study the peptide profile of a group of cyanobacteria isolated from the Southeastern Brazilian coastal forest. A total of 38 peptides belonging to three different families (anabaenopeptins, aeruginosins, and cyanopeptolins) were detected in the extracts. Of the 38 peptides, 37 were detected here for the first time. New structural features were proposed based on mass accuracy data and isotopic patterns derived from full scan and MS/MS spectra. Interestingly, of the 40 surveyed strains only nine were confirmed to be peptide producers; all of these strains belonged to the order Nostocales (three Nostoc sp., two Desmonostoc sp. and four Brasilonema sp.). PMID:26096276

Electron impact action spectroscopy of mass/charge selected macromolecular ions: Inner-shell excitation of ubiquitin protein

NASA Astrophysics Data System (ADS)

Ranković, Miloš Lj.; Giuliani, Alexandre; Milosavljević, Aleksandar R.

2016-02-01

We have performed inner-shell electron impact action spectroscopy of mass and charge selected macromolecular ions. For this purpose, we have coupled a focusing electron gun with a linear quadrupole ion trap mass spectrometer. This experiment represents a proof of principle that an energy-tunable electron beam can be used in combination with radio frequency traps as an activation method in tandem mass spectrometry (MS2) and allows performing action spectroscopy. Electron impact MS2 spectra of multiply protonated ubiquitin protein ion have been recorded at incident electron energies around the carbon 1 s excitation. Both MS2 and single ionization energy dependence spectra are compared with literature data obtained using the soft X-ray activation conditions.

Tandem mass spectrometry: analysis of complex mixtures

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

Singleton, K.E.

1985-01-01

Applications of tandem mass spectrometry (MS/MS) for the analysis of complex mixtures results in increased specificity and selectivity by using a variety of reagent gases in both negative and positive ion modes. Natural isotopic abundance ratios were examined in both simple and complex mixtures using parent, daughter and neutral loss scans. MS/MS was also used to discover new compounds. Daughter scans were used to identify seven new alkaloids in a cactus species. Three of these alkaloids were novel compounds, and included the first simple, fully aromatic isoquinoline alkaloids reported in Cactaceae. MS/MS was used to characterize the chemical reaction productsmore » of coal in studies designed to probe its macromolecular structure. Negative ion chemical ionization was utilized to study reaction products resulting from the oxidation of coal. Possible structural units in the precursor coal were predicted based on the reaction products identified, aliphatic and aromatic acids and their anhydrides. The MS/MS method was also used to characterize reaction products resulting from coal liquefaction and/or extraction. These studies illustrate the types of problems for which MS/MS is useful. Emphasis has been placed on characterization of complex mixtures by selecting experimental parameters which enhance the information obtained. The value of using MS/MS in conjunction with other analytical techniques as well as the chemical pretreatment is demonstrated.« less

White-emissive tandem-type hybrid organic/polymer diodes with (0.33, 0.33) chromaticity coordinates.

PubMed

Guo, Tzung-Fang; Wen, Ten-Chin; Huang, Yi-Shun; Lin, Ming-Wei; Tsou, Chuan-Cheng; Chung, Chia-Tin

2009-11-09

This study reports fabrication of white-emissive, tandem-type, hybrid organic/polymer light-emitting diodes (O/PLED). The tandem devices are made by stacking a blue-emissive OLED on a yellow-emissive phenyl-substituted poly(para-phenylene vinylene) copolymer-based PLED and applying an organic oxide/Al/molybdenum oxide (MoO(3)) complex structure as a connecting structure or charge-generation layer (CGL). The organic oxide/Al/MoO(3) CGL functions as an effective junction interface for the transport and injection of opposite charge carriers through the stacked configuration. The electroluminescence (EL) spectra of the tandem-type devices can be tuned by varying the intensity of the emission in each emissive component to yield the visible-range spectra from 400 to 750 nm, with Commission Internationale de l'Eclairage chromaticity coordinates of (0.33, 0.33) and a high color rendering capacity as used for illumination. The EL spectra also exhibit good color stability under various bias conditions. The tandem-type device of emission with chromaticity coordinates, (0.30, 0.31), has maximum brightness and luminous efficiency over 25,000 cd/m(2) and approximately 4.2 cd/A, respectively.

Simultaneous drug identification in urine of sexual assault victims by using liquid chromatography tandem mass spectrometry.

PubMed

Lee, Hei Hwa; Chen, Suen Chi; Lee, Jong Feng; Lin, Hsin Yu; Chen, Bai Hsiun

2018-01-01

According to domestic and international epidemiological investigation, the proportion of substance involved sexual assault has the trend of ascent. In the past, laboratory methods that investigated urine sample of the sexual assault victims was to screen with enzyme immunoassay and then confirmed with mass spectrometry. The objective of the study is to simultaneously identify abused drugs in 126 decoded urine samples of sexual assault victims by liquid chromatography tandem mass spectrometry. The instrument was operated in multiple-reaction monitoring with an electro-spray positive ionization mode. Chromatograms were separated with ACE5 C18 column on a gradient of acetonitrile. After liquid-liquid extraction, samples were passed through a 0.22μm PVDF filter before injection into the system. The limits of quantitation ranged from 0.2 to 10ng/mL. The precision (CV) results were below 12.9% (intraday) and 15.0% (interday). The intraday accuracy ranged from 84.8 to 121.0%, interday accuracy ranged from 72.0 to 117.3%. We found that 29 (23.0%) were positive for drugs. The most common drug identified is flunitrazepam (11.1%), followed by nimetazepam and ketamine (7.9%), some new psychoactive substances, such as 2C-B, mephedrone, methylone, PMA and PMMA were also identified. We identified abused drugs, benzodiazepines, and new psychoactive substances in urine of sexual assault victims by using liquid chromatography tandem mass spectrometry. Copyright © 2017 Elsevier B.V. All rights reserved.

Optimization of Sample Preparation for the Identification and Quantification of Saxitoxin in Proficiency Test Mussel Sample using Liquid Chromatography-Tandem Mass Spectrometry

PubMed Central

Harju, Kirsi; Rapinoja, Marja-Leena; Avondet, Marc-André; Arnold, Werner; Schär, Martin; Burrell, Stephen; Luginbühl, Werner; Vanninen, Paula

2015-01-01

Saxitoxin (STX) and some selected paralytic shellfish poisoning (PSP) analogues in mussel samples were identified and quantified with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Sample extraction and purification methods of mussel sample were optimized for LC-MS/MS analysis. The developed method was applied to the analysis of the homogenized mussel samples in the proficiency test (PT) within the EQuATox project (Establishment of Quality Assurance for the Detection of Biological Toxins of Potential Bioterrorism Risk). Ten laboratories from eight countries participated in the STX PT. Identification of PSP toxins in naturally contaminated mussel samples was performed by comparison of product ion spectra and retention times with those of reference standards. The quantitative results were obtained with LC-MS/MS by spiking reference standards in toxic mussel extracts. The results were within the z-score of ±1 when compared to the results measured with the official AOAC (Association of Official Analytical Chemists) method 2005.06, pre-column oxidation high-performance liquid chromatography with fluorescence detection (HPLC-FLD). PMID:26610567

Peptides derivatized with bicyclic quaternary ammonium ionization tags. Sequencing via tandem mass spectrometry.

PubMed

Setner, Bartosz; Rudowska, Magdalena; Klem, Ewelina; Cebrat, Marek; Szewczuk, Zbigniew

2014-10-01

Improving the sensitivity of detection and fragmentation of peptides to provide reliable sequencing of peptides is an important goal of mass spectrometric analysis. Peptides derivatized by bicyclic quaternary ammonium ionization tags: 1-azabicyclo[2.2.2]octane (ABCO) or 1,4-diazabicyclo[2.2.2]octane (DABCO), are characterized by an increased detection sensitivity in electrospray ionization mass spectrometry (ESI-MS) and longer retention times on the reverse-phase (RP) chromatography columns. The improvement of the detection limit was observed even for peptides dissolved in 10 mM NaCl. Collision-induced dissociation tandem mass spectrometry of quaternary ammonium salts derivatives of peptides showed dominant a- and b-type ions, allowing facile sequencing of peptides. The bicyclic ionization tags are stable in collision-induced dissociation experiments, and the resulted fragmentation pattern is not significantly influenced by either acidic or basic amino acid residues in the peptide sequence. Obtained results indicate the general usefulness of the bicyclic quaternary ammonium ionization tags for ESI-MS/MS sequencing of peptides. Copyright © 2014 John Wiley & Sons, Ltd.

Determination of glutathione in spruce needles by liquid chromatography/tandem mass spectrometry.

PubMed

Gucek, Marjan; Makuc, Simon; Mlakar, Anita; Bericnik-Vrbovsek, Julija; Marsel, Joze

2002-01-01

For the determination of glutathione (GSH) and its oxidized form (GSSG) in spruce needles their electrospray mass and MS/MS spectra were recorded with an ion trap mass spectrometer (ITMS, LCQ, Finnigan) and a triple stage quadrupole mass spectrometer (TSQ, Quattro II, Micromass). A study of the stability of GSH in aqueous solutions shows the presence of dimeric and trimeric forms of GSH, as well as GSSG, GSH-sulfonate and GSH-sulfinic acid. The same components were also found in extracts of spruce needles. We developed an assay which is suitable for monitoring low concentrations of GSH and similar compounds in plant tissues, employing the sensitivity and specificity of LC/MS/MS. Preliminary results on the mass spectrometric determination of GSH in spruce needles are given. Copyright 2002 John Wiley & Sons, Ltd.

Molecular resolution and fragmentation of fulvic acid by electrospray ionization/multistage tandem mass spectrometry

USGS Publications Warehouse

Leenheer, J.A.; Rostad, C.E.; Gates, Paul M.; Furlong, E.T.; Ferrer, I.

2001-01-01

Molecular weight distributions of fulvic acid from the Suwannee River, Georgia, were investigated by electrospray ionization/quadrupole mass spectrometry (ESI/QMS), and fragmentation pathways of specific fulvic acid masses were investigated by electrospray ionization/ion trap multistage tandem mass spectrometry (ESI/MST/MS). ESI/QMS studies of the free acid form of low molecular weight poly(carboxylic acid) standards in 75% methanol/25% water mobile phase found that negative ion detection gave the optimum generation of parent ions that can be used for molecular weight determinations. However, experiments with poly(acrylic acid) mixtures and specific high molecular weight standards found multiply charged negative ions that gave a low bias to molecular mass distributions. The number of negative charges on a molecule is dependent on the distance between charges. ESI/MST/MS of model compounds found characteristic water loss from alcohol dehydration and anhydride formation, as well as CO2 loss from decarboxylation, and CO loss from ester structures. Application of these fragmentation pathways to specific masses of fulvic acid isolated and fragmented by ESI/MST/MS is indicative of specific structures that can serve as a basis for future structural confirmation after these hypothesized structures are synthesized.

Recent advances of liquid chromatography-(tandem) mass spectrometry in clinical and forensic toxicology.

PubMed

Peters, Frank T

2011-01-01

Liquid chromatography (LC) coupled to mass spectrometry (MS) or tandem mass spectrometry (MS/MS) has become increasingly important in clinical and forensic toxicology as well as doping control and is now a robust and reliable technique for routine analysis in these fields. In recent years, methods for LC-MS(/MS)-based systematic toxicological analysis using triple quadrupole or ion trap instruments have been considerably improved and a new screening approach based on high-resolution MS analysis using benchtop time-of-flight MS instruments has been developed. Moreover, many applications for so-called multi-target screening and/or quantification of drugs, poisons, and or their metabolites in various biomatrices have been published. The present paper will provide an overview and discuss these recent developments focusing on the literature published after 2006. Copyright © 2010 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Sensitive liquid chromatography-tandem mass spectrometry method for the simultaneous determination of paracetamol and guaifenesin in human plasma.

PubMed

Chen, Xiaoyan; Huang, Jia; Kong, Zhang; Zhong, Dafang

2005-03-25

A rapid and sensitive method for the simultaneous determination of paracetamol and guaifenesin in human plasma was developed and validated, using high-performance liquid chromatographic separation with tandem mass spectrometric detection. After extracted from plasma samples by diethyl ether-dichloromethane (3:2, v/v), the analytes and internal standard osalmide were chromatographed on a C18 column. Detection was performed on a triple quadrupole tandem mass spectrometer by selected reaction monitoring (SRM) mode via atmospheric pressure chemical ionization (APCI). The method was linear in the concentration range of 0.05-20.0 microg/ml for paracetamol and 5.0-2000.0 ng/ml for guaifenesin. The intra- and inter-day precision was within 14% for both paracetamol and guaifenesin. The assay accuracy was within +/-2.4% for the analytes. This is the first assay method described for the simultaneous determination of paracetamol and guaifenesin in plasma using one chromatographic run. The method was successfully employed in a pharmacokinetic study after an oral administration of a multicomponent formulation, containing 650 mg paracetamol, 200 mg guaifenesin, 60 mg pseudoephedrine and 20 mg dextrorphan.

Improved Reagents for Newborn Screening of Mucopolysaccharidosis Types I, II, and VI by Tandem Mass Spectrometry

PubMed Central

2015-01-01

Tandem mass spectrometry for the multiplex and quantitative analysis of enzyme activities in dried blood spots on newborn screening cards has emerged as a powerful technique for early assessment of lysosomal storage diseases. Here we report the design and process-scale synthesis of substrates for the enzymes α-l-iduronidase, iduronate-2-sulfatase, and N-acetylgalactosamine-4-sulfatase that are used for newborn screening of mucopolysaccharidosis types I, II, and VI. The products contain a bisamide unit that is hypothesized to readily protonate in the gas phase, which improves detection sensitivity by tandem mass spectrometry. The products contain a benzoyl group, which provides a useful site for inexpensive deuteration, thus facilitating the preparation of internal standards for the accurate quantification of enzymatic products. Finally, the reagents are designed with ease of synthesis in mind, thus permitting scale-up preparation to support worldwide newborn screening of lysosomal storage diseases. The new reagents provide the most sensitive assay for the three lysosomal enzymes reported to date as shown by their performance in reactions using dried blood spots as the enzyme source. Also, the ratio of assay signal to that measured in the absence of blood (background) is superior to all previously reported mucopolysaccharidosis types I, II, and VI assays. PMID:24694010

The utility of ultra-high performance supercritical fluid chromatography-tandem mass spectrometry (UHPSFC-MS/MS) for clinically relevant steroid analysis.

PubMed

Storbeck, Karl-Heinz; Gilligan, Lorna; Jenkinson, Carl; Baranowski, Elizabeth S; Quanson, Jonathan L; Arlt, Wiebke; Taylor, Angela E

2018-05-15

Liquid chromatography tandem mass spectrometry (LC-MS/MS) assays are considered the reference standard for serum steroid hormone analyses, while full urinary steroid profiles are only achievable by gas chromatography (GC-MS). Both LC-MS/MS and GC-MS have well documented strengths and limitations. Recently, commercial ultra-high performance supercritical fluid chromatography-tandem mass spectrometry (UHPSFC-MS/MS) systems have been developed. These systems combine the resolution of GC with the high-throughput capabilities of UHPLC. Uptake of this new technology into research and clinical labs has been slow, possibly due to the perceived increase in complexity. Here we therefore present fundamental principles of UHPSFC-MS/MS and the likely applications for this technology in the clinical research setting, while commenting on potential hurdles based on our experience to date. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Functional Groups and Structural Insights of Water-Soluble Organic Carbon using Ultrahigh Resolution FT-ICR Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Mazzoleni, L. R.; Habib, D.; Zhao, Y.; Dalbec, M.; Samburova, V.; Hallar, G.; Zielinska, B.; Lowenthal, D.

2013-12-01

Water-soluble organic carbon (WSOC) is a complex mixture of thousands of organic compounds which may have significant influence on the climate-relevant properties of atmospheric aerosols. An improved understanding of the molecular composition of WSOC is needed to evaluate the effect of aerosol composition upon aerosol physical properties. Products of gas phase, aqueous phase and particle phase reactions contribute to pre-existing aerosol organic mass or nucleate new aerosol particles. Thus, ambient aerosols carry a complex array of WSOC components with variable chemical signatures depending upon its origin and aerosol life-cycle processes. In this work, ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) was used to characterize aerosol WSOC collected during the summer of 2010 at the Storm Peak Laboratory (3210 m a.s.l.) near Steamboat Springs, CO. Approximately 4000 molecular formulas were assigned in the mass range of m/z 100-800 after negative-ion electrospray ionization. The observed trends indicate significant non-oxidative accretion reaction pathways for the formation of high molecular weight WSOC components closely associated with terpene ozonolysis secondary organic aerosol (SOA). The aerosol WSOC was further characterized using ultrahigh resolution tandem MS analysis with infrared multiphoton dissociation to determine the functional groups and structural properties of 1700 WSOC species up to m/z 600. Due to the complex nature of the WSOC, multiple precursor ions were simultaneously fragmented. The exact mass measurements of the precursor and product ions facilitated molecular formula assignments and matching of neutral losses. The most important neutral losses are CO2, H2O, CH3OH, HNO3, CH3NO3, SO3 and SO4. The presence and frequency of these losses indicate the type of functional groups contained in the precursor structures. Consistent with the acidic nature of WSOC compounds, the most frequently observed losses

The proteins cleaved by endogenous tryptic proteases in normal EDTA plasma by C18 collection of peptides for liquid chromatography micro electrospray ionization and tandem mass spectrometry.

PubMed

Dufresne, Jaimie; Florentinus-Mefailoski, Angelique; Ajambo, Juliet; Ferwa, Ammara; Bowden, Peter; Marshall, John

2017-01-01

The tryptic peptides from ice cold versus room temperature plasma were identified by C18 liquid chromatography and micro electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). Samples collected on ice showed low levels of endogenous tryptic peptides compared to the same samples incubated at room temperature. Plasma on ice contained peptides from albumin, complement, and apolipoproteins and others that were observed by the X!TANDEM and SEQUEST algorithms. In contrast to ice cold samples, after incubation at room temperature, greater numbers of tryptic peptides from well characterized plasma proteins, and from cellular proteins were observed. A total of 583,927 precursor ions and MS/MS spectra were correlated to 94,669 best fit peptides that reduced to 22,287 correlations to the best accession within a gene symbol and to 7174 correlations to at least 510 gene symbols with ≥ 5 independent MS/MS correlations (peptide counts) that showed FDR q-values ranging from E-9 (i.e. FDR = 0.000000001) to E-227. A set of 528 gene symbols identified by X!TANDEM and SEQUEST including C4B showed ≥ fivefold variation between ice cold versus room temperature incubation. STRING analysis of the protein gene symbols observed from endogenous peptides in normal plasma revealed an extensive protein-interaction network of cellular factors associated with cell signalling and regulation, the formation of membrane bound organelles, cellular exosomes and exocytosis network proteins. Taken together the results indicated that a pool of cellular proteins, or protein complexes, in plasma are apparently not stable and degrade soon after incubation at room temperature.

Sequence analysis of the pyruvylated galactan sulfate-derived oligosaccharides by negative-ion electrospray tandem mass spectrometry.

PubMed

Li, Na; Mao, Wenjun; Liu, Xue; Wang, Shuyao; Xia, Zheng; Cao, Sujian; Li, Lin; Zhang, Qi; Liu, Shan

2016-10-04

Five sulfated oligosaccharide fragments, F1-F5, were prepared from a pyruvylated galactan sulfate from the green alga Codium divaricatum, by partial depolymerization using mild acid hydrolysis and purification with gel-permeation chromatography. Negative-ion electrospray tandem mass spectrometry with collision-induced dissociation (ES-CID-MS/MS) is attempted for sequence determination of the sulfated oligosaccharides. The sequence of F1 with homogeneous disaccharide composition was first characterized to be Galp-(4SO4)-(1 → 3)-Galp by detailed nuclear magnetic resonance spectroscopic analyses. The fragmentation pattern of F1 in the product ion spectra was established on the basis of negative-ion ES-CID MS/MS, which was then applied to sequence analysis of other sulfated oligosaccharides. The sequences of F2 and F3 were deduced to be Galp-(4SO4)-(1 → 3)-Galp-(1 → 3)-Galp-(1 → 3)-Galp and 3,4-O-(1-carboxyethylidene)-Galp-(6SO4)-(1 → 3)-Galp, respectively. The sequences of major fragments in F4 and F5 were also deduced. The investigation demonstrated that negative-ion ES-CID-MS/MS was an efficient method for the sequence analysis of the pyruvylated galactan sulfate-derived oligosaccharides which revealed the patterns of substitution and glycosidic linkages. The pyruvylated galactan sulfate-derived oligosaccharides were novel sulfated oligosaccharides different from other algal polysaccharide-derived oligosaccharides. Copyright © 2016 Elsevier Ltd. All rights reserved.

Detection and identification of drugs and toxicants in human body fluids by liquid chromatography-tandem mass spectrometry under data-dependent acquisition control and automated database search.

PubMed

Oberacher, Herbert; Schubert, Birthe; Libiseller, Kathrin; Schweissgut, Anna

2013-04-03

Systematic toxicological analysis (STA) is aimed at detecting and identifying all substances of toxicological relevance (i.e. drugs, drugs of abuse, poisons and/or their metabolites) in biological material. Particularly, gas chromatography-mass spectrometry (GC/MS) represents a competent and commonly applied screening and confirmation tool. Herein, we present an untargeted liquid chromatography-tandem mass spectrometry (LC/MS/MS) assay aimed to complement existing GC/MS screening for the detection and identification of drugs in blood, plasma and urine samples. Solid-phase extraction was accomplished on mixed-mode cartridges. LC was based on gradient elution in a miniaturized C18 column. High resolution electrospray ionization-MS/MS in positive ion mode with data-dependent acquisition control was used to generate tandem mass spectral information that enabled compound identification via automated library search in the "Wiley Registry of Tandem Mass Spectral Data, MSforID". Fitness of the developed LC/MS/MS method for application in STA in terms of selectivity, detection capability and reliability of identification (sensitivity/specificity) was demonstrated with blank samples, certified reference materials, proficiency test samples, and authentic casework samples. Copyright © 2013 Elsevier B.V. All rights reserved.

Method for the Simultaneous Quantitation of Apolipoprotein E Isoforms using Tandem Mass Spectrometry

PubMed Central

Wildsmith, Kristin R.; Han, Bomie; Bateman, Randall J.

2009-01-01

Using Apolipoprotein E (ApoE) as a model protein, we developed a protein isoform analysis method utilizing Stable Isotope Labeling Tandem Mass Spectrometry (SILT MS). ApoE isoforms are quantitated using the intensities of the b and y ions of the 13C-labeled tryptic isoform-specific peptides versus unlabeled tryptic isoform-specific peptides. The ApoE protein isoform analysis using SILT allows for the simultaneous detection and relative quantitation of different ApoE isoforms from the same sample. This method provides a less biased assessment of ApoE isoforms compared to antibody-dependent methods, and may lead to a better understanding of the biological differences between isoforms. PMID:19653990

CAPILLARY ELECTROPHORESIS-ELECTROSPRAY MASS SPECTRA OF THE HERBICIDES PARAQUAT AND DIQUAT

EPA Science Inventory

The positive ion electrospray mass spectra of the quaternary ammonium salt herbicides paraquat and diquat are examined by on-line separation with capillary electrophoresis (CE) and by direct infusion of the analytes. The analytes are separated by CE in 7-10 min at pH 3.9 in 50% m...

A novel high-throughput method for supported liquid extraction of retinol and alpha-tocopherol from human serum and simultaneous quantitation by liquid chromatography tandem mass spectrometry.

PubMed

Hinchliffe, Edward; Rudge, James; Reed, Paul

2016-07-01

Measurement of vitamin A (retinol) and E (alpha-tocopherol) in UK clinical laboratories is currently performed exclusively by high-performance liquid chromatography with ultraviolet detection. We investigated whether retinol and alpha-tocopherol could be measured simultaneously by liquid chromatography tandem mass spectrometry. Serum samples (100 μL) were extracted using Isolute + Supported Liquid Extraction plates. Chromatography was performed on a Phenomenex Kinetex Biphenyl 2.6 μm, 50 × 2.1 mm column, and liquid chromatography tandem mass spectrometry on a Waters Acquity TQD. Injection-to-injection time was 4.3 min. The assay was validated according to published guidelines. Patient samples were used to compare liquid chromatography tandem mass spectrometry and high-performance liquid chromatography with ultraviolet detection methods. For retinol and alpha-tocopherol, respectively, the assay was linear up to 6.0 and 80.0 μmol/L, and lower limit of quantification was 0.07 and 0.26 μmol/L. Intra and interassay imprecision were within desirable analytical specifications. Analysis of quality control material aligned to NIST SRM 968e, and relative spiked recovery from human serum, both yielded results within 15% of target values. Method comparison with high-performance liquid chromatography with ultraviolet detection methodology demonstrated a negative bias for retinol and alpha-tocopherol by the liquid chromatography tandem mass spectrometry method. Analysis of United Kingdom National External Quality Assurance Scheme samples yielded mean bias from the target value of +3.0% for retinol and -11.2% for alpha-tocopherol. We have developed a novel, high-throughput method for extraction of retinol and alpha-tocopherol from human serum followed by simultaneous quantitation by liquid chromatography tandem mass spectrometry. The method offers a rapid, sensitive, specific and cost-effective alternative to high-performance liquid chromatography with

Structural Characterisation of Acetogenins from Annona muricata by Supercritical Fluid Chromatography Coupled to High-Resolution Tandem Mass Spectrometry.

PubMed

Laboureur, Laurent; Bonneau, Natacha; Champy, Pierre; Brunelle, Alain; Touboul, David

2017-11-01

Acetogenins are plant polyketides known to be cytotoxic and proposed as antitumor candidates. They are also suspected to be alimentary neurotoxins. Their occurrence as complex mixtures renders their dereplication and structural identification difficult using liquid chromatography coupled to tandem mass spectrometry and efforts are required to improve the methodology. To develop a supercritical fluid chromatography (SFC) high-resolution tandem mass spectrometry method, involving lithium post-column cationisation, for the structural characterisation of Annonaceous acetogenins in crude extracts. The seeds of Annona muricata L. were extracted with methanol. Supercritical fluid chromatography of the extract, using a 2-ethylpyridine stationary phase column, was monitored using a high-resolution quadrupole time-of-flight mass spectrometer. Lithium iodide was added post-column in the make-up solvent. For comparison, the same extract was analysed using high-pressure liquid chromatography coupled to the same mass spectrometer, with a column based on solid core particles. Sensitivity was similar for both HPLC and SFC approaches. Retention behaviour and fragmentation pathways of three different isomer groups are described. A previously unknown group of acetogenins was also evidenced for the first time. The use of SFC-MS/MS allows the reduction of the time of analysis, of environmental impact and an increase in the chromatographic resolution, compared to liquid chromatography. This new methodology enlightened a new group of acetogenins, isomers of montanacin-D. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Purification of pharmaceutical preparations using thin-layer chromatography to obtain mass spectra with Direct Analysis in Real Time and accurate mass spectrometry.

PubMed

Wood, Jessica L; Steiner, Robert R

2011-06-01

Forensic analysis of pharmaceutical preparations requires a comparative analysis with a standard of the suspected drug in order to identify the active ingredient. Purchasing analytical standards can be expensive or unattainable from the drug manufacturers. Direct Analysis in Real Time (DART™) is a novel, ambient ionization technique, typically coupled with a JEOL AccuTOF™ (accurate mass) mass spectrometer. While a fast and easy technique to perform, a drawback of using DART™ is the lack of component separation of mixtures prior to ionization. Various in-house pharmaceutical preparations were purified using thin-layer chromatography (TLC) and mass spectra were subsequently obtained using the AccuTOF™- DART™ technique. Utilizing TLC prior to sample introduction provides a simple, low-cost solution to acquiring mass spectra of the purified preparation. Each spectrum was compared against an in-house molecular formula list to confirm the accurate mass elemental compositions. Spectra of purified ingredients of known pharmaceuticals were added to an in-house library for use as comparators for casework samples. Resolving isomers from one another can be accomplished using collision-induced dissociation after ionization. Challenges arose when the pharmaceutical preparation required an optimized TLC solvent to achieve proper separation and purity of the standard. Purified spectra were obtained for 91 preparations and included in an in-house drug standard library. Primary standards would only need to be purchased when pharmaceutical preparations not previously encountered are submitted for comparative analysis. TLC prior to DART™ analysis demonstrates a time efficient and cost saving technique for the forensic drug analysis community. Copyright © 2011 John Wiley & Sons, Ltd. Copyright © 2011 John Wiley & Sons, Ltd.

Silver complexation and tandem mass spectrometry for differentiation of isomeric flavonoid diglycosides.

PubMed

Zhang, Junmei; Brodbelt, Jennifer S

2005-03-15

For detection and differentiation of isomeric flavonoids, electrospray ionization mass spectrometry is used to generate silver complexes of the type (Ag + flavonoid)+. Collisionally activated dissociation (CAD) of the resulting 1:1 silver/flavonoid complexes allows isomer differentiation of flavonoids. Eighteen flavonoid diglycosides constituting seven isomeric series are distinguishable from each other based on the CAD patterns of their silver complexes. Characteristic dissociation pathways allow identification of the site of glycosylation, the type of disaccharide (rutinose versus neohesperidose), and the type of aglycon (flavonol versus flavone versus flavanone). This silver complexation method is more universal than previous metal complexation methods, as intense silver complexes are observed even for flavonoids that lack the typical metal chelation sites. To demonstrate the feasibility of using silver complexation and tandem mass spectrometry to characterize flavonoids in complex mixtures, flavonoids extracted from grapefruit juice are separated by high-performance liquid chromatography and analyzed via a postcolumn complexation ESI-MS/MS strategy. Diagnostic fragmentation pathways of the silver complexes of the individual eluting flavonoids allow successful identification of the six flavonoids in the extract.

Electron impact action spectroscopy of mass/charge selected macromolecular ions: Inner-shell excitation of ubiquitin protein

DOE PAGES

Rankovic, Milos Lj.; Giuliani, Alexandre; Milosavljevic, Aleksandar R.

2016-02-11

In this study, we have performed inner-shell electron impact action spectroscopy of mass and charge selected macromolecular ions. For this purpose, we have coupled a focusing electron gun with a linear quadrupole ion trap mass spectrometer. This experiment represents a proof of principle that an energy-tunable electron beam can be used in combination with radio frequency traps as an activation method in tandem mass spectrometry (MS 2) and allows performing action spectroscopy. Electron impact MS 2 spectra of multiply protonated ubiquitin protein ion have been recorded at incident electron energies around the carbon 1s excitation. Both MS 2 and singlemore » ionization energy dependence spectra are compared with literature data obtained using the soft X-ray activation conditions.« less

Electron impact action spectroscopy of mass/charge selected macromolecular ions: Inner-shell excitation of ubiquitin protein

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

Rankovic, Milos Lj.; Giuliani, Alexandre; Milosavljevic, Aleksandar R.

In this study, we have performed inner-shell electron impact action spectroscopy of mass and charge selected macromolecular ions. For this purpose, we have coupled a focusing electron gun with a linear quadrupole ion trap mass spectrometer. This experiment represents a proof of principle that an energy-tunable electron beam can be used in combination with radio frequency traps as an activation method in tandem mass spectrometry (MS 2) and allows performing action spectroscopy. Electron impact MS 2 spectra of multiply protonated ubiquitin protein ion have been recorded at incident electron energies around the carbon 1s excitation. Both MS 2 and singlemore » ionization energy dependence spectra are compared with literature data obtained using the soft X-ray activation conditions.« less

Mass Spectrometry Parameters Optimization for the 46 Multiclass Pesticides Determination in Strawberries with Gas Chromatography Ion-Trap Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Fernandes, Virgínia C.; Vera, Jose L.; Domingues, Valentina F.; Silva, Luís M. S.; Mateus, Nuno; Delerue-Matos, Cristina

2012-12-01

Multiclass analysis method was optimized in order to analyze pesticides traces by gas chromatography with ion-trap and tandem mass spectrometry (GC-MS/MS). The influence of some analytical parameters on pesticide signal response was explored. Five ion trap mass spectrometry (IT-MS) operating parameters, including isolation time (IT), excitation voltage (EV), excitation time (ET), maximum excitation energy or " q" value (q), and isolation mass window (IMW) were numerically tested in order to maximize the instrument analytical signal response. For this, multiple linear regression was used in data analysis to evaluate the influence of the five parameters on the analytical response in the ion trap mass spectrometer and to predict its response. The assessment of the five parameters based on the regression equations substantially increased the sensitivity of IT-MS/MS in the MS/MS mode. The results obtained show that for most of the pesticides, these parameters have a strong influence on both signal response and detection limit. Using the optimized method, a multiclass pesticide analysis was performed for 46 pesticides in a strawberry matrix. Levels higher than the limit established for strawberries by the European Union were found in some samples.

Accurate proteome-wide protein quantification from high-resolution 15N mass spectra

PubMed Central

2011-01-01

In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods. PMID:22182234

Simultaneous separation and identification of limonoids from citrus using liquid chromatography-collision-induced dissociation mass spectra.

PubMed

Jayaprakasha, Guddadarangavvanahally K; Dandekar, Deepak V; Tichy, Shane E; Patil, Bhimanagouda S

2011-01-01

Limonoids are considered as potential cancer chemopreventive agents and are widely distributed in the Citrus genus as aglycones and glucosides. In the present study, reversed-phase HPLC coupled with CID mass spectra was developed for the simultaneous separation and identification of aglycones and glucosides of limonoids from citrus. Five aglycones such as limonin, deacetyl nomilin, ichangin, isolimonoic acid and nomilin were identified by positive ion CID MS/MS, whereas five glucosides, viz. limonin glucoside, isoobacunoic acid glucoside, obacunone glucoside, deacetyl nomilinic acid glucoside and nomilinic acid glucoside were analyzed by negative ion CID mass spectra. The developed method was successfully applied to complex citrus samples for the separation and identification of aglycones and glucosides. Citrus seeds were extracted with methanol and partially purified and analyzed by LC-CID mass spectra. The separation was achieved by C-18 column; eight limonoids were identified by comparing the retention times and mass spectral fragmentation. To the best of our knowledge, this is the first report on the identification of citrus limonoids using CID technique. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming.

PubMed

Baran, Richard; Northen, Trent R

2013-10-15

Untargeted metabolite profiling using liquid chromatography and mass spectrometry coupled via electrospray ionization is a powerful tool for the discovery of novel natural products, metabolic capabilities, and biomarkers. However, the elucidation of the identities of uncharacterized metabolites from spectral features remains challenging. A critical step in the metabolite identification workflow is the assignment of redundant spectral features (adducts, fragments, multimers) and calculation of the underlying chemical formula. Inspection of the data by experts using computational tools solving partial problems (e.g., chemical formula calculation for individual ions) can be performed to disambiguate alternative solutions and provide reliable results. However, manual curation is tedious and not readily scalable or standardized. Here we describe an automated procedure for the robust automated mass spectra interpretation and chemical formula calculation using mixed integer linear programming optimization (RAMSI). Chemical rules among related ions are expressed as linear constraints and both the spectra interpretation and chemical formula calculation are performed in a single optimization step. This approach is unbiased in that it does not require predefined sets of neutral losses and positive and negative polarity spectra can be combined in a single optimization. The procedure was evaluated with 30 experimental mass spectra and was found to effectively identify the protonated or deprotonated molecule ([M + H](+) or [M - H](-)) while being robust to the presence of background ions. RAMSI provides a much-needed standardized tool for interpreting ions for subsequent identification in untargeted metabolomics workflows.

Electrospray-assisted laser desorption/ionization and tandem mass spectrometry of peptides and proteins.

PubMed

Peng, Ivory X; Shiea, Jentaie; Ogorzalek Loo, Rachel R; Loo, Joseph A

2007-01-01

We have constructed an electrospray-assisted laser desorption/ionization (ELDI) source which utilizes a nitrogen laser pulse to desorb intact molecules from matrix-containing sample solution droplets, followed by electrospray ionization (ESI) post-ionization. The ELDI source is coupled to a quadrupole ion trap mass spectrometer and allows sampling under ambient conditions. Preliminary data showed that ELDI produces ESI-like multiply charged peptides and proteins up to 29 kDa carbonic anhydrase and 66 kDa bovine albumin from single-protein solutions, as well as from complex digest mixtures. The generated multiply charged polypeptides enable efficient tandem mass spectrometric (MS/MS)-based peptide sequencing. ELDI-MS/MS of protein digests and small intact proteins was performed both by collisionally activated dissociation (CAD) and by nozzle-skimmer dissociation (NSD). ELDI-MS/MS may be a useful tool for protein sequencing analysis and top-down proteomics study, and may complement matrix-assisted laser desorption/ionization (MALDI)-based measurements. Copyright (c) 2007 John Wiley & Sons, Ltd.

Characterization of physalins and fingerprint analysis for the quality evaluation of Physalis alkekengi L. var. franchetii by ultra-performance liquid chromatography combined with diode array detection and electrospray ionization tandem mass spectrometry.

PubMed

Zheng, Yunliang; Luan, Lianjun; Chen, Yong; Ren, Yiping; Wu, Yongjiang

2012-12-01

Physalins are important bioactive compounds from genus Physalis. They often occur as isomers, which makes the structural elucidation difficult. In the present study, the fragmentation behavior and UV characteristics of seven physalins from genus Physalis were firstly investigated using electrospray ionization tandem mass spectrometry (ESI-MS/MS) and diode array detection (DAD). Combined with ultra-performance liquid chromatography (UPLC) and DAD, the established approach to the structural identification of physalins by ESI-MS/MS was then applied to the analysis of Physalis alkekengi L. According to the UPLC retention behavior, the diagnostic UV spectra and the molecular structural information provided by MS/MS spectra, about 19 fingerprint peaks were identified, including 14 physalins and 5 other compounds. Finally, the established fingerprint method was applied to the analysis of 31 P. alkekengi L. samples collected from different locations, which reflected their similar chemical constituent properties. The proposed method provides a scientific and technical platform to the herbal industry for quality control and safety assurance of herbal preparations that contain this class of physalins. Copyright © 2012 Elsevier B.V. All rights reserved.

Diclofenac in municipal wastewater treatment plant: quantification using laser diode thermal desorption--atmospheric pressure chemical ionization--tandem mass spectrometry approach in comparison with an established liquid chromatography-electrospray ionization-tandem mass spectrometry method.

PubMed

Lonappan, Linson; Pulicharla, Rama; Rouissi, Tarek; Brar, Satinder K; Verma, Mausam; Surampalli, Rao Y; Valero, José R

2016-02-12

Diclofenac (DCF), a prevalent non-steroidal anti-inflammatory drug (NSAID) is often detected in wastewater and surface water. Analysis of the pharmaceuticals in complex matrices is often laden with challenges. In this study a reliable, rapid and sensitive method based on laser diode thermal desorption/atmospheric pressure chemical ionization (LDTD/APCI) coupled with tandem mass spectrometry (MS/MS) has been developed for the quantification of DCF in wastewater and wastewater sludge. An established conventional LC-ESI-MS/MS (liquid chromatography-electrospray ionization-tandem mass spectrometry) method was compared with LDTD-APCI-MS/MS approach. The newly developed LDTD-APCI-MS/MS method reduced the analysis time to 12s in lieu of 12 min for LC-ESI-MS/MS method. The method detection limits for LDTD-APCI-MS/MS method were found to be 270 ng L(-1) (LOD) and 1000 ng L(-1) (LOQ). Furthermore, two extraction procedures, ultrasonic assisted extraction (USE) and accelerated solvent extraction (ASE) for the extraction of DCF from wastewater sludge were compared and ASE with 95.6 ± 7% recovery was effective over USE with 86 ± 4% recovery. The fate and partitioning of DCF in wastewater (WW) and wastewater sludge (WWS) in wastewater treatment plant was also monitored at various stages of treatment in Quebec Urban community wastewater treatment plant. DCF exhibited affinity towards WW than WWS with a presence about 60% of DCF in WW in contrary with theoretical prediction (LogKow=4.51). Copyright © 2016 Elsevier B.V. All rights reserved.

Tandem mass spectrometry approach for the investigation of the steroidal metabolism: structure-fragmentation relationship (SFR) in anabolic steroids and their metabolites by ESI-MS/MS analysis.

PubMed

Musharraf, Syed Ghulam; Ali, Arslan; Khan, Naik Tameem; Yousuf, Maria; Choudhary, Muhammad Iqbal; Atta-ur-Rahman

2013-02-01

Electrospray ionization tandem mass spectrometry (ESI-MS/MS) was used to investigate the effect of different substitutions introduced during metabolism on fragmentation patterns of four anabolic steroids including methyltestosterone, methandrostenolone, cis-androsterone and adrenosterone, along with their metabolites. Collision-induced dissociation (CID) analysis was performed to correlate the major product ions of 19 steroids with structural features. The analysis is done to portray metabolic alteration, such as incorporation or reduction of double bonds, hydroxylations, and/or oxidation of hydroxyl moieties to keto functional group on steroidal skeleton which leads to drastically changed product ion spectra from the respective classes of steroids, therefore, making them difficult to identify. The comparative ESI-MS/MS study also revealed some characteristic peaks to differentiate different steroidal metabolites and can be useful for the unambiguous identification of anabolic steroids in biological fluid. Moreover, LC-ESI-MS/MS analysis of fermented extract of methyltestosterone, obtained by Macrophomina phaseolina was also investigated. Copyright © 2012 Elsevier Inc. All rights reserved.

MEASUREMENT OF PYRETHROID RESIDUES IN ENVIRONMENTAL AND FOOD SAMPLES BY ENHANCED SOLVENT EXTRACTION/SUPERCRITICAL FLUID EXTRACTION COUPLED WITH GAS CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY

EPA Science Inventory

The abstract summarizes pyrethorid methods development research. It provides a summary of sample preparation and analytical techniques such as supercritical fluid extraction, enhance solvent extraction, gas chromatography and tandem mass spectrometry.

Single Laboratory Validated Method for Determination of Cylindrospermopsin and Anatoxin-a in Ambient Freshwaters by Liquid Chromatography/Tandem Mass Spectrometry (LC/MS/MS)

EPA Pesticide Factsheets

This document is a standardized single laboratory validated liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the detection and quantification of cyanotoxins (combined intracellular and extracellular) in ambient freshwaters.

Multiresidue analysis of 47 pesticides in cooked wheat flour and polished rice by liquid chromatography with tandem mass spectrometry.

PubMed

Lee, Sung Jung; Park, Hyeong Jin; Kim, Wooseong; Jin, Jong Sung; Abd El-Aty, A M; Shim, Jae-Han; Shin, Sung Chul

2009-04-01

Liquid chromatography in conjunction with tandem mass spectrometry was used to directly quantify of 47 pesticide residues from cooked wheat flour and polished rice, which are the most widely consumed cereals in the Republic of Korea. The sample clean-up was carried out according to the method established by the Korea Food and Drug Administration. The mobile phase for liquid chromatography separation consisted of water and 5 mm methanolic ammonium formate. Tandem mass spectroscopy experiments were performed in electrospray ionization positive mode and the multiple reaction monitoring mode. The matrix effects estimated for the 47 pesticides had a mean value of 99% and ranged from 45 to 147%. High recoveries (70-140%) and relative standard deviations (< or = 20%) were achieved for most of the pesticides tested. The method used in this study allowed for rapid quantification and identification of low levels of pesticides in cooked wheat flour and polished rice samples. Of the screened pesticide residues, only tricyclazole and fenobucarb were found in polished rice samples. However, no samples contained residues above the MRL established by the Korea Food and Drug Administration.

Simultaneous determination of three pesticides and their metabolites in unprocessed foods using ultraperformance liquid chromatography-tandem mass spectrometry.

PubMed

Rong, Lili; Wu, Xiaohu; Xu, Jun; Dong, Fengshou; Liu, Xingang; Pan, Xinglu; Du, Pengqiang; Wei, Dongmei; Zheng, Yongquan

2018-02-01

We have developed a rapid, multi-compound analytical method for measuring residues of the pesticides thiamethoxam and its metabolite, clothianidin; fipronil and its three metabolites, fipronil sulfone, fipronil sulfide, and fipronil desulfinyl; and pyraclostrobin in unprocessed foods (rice, corn, cucumbers, tomatoes, apples, and bananas) by ultra-performance liquid chromatography coupled to tandem mass spectrometry. Acetonitrile was used as the extraction solvent, and an octadecylsilane-dispersive SPE was used to clean up the analytes, which were then separated through a UPLC HSS T3 column connected to a tandem mass spectrometer via an electrospray ionisation source. The linearity of this method for the target analytes was excellent (R 2  ≥0.990) in the concentration range of 5-1000 μg kg -1 . The average recoveries of the seven compounds at concentrations of 10, 100, and 1000 μg kg -1 from six spiked matrix samples ranged from 73.6 to 110.6%, all with RSD values of ≤19.7%. The limit of quantification was 10 μg kg -1 . The method validated the effectiveness of the method for routine monitoring the residue of these pesticides and their metabolites in foods.

Quantitation of phlorizin and phloretin using an ultra high performance liquid chromatography-electrospray ionization tandem mass spectrometric method.

PubMed

Lijia, Xu; Guo, Jianru; Chen, QianQian; Baoping, Jiang; Zhang, Wei

2014-06-01

A sensitive and selective ultra high performance liquid chromatography-tandem mass spectrometric (UHPLC-MS/MS) method for the determination of phlorizin and phloretin in human plasma has been firstly developed. Samples were prepared after protein precipitation and analyzed on a C18 column interfaced with a triple quadrupole tandem mass spectrometer. Negative electrospray ionization was employed as the ionization source. The mobile phase consisted of acetonitrile-water (0.02% formic acid), using a gradient procedure. The analytes and internal standard dihydroquercetin were both detected by use of multiple reaction monitoring mode. The method was linear in the concentration range of 2.5-1000.0 ng/mL. The lower limit of quantification (LLOQ) was 2.5 ng/mL. The intra- and inter-day relative standard deviation across three validation runs over the entire concentration range was less than 9.2%. The accuracy determined at three concentrations was within ± 7.3% in terms of relative error. The total run time was 12.0 min. This assay offers advantages in terms of expediency, and suitability for the analysis of phlorizin and phloretin in various biological fluids. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Liquid chromatography tandem mass spectrometry for the simultaneous determination of mequindox and its metabolites in porcine tissues.

PubMed

Zeng, Dongping; Shen, Xiangguang; He, Limin; Ding, Huanzhong; Tang, Youzhi; Sun, Yongxue; Fang, Binghu; Zeng, Zhenling

2012-06-01

A rapid liquid chromatography tandem mass spectrometric method was developed for the simultaneous determination of mequindox and its five metabolites (2-isoethanol mequindox, 2-isoethanol 1-desoxymequindox, 1-desoxymequindox, 1,4-bisdesoxymequindox, and 2-isoethanol bisdesoxymequindox) in porcine muscle, liver, and kidney, fulfilling confirmation criteria with two transitions for each compound with acceptable relative ion intensities. The method involved acid hydrolysis, purification by solid-phase extraction, and subsequent analysis with liquid chromatography tandem mass spectrometry using electrospray ionization operated in positive polarity with a total run time of 15 min. The decision limit values of five analytes in porcine tissues ranged from 0.6 to 2.9 μg/kg, and the detection capability values ranged from 1.2 to 5.7 μg/kg. The results of the inter-day study, which was performed by fortifying porcine muscle (2, 4, and 8 μg/kg), liver, and kidney (10, 20, and 40 μg/kg) samples on three separate days, showed that the accuracy of the method for the various analytes ranged between 75.3 and 107.2% with relative standard deviation less than 12% for each analyte. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A new application of hierarchical cluster analysis to investigate organic peaks in bulk mass spectra obtained with an Aerodyne Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Middlebrook, A. M.; Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M. L.; Bertman, S. B.

2006-12-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel Ronald H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter probably originating from both anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent on average 17% of the total organic mass that stems likely from biogenic sources during the ship's cruise. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

High-performance liquid chromatography coupled with tandem mass spectrometry technology in the analysis of Chinese Medicine Formulas: A bibliometric analysis (1997-2015).

PubMed

He, Xi-Ran; Li, Chun-Guang; Zhu, Xiao-Shu; Li, Yuan-Qing; Jarouche, Mariam; Bensoussan, Alan; Li, Ping-Ping

2017-01-01

There is a recognized challenge in analyzing traditional Chinese medicine formulas because of their complex chemical compositions. The application of modern analytical techniques such as high-performance liquid chromatography coupled with a tandem mass spectrometry has improved the characterization of various compounds from traditional Chinese medicine formulas significantly. This study aims to conduct a bibliometric analysis to recognize the overall trend of high-performance liquid chromatography coupled with tandem mass spectrometry approaches in the analysis of traditional Chinese medicine formulas, its significance and possible underlying interactions between individual herbs in these formulas. Electronic databases were searched systematically, and the identified studies were collected and analyzed using Microsoft Access 2010, Graph Pad 5.0 software and Ucinet software package. 338 publications between 1997 and 2015 were identified, and analyzed in terms of annual growth and accumulated publications, top journals, forms of traditional Chinese medicine preparations and highly studied formulas and single herbs, as well as social network analysis of single herbs. There is a significant increase trend in using high-performance liquid chromatography coupled with tandem mass spectrometry related techniques in analysis of commonly used forms of traditional Chinese medicine formulas in the last 3 years. Stringent quality control is of great significance for the modernization and globalization of traditional Chinese medicine, and this bibliometric analysis provided the first and comprehensive summary within this field. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mass spectra of the particle-antiparticle system with a Dirac oscillator interaction

NASA Technical Reports Server (NTRS)

Moshinsky, M.; Loyola, G.

1993-01-01

The present view about the structure of mesons is that they are a quark-antiquark system. The mass spectrum corresponding to this system should, in principle, be given by chromodynamics, but this turns out to be a complex affair. Thus it is of some interest to consider relativistic systems of particle-antiparticle, with a simple type of interaction, which could give some insight on the spectra we can expect for mesons. This analysis is carried out when the interaction is of the Dirac oscillator type. It is shown that the Dirac equation of the antiparticle can be obtained from that of the particle by just changing the frequency omega into -omega. Following a procedure suggested by Barut, the equation for the particle-antiparticle system is derived and it is solved by a perturbation procedure. Thus, explicit expressions for the square of the mass spectra are obtained and its implications in the meson case is discussed.

Direct evidence for tautomerization of the uracil moiety within the Pb2+/uridine-5'-monophosphate complex: a combined tandem mass spectrometry and IRMPD study.

PubMed

Salpin, Jean-Yves; Guillaumont, Sébastien; Ortiz, Daniel; Tortajada, Jeanine; Maître, Philippe

2011-08-15

The structure of the [Pb(UMP)-H](+) (UMP = uridine-5'-monophosphate) complex was studied in the gas phase by combining electrospray ionization (ESI), tandem mass spectrometry, and mid-infrared multiple photon dissociation (IRMPD) spectroscopy. The results obtained show that Pb(2+) ions interact not only with the deprotonated phosphate group but also with a carbonyl group of the nucleobase moiety by folding of the mononucleotide, resulting in macrochelates that are not likely to be present in solution. Comparison between the IRMPD and DFT-computed spectra suggests that the ESI-generated complex likely corresponds to a mixture of several structures, and establishes the enolic tautomers as the most abundant species for the [Pb(UMP)-H](+) ion, while the very weak IRMPD signal observed at ∼1763 cm(-1) points to a minor population of oxo forms. Our data also suggest that losing the nucleobase residue under CID conditions does not necessarily mean a lack of interaction between the metal and the nucleobase moiety, as commonly reported in the literature for large oligonucleotides. © 2011 American Chemical Society

Determination of albendazole sulfoxide in human plasma by using liquid chromatography-tandem mass spectrometry.

PubMed

Saraner, Nihal; Özkan, Güler Yağmur; Güney, Berrak; Alkan, Erkin; Burul-Bozkurt, Nihan; Sağlam, Onursal; Fikirdeşici, Ezgi; Yıldırım, Mevlüt

2016-06-01

A rapid, simple and sensitive method was developed and validated using liquid chromatography-tandem mass spectrometry (LC-MS/MS) for determination of albendazole sulfoxide (ABZOX) in human plasma. The plasma samples were extracted by protein precipitation using albendazole sulfoxide-d3 as internal standard (IS). The chromatographic separation was performed on Waters Xbridge C18Column (100×4.6mm, 3.5μm) with a mobile phase consisting of ammonia solution, water and methanol at a flow rate of 0.70mL/min. ABZOX was detected and identified by mass spectrometry with electrospray ionization (ESI) in positive ion and multiple-reaction monitoring (MRM) mode. The method was linear in the range of 3-1500ng/mL for ABZOX. This method was successfully applied to the bioequivalence study in human plasma samples. Copyright © 2016 Elsevier B.V. All rights reserved.

MixGF: Spectral Probabilities for Mixture Spectra from more than One Peptide*

PubMed Central

Wang, Jian; Bourne, Philip E.; Bandeira, Nuno

2014-01-01

In large-scale proteomic experiments, multiple peptide precursors are often cofragmented simultaneously in the same mixture tandem mass (MS/MS) spectrum. These spectra tend to elude current computational tools because of the ubiquitous assumption that each spectrum is generated from only one peptide. Therefore, tools that consider multiple peptide matches to each MS/MS spectrum can potentially improve the relatively low spectrum identification rate often observed in proteomics experiments. More importantly, data independent acquisition protocols promoting the cofragmentation of multiple precursors are emerging as alternative methods that can greatly improve the throughput of peptide identifications but their success also depends on the availability of algorithms to identify multiple peptides from each MS/MS spectrum. Here we address a fundamental question in the identification of mixture MS/MS spectra: determining the statistical significance of multiple peptides matched to a given MS/MS spectrum. We propose the MixGF generating function model to rigorously compute the statistical significance of peptide identifications for mixture spectra and show that this approach improves the sensitivity of current mixture spectra database search tools by a ≈30–390%. Analysis of multiple data sets with MixGF reveals that in complex biological samples the number of identified mixture spectra can be as high as 20% of all the identified spectra and the number of unique peptides identified only in mixture spectra can be up to 35.4% of those identified in single-peptide spectra. PMID:25225354

Ultra-Trace Analysis of Nine Macrolides, including Tulathromycin A (Draxxin), in Edible Animal Tissues with Mini-Column Liquid Chromatography Tandem Mass Spectrometry

USDA-ARS?s Scientific Manuscript database

Analysis of 9 macrolides is presented, including tulathromycin A (Draxxin), in beef, poultry and pork muscle with a simple multi-residue extraction and analysis method using high performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry. The extraction method inv...

Determination of amphetamine and methamphetamine in umbilical cord using liquid chromatography-tandem mass spectrometry

PubMed Central

Jones, Joseph; Rios, Rosemarie; Jones, Mary; Lewis, Douglas; Plate, Charles

2009-01-01

The use of meconium as a drug-screening matrix for newborns has been the gold standard of care for the past two decades. A recent study using matched pairs of meconium and umbilical cord demonstrated a high degree of agreement. The use of liquid chromatography-tandem mass spectrometry as a means to confirm amphetamines presumptive positive umbilical cord specimens for amphetamine and methamphetamine is described here for the first time. The limit of detection for both compounds was 0.2 ng/g. The limit of quantitation for both compounds was 0.6 ng/g. The assay was linear for both compounds up to 100 ng/g. PMID:19783234

Residue analysis of sixty pesticides in red swamp crayfish using QuEChERS with high-performance liquid chromatography-tandem mass spectrometry

USDA-ARS?s Scientific Manuscript database

In this study, a multi-residue analytical method using QuEChERS extraction and dispersive solid-phase extraction (d-SPE) cleanup followed by high-performance liquid chromatography–tandem mass spectrometry (HPLC-MS/MS) was developed for rapid determination of 60 pesticide residues in whole crayfish a...

Comparison of pulse glow discharge-ion mobility spectrometry and liquid chromatography with tandem mass spectrometry based on multiplug filtration cleanup for the analysis of tricaine mesylate residues in fish and water.

PubMed

Zou, Nan; Chen, Ronghua; Qin, Yuhong; Song, Shuangyu; Tang, Xinglin; Pan, Canping

2016-09-01

Analytical methods based on multiplug filtration cleanup coupled with pulse glow discharge-ion mobility spectrometry and liquid chromatography tandem mass spectrometry were developed for the analysis of tricaine mesylate residue in fish and fish-raising water samples. A silica fiber holder and an appropriate new interface were designed to make the direct introduction of the fiber into the pulse glow discharge-ion mobility spectrometry introduction mechanism. The multiplug filtration cleanup method with adsorption mixtures was optimized for the determination of tricaine mesylate in fish samples. Good linear relationships were obtained by the two methods. For fish samples, limits of detection were 6 and 0.6 μg/kg by ion mobility spectrometry and liquid chromatography with tandem mass spectrometry, respectively. The matrix effect of the established liquid chromatography tandem mass spectrometry method was negligible for fish samples but that of the ion mobility spectrometry method was not. The two methods were compared. The ion mobility spectrometry system could be used a rapid screening tool on site with the advantage of rapidity, simplicity, and portability, and the liquid chromatography tandem mass spectrometry system could be used for validation in laboratory conditions with the advantage of lower limit of detection, stability, and precision. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Rapid screening the alkaloids of poppy shell in hot pot condiment, beef noodle soup and seasoning by direct analysis in real time-tandem mass spectrometry].

PubMed

Zhang, Baile; Gao, Lihong; Xie, Yingshuang; Zhou, Wei; Chen, Xiaofeng; Lei, Chunni; Zhang, Huan

2017-07-08

A direct analysis in real time tandem mass spectrometry (DART-MS/MS) method was established for quickly screening five illegally added alkaloids of poppy shell from the hot pot condiment, beef noodle soup and seasoning. The samples were extracted and purified by acetonitrile, and then injected under the conditions of ionization temperature of 300℃, grid electrode voltage of 150 V and sampling rate of 0.8 mm/s using DART in the positive ion mode. The determination was conducted by tandem mass spectrometry in positive ESI mode under multiple reaction monitoring (MRM) mode. The method is simple and rapid, and can meet the requirement of rapid screening and analysis of large quantities of samples.

[Qualitative and quantitative analysis of amygdalin and its metabolite prunasin in plasma by ultra-high performance liquid chromatography-tandem quadrupole time of flight mass spectrometry and ultra-high performance liquid chromatography-tandem triple quadrupole mass spectrometry].

PubMed

Gao, Meng; Wang, Yuesheng; Wei, Huizhen; Ouyang, Hui; He, Mingzhen; Zeng, Lianqing; Shen, Fengyun; Guo, Qiang; Rao, Yi

2014-06-01

A method was developed for the determination of amygdalin and its metabolite prunasin in rat plasma after intragastric administration of Maxing shigan decoction. The analytes were identified by ultra-high performance liquid chromatography-tandem quadrupole time of flight mass spectrometry and quantitatively determined by ultra-high performance liquid chromatography-tandem triple quadrupole mass spectrometry. After purified by liquid-liquid extraction, the qualitative analysis of amygdalin and prunasin in the plasma sample was performed on a Shim-pack XR-ODS III HPLC column (75 mm x 2.0 mm, 1.6 microm), using acetonitrile-0.1% (v/v) formic acid aqueous solution. The detection was performed on a Triple TOF 5600 quadrupole time of flight mass spectrometer. The quantitative analysis of amygdalin and prunasin in the plasma sample was performed by separation on an Agilent C18 HPLC column (50 mm x 2.1 mm, 1.7 microm), using acetonitrile-0.1% (v/v) formic acid aqueous solution. The detection was performed on an AB Q-TRAP 4500 triple quadrupole mass spectrometer utilizing electrospray ionization (ESI) interface operated in negative ion mode and multiple-reaction monitoring (MRM) mode. The qualitative analysis results showed that amygdalin and its metabolite prunasin were detected in the plasma sample. The quantitative analysis results showed that the linear range of amygdalin was 1.05-4 200 ng/mL with the correlation coefficient of 0.999 0 and the linear range of prunasin was 1.25-2 490 ng/mL with the correlation coefficient of 0.997 0. The method had a good precision with the relative standard deviations (RSDs) lower than 9.20% and the overall recoveries varied from 82.33% to 95.25%. The limits of detection (LODs) of amygdalin and prunasin were 0.50 ng/mL. With good reproducibility, the method is simple, fast and effective for the qualitative and quantitative analysis of the amygdalin and prunasin in plasma sample of rats which were administered by Maxing shigan decoction.

Pivotal role of computers and software in mass spectrometry - SEQUEST and 20 years of tandem MS database searching.

PubMed

Yates, John R

2015-11-01

Advances in computer technology and software have driven developments in mass spectrometry over the last 50 years. Computers and software have been impactful in three areas: the automation of difficult calculations to aid interpretation, the collection of data and control of instruments, and data interpretation. As the power of computers has grown, so too has the utility and impact on mass spectrometers and their capabilities. This has been particularly evident in the use of tandem mass spectrometry data to search protein and nucleotide sequence databases to identify peptide and protein sequences. This capability has driven the development of many new approaches to study biological systems, including the use of "bottom-up shotgun proteomics" to directly analyze protein mixtures. Graphical Abstract ᅟ.

CREATININE DETERMINATION IN URINE BY LIQUID CHROMATOGRAPHY-ELECTROSPRAY IONIZATION-TANDEM MASS SPECTROMETRY METHOD.

PubMed

Dereziński, Paweł; Klupczyńska, Agnieszka; Sawicki, Wojciech; Kokot, Zenon J

2016-01-01

Creatinine determination in urine is used to estimate the completeness of the 24-h urine collection, compensation for variable diuresis and as a preliminary step in protein profiling in urine. Despite the fact that a wide range of methods of measuring creatinine level in biofluids has been developed, many of them are adversely affected by interfering substances. A new liquid chromatography-tandem mass spectrometry method for creatinine determination in urine has been developed. Chromatographic separation was performed by applying C18 column and a gradient elution. Analyses were carried out on a triple quadrupole mass spectrometer equipped with an electrospray ion source. The developed method was fully validated according to the international guidelines. The quantification range of the method was 5-1500 ng/mL, which corresponds to 1-300 mg/dL in urine. Limit of detection and quantitation were 2 and 5 ng/mL, respectively. Additionally, the comparison of creatinine determination by newly developed method to the colorimetric method was performed. The method enables the determination of creatinine in urine samples with a minimal sample preparation, excellent sensitivity and prominent selectivity. Since mass spectrometry allows to measure a number of compounds simultaneously, a future perspective would be to incorporate the determination of other clinically important compounds excreted in urine.

Quantification of 11-Nor-9-Carboxy-Δ9-Tetrahydrocannabinol in Human Oral Fluid by Gas Chromatography–Tandem Mass Spectrometry

PubMed Central

Barnes, Allan J.; Scheidweiler, Karl B.; Huestis, Marilyn A.

2015-01-01

A sensitive and specific method for the quantification of 11-nor-9-carboxy-Δ9-tetrahydrocannabinol (THCCOOH) in oral fluid collected with the Quantisal and Oral-Eze devices was developed and fully validated. Extracted analytes were derivatized with hexafluoroisopropanol and trifluoroacetic anhydride and quantified by gas chromatography–tandem mass spectrometry with negative chemical ionization. Standard curves, using linear least-squares regression with 1/x2 weighting were linear from 10 to 1000 ng/L with coefficients of determination >0.998 for both collection devices. Bias was 89.2%–112.6%, total imprecision 4.0%–5.1% coefficient of variation, and extraction efficiency >79.8% across the linear range for Quantisal-collected specimens. Bias was 84.6%–109.3%, total imprecision 3.6%–7.3% coefficient of variation, and extraction efficiency >92.6% for specimens collected with the Oral-Eze device at all 3 quality control concentrations (10, 120, and 750 ng/L). This effective high-throughput method reduces analysis time by 9 minutes per sample compared with our current 2-dimensional gas chromatography–mass spectrometry method and extends the capability of quantifying this important oral fluid analyte to gas chromatography–tandem mass spectrometry. This method was applied to the analysis of oral fluid specimens collected from individuals participating in controlled cannabis studies and will be effective for distinguishing passive environmental contamination from active cannabis smoking. PMID:24622724

Separate Spectra of the Components of the Low-mass Binary L722-22

NASA Astrophysics Data System (ADS)

Chance, D.; Hershey, J.

1996-12-01

Separate spectra have been acquired of the components of the low-mass binary L722-22A,B. Using the Hubble Space Telescope Faint Object Spectrograph in the same manner described in BAAS 27,1341 for Ross 614A,B a small aperture was placed on each star, excluding the light from the other. L722-22 was discovered to be a binary by Ianna (1988, AJ 95,1226) from a small photographic photocentric orbit found in parallax observations. The ground-based work indicated L722-22B might have a mass in the brown-dwarf range, at 0.06 M_⊙ which motivated the FOS observations. However, current HST astrometric work indicates L722-22B is at the 0.1 M_⊙ level (Taff, Hershey Space Telescope Astrometry Team 75th Meeting Report, Apr 1996). Ground based CCD spectra of M dwarf standards have been provided to us by J. Davy Kirkpatrick in the 6300 to 8500 Angstroms range. Apart from the telluric lines the FOS spectra interpolate very closely into the ground-based series across this spectral range. A classification program has been written which defines a series of spectral interval ratios, does fits for the indices of the standards as a function of spectral subtype across the M3 to M7 range of standards, and inverts the fits for the four unknown spectra of Ross 614A,B and L722-22A,B. The internal formal error of the mean from the series of indices is a small fraction of a spectral subtype. The spectral types of L722-22A and B are found to be earlier by about 3/4 of a spectral subtype than Ross 614A and B, respectively. The HST astrometry and spectroscopy yield points for these 4 binary members which lie in a very narrow locus in the mass-spectral type plane and imply that single stars of types dM6 and later, have masses less than 0.08 M_⊙, presumably substellar. Support for this work was provided by NASA through grant number 06048 from the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc. under NASA contract NAS5-26555.

Ultra-performance liquid chromatography-tandem mass spectrometry for the determination of atypical antipsychotics and some metabolites in in vitro samples.

PubMed

Li, Kun-Yan; Zhou, Yan-Gang; Ren, Hua-Yi; Wang, Feng; Zhang, Bi-Kui; Li, Huan-De

2007-05-01

The ultra-performance liquid chromatography-electrospray tandem mass spectrometry (UPLC-ESI-MS/MS) method has been developed to perform the determination of quetiapine, perospirone, aripiprazole and quetiapine sulfoxide in in vitro samples in less than 3 min. The UPLC separation was carried out using an Acquity UPLC BEH C18 column (100 mm x 2.1mm i.d., 1.7 microm particle size) that provided high efficiency and resolution in combination with high linear velocities. The UPLC system was coupled to a Waters Micromass Quattro Premier XE tandem quadrupole mass spectrometer. This system permits high-speed data acquisition without peak intensity degradation, and produces sharp and narrow chromatographic peaks (w(h) about 2.5s) of compounds. The determination was performed in multiple reaction monitoring (MRM) mode. The quantification parameters of the developed method were established, obtaining instrumental LODs lower than 0.005 microg/l and a repeatability at a low concentration level lower than 10% CV (n=10). Finally, the method was successfully applied to the analysis of atypical antipsychotics and some metabolites in in vitro samples.

Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin

NASA Astrophysics Data System (ADS)

Floris, Federico; Chiron, Lionel; Lynch, Alice M.; Barrow, Mark P.; Delsuc, Marc-André; O'Connor, Peter B.

2018-06-01

Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about 23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from 23% to 42%.

Electrical and optical analyses of tandem organic light-emitting diodes with organic charge-generation layer

NASA Astrophysics Data System (ADS)

Kim, Bong Sung; Chae, Heeyeop; Chung, Ho Kyoon; Cho, Sung Min

2018-06-01

The electrical and optical properties of tandem organic light-emitting diodes (OLEDs), in which a fluorescent and phosphorescent emitting units are connected by an organic charge-generation layer (CGL), were experimentally analyzed. To investigate the internal properties of the tandem OLEDs, we fabricated and compared two single, two homo-tandem, and two hetero-tandem OLEDs using the fluorescent and phosphorescent units. From the experimental results of the OLEDs obtained at the same current density, the voltage across the CGL as well as the individual emission spectra and luminance of each unit of tandem OLEDs were obtained and compared with the theoretical simulation results. The analysis method proposed in this study can be utilized as a method to verify the accuracy of optical or electrical computer simulation of tandem OLED and it will be useful to understand the overall electrical and optical characteristics of tandem OLEDs.

Characterization of signatures from organic compounds in CDA mass spectra of ice particles in Saturn's E-ring

NASA Astrophysics Data System (ADS)

Khawaja, Nozair; Postberg, Frank; Reviol, Rene; Srama, Ralf

2015-04-01

The major source of ice particles in Saturn's E-ring is Enceladus - a geological active moon of Saturn. Enceladus is emanating ice particles from its fractured south polar terrain (SPT), the so-called "Tiger Stripes". The source of Enceladus activity and many of the ice particles is a subsurface ocean. The Cosmic Dust Analyzer (CDA) onboard the Cassini spacecraft is sampling these icy particles and producing TOF mass spectra of cations of impinging particles [1]. Three compositional types of ice particles have been identified from CDA-mass spectra: (i) pure water ice (Type-1) (ii) organic rich (Type-2) (iii) salt rich (Type-3) [2][3]. These organic rich (Type-2) spectra are particularly abundant in the icy jets of Enceladus as we found out during the Cassini's Enceladus flybys (E17 and E18) in 2012 [4]. We present a compositional analysis of the CDA spectra of these organic rich icy grains sampled in the E ring. We have characterized hundreds of Type-2 spectra of impinging ice particles. These were recorded at different impact velocities causing different molecular fragmentation patterns observed in the mass spectra. We defined 3 typical impact speed intervals: (i) 4-7 km/s (ii) 8-11 km/s and (iii) 12-16km/s. Organic features best observed at slow (4-7 km/s) or at intermediate (8-11 km/s) impact velocity ranges. Several classes of organic rich spectra are identified. Classifying Type-2 spectra are according to their characteristic mass lines of possible organic species. We try to infer the composition of each class of organic rich spectra is inferred by using an experimental setup (IR-FL-MALDI) to simulate the CDA spectra of different compositional types. In the laboratory we have used infrared laser to disperse a micro-beam of a water solution [5]. The laser energy is adjusted to simulate different impact velocities of ice particles on the CDA. Four families of organic compounds including alcohols, fatty acids, amines and aromatic, with varying number of carbon

Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin.

PubMed

Floris, Federico; Chiron, Lionel; Lynch, Alice M; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B

2018-06-04

Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about ~23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from ~23% to ~42%. Graphical Abstract Two-dimensional mass spectrometry, when applied to primary fragment ions from the source, allows deep-sequencing of the protein calmodulin.

Rapid qualitative and quantitative analysis of proanthocyanidin oligomers and polymers by ultra-performance liquid chromatography – tandem mass spectrometry (UPLC-MS/MS)

USDA-ARS?s Scientific Manuscript database

We developed a rapid method with ultra-performance liquid chromatography – tandem mass spectrometry (UPLC-MS/MS) for the qualitative and quantitative analysis of plant proanthocyanidins (PAs) directly from crude plant extracts. The method utilizes a range of cone voltages to achieve the depolymeriza...

[Simultaneous determination of four alkaloids in Corydalis decumbens (Thunb.) Pers. by high performance liquid chromatography-tandem mass spectrometry].

PubMed

Shen, Yan; Han, Chao; Liu, Cuiping; Zhou, Yongfang; Xia, Biqi; Zhu, Zhenou; Liu, Aili

2011-02-01

A method for the analysis of 4 alkaloids in Corydalis decumbens (Thunb.) Pers. was developed by high performance liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-MS/MS). The sample was extracted in methanol by ultrasonic, filtered and diluted with methanol for further analysis. The analysis was performed on a C18 column (150 mm x 2.1 mm, 3.5 microm) using a gradient elution program with the mobile phase of 0.2% acetic acid solution and acetonitrile. The analyte was determined by an electrospray ionization tandem mass spectrometry in multiple reactions monitoring (MRM) mode. The qualitative and quantitative analyses were based on the retention times and characteristic ion pairs consisting of one parent ion and two fragment ions of the analyte. The limits of detection (LODs) for 4 alkaloids were in the range of 0.02 - 0.2 microg/L, and the limits of quantification (LOQs) were in the range of 0.07 - 0.66 microg/L. The average recoveries were in the range of 93.6% - 103.5% for 4 alkaloids with the relative standard deviations below 3.8%. This method is reliable, sensitive and reproducible, and it can be used for the quality control of Corydalis decumbens (Thunb.) Pers. sample.

An accurate proteomic quantification method: fluorescence labeling absolute quantification (FLAQ) using multidimensional liquid chromatography and tandem mass spectrometry.

PubMed

Liu, Junyan; Liu, Yang; Gao, Mingxia; Zhang, Xiangmin

2012-08-01

A facile proteomic quantification method, fluorescent labeling absolute quantification (FLAQ), was developed. Instead of using MS for quantification, the FLAQ method is a chromatography-based quantification in combination with MS for identification. Multidimensional liquid chromatography (MDLC) with laser-induced fluorescence (LIF) detection with high accuracy and tandem MS system were employed for FLAQ. Several requirements should be met for fluorescent labeling in MS identification: Labeling completeness, minimum side-reactions, simple MS spectra, and no extra tandem MS fragmentations for structure elucidations. A fluorescence dye, 5-iodoacetamidofluorescein, was finally chosen to label proteins on all cysteine residues. The fluorescent dye was compatible with the process of the trypsin digestion and MALDI MS identification. Quantitative labeling was achieved with optimization of reacting conditions. A synthesized peptide and model proteins, BSA (35 cysteines), OVA (five cysteines), were used for verifying the completeness of labeling. Proteins were separated through MDLC and quantified based on fluorescent intensities, followed by MS identification. High accuracy (RSD% < 1.58) and wide linearity of quantification (1-10(5) ) were achieved by LIF detection. The limit of quantitation for the model protein was as low as 0.34 amol. Parts of proteins in human liver proteome were quantified and demonstrated using FLAQ. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comprehensive analysis of ß-lactam antibiotics including penicillins, cephalosporins, and carbapenems in poultry muscle using liquid chromatography coupled to tandem mass spectrometry.

PubMed

Berendsen, Bjorn J A; Gerritsen, Henk W; Wegh, Robin S; Lameris, Steven; van Sebille, Ralph; Stolker, Alida A M; Nielen, Michel W F

2013-09-01

A comprehensive method for the quantitative residue analysis of trace levels of 22 ß-lactam antibiotics, including penicillins, cephalosporins, and carbapenems, in poultry muscle by liquid chromatography in combination with tandem mass spectrometric detection is reported. The samples analyzed for ß-lactam residues are hydrolyzed using piperidine in order to improve compound stability and to include the total residue content of the cephalosporin ceftifour. The reaction procedure was optimized using a full experimental design. Following detailed isotope labeling, tandem mass spectrometry studies and exact mass measurements using high-resolution mass spectrometry reaction schemes could be proposed for all ß-lactams studied. The main reaction occurring is the hydrolysis of the ß-lactam ring under formation of the piperidine substituted amide. For some ß-lactams, multiple isobaric hydrolysis reaction products are obtained, in accordance with expectations, but this did not hamper quantitative analysis. The final method was fully validated as a quantitative confirmatory residue analysis method according to Commission Decision 2002/657/EC and showed satisfactory quantitative performance for all compounds with trueness between 80 and 110% and within-laboratory reproducibility below 22% at target level, except for biapenem. For biapenem, the method proved to be suitable for qualitative analysis only.

Differentiation of regioisomeric aromatic ketocarboxylic acids by atmospheric pressure chemical ionization CAD tandem mass spectrometry in a linear quadrupole ion trap mass spectrometer

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

Amundson, Lucas M.; Owen, Ben C.; Gallardo, Vanessa A.

2011-01-01

Positive-mode atmospheric pressure chemical ionization tandem mass spectrometry (APCI-MS n ) was tested for the differentiation of regioisomeric aromatic ketocarboxylic acids. Each analyte forms exclusively an abundant protonated molecule upon ionization via positive-mode APCI in a commercial linear quadrupole ion trap (LQIT) mass spectrometer. Energy-resolved collision-activated dissociation (CAD) experiments carried out on the protonated analytes revealed fragmentation patterns that varied based on the location of the functional groups. Unambiguous differentiation between the regioisomers was achieved in each case by observing different fragmentation patterns, different relative abundances of ion-molecule reaction products, or different relative abundances of fragment ions formed at differentmore » collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.« less

Unravelling associations between unassigned mass spectrometry peaks with frequent itemset mining techniques.

PubMed

Vu, Trung Nghia; Mrzic, Aida; Valkenborg, Dirk; Maes, Evelyne; Lemière, Filip; Goethals, Bart; Laukens, Kris

2014-01-01

Mass spectrometry-based proteomics experiments generate spectra that are rich in information. Often only a fraction of this information is used for peptide/protein identification, whereas a significant proportion of the peaks in a spectrum remain unexplained. In this paper we explore how a specific class of data mining techniques termed "frequent itemset mining" can be employed to discover patterns in the unassigned data, and how such patterns can help us interpret the origin of the unexpected/unexplained peaks. First a model is proposed that describes the origin of the observed peaks in a mass spectrum. For this purpose we use the classical correlative database search algorithm. Peaks that support a positive identification of the spectrum are termed explained peaks. Next, frequent itemset mining techniques are introduced to infer which unexplained peaks are associated in a spectrum. The method is validated on two types of experimental proteomic data. First, peptide mass fingerprint data is analyzed to explain the unassigned peaks in a full scan mass spectrum. Interestingly, a large numbers of experimental spectra reveals several highly frequent unexplained masses, and pattern mining on these frequent masses demonstrates that subsets of these peaks frequently co-occur. Further evaluation shows that several of these co-occurring peaks indeed have a known common origin, and other patterns are promising hypothesis generators for further analysis. Second, the proposed methodology is validated on tandem mass spectrometral data using a public spectral library, where associations within the mass differences of unassigned peaks and peptide modifications are explored. The investigation of the found patterns illustrates that meaningful patterns can be discovered that can be explained by features of the employed technology and found modifications. This simple approach offers opportunities to monitor accumulating unexplained mass spectrometry data for emerging new patterns

Tandem Mass Spectrometry of Modified and Platinated Oligoribonucleotides

NASA Astrophysics Data System (ADS)

Nyakas, Adrien; Stucki, Silvan R.; Schürch, Stefan

2011-05-01

Therapeutic approaches for treatment of various diseases aim at the interruption of transcription or translation. Modified oligonucleotides, such as 2'- O-methyl- and methylphosphonate-derivatives, exhibit high resistance against cellular nucleases, thus rendering application for, e.g., antigene or antisense purposes possible. Other approaches are based on administration of cross-linking agents, such as cis-diamminedichloroplatinum(II) (cisplatin, DDP), which is still the most widely used anticancer drug worldwide. Due to the formation of 1,2-intrastrand cross links at adjacent guanines, replication of the double-strand is disturbed, thus resulting in significant cytotoxicity. Evidence for the gas-phase dissociation mechanism of platinated RNA is given, based on nano-electrospray ionization high-resolution multistage tandem mass spectrometry (MS n ). Confirmation was found by investigating the fragmentation pattern of platinated and unplatinated 2'-methoxy oligoribonucleotide hexamers and their corresponding methylphosphonate derivatives. Platinated 2'-methoxy oligoribonucleotides exhibit a similar gas-phase dissociation behavior as the corresponding DNA and RNA sequences, with the 3'-C-O bond adjacent to the vicinal guanines being cleaved preferentially, leading to wx-ion formation. By examination of the corresponding platinated methylphosphonate derivatives of the 2'-methoxy oligoribonucleotides, the key role of the negatively charged phosphate oxygen atoms in direct proximity to the guanines was proven. The significant alteration of fragmentation due to platination is demonstrated by comparison of the fragment ion patterns of unplatinated and platinated 2'- O-methyl- and 2'- O-methyl methylphosphonate oligoribonucleotides, and the results obtained by H/D exchange experiments.

Observation of T-2 and HT-2 glucosides from Fusarium sporotrichioides by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS)

USDA-ARS?s Scientific Manuscript database

Cultures of Fusarium sporotrichioides were extracted and subjected to evaluation by high performance liquid chromatography – tandem mass spectrometry (LC-MS/MS). Along with the expected T-2 and HT-2 toxins, compounds 162 m/z higher than the toxins were observed. Fragmentation behavior of the larger ...

Monitoring salivary melatonin concentrations in children with sleep disorders using liquid chromatography-tandem mass spectrometry.

PubMed

Khan, Sohil A; George, Rani; Charles, Bruce G; Taylor, Paul J; Heussler, Helen S; Cooper, David M; McGuire, Treasure M; Pache, David; Norris, Ross L G

2013-06-01

Melatonin is synthesized in the pineal gland and is an important circadian phase marker, especially in the determination of sleep patterns. Both temporary and permanent abnormal sleep patterns occur in children; therefore, it is desirable to have methods for monitoring melatonin in biological fluids in the diagnosis and treatment of such disorders. The objective of the study is to develop a liquid chromatography-tandem mass spectrometry method for the determination of melatonin in saliva and to apply it to monitoring salivary concentrations in children with sleep disorders. A deuterated internal standard (d7-melatonin) was added to a diluted saliva sample (20 µL) in an autosampler vial insert, and 50 µL were injected. Plasticware was strictly avoided, and all glassware was scrupulously cleaned and then baked at 120°C for at least 48 hours to obtain satisfactory performance. Reverse-phase chromatography was performed on a C8 column using a linear gradient elution profile comprising mobile phases A (0.1% aqueous formic acid) and B (15% methanol in acetonitrile containing 0.1% formic acid), pumped at a total flow rate of 0.8 mL/min. The run time was 8 minutes. After atmospheric pressure chemical ionization, mass spectrometric detection was in positive ion mode. Mass detection was by selected reaction monitoring mode with the following mass transitions used for quantification: melatonin, m/z 233.0 → 173.8 and d7-melatonin, m/z 240.0 → 178.3. Linearity (r > 0.999) was established from 3.9 to 1000 pg/mL. Imprecision (coefficient of variation percent) was less than 11%, and accuracy was 100-105% (7.0-900 pg/mL). The method was selective, and the mean (range) ratio of the slopes of calibrations in water to those in daytime saliva samples collected from 10 healthy adult subjects was 0.989 (0.982-0.997), indicating negligible matrix effects. The application of the assay was demonstrated in healthy adults and in children being clinically investigated for sleep

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.

Quantitative determination of tilmicosin in canine serum by high performance liquid chromatography-tandem mass spectrometry.

PubMed

Herrera, Michael; Ding, Haiqing; McClanahan, Robert; Owens, Jane G; Hunter, Robert P

2007-09-15

A highly sensitive and quantitative LC/MS/MS assay for the determination of tilmicosin in serum has been developed and validated. For sample preparation, 0.2 mL of canine serum was extracted with 3 mL of methyl tert-butyl ether. The organic layer was transferred to a new vessel and dried under nitrogen. The sample was then reconstituted for analysis by high performance liquid chromatography-tandem mass spectrometry. A Phenomenex Luna C8(2) analytical column was used for the chromatographic separation. The eluent was subsequently introduced to the mass spectrometer by electrospray ionization. A single range was validated for 50-5000 ng/mL for support of toxicokinetic studies. The inter-day relative error (inaccuracy) for the LLOQ samples ranged from -5.5% to 0.3%. The inter-day relative standard deviations (imprecision) at the respective LLOQ levels were < or =10.1%.

Measurement of tamsulosin in human serum by liquid chromatography–tandem mass spectrometry☆

PubMed Central

Upreti, Rita; Homer, Natalie Z.M.; Naredo, Gregorio; Cobice, Diego F.; Hughes, Katherine A.; Stewart, Laurence H.; Walker, Brian R.; Andrew, Ruth

2013-01-01

A simple, sensitive and robust method to extract tamsulosin from human serum, and quantify by liquid chromatography–tandem mass spectrometry (LC–MS/MS) was developed and validated and is applicable as a measure of compliance in clinical research. Tamsulosin was extracted from human serum (100 μL) via liquid–liquid extraction with methyl tert-butyl ether (2 mL) following dilution with 0.1 M ammonium hydroxide (100 μL), achieving 99.9% analyte recovery. Internal standard, d9-finasteride, was synthesised in-house. Analyte and internal standard were separated on an Ascentis® Express C18 (100 mm × 3 mm, 2.7 μm) column using a gradient elution with mobile phases methanol and 2 mM aqueous ammonium acetate (5:95, v/v). Total run-time was 6 min. Tamsulosin was quantified using a triple quadrupole mass spectrometer operated in multi-reaction-monitoring (MRM) mode using positive electrospray ionisation. Mass transitions monitored for quantitation were: tamsulosin m/z 409 → 228 and d9-finasteride m/z 382 → 318, with the structural formulae of ions confirmed by Fourier transform ion cyclotron resonance mass spectrometry (within 10 ppm). The limit of quantitation was 0.2 ng/mL, and the method was validated in the linear range 0.2–50 ng/mL with acceptable inter- and intra-assay precision and accuracy and stability suitable for routine laboratory practice. The method was successfully applied to samples taken from research volunteers in a clinical study of benign prostatic hyperplasia. PMID:23743242

Measurement of tamsulosin in human serum by liquid chromatography-tandem mass spectrometry.

PubMed

Upreti, Rita; Homer, Natalie Z M; Naredo, Gregorio; Cobice, Diego F; Hughes, Katherine A; Stewart, Laurence H; Walker, Brian R; Andrew, Ruth

2013-07-01

A simple, sensitive and robust method to extract tamsulosin from human serum, and quantify by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed and validated and is applicable as a measure of compliance in clinical research. Tamsulosin was extracted from human serum (100μL) via liquid-liquid extraction with methyl tert-butyl ether (2mL) following dilution with 0.1M ammonium hydroxide (100μL), achieving 99.9% analyte recovery. Internal standard, d9-finasteride, was synthesised in-house. Analyte and internal standard were separated on an Ascentis(®) Express C18 (100mm×3mm, 2.7μm) column using a gradient elution with mobile phases methanol and 2mM aqueous ammonium acetate (5:95, v/v). Total run-time was 6min. Tamsulosin was quantified using a triple quadrupole mass spectrometer operated in multi-reaction-monitoring (MRM) mode using positive electrospray ionisation. Mass transitions monitored for quantitation were: tamsulosin m/z 409→228 and d9-finasteride m/z 382→318, with the structural formulae of ions confirmed by Fourier transform ion cyclotron resonance mass spectrometry (within 10ppm). The limit of quantitation was 0.2ng/mL, and the method was validated in the linear range 0.2-50ng/mL with acceptable inter- and intra-assay precision and accuracy and stability suitable for routine laboratory practice. The method was successfully applied to samples taken from research volunteers in a clinical study of benign prostatic hyperplasia. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

MixGF: spectral probabilities for mixture spectra from more than one peptide.

PubMed

Wang, Jian; Bourne, Philip E; Bandeira, Nuno

2014-12-01

In large-scale proteomic experiments, multiple peptide precursors are often cofragmented simultaneously in the same mixture tandem mass (MS/MS) spectrum. These spectra tend to elude current computational tools because of the ubiquitous assumption that each spectrum is generated from only one peptide. Therefore, tools that consider multiple peptide matches to each MS/MS spectrum can potentially improve the relatively low spectrum identification rate often observed in proteomics experiments. More importantly, data independent acquisition protocols promoting the cofragmentation of multiple precursors are emerging as alternative methods that can greatly improve the throughput of peptide identifications but their success also depends on the availability of algorithms to identify multiple peptides from each MS/MS spectrum. Here we address a fundamental question in the identification of mixture MS/MS spectra: determining the statistical significance of multiple peptides matched to a given MS/MS spectrum. We propose the MixGF generating function model to rigorously compute the statistical significance of peptide identifications for mixture spectra and show that this approach improves the sensitivity of current mixture spectra database search tools by a ≈30-390%. Analysis of multiple data sets with MixGF reveals that in complex biological samples the number of identified mixture spectra can be as high as 20% of all the identified spectra and the number of unique peptides identified only in mixture spectra can be up to 35.4% of those identified in single-peptide spectra. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Use of oleic-acid functionalized nanoparticles for the magnetic solid-phase microextraction of alkylphenols in fruit juices using liquid chromatography-tandem mass spectrometry.

PubMed

Viñas, Pilar; Pastor-Belda, Marta; Torres, Aitor; Campillo, Natalia; Hernández-Córdoba, Manuel

2016-05-01

Magnetic nanoparticles of cobalt ferrite with oleic acid as the surfactant (CoFe2O4/oleic acid) were used as sorbent material for the determination of alkylphenols in fruit juices. High sensitivity and specificity were achieved by liquid chromatography and detection using both diode-array (DAD) and electrospray-ion trap-tandem mass spectrometry (ESI-IT-MS/MS) in the selected reaction monitoring (SRM) mode of the negative fragment ions for alkylphenols (APs) and in positive mode for ethoxylate APs (APEOs). The optimized conditions for the different variables influencing the magnetic separation procedure were: mass of magnetic nanoparticles, 50mg, juice volume, 10mL diluted to 25mL with water, pH 6, stirring for 10min at room temperature, separation with an external neodymium magnet, desorption with 3mL of methanol and orbital shaking for 5min. The enriched organic phase was evaporated and reconstituted with 100µL acetonitrile before injecting 30µL into a liquid chromatograph with a mobile phase composed of acetonitrile/0.1% (v/v) formic acid under gradient elution. Quantification limits were in the range 3.6 to 125ngmL(-1). The recoveries obtained were in the 91-119% range, with RSDs lower than 14%. The ESI-MS/MS spectra permitted the correct identification of both APs and APEOs in the fruit juice samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Liquid chromatography with tandem mass spectrometry quantification of urinary proanthocyanin A2 dimer and its potential use as a biomarker of cranberry intake

USDA-ARS?s Scientific Manuscript database

The lack of a biomarker for the consumption of cranberries has confounded the interpretation of several studies investigating the effect of cranberry products, especially juices, on health outcomes. The objectives of this pilot study were to develop a liquid chromatography tandem mass spectrometric ...

Characterisation of homoflavonoids from three Ophioglossum species using liquid chromatography with diode array detection and electrospray ionisation tandem mass spectrometry.

PubMed

Wan, Chuan-Xing; Luo, Jian-Guang; Gu, Yu-Cheng; Xu, De-Ran; Kong, Ling-Yi

2013-01-01

Homoflavonoids, characterised by one more carbon atom directly added to C6 -C3 -C6 backbone of flavonoids, are rich in the species of genus Ophioglossum. Up to now we have little knowledge about their MS fragmentation patterns. It is therefore necessary to investigate their MS fragmentation pathways so as to distinguish them from other types of flavonoids. To develop a rapid method for identifying homoflavonoids from Ophioglossum based on their characteristic MS fragmentation. Mass spectrometry fragmentation pathways and qualitative analysis of homoflavonoids in three ferns of Ophioglosssum were investigated by using high-performance liquid chromatography coupled with diode-array detection and electrospray ionisation tandem mass spectrometry (HPLC-DAD-ESI/MS(n) ). The analyses of the MS(n) spectra of the homoflavonoids allowed us to classify them into two types according to their fragmentation characteristics. The type I homoflavonoids, with an attached additional carbon atom to the C-3 position of the C-ring, presented the initial competing loss of H2 O and CH2 O from their aglycone ions, compared to the initial removal of H2 O or CO in the case of the type II homoflavonoids, which bear the additional carbon atom at the C-2' site of the B-ring and forming ring D. The above characteristic fragmentations of homoflavonoids were quite different from those of other flavonoids, and were successfully applied to identify homoflavonoids in the crude extracts of three Ophioglossum species. The HPLC-DAD-ESI/MS(n) method obtained in the present study provided a powerful tool for identifying homoflavonoids from ferns in the genus Ophioglossum. Copyright © 2013 John Wiley & Sons, Ltd.

Hyphenation of supercritical fluid chromatography with tandem mass spectrometry for fast determination of four aflatoxins in edible oil.

PubMed

Lei, Fang; Li, Chenglong; Zhou, Shuang; Wang, Dan; Zhao, Yunfeng; Wu, Yongning

2016-08-01

Aflatoxins (AFTs) are of great concern all over the world. Supercritical fluid chromatography (SFC) has the advantage of fast, high resolution and excellent compatibility with a broad range of organic solvents and samples, thus hyphenating SFC with tandem mass spectrometry (MS/MS) can be used for the easy and fast determination of AFTs in edible oils. Edible oil was spiked with isotope-labeled aflatoxin standards, diluted with hexane and extracted with acetonitrile. The extraction was directly loaded to an SFC apparatus and separated on a UPC(2) 2-EP column with CO2 -methanol gradient elution. A post-column make-up flow was introduced to facilitate mass spectrometry performance, and the mixture was analyzed by MS/MS with an electrospray ionization (ESI) source. The SFC conditions including separation column, modifier and sample solvent were optimized, and the four target aflatoxins were baseline separated. The ESI interface parameters were also investigated, implicating the make-up flow as a critical factor for sensitive determination by SFC-MS/MS. The LOQs for the AFTs were 0.05-0.12 μg L(-1) , while the RSDs were lower than 8.5%. Supercritical fluid chromatography was successfully coupled to tandem mass spectrometry to establish a simple, fast and sensitive method for the analysis of four aflatoxins in edible oil. This shows the combination of SFC-MS/MS has great potential in determination of trace contaminants in food. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Investigation of an enhanced resolution triple quadrupole mass spectrometer for high-throughput liquid chromatography/tandem mass spectrometry assays.

PubMed

Yang, Liyu; Amad, Ma'an; Winnik, Witold M; Schoen, Alan E; Schweingruber, Hans; Mylchreest, Iain; Rudewicz, Patrick J

2002-01-01

Triple quadrupole mass spectrometers, when operated in multiple reaction monitoring (MRM) mode, offer a unique combination of sensitivity, specificity, and dynamic range. Consequently, the triple quadrupole is the workhorse for high-throughput quantitation within the pharmaceutical industry. However, in the past, the unit mass resolution of quadrupole instruments has been a limitation when interference from matrix or metabolites cannot be eliminated. With recent advances in instrument design, triple quadrupole instruments now afford mass resolution of less than 0.1 Dalton (Da) full width at half maximum (FWHM). This paper describes the evaluation of an enhanced resolution triple quadrupole mass spectrometer for high-throughput bioanalysis with emphasis on comparison of selectivity, sensitivity, dynamic range, precision, accuracy, and stability under both unit mass (1 Da FWHM) and enhanced (mass resolution, the transmitted precursor ion from the first quadrupole contained not only protonated molecules from mometasone, but also PPG interference. At enhanced resolution only selected mometasone peaks were transmitted, and no interference from PPG was detected. Sensitivity of the instrument was demonstrated with 10 femtograms of descarboethoxyloratadine injected on-column, for which a signal-to-noise (S/N) ratio of 24 was obtained for MRM chromatograms at both unit and enhanced resolution. Absolute signals obtained at enhanced resolution were about one-third those obtained at unit mass resolution. However, S/N was maintained at enhanced resolution due to the proportional decrease in noise level. Finally, the stability of the instrument operating at enhanced resolution was demonstrated during an overnight 17 h period that was used to validate a liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay for

Newborn screening by tandem mass spectrometry: ethical and social issues.

PubMed

Avard, Denise; Vallance, Hilary; Greenberg, Cheryl; Potter, Beth

2007-01-01

Emerging technologies like Tandem Mass Spectrometry (TMS) enable multiple tests on a single blood sample and allow the expansion of Newborn Screening (NBS) to include various metabolic diseases. Introducing TMS for NBS raises important social and ethical questions: what are the criteria for adding disorders to screening panels? What evidence justifies expansion of screening? How can equity in NBS access and standards be ensured? How can policy standards be set, given the multiplicity of stakeholders? To address emerging issues, policy-makers, patient advocates, clinicians and researchers had a workshop during the 2005 Garrod Symposium. The participants received a summary of the discussion and understood the workshop's goal was to provide a basis for further discussion. This article contributes to this ongoing discussion. Several proposed recommendations assert the centrality of including social and ethical issues in the assessment of whether or not to introduce TMS. The article outlines five key recommendations for advancing the NBS agenda: national public health leadership; transparency; increased national consistency in NBS strategy, including minimum standards; collaboration between the federal and provincial/territorial governments and diverse stakeholders; and supporting research and/or programs based on effectiveness, which integrate ethical and social issues into assessment.

[Simultaneous determination of 16 flavonoids in the ginkgo dietary supplement tea by high performance liquid chromatography-tandem mass spectrometry].

PubMed

Jiang, Yalan; Huang, Fang; Wu, Fuhai; Wu, Huiqin; Huang, Xiaolan; Deng, Xin

2015-10-01

A method for the determination of 16 functional components of ginkgo dietary supplement tea such as catechin, vitexin, puerarin, isoflavoues aglycone, silymarin, quercetin, luteolin, apigenin, naringenin, hesperitin dihydrochalcone, kaempferol, hesperitin, isorhamnetin, baicalein, nobiletin and tangeretin by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was proposed. The conditions of chromatography and mass spectrometry were optimized. The 16 flavonoids were separated on a C18 chromatographic column with acetonitrile and water (additional 0.1% formic acid) as mobile phases under gradient elution at a flow rate of 0.25 mL/min. The determination was conducted by tandem mass spectrometry in positive ESI mode under multiple reaction monitoring (MRM) mode. Good linearities for all the compounds, with correlation coefficients over 0.996, were acquired. The recoveries were in the range of 70.9% to 100.0% (n = 6), while the relative standard deviations (RSDs) were less than 10%. The results showed that the nine flavonoids, which were kaempferol, quercetin, hesperitin, vitexin, luteolin, catechin, apigenin, naringenin and isorhamnetin, were higher in contents among the 16 flavonoids in real samples, and they constituted up to 99.6% of the total flavonoids. The contents of these nine flavonoids can be considered as the quality control index of the ginkgo dietary supplement tea. The method proved to be rapid, selective, sensitive and stable, and it can be applied to control the quality of the ginkgo dietary supplement tea.

Quantification of citalopram or escitalopram and their demethylated metabolites in neonatal hair samples by liquid chromatography-tandem mass spectrometry.

PubMed

Frison, Giampietro; Favretto, Donata; Vogliardi, Susanna; Terranova, Claudio; Ferrara, Santo Davide

2008-08-01

Citalopram and escitalopram are highly selective serotonin reuptake inhibitors widely used in the treatment of depression. They exhibit adverse drug reactions and side effects, however, and the development of specific methods for their determination is of great interest in clinical and forensic toxicology. A liquid chromatography-tandem mass spectrometry method has been developed and validated for the assay of citalopram, escitalopram, and their demethylated metabolites in 10-mg hair samples. The analytes were extracted by incubation in methanol and liquid/liquid extraction with diethyl ether/dichloromethane. Gradient elution on a narrow bore C18 column was realized using clomipramine-d3 as an internal standard. Positive ion electrospray ionization and tandem mass spectrometry determination by collision-induced dissociation were performed in an ion trap mass spectrometer. The method exhibited a linear range of 25 to 2000 pg/mg, a quantification limit of 25 pg/mg for all analytes, relative standard deviations in the range of 12.10 to 9.80 (intraassay), and 13.80 to 11.78 (interassay), and accuracies (as percent recovery of the spiked standards) in the range of 90% to 110%; it was applied to the determination of citalopram and escitalopram and their metabolites in hair samples of two newborns to document their in utero exposure to the drugs. The method proved suitable for neonatal hair analysis of citalopram or escitalopram and was applied to two real cases of gestational exposure.

Combinatorial Labeling Method for Improving Peptide Fragmentation in Mass Spectrometry

NASA Astrophysics Data System (ADS)

Kuchibhotla, Bhanuramanand; Kola, Sankara Rao; Medicherla, Jagannadham V.; Cherukuvada, Swamy V.; Dhople, Vishnu M.; Nalam, Madhusudhana Rao

2017-06-01

Annotation of peptide sequence from tandem mass spectra constitutes the central step of mass spectrometry-based proteomics. Peptide mass spectra are obtained upon gas-phase fragmentation. Identification of the protein from a set of experimental peptide spectral matches is usually referred as protein inference. Occurrence and intensity of these fragment ions in the MS/MS spectra are dependent on many factors such as amino acid composition, peptide basicity, activation mode, protease, etc. Particularly, chemical derivatizations of peptides were known to alter their fragmentation. In this study, the influence of acetylation, guanidinylation, and their combination on peptide fragmentation was assessed initially on a lipase (LipA) from Bacillus subtilis followed by a bovine six protein mix digest. The dual modification resulted in improved fragment ion occurrence and intensity changes, and this resulted in the equivalent representation of b- and y-type fragment ions in an ion trap MS/MS spectrum. The improved representation has allowed us to accurately annotate the peptide sequences de novo. Dual labeling has significantly reduced the false positive protein identifications in standard bovine six peptide digest. Our study suggests that the combinatorial labeling of peptides is a useful method to validate protein identifications for high confidence protein inference. [Figure not available: see fulltext.

Site-specific N-glycosylation analysis: matrix-assisted laser desorption/ionization quadrupole-quadrupole time-of-flight tandem mass spectral signatures for recognition and identification of glycopeptides.

PubMed

Krokhin, Oleg; Ens, Werner; Standing, Kenneth G; Wilkins, John; Perreault, Hélène

2004-01-01

The identification of glycosylation sites in proteins is often possible through a combination of proteolytic digestion, separation, mass spectrometry (MS) and tandem MS (MS/MS). Liquid chromatography (LC) in combination with MS/MS has been a reliable method for detecting glycopeptides in digestion mixtures, and for assigning glycosylation sites and glycopeptide sequences. Direct interfacing of LC with MS relies on electrospray ionization, which produces ions with two, three or four charges for most proteolytic peptides and glycopeptides. MS/MS spectra of such glycopeptide ions often lead to ambiguous interpretation if deconvolution to the singly charged level is not used. In contrast, the matrix-assisted laser desorption/ionization (MALDI) technique usually produces singly charged peptide and glycopeptide ions. These ions require an extended m/z range, as provided by the quadrupole-quadrupole time-of-flight (QqTOF) instrument used in these experiments, but the main advantages of studying singly charged ions are the simplicity and consistency of the MS/MS spectra. A first aim of the present study is to develop methods to recognize and use glycopeptide [M+H]+ ions as precursors for MS/MS, and thus for glycopeptide/glycoprotein identification as part of wider proteomics studies. Secondly, this article aims at demonstrating the usefulness of MALDI-MS/MS spectra of N-glycopeptides. Mixtures of diverse types of proteins, obtained commercially, were prepared and subjected to reduction, alkylation and tryptic digestion. Micro-column reversed-phase separation allowed deposition of several fractions on MALDI plates, followed by MS and MS/MS analysis of all peptides. Glycopeptide fractions were identified after MS by their specific m/z spacing patterns (162, 203, 291 u) between glycoforms, and then analyzed by MS/MS. In most cases, MS/MS spectra of [M+H]+ ions of glycopeptides featured peaks useful for determining sugar composition, peptide sequence, and thus probable

EPA CRL MS014: Analysis of Aldicarb, Bromadiolone, Carbofuran, Oxamyl and Methomyl in Water by Multiple Reaction Monitoring Liquid Chromatography / Tandem Mass Spectrometry (LC/MS/MS)

EPA Pesticide Factsheets

Method MS014 describes procedures for solvent extraction of aldicarb, bromadiolone, carbofuran, oxamyl and methomyl from water samples, followed by analysis using liquid chromatography tandem mass spectrometry (LC-MS-MS).

Broad Separation of Isomeric Lipids by High-Resolution Differential Ion Mobility Spectrometry with Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Bowman, Andrew P.; Abzalimov, Rinat R.; Shvartsburg, Alexandre A.

2017-08-01

Maturation of metabolomics has brought a deeper appreciation for the importance of isomeric identity of lipids to their biological role, mirroring that for proteoforms in proteomics. However, full characterization of the lipid isomerism has been thwarted by paucity of rapid and effective analytical tools. A novel approach is ion mobility spectrometry (IMS) and particularly differential or field asymmetric waveform IMS (FAIMS) at high electric fields, which is more orthogonal to mass spectrometry. Here we broadly explore the power of FAIMS to separate lipid isomers, and find a 75% success rate across the four major types of glycero- and phospho- lipids ( sn, chain length, double bond position, and cis/ trans). The resolved isomers were identified using standards, and (for the first two types) tandem mass spectrometry. These results demonstrate the general merit of incorporating high-resolution FAIMS into lipidomic analyses.

Forensic analysis of printing inks using tandem Laser Induced Breakdown Spectroscopy and Laser Ablation Inductively Coupled Plasma Mass Spectrometry

NASA Astrophysics Data System (ADS)

Subedi, Kiran; Trejos, Tatiana; Almirall, José

2015-01-01

Elemental analysis, using either LA-ICP-MS or LIBS, can be used for the chemical characterization of materials of forensic interest to discriminate between source materials originating from different sources and also for the association of materials known to originate from the same source. In this study, a tandem LIBS/LA-ICP-MS system that combines the benefits of both LIBS and LA-ICP-MS was evaluated for the characterization of samples of printing inks (toners, inkjets, intaglio and offset.). The performance of both laser sampling methods is presented. A subset of 9 black laser toners, 10 colored (CMYK) inkjet samples, 12 colored (CMYK) offset samples and 12 intaglio inks originating from different manufacturing sources were analyzed to evaluate the discrimination capability of the tandem method. These samples were selected because they presented a very similar elemental profile by LA-ICP-MS. Although typical discrimination between different ink sources is found to be > 99% for a variety of inks when only LA-ICP-MS was used for the analysis, additional discrimination was achieved by combining the elemental results from the LIBS analysis to the LA-ICP-MS analysis in the tandem technique, enhancing the overall discrimination capability of the individual laser ablation methods. The LIBS measurements of the Ca, Fe, K and Si signals, in particular, improved the discrimination for this specific set of different ink samples previously shown to exhibit very similar LA-ICP-MS elemental profiles. The combination of these two techniques in a single setup resulted in better discrimination of the printing inks with two distinct fingerprint spectra, providing information from atomic/ionic emissions and isotopic composition (m/z) for each ink sample.

21 CFR 862.1055 - Newborn screening test system for amino acids, free carnitine, and acylcarnitines using tandem...

Code of Federal Regulations, 2012 CFR

2012-04-01

... mass spectrometry is a device that consists of stable isotope internal standards, control materials..., free carnitine, and acylcarnitines using tandem mass spectrometry. 862.1055 Section 862.1055 Food and... screening test system for amino acids, free carnitine, and acylcarnitines using tandem mass spectrometry. (a...

21 CFR 862.1055 - Newborn screening test system for amino acids, free carnitine, and acylcarnitines using tandem...

Code of Federal Regulations, 2014 CFR

2014-04-01

... mass spectrometry is a device that consists of stable isotope internal standards, control materials..., free carnitine, and acylcarnitines using tandem mass spectrometry. 862.1055 Section 862.1055 Food and... screening test system for amino acids, free carnitine, and acylcarnitines using tandem mass spectrometry. (a...

The direct analysis of drug distribution of rotigotine-loaded microspheres from tissue sections by LESA coupled with tandem mass spectrometry.

PubMed

Xu, Li-Xiao; Wang, Tian-Tian; Geng, Yin-Yin; Wang, Wen-Yan; Li, Yin; Duan, Xiao-Kun; Xu, Bin; Liu, Charles C; Liu, Wan-Hui

2017-09-01

The direct analysis of drug distribution of rotigotine-loaded microspheres (RoMS) from tissue sections by liquid extraction surface analysis (LESA) coupled with tandem mass spectrometry (MS/MS) was demonstrated. The RoMS distribution in rat tissues assessed by the ambient LESA-MS/MS approach without extensive or tedious sample pretreatment was compared with that obtained by a conventional liquid chromatography tandem mass spectrometry (LC-MS/MS) method in which organ excision and subsequent solvent extraction were commonly employed before analysis. Results obtained from the two were well correlated for a majority of the organs, such as muscle, liver, stomach, and hippocampus. The distribution of RoMS in the brain, however, was found to be mainly focused in the hippocampus and striatum regions as shown by the LESA-imaged profiles. The LESA approach we developed is sensitive enough, with an estimated LLOQ at 0.05 ng/mL of rotigotine in brain tissue, and information-rich with minimal sample preparation, suitable, and promising in assisting the development of new drug delivery systems for controlled drug release and protection. Graphical abstract Workflow for the LESA-MS/MS imaging of brain tissue section after intramuscular RoMS administration.

Identification of glyceollin metabolites derived from conjugation with glutathione and glucuronic acid in rats by on-line liquid chromatography-electrospray ionization tandem mass spectrometry

USDA-ARS?s Scientific Manuscript database

Glyceollin-related metabolites produced in rats following oral glyceollin administration were screened and identified by precursor and product ion scanning using liquid chromatography, coupled on-line with electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS), to identify all glyceollin me...

A mass spectrometric system for analyzing thermal desorption spectra of ion-implanted argon and cesium in tungsten. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Wood, G. M., Jr.

1974-01-01

A mass spectrometric system for determining the characteristics of materials used in instrumental development and aerospace applications was developed. The desorption spectra of cesium that was ion-implanted into polycrystalline tungsten and the effects on the spectra of bombardment of the tungsten by low energy (70 eV) electrons were investigated. Work function changes were measured by the retarding potential diode method. Flash desorption characteristics were observed and gas-reaction mechanisms of the surface of heated metal filaments were studied. Desorption spectra were measured by linearly increasing the sample temperature at a selected rate, the temperature cycling being generated from a ramp-driven dc power supply, with the mass spectrometer tuned to a mass number of interest. Results of the study indicate an anomolous desorption mechanism following an electron bombardment of the sample surface. The enhanced spectra are a function of the post-bombardment time and energy and are suggestive of an increased concentration of cesium atoms, up to 10 or more angstroms below the surface.

De Novo Peptide Sequencing: Deep Mining of High-Resolution Mass Spectrometry Data.

PubMed

Islam, Mohammad Tawhidul; Mohamedali, Abidali; Fernandes, Criselda Santan; Baker, Mark S; Ranganathan, Shoba

2017-01-01

High resolution mass spectrometry has revolutionized proteomics over the past decade, resulting in tremendous amounts of data in the form of mass spectra, being generated in a relatively short span of time. The mining of this spectral data for analysis and interpretation though has lagged behind such that potentially valuable data is being overlooked because it does not fit into the mold of traditional database searching methodologies. Although the analysis of spectra by de novo sequences removes such biases and has been available for a long period of time, its uptake has been slow or almost nonexistent within the scientific community. In this chapter, we propose a methodology to integrate de novo peptide sequencing using three commonly available software solutions in tandem, complemented by homology searching, and manual validation of spectra. This simplified method would allow greater use of de novo sequencing approaches and potentially greatly increase proteome coverage leading to the unearthing of valuable insights into protein biology, especially of organisms whose genomes have been recently sequenced or are poorly annotated.

Simultaneous quantitation and identification of organic and inorganic selenium in diet supplements by liquid chromatography with tandem mass spectrometry.

PubMed

Zembrzuska, Joanna; Matusiewicz, Henryk; Polkowska-Motrenko, Halina; Chajduk, Ewelina

2014-01-01

A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for selenium speciation in dietary supplements. Chromatographic separation was performed on a TSK-Gel ODS-100V column using a mixture of 5mM ammonium acetate water solution and methanol as a mobile phase. Conditions chosen for this process allowed to separate all investigated chemical compounds of selenium: seleno-l-methionine, methyl-seleno-l-cysteine, l-selenocystine, methaneseleninic acid, selenite and selenate. A tandem mass spectrometer with an ion trap operating in negative or positive ion mode according to the selenium form being determined was used as a detector. Three extraction procedures: water extraction, enzymatic hydrolysis and sequential extraction were used for preparation of samples for the determination of the actual forms of selenium in diet supplements. The developed method was used for analysis of six dietary supplements containing selenium bought in a pharmacy and supermarket. Apart from speciation analysis of selenium content in supplements total selenium content was determined using instrumental neutron activation analysis (INAA). All expected forms of selenium except for selenite were determined using LC-MS/MS technique. It should be stressed that amounts of selenate were smaller than expected. Copyright © 2013 Elsevier Ltd. All rights reserved.

Multidimensional gas chromatography in combination with accurate mass, tandem mass spectrometry, and element-specific detection for identification of sulfur compounds in tobacco smoke.

PubMed

Ochiai, Nobuo; Mitsui, Kazuhisa; Sasamoto, Kikuo; Yoshimura, Yuta; David, Frank; Sandra, Pat

2014-09-05

A method is developed for identification of sulfur compounds in tobacco smoke extract. The method is based on large volume injection (LVI) of 10μL of tobacco smoke extract followed by selectable one-dimensional ((1)D) or two-dimensional ((2)D) gas chromatography (GC) coupled to a hybrid quadrupole time-of-flight mass spectrometer (Q-TOF-MS) using electron ionization (EI) and positive chemical ionization (PCI), with parallel sulfur chemiluminescence detection (SCD). In order to identify each individual sulfur compound, sequential heart-cuts of 28 sulfur fractions from (1)D GC to (2)D GC were performed with the three MS detection modes (SCD/EI-TOF-MS, SCD/PCI-TOF-MS, and SCD/PCI-Q-TOF-MS). Thirty sulfur compounds were positively identified by MS library search, linear retention indices (LRI), molecular mass determination using PCI accurate mass spectra, formula calculation using EI and PCI accurate mass spectra, and structure elucidation using collision activated dissociation (CAD) of the protonated molecule. Additionally, 11 molecular formulas were obtained for unknown sulfur compounds. The determined values of the identified and unknown sulfur compounds were in the range of 10-740ngmg total particulate matter (TPM) (RSD: 1.2-12%, n=3). Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Proteomic profiling of human pleural effusion using two-dimensional nano liquid chromatography tandem mass spectrometry.

PubMed

Tyan, Yu-Chang; Wu, Hsin-Yi; Lai, Wu-Wei; Su, Wu-Chou; Liao, Pao-Chi

2005-01-01

Pleural effusion, an accumulation of pleural fluid, contains proteins originated from plasma filtrate and, especially when tissues are damaged, parenchyma interstitial spaces of lungs and/or other organs. This study details protein profiles in human pleural effusion from 43 lung adenocarcinoma patients by a two-dimensional nano-high performance liquid chromatography electrospray ionization tandem mass spectrometry (2D nano-HPLC-ESI-MS/MS) system. The experimental results revealed the identification of 1415 unique proteins from human pleural effusion. Among these 124 proteins identified with higher confidence levels, some proteins have not been reported in plasma and may represent proteins specifically present in pleural effusion. These proteins are valuable for mass identification of differentially expressed proteins involved in proteomics database and screening biomarker to further study in human lung adenocarcinoma. The significance of the use of proteomics analysis of human pleural fluid for the search of new lung cancer marker proteins, and for their simultaneous display and analysis in patients suffering from lung disorders has been examined.

Liquid chromatography tandem mass spectrometry assay to determine the pharmacokinetics of aildenafil in human plasma.

PubMed

Wang, Jiang; Jiang, Yao; Wang, Yingwu; Zhao, Xia; Cui, Yimin; Gu, Jingkai

2007-05-09

A simple, sensitive and specific liquid chromatography/tandem mass spectrometry method for the quantitation of aildenafil, a new phosphodiesterase V inhibitor, in human plasma is presented. The analyte and internal standard, sildenafil, were extracted by a one-step liquid-liquid extraction in alkaline conditions and separated on a C(18) column using ammonia:10mM ammonium acetate buffer:methanol (0.1:15:85, v/v/v) as the mobile phase. The detection by an API 4000 triple quadrupole mass spectrometer in multiple-reaction monitoring mode was completed within 2.5 min. The calibration curve exhibited a linear dynamic range of 0.05-100 ng/ml with a 10 pg/ml limit of detection. The intra- and inter-day precisions measured as relative standard deviation were within 8.04% and 5.72%, respectively. This method has been used in a pharmacokinetic study of aildenafil in healthy male volunteers each given an oral administration of one of the three dosages.

Recent advances of liquid chromatography-(tandem) mass spectrometry in clinical and forensic toxicology - An update.

PubMed

Remane, Daniela; Wissenbach, Dirk K; Peters, Frank T

2016-09-01

Liquid chromatography (LC) coupled to mass spectrometry (MS) or tandem mass spectrometry (MS/MS) is a well-established and widely used technique in clinical and forensic toxicology as well as doping control especially for quantitative analysis. In recent years, many applications for so-called multi-target screening and/or quantification of drugs, poisons, and or their metabolites in biological matrices have been developed. Such methods have proven particularly useful for analysis of so-called new psychoactive substances that have appeared on recreational drug markets throughout the world. Moreover, the evolvement of high resolution MS techniques and the development of data-independent detection modes have opened new possibilities for applications of LC-(MS/MS) in systematic toxicological screening analysis in the so called general unknown setting. The present paper will provide an overview and discuss these recent developments focusing on the literature published after 2010. Copyright © 2016 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Hydrophilic Interaction Liquid Chromatography-Tandem Mass Spectrometry Analysis of Fosetyl-Aluminum in Airborne Particulate Matter

PubMed Central

Di Filippo, Patrizia; Riccardi, Carmela; Pomata, Donatella; Marsiglia, Riccardo; Console, Carla; Puri, Daniele

2018-01-01

Fosetyl-aluminum is a synthetic fungicide administered to plants especially to prevent diseases caused by the members of the Peronosporales and several Phytophthora species. Herein, we present a selective liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to analyze residues of fosetyl-A1 in air particulate matter. This study was performed in perspective of an exposure assessment of this substance of health concern in environments where high levels of fosetly-Al, relatively to airborne particulate matter, can be found after spraying it. The cleanup procedure of the analyte, from sampled filters of atmospheric particulate matter, was optimized using a Strata X solid-phase extraction cartridge, after accelerated extraction by using water. The chromatographic separation was achieved using a polymeric column based on hydrophilic interaction in step elution with water/acetonitrile, whereas the mass spectrometric detection was performed in negative electrospray ionization. The proposed method resulted to be a simple, fast, and suitable method for confirmation purposes. PMID:29686933

End-group characterisation of poly(propylene glycol)s by means of electrospray ionisation-tandem mass spectrometry (ESI-MS/MS).

PubMed

Jackson, Anthony T; Slade, Susan E; Thalassinos, Konstantinos; Scrivens, James H

2008-10-01

The end-group functionalisation of a series of poly(propylene glycol)s has been characterised by means of electrospray ionisation-tandem mass spectrometry (ESI-MS/MS). A series of peaks with mass-to-charge ratios that are close to that of the precursor ion were used to generate information on the end-group functionalities of the poly(propylene glycol)s. Fragment ions resulting from losses of both of the end groups were noted from some of the samples. An example is presented of how software can be used to significantly reduce the length of time involved in data interpretation (which is typically the most time-consuming part of the analysis).

Improved Tandem Measurement Techniques for Aerosol Particle Analysis

NASA Astrophysics Data System (ADS)

Rawat, Vivek Kumar

Non-spherical, chemically inhomogeneous (complex) nanoparticles are encountered in a number of natural and engineered environments, including combustion systems (which produces highly non-spherical aggregates), reactors used in gas-phase materials synthesis of doped or multicomponent materials, and in ambient air. These nanoparticles are often highly diverse in size, composition and shape, and hence require determination of property distribution functions for accurate characterization. This thesis focuses on development of tandem mobility-mass measurement techniques coupled with appropriate data inversion routines to facilitate measurement of two dimensional size-mass distribution functions while correcting for the non-idealities of the instruments. Chapter 1 provides the detailed background and motivation for the studies performed in this thesis. In chapter 2, the development of an inversion routine is described which is employed to determine two dimensional size-mass distribution functions from Differential Mobility Analyzer-Aerosol Particle Mass analyzer tandem measurements. Chapter 3 demonstrates the application of the two dimensional distribution function to compute cumulative mass distribution function and also evaluates the validity of this technique by comparing the calculated total mass concentrations to measured values for a variety of aerosols. In Chapter 4, this tandem measurement technique with the inversion routine is employed to analyze colloidal suspensions. Chapter 5 focuses on application of a transverse modulation ion mobility spectrometer coupled with a mass spectrometer to study the effect of vapor dopants on the mobility shifts of sub 2 nm peptide ion clusters. These mobility shifts are then compared to models based on vapor uptake theories. Finally, in Chapter 6, a conclusion of all the studies performed in this thesis is provided and future avenues of research are discussed.

Determination of caprolactam and 6-aminocaproic acid in human urine using hydrophilic interaction liquid chromatography-tandem mass spectrometry.

PubMed

Wu, Ya-Hsueh; Wu, Ming-Ling; Lin, Chun-Chi; Chu, Wei-Lan; Yang, Chen-Chang; Lin, Robert Tate; Deng, Jou-Fang

2012-02-15

A simple and rapid assay based on hydrophilic interaction liquid chromatography with tandem mass spectrometry has been first developed and validated for simultaneous determination of caprolactam (CA) and 6-aminocaproic acid (6-ANCA) in human urine using 8-aminocaprylic acid as internal standard. A 20μL aliquot of urine was injected directly into the liquid chromatography tandem mass spectrometry (LC-MS-MS) system. The analytes were separated on a Phenomenex Luna HILIC column with gradient elution. Detection was performed on Triple Quadrupole LC-MS in positive ions multiple reaction monitoring mode using electrospray ionization. The calibration curves were linear (r(2)≥0.995) over the concentration range from 62.5 to 1250ng/mL for CA and 31.25 to 1000ng/mL for 6-ANCA. The detection limits of CA and 6-ANCA were 62.5 and 15.6ng/mL, respectively. The intra-day and inter-day precisions were within 8.7% and 9.9%, respectively. The intra-day and inter-day accuracy were between 5.3% and 3.5%, and between 6.1% and 6.6%, respectively. The method proved to be simple and time efficient, and was successfully applied to evaluate the kinetics of caprolactam in one unusual case of caprolactam poisoning. Copyright © 2011 Elsevier B.V. All rights reserved.

Microorganism gram-type differentiation based on pyrolysis-mass spectrometry of bacterial Fatty Acid methyl ester extracts.

PubMed

Basile, F; Voorhees, K J; Hadfield, T L

1995-04-01

Curie-point pyrolysis (Py)-mass spectrometry has been used to differentiate 19 microorganisms by Gram type on the basis of the methyl esters of their fatty acid distribution. The mass spectra of gram-negative microorganisms were characterized by the presence of palmitoleic acid (C(inf16:1)) and oleic acid (C(inf18:1)), as well as a higher abundance of palmitic acid (C(inf16:0)) than pentadecanoic acid (C(inf15:0)). For gram-positive microorganisms, a signal of branched C(inf15:0) (isoC(inf15:0) and/or anteisoC(inf15:0)) more intense than that of palmitic acid was observed in the mass spectra. Principal components analysis of these mass spectral data segregated the microorganisms investigated in this study into three discrete clusters that correlated to their gram reactions and pathogenicities. Further tandem mass spectrometric analysis demonstrated that the nature of the C(inf15:0) fatty acid isomer (branched or normal) present in the mass spectrum of each microorganism was important for achieving the classification into three clusters.

METHOD 544. DETERMINATION OF MICROCYSTINS AND NODULARIN IN DRINKING WATER BY SOLID PHASE EXTRACTION AND LIQUID CHROMATOGRAPHY/TANDEM MASS SPECTROMETRY (LC/MS/MS)

EPA Science Inventory

Method 544 is an accurate and precise analytical method to determine six microcystins (including MC-LR) and nodularin in drinking water using solid phase extraction and liquid chromatography tandem mass spectrometry (SPE-LC/MS/MS). The advantage of this SPE-LC/MS/MS is its sensi...

Targeted Quantitation of Proteins by Mass Spectrometry

PubMed Central

2013-01-01

Quantitative measurement of proteins is one of the most fundamental analytical tasks in a biochemistry laboratory, but widely used immunochemical methods often have limited specificity and high measurement variation. In this review, we discuss applications of multiple-reaction monitoring (MRM) mass spectrometry, which allows sensitive, precise quantitative analyses of peptides and the proteins from which they are derived. Systematic development of MRM assays is permitted by databases of peptide mass spectra and sequences, software tools for analysis design and data analysis, and rapid evolution of tandem mass spectrometer technology. Key advantages of MRM assays are the ability to target specific peptide sequences, including variants and modified forms, and the capacity for multiplexing that allows analysis of dozens to hundreds of peptides. Different quantitative standardization methods provide options that balance precision, sensitivity, and assay cost. Targeted protein quantitation by MRM and related mass spectrometry methods can advance biochemistry by transforming approaches to protein measurement. PMID:23517332

Targeted quantitation of proteins by mass spectrometry.

PubMed

Liebler, Daniel C; Zimmerman, Lisa J

2013-06-04

Quantitative measurement of proteins is one of the most fundamental analytical tasks in a biochemistry laboratory, but widely used immunochemical methods often have limited specificity and high measurement variation. In this review, we discuss applications of multiple-reaction monitoring (MRM) mass spectrometry, which allows sensitive, precise quantitative analyses of peptides and the proteins from which they are derived. Systematic development of MRM assays is permitted by databases of peptide mass spectra and sequences, software tools for analysis design and data analysis, and rapid evolution of tandem mass spectrometer technology. Key advantages of MRM assays are the ability to target specific peptide sequences, including variants and modified forms, and the capacity for multiplexing that allows analysis of dozens to hundreds of peptides. Different quantitative standardization methods provide options that balance precision, sensitivity, and assay cost. Targeted protein quantitation by MRM and related mass spectrometry methods can advance biochemistry by transforming approaches to protein measurement.

Formation and reactions of negative ions relevant to chemical ionization mass spectrometry. I. Cl mass spectra of organic compounds produced by F− reactions

PubMed Central

Tiernan, T. O.; Chang, C.; Cheng, C. C.

1980-01-01

A systematic study of the negative-ion chemical ionization mass spectra produced by the reaction of F− with a wide variety of organic compounds has been accomplished. A time-of-flight mass spectrometer fitted with a modified high pressure ion source was employed for these experiments. The F− reagent ion was generated from CF3H or NF3, typically at an ion source pressure of 100 μm. In pure NF3, F− is the major ion formed and constitutes more than 90% of the total ion intensity. While F− is also the major primary ion formed in pure CF3H, it undergoes rapid ion-molecule reactions at elevated source pressures, yielding (HF)nF− (n = 1−3) ions, which makes CF3H less suitable as a chemical ionization reagent gas. Among the organic compounds investigated were carboxylic acids, ketones, aldehydes, esters, alcohols, phenols, halides, nitriles, nitrobenzene, ethers, amines and hydrocarbons. An intense (M − 1)− ion was observed in the F− chemical ionization mass spectra of carboxylic acids, ketones, aldehydes and phenols. Alcohols yield only (M + F)− ions upon reaction with F−. A weaker (M + F)− ion was also detected in the F− chemical ionization spectra of carboxylic acids, aldehydes, ketones and nitriles. The F− chemical ionization mass spectra of esters, halides, nitriles, nitrobenzene and ethers are characterized primarily by the ions, RCOO−, X−, CN−, NO2−, and OR−, respectively. In addition, esters show a very weak (M − 1)− ion (except formates). In the F− chemical ionization spectra of some aliphatic alkanes and o-xylene, a very weak (M + F)− ion was observed. Amines and aliphatic alkenes exhibit only insignificant fragment ions under similar conditions, while aromatic hydrocarbons, such as benzene and toluene are not reactive at all with the F− ion. The mechanisms of the various reactions mentioned are discussed, and several experimental complications are noted. In still other studies, the effects of varying several

Acrylamide levels in Finnish foodstuffs analysed with liquid chromatography tandem mass spectrometry.

PubMed

Eerola, Susanna; Hollebekkers, Koen; Hallikainen, Anja; Peltonen, Kimmo

2007-02-01

Sample clean-up and HPLC with tandem mass spectrometric detection (LC-MS/MS) was validated for the routine analysis of acrylamide in various foodstuffs. The method used proved to be reliable and the detection limit for routine monitoring was sensitive enough for foods and drinks (38 microg/kg for foods and 5 microg/L for drinks). The RSDs for repeatability and day-to-day variation were below 15% in all food matrices. Two hundred and one samples which included more than 30 different types of food and foods manufactured and prepared in various ways were analysed. The main types of food analysed were potato and cereal-based foods, processed foods (pizza, minced beef meat, meat balls, chicken nuggets, potato-ham casserole and fried bacon) and coffee. Acrylamide was detected at levels, ranging from nondetectable to 1480 microg/kg level in solid food, with crisp bread exhibiting the highest levels. In drinks, the highest value (29 microg/L) was found in regular coffee drinks.

Characterization of protein N-glycosylation by tandem mass spectrometry using complementary fragmentation techniques

DOE PAGES

Ford, Kristina L.; Zeng, Wei; Heazlewood, Joshua L.; ...

2015-08-28

The analysis of post-translational modifications (PTMs) by proteomics is regarded as a technically challenging undertaking. While in recent years approaches to examine and quantify protein phosphorylation have greatly improved, the analysis of many protein modifications, such as glycosylation, are still regarded as problematic. Limitations in the standard proteomics workflow, such as use of suboptimal peptide fragmentation methods, can significantly prevent the identification of glycopeptides. The current generation of tandem mass spectrometers has made available a variety of fragmentation options, many of which are becoming standard features on these instruments. Lastly, we have used three common fragmentation techniques, namely CID, HCD,more » and ETD, to analyze a glycopeptide and highlight how an integrated fragmentation approach can be used to identify the modified residue and characterize the N-glycan on a peptide.« less

Transformation of chlorinated paraffins to olefins during metal work and thermal exposure - Deconvolution of mass spectra and kinetics.

PubMed

Schinkel, Lena; Lehner, Sandro; Knobloch, Marco; Lienemann, Peter; Bogdal, Christian; McNeill, Kristopher; Heeb, Norbert V

2018-03-01

Chlorinated paraffins (CPs) are high production volume chemicals widely used as additives in metal working fluids. Thereby, CPs are exposed to hot metal surfaces which may induce degradation processes. We hypothesized that the elimination of hydrochloric acid would transform CPs into chlorinated olefins (COs). Mass spectrometry is widely used to detect CPs, mostly in the selected ion monitoring mode (SIM) evaluating 2-3 ions at mass resolutions R < 20'000. This approach is not suited to detected COs, because their mass spectra strongly overlap with CPs. We applied a mathematical deconvolution method based on full-scan MS data to separate interfered CP/CO spectra. Metal drilling indeed induced HCl-losses. CO proportions in exposed mixtures of chlorotridecanes increased. Thermal exposure of chlorotridecanes at 160, 180, 200 and 220 °C also induced dehydrohalogenation reactions and CO proportions also increased. Deconvolution of respective mass spectra is needed to study the CP transformation kinetics without bias from CO interferences. Apparent first-order rate constants (k app ) increased up to 0.17, 0.29 and 0.46 h -1 for penta-, hexa- and heptachloro-tridecanes exposed at 220 °C. Respective half-life times (τ 1/2 ) decreased from 4.0 to 2.4 and 1.5 h. Thus, higher chlorinated paraffins degrade faster than lower chlorinated ones. In conclusion, exposure of CPs during metal drilling and thermal treatment induced HCl losses and CO formation. It is expected that CPs and COs are co-released from such processes. Full-scan mass spectra and subsequent deconvolution of interfered signals is a promising approach to tackle the CP/CO problem, in case of insufficient mass resolution. Copyright © 2017 Elsevier Ltd. All rights reserved.

Simultaneous determination of phenolic compounds in Equisetum palustre L. by ultra high performance liquid chromatography with tandem mass spectrometry combined with matrix solid-phase dispersion extraction.

PubMed

Wei, Zuofu; Pan, Youzhi; Li, Lu; Huang, Yuyang; Qi, Xiaolin; Luo, Meng; Zu, Yuangang; Fu, Yujie

2014-11-01

A method based on matrix solid-phase dispersion extraction followed by ultra high performance liquid chromatography with tandem mass spectrometry is presented for the extraction and determination of phenolic compounds in Equisetum palustre. This method combines the high efficiency of matrix solid-phase dispersion extraction and the rapidity, sensitivity, and accuracy of ultra high performance liquid chromatography with tandem mass spectrometry. The influential parameters of the matrix solid-phase dispersion extraction were investigated and optimized. The optimized conditions were as follows: silica gel was selected as dispersing sorbent, the ratio of silica gel to sample was selected to be 2:1 (400/200 mg), and 8 mL of 80% methanol was used as elution solvent. Furthermore, a fast and sensitive ultra high performance liquid chromatography with tandem mass spectrometry method was developed for the determination of nine phenolic compounds in E. palustre. This method was carried out within <6 min, and exhibited satisfactory linearity, precision, and recovery. Compared with ultrasound-assisted extraction, the proposed matrix solid-phase dispersion procedure possessed higher extraction efficiency, and was more convenient and time saving with reduced requirements on sample and solvent amounts. All these results suggest that the developed method represents an excellent alternative for the extraction and determination of active components in plant matrices. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of Growth Medium on Matrix-Assisted Laser Desorption–Ionization Time of Flight Mass Spectra: a Case Study of Acetic Acid Bacteria

PubMed Central

Wieme, Anneleen D.; Spitaels, Freek; Aerts, Maarten; De Bruyne, Katrien; Van Landschoot, Anita

2014-01-01

The effect of the growth medium used on the matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectra generated and its consequences for species and strain level differentiation of acetic acid bacteria (AAB) were determined by using a set of 25 strains. The strains were grown on five different culture media that yielded a total of more than 600 mass spectra, including technical and biological replicates. The results demonstrate that the culture medium can have a profound effect on the mass spectra of AAB as observed in the presence and varying signal intensities of peak classes, in particular when culture media do not sustain optimal growth. The observed growth medium effects do not disturb species level differentiation but strongly affect the potential for strain level differentiation. The data prove that a well-constructed and robust MALDI-TOF mass spectrometry identification database should comprise mass spectra of multiple reference strains per species grown on different culture media to facilitate species and strain level differentiation. PMID:24362425

Protein mass spectra data analysis for clinical biomarker discovery: a global review.

PubMed

Roy, Pascal; Truntzer, Caroline; Maucort-Boulch, Delphine; Jouve, Thomas; Molinari, Nicolas

2011-03-01

The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. In recent years there has been a growing interest in using high throughput technologies for the detection of such biomarkers. In particular, mass spectrometry appears as an exciting tool with great potential. However, to extract any benefit from the massive potential of clinical proteomic studies, appropriate methods, improvement and validation are required. To better understand the key statistical points involved with such studies, this review presents the main data analysis steps of protein mass spectra data analysis, from the pre-processing of the data to the identification and validation of biomarkers.

Screening of carnitine and biotin deficiencies on tandem mass spectrometry.

PubMed

Hagiwara, Shin-Ichiro; Kubota, Mitsuru; Nambu, Ryusuke; Kagimoto, Seiichi

2017-04-01

It is important to assess pediatric patients for nutritional deficiency when they are receiving specific interventions, such as enteral feeding. We focused on measurement of C0 and 3-hydroxyisovalerylcarnitine (C5-OH) with tandem mass spectrometry (MS/MS), which is performed as part of the newborn mass screening. The purpose of this study was to investigate the usefulness of MS/MS for screening carnitine and biotin deficiencies. Forty-two children (24 boys, 18 girls) were enrolled between December 2013 and December 2015. Blood tests, including measurement of serum free carnitine via the enzyme cycling method, and acylcarnitine analysis on MS/MS of dried blood spot (DBS), were performed for the evaluation of nutrition status. Median patient age was 2 years (range, 2 months-14 years). Mean serum free carnitine was 41.8 ± 19.2 μmol/L. In six of the 42 patients, serum free carnitine was <20 μmol/L (range, 4.0-18.7 μmol/L). C0 and C5-OH measured on MS/MS of DBS were 33.8 ± 20.2 nmol/mL and 0.48 ± 0.22 nmol/mL, respectively. There was a strong positive correlation (r = 0.89, P < 0.001) between serum free carnitine and C0 measured on the same day. In one patient on hydrolyzed formula, C5-OH was >1.00 nmol/L. Therapy-resistant eczema was improved by treatment with additional biotin and a non-hydrolyzed formula. C0 and C5-OH, measured on MS/MS of DBS, were useful for screening carnitine and biotin deficiencies. © 2016 Japan Pediatric Society.

Detection of nicotine as an indicator of tobacco smoke by direct analysis in real time (DART) tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Kuki, Ákos; Nagy, Lajos; Nagy, Tibor; Zsuga, Miklós; Kéki, Sándor

2015-01-01

The residual tobacco smoke contamination (thirdhand smoke, THS) on the clothes of a smoker was examined by direct analysis in real time (DART) mass spectrometry. DART-MS enabled sensitive and selective analysis of nicotine as the indicator of tobacco smoke pollution. Tandem mass spectrometric (MS/MS) experiments were also performed to confirm the identification of nicotine. Transferred thirdhand smoke originated from the fingers of a smoker onto other objects was also detected by DART mass spectrometry. DART-MS/MS was utilized for monitoring the secondhand tobacco smoke (SHS) in the air of the laboratory using nicotine as an indicator. To the best of our knowledge, this is the first report on the application of DART-MS and DART-MS/MS to the detection of thirdhand smoke and to the monitoring of secondhand smoke.

Single Laboratory Validated Method for Determination of Microcystins and Nodularin in Ambient Freshwaters by Solid Phase Extraction and Liquid Chromatography/ Tandem Mass Spectrometry (LC/MS/MS)

EPA Pesticide Factsheets

This document is a standardized, single laboratory validated liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for the detection of cyanotoxins—microsystins and nodularin (combined intracellular and extracellular)—in ambient freshwaters.

Cluster Analysis of the Organic Peaks in Bulk Mass Spectra Obtained During the 2002 New England Air Quality Study with an Aerodyne Aerosol Mass Spectrometer

NASA Astrophysics Data System (ADS)

Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M.; Bertman, S. B.; Middlebrook, A. M.

2006-12-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel R. H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter probably originating from both anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent on average 17% of the total organic mass that stems likely from biogenic sources during the ship's cruise. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

Metabolite identification of the antimalarial naphthoquine using liquid chromatography-tandem high-resolution mass spectrometry in combination with multiple data-mining tools.

PubMed

Sun, Yanhong; Wang, Shuqi; Ji, Jianbo; Zhai, Guangxi; Xing, Jie

2018-06-01

Naphthoquine (NQ) is one of important partner drugs of artemisinin-based combination therapy (ACT), which is recommended for the treatment of uncomplicated Plasmodium falciparum. NQ shows a high cure rate after a single oral administration. It is absorbed quickly (time to peak concentration 2-4 h) and has a long elimination half-life (255 h). However, the metabolism of NQ has not been clarified. In this work, the metabolite profiling of NQ was studied in six liver microsomal incubates (human, cynomolgus monkey, beagle dog, mini pig, rat and CD1 mouse), seven recombinant CYP enzymes (1A2, 2B6, 2C8, 2C9, 2C19, 2D6 and 3A4) and rat (plasma, urine, bile and feces) using liquid chromatography tandem high-resolution LTQ-Orbitrap mass spectrometry (HRMS n ) in conjunction with online hydrogen/deuterium exchange. The biological samples were pretreated by protein precipitation and solid-phase extraction. For data processing, multiple data-mining tools were applied in tandem, i.e. background subtraction and followed by mass defect filter. NQ metabolites were characterized by accurate MS/MS fragmentation characteristics, the hydrogen/deuterium exchange data and cLogP simulation. As a result, five phase I metabolites (M1-M5) of NQ were characterized for the first time. Two metabolic pathways were involved: hydroxylation and N-oxidation. This study demonstrates that LC-HRMS n in combination with multiple data-mining tools in tandem can be a valuable analytical strategy for rapid metabolite profiling of drugs. Copyright © 2018 John Wiley & Sons, Ltd.

Cluster analysis of the organic peaks in bulk mass spectra obtained during the 2002 New England Air Quality Study with an Aerodyne aerosol mass spectrometer

NASA Astrophysics Data System (ADS)

Marcolli, C.; Canagaratna, M. R.; Worsnop, D. R.; Bahreini, R.; de Gouw, J. A.; Warneke, C.; Goldan, P. D.; Kuster, W. C.; Williams, E. J.; Lerner, B. M.; Roberts, J. M.; Meagher, J. F.; Fehsenfeld, F. C.; Marchewka, M. L.; Bertman, S. B.; Middlebrook, A. M.

2006-06-01

We applied hierarchical cluster analysis to an Aerodyne aerosol mass spectrometer (AMS) bulk mass spectral dataset collected aboard the NOAA research vessel Ronald H. Brown during the 2002 New England Air Quality Study off the east coast of the United States. Emphasizing the organic peaks, the cluster analysis yielded a series of categories that are distinguishable with respect to their mass spectra and their occurrence as a function of time. The differences between the categories mainly arise from relative intensity changes rather than from the presence or absence of specific peaks. The most frequent category exhibits a strong signal at m/z 44 and represents oxidized organic matter most probably originating from both, anthropogenic as well as biogenic sources. On the basis of spectral and trace gas correlations, the second most common category with strong signals at m/z 29, 43, and 44 contains contributions from isoprene oxidation products. The third through the fifth most common categories have peak patterns characteristic of monoterpene oxidation products and were most frequently observed when air masses from monoterpene rich regions were sampled. Taken together, the second through the fifth most common categories represent as much as 5 µg/m3 organic aerosol mass - 17% of the total organic mass - that can be attributed to biogenic sources. These numbers have to be viewed as lower limits since the most common category was attributed to anthropogenic sources for this calculation. The cluster analysis was also very effective in identifying a few contaminated mass spectra that were not removed during pre-processing. This study demonstrates that hierarchical clustering is a useful tool to analyze the complex patterns of the organic peaks in bulk aerosol mass spectra from a field study.

Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data.

PubMed

Kumar, Dhirendra; Yadav, Amit Kumar; Dash, Debasis

2017-01-01

Database searching is the preferred method for protein identification from digital spectra of mass to charge ratios (m/z) detected for protein samples through mass spectrometers. The search database is one of the major influencing factors in discovering proteins present in the sample and thus in deriving biological conclusions. In most cases the choice of search database is arbitrary. Here we describe common search databases used in proteomic studies and their impact on final list of identified proteins. We also elaborate upon factors like composition and size of the search database that can influence the protein identification process. In conclusion, we suggest that choice of the database depends on the type of inferences to be derived from proteomics data. However, making additional efforts to build a compact and concise database for a targeted question should generally be rewarding in achieving confident protein identifications.

Liquid chromatography with tandem mass spectrometry for the simultaneous identification and quantification of cardiovascular drugs applied to the detection of substandard and falsified drugs.

PubMed

Bernard, Mélisande; Akrout, Wiem; Van Buu, Christelle Tran; Metz, Carole; Antignac, Marie; Yagoubi, Najet; Do, Bernard

2015-02-01

The counterfeiting of pharmaceuticals has been detected since about 1990 and has alarmingly continued to pick up steam. We have been recently involved in an evaluation program of some of the most commonly prescribed cardiovascular drugs in Africa, for analysing an important number of tablets or capsules obtained from different places in seven African countries. A reversed-phase high-performance liquid chromatography with tandem mass spectrometry method was developed and validated to simultaneously control the identity and the quantity of acenocoumarol, amlodipine, atenolol, captopril, furosemide, hydrochlorothiazide and simvastatin in tablets. Their separation was performed on a Kinetex® C(18) (100 mm × 2.1 mm inside diameter, 2.6 μm) column using a gradient elution of 20 mM ammonium formate buffer and acetonitrile (90:10 10:90 v/v) at a flow rate of 0.5 mL/min. The analytes were detected using electrospray ionisation tandem mass spectrometry in both positive and negative modes with multiple reaction monitoring. Tandem mass spectrometry fragmentation patterns of captopril, furosemide and acenocoumarol, up to now not detailed in the literature, were also studied to assist in the selection of the most relevant transitions towards the objectives. The developed method was validated as per International Conference on Harmonisation guidelines with respect to specificity, linearity, trueness, precision, limits of detection and quantification. It has been successfully applied to the control of oral forms of seven cardiovascular drugs collected in African countries. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of triterpenoids and phytosterols in vegetables by thin-layer chromatography coupled to tandem mass spectrometry.

PubMed

Naumoska, Katerina; Vovk, Irena

2015-02-13

Three TLC methods were used for an initial screening of some common plant triterpenoids and phytosterols in cuticular wax extracts of different vegetables (zucchini, eggplant, tomato, red pepper, mangold, spinach, lettuce, white-colored radicchio di Castelfranco, raddichio Leonardo, white cabbage, red cabbage and savoy cabbage). The preliminary experiments showed that the studied vegetables are potential sources of triterpenoids and phytosterols. To identify the compounds present in the extracts with high certainty, the first TLC-MS(2) method was developed for the analysis of eight triterpenoids (lupeol, α-amyrin, β-amyrin, cycloartenol, cycloartenol acetate, lupeol acetate, lupenone and friedelin) and two phytosterols (β-sitosterol and stigmasterol). This method takes the advantages of: (1) a satisfactory separation of the target compounds; (2) their differentiation according to the band colors; and (3) the potential of their discrimination by the acquired first-order mass (MS) and product ion (MS(2)) spectra. Since the closely eluting compounds have complex and similar MS(2) spectra, distinguishing between them was possible by the proposed characteristic ions. Using a custom-built mass spectral library, the head to tail MS(2) spectra comparison of sample test solution zones and standard aided the compound identification. In addition to the molecular mass information, the developed atmospheric pressure chemical ionization method (APCI) in positive ion mode provided structural information, regarding the presence of functional group in the molecule. This approach resulted in many positively assigned compounds in the investigated vegetable waxes, from which more than a half are reported for the first time. Copyright © 2015 Elsevier B.V. All rights reserved.

Determination of artemisitene in rat plasma by ultra-performance liquid chromatography/tandem mass spectrometry and its application in pharmacokinetics.

PubMed

Wu, Li-Lan; Wu, Yun-Shan; Chen, Wei-Ying; Zhou, Wen; Tang, Lipeng; Li, Ben; Liu, Bo

2017-07-15

Artemisitene shows a wide variety of pharmacological activities, such as antioxidant protection in vitro and in vivo. It has been identified as a novel Nrf2 inducer. However, there is no report on an ultra-performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) method to quantitate artemisitene in rat plasma and its application to a pharmacokinetic profile study. An ACQUITY UPLC™ BEH Symmetry Shield RP18 column (1.7 μm, 2.1 mm × 100 mm) was used at a flow rate of 0.3 mL·min -1 . Mass detection was performed by electrospray ionization tandem mass spectrometry via multiple reaction monitoring (MRM) in positive mode. Plasma samples were pre-treated by a single-step extraction with 0.1% formic acid aqueous solutions-acetonitrile, and tolbutamide was used as internal standard. The calibration curve was from 0.98 to 1000 ng∙mL -1 (r 2  = 0.995). The extraction recoveries were 61.5-79.4% and 81.7-94.6% for artemisitene and tolbutamide, respectively. The lower limit of quantification (LLOQ) was 0.98 ng∙mL -1 . The absolute bioavailability of artemisitene was 3.7% after intravenous and oral administration in rats. The UPLC/MS/MS assay was validated for linearity, accuracy, stability, extraction recovery, matrix effects, and intra-day and inter-day precision. The method, for the first time, achieved some pharmacokinetic parameters and was successfully applied to a pharmacokinetic study Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

LESSONS IN DE NOVO PEPTIDE SEQUENCING BY TANDEM MASS SPECTROMETRY

PubMed Central

Medzihradszky, Katalin F.; Chalkley, Robert J.

2015-01-01

Mass spectrometry has become the method of choice for the qualitative and quantitative characterization of protein mixtures isolated from all kinds of living organisms. The raw data in these studies are MS/MS spectra, usually of peptides produced by proteolytic digestion of a protein. These spectra are “translated” into peptide sequences, normally with the help of various search engines. Data acquisition and interpretation have both been automated, and most researchers look only at the summary of the identifications without ever viewing the underlying raw data used for assignments. Automated analysis of data is essential due to the volume produced. However, being familiar with the finer intricacies of peptide fragmentation processes, and experiencing the difficulties of manual data interpretation allow a researcher to be able to more critically evaluate key results, particularly because there are many known rules of peptide fragmentation that are not incorporated into search engine scoring. Since the most commonly used MS/MS activation method is collision-induced dissociation (CID), in this article we present a brief review of the history of peptide CID analysis. Next, we provide a detailed tutorial on how to determine peptide sequences from CID data. Although the focus of the tutorial is de novo sequencing, the lessons learned and resources supplied are useful for data interpretation in general. PMID:25667941

AUTOMATED DECONVOLUTION OF COMPOSITE MASS SPECTRA OBTAINED WITH AN OPEN-AIR IONIZATIONS SOURCE BASED ON EXACT MASSES AND RELATIVE ISOTIPIC ABUNDANCES

EPA Science Inventory

Chemicals dispersed by accidental, deliberate, or weather-related events must be rapidly identified to assess health risks. Mass spectra from high levels of analytes obtained using rapid, open-air ionization by a Direct Analysis in Real Time (DART®) ion source often contain

Tandem mass spectrometry, but not T-cell receptor excision circle analysis, identifies newborns with late-onset adenosine deaminase deficiency.

PubMed

la Marca, Giancarlo; Canessa, Clementina; Giocaliere, Elisa; Romano, Francesca; Duse, Marzia; Malvagia, Sabrina; Lippi, Francesca; Funghini, Silvia; Bianchi, Leila; Della Bona, Maria Luisa; Valleriani, Claudia; Ombrone, Daniela; Moriondo, Maria; Villanelli, Fabio; Speckmann, Carsten; Adams, Stuart; Gaspar, Bobby H; Hershfield, Michael; Santisteban, Ines; Fairbanks, Lynette; Ragusa, Giovanni; Resti, Massimo; de Martino, Maurizio; Guerrini, Renzo; Azzari, Chiara

2013-06-01

Adenosine deaminase (ADA)-severe combined immunodeficiency (SCID) is caused by genetic variants that disrupt the function of ADA. In its early-onset form, it is rapidly fatal to infants. Delayed or late-onset ADA-SCID is characterized by insidious progressive immunodeficiency that leads to permanent organ damage or death. Quantification of T-cell receptor excision circles (TRECs) or tandem mass spectrometry (tandem-MS) analysis of dried blood spots (DBSs) collected at birth can identify newborns with early-onset ADA-SCID and are used in screening programs. However, it is not clear whether these analyses can identify newborns who will have delayed or late-onset ADA-SCID before symptoms appear. We performed a retrospective study to evaluate whether tandem-MS and quantitative TREC analyses of DBSs could identify newborns who had delayed-onset ADA-SCID later in life. We tested stored DBSs collected at birth from 3 patients with delayed-onset ADA-SCID using tandem-MS (PCT EP2010/070517) to evaluate levels of adenosine and 2'-deoxyadenosine and real-time PCR to quantify TREC levels. We also analyzed DBSs from 3 newborns with early-onset ADA-SCID and 2 healthy newborn carriers of ADA deficiency. The DBSs taken at birth from the 3 patients with delayed-onset ADA-SCID had adenosine levels of 10, 25, and 19 μmol/L (normal value, <1.5 μmol/L) and 2'-deoxyadenosine levels of 0.7, 2.7, and 2.4 μmol/L (normal value, <0.07 μmol/L); the mean levels of adenosine and 2'-deoxyadenosine were respectively 12.0- and 27.6-fold higher than normal values. DBSs taken at birth from all 3 patients with delayed-onset ADA deficiency had normal TREC levels, but TRECs were undetectable in blood samples taken from the same patients at the time of diagnosis. Tandem-MS but not TREC quantification identifies newborns with delayed- or late-onset ADA deficiency. Copyright © 2013 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. 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

AUTOMATED DETERMINATION OF PRECURSOR ION, PRODUCT ION, AND NEUTRAL LOSS COMPOSITIONS AND DECONVOLUTION OF COMPOSITE MASS SPECTRA USING ION CORRELATION BASED ON EXACT MASSES AND RELATIVE ISOTOPIC ABUNDANCES

EPA Science Inventory

After a dispersive event, rapid determination of elemental compositions of ions in mass spectra is essential for tentatively identifying compounds. A Direct Analysis in Real Time (DART)® ion source interfaced to a JEOL AccuTOF® mass spectrometer provided exact masses accurate to ...

Ion/Neutral, Ion/Electron, Ion/Photon, and Ion/Ion Interactions in Tandem Mass Spectrometry: Do we need them all? Are they enough?

PubMed Central

McLuckey, Scott A.; Mentinova, Marija

2011-01-01

A range of strategies and tools has been developed to facilitate the determination of primary structures of analyte molecules of interest via tandem mass spectrometry (MS/MS). The two main factors that determine the primary structural information present in an MS/MS spectrum are the type of ion generated from the analyte molecule and the dissociation method. The ion-type subjected to dissociation is determined by the ionization method/conditions and ion transformation processes that might take place after initial gas-phase ion formation. Furthermore, the range of analyte-related ion types can be expanded via derivatization reactions prior to mass spectrometry. Dissociation methods include those that simply alter the population of internal states of the mass-selected ion (i.e., activation methods like collision-induced dissociation) as well as processes that rely on transformation of the ion-type prior to dissociation (e.g., electron capture dissociation). A variety of ionic interactions has been studied for the purpose of ion dissociation and ion transformation that include ion/neutral, ion/photon, ion/electron, and ion/ion interactions. A wide range of phenomena has been observed, many of which have been explored/developed as means for structural analysis. The techniques arising from these phenomena are discussed within the context of the elements of structure determination in tandem mass spectrometry, viz., ion-type definition and dissociation. Unique aspects of the various ion interactions are emphasized along with any barriers to widespread implementation. PMID:21472539

Proposal for a common nomenclature for fragment ions in mass spectra of lipids

PubMed Central

Hartler, Jürgen; Christiansen, Klaus; Gallego, Sandra F.; Peng, Bing; Ahrends, Robert

2017-01-01

Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines. PMID:29161304

Proposal for a common nomenclature for fragment ions in mass spectra of lipids.

PubMed

Pauling, Josch K; Hermansson, Martin; Hartler, Jürgen; Christiansen, Klaus; Gallego, Sandra F; Peng, Bing; Ahrends, Robert; Ejsing, Christer S

2017-01-01

Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines.

Determination of selected non-authorized insecticides in peppers by liquid chromatography time-of-flight mass spectrometry and tandem mass spectrometry.

PubMed

Mezcua, Milagros; Ferrer, Carmen; García-Reyes, Juan F; Martínez-Bueno, María Jesús; Albarracín, Micaela; Claret, María; Fernández-Alba, Amadeo R

2008-05-01

In this work, two analytical methods based on liquid chromatography coupled to electrospray time-of-flight mass spectrometry (LC/ESI-TOFMS) and tandem mass spectrometry (LC/ESI-MS/MS) are described for the identification, confirmation and quantitation of three insecticides non-authorized in the European Union (nitenpyram, isocarbophos and isofenphos-methyl) but detected in recent monitoring programmes in pepper samples. The proposed methodologies involved a sample extraction procedure using liquid-liquid partition with acetonitrile followed by a cleanup step based on dispersive solid-phase extraction. Recovery studies performed on peppers spiked at different fortification levels (10 and 50 microg kg(-1)) yielded average recoveries in the range 76-100% with relative standard deviation (RSD) (%) values below 10%. Identification, confirmation and quantitation were carried out by LC/TOFMS and LC/MS/MS using a hybrid triple quadrupole linear ion trap (QqLIT) instrument in multiple-reaction monitoring (MRM) mode. The obtained limits of quantitation (LOQs) were in the range 0.1-5 microg kg(-1), depending on each individual technique. Finally, the proposed methods were successfully applied to the analysis of suspected pepper samples. Copyright (c) 2008 John Wiley & Sons, Ltd.

Detection of Stimulants and Narcotics by Liquid Chromatography-Tandem Mass Spectrometry and Gas Chromatography-Mass Spectrometry for Sports Doping Control.

PubMed

Ahrens, Brian D; Kucherova, Yulia; Butch, Anthony W

2016-01-01

Sports drug testing laboratories are required to detect several classes of compounds that are prohibited at all times, which include anabolic agents, peptide hormones, growth factors, beta-2 agonists, hormones and metabolic modulators, and diuretics/masking agents. Other classes of compounds such as stimulants, narcotics, cannabinoids, and glucocorticoids are also prohibited, but only when an athlete is in competition. A single class of compounds can contain a large number of prohibited substances and all of the compounds should be detected by the testing procedure. Since there are almost 70 stimulants on the prohibited list it can be a challenge to develop a single screening method that will optimally detect all the compounds. We describe a combined liquid chromatography-tandem mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) testing method for detection of all the stimulants and narcotics on the World Anti-Doping Agency prohibited list. Urine for LC-MS/MS testing does not require sample pretreatment and is a direct dilute and shoot method. Urine samples for the GC-MS method require a liquid-liquid extraction followed by derivatization with trifluoroacetic anhydride.

Determination of azithromycin residue in pork using a molecularly imprinted monolithic microcolumn coupled to liquid chromatography with tandem mass spectrometry.

PubMed

Zhou, Tong; Yang, Haicui; Jin, Zhen; Liu, Qingying; Song, Xuqin; He, Limin; Fang, Binghu; Meng, Chenying

2016-04-01

Using spiramycin as a dummy template, a molecularly imprinted polymer monolithic micro-column with high selection to azithromycin was prepared in a micropipette tip. The imprinting factor of the monolithic micro-column prepared was approximately 2.67 and the morphological structure of the polymers was characterized by scanning electron microscopy. A simple, sensitive, and reproducible method based on the imprinted monolithic micro-column coupled to liquid chromatography with tandem mass spectrometry was developed for determining the residues of azithromycin in pork. Pork samples were extracted with acetonitrile, cleaned up under the optimal monolithic micro-column conditions, and analyzed using liquid chromatography with tandem mass spectrometry in the multiple reaction monitoring mode. The assay exhibited a linear dynamic range of 0.50-50 μg/L with the correlation coefficient (r(2) ) above 0.99. In the three spiking levels of 0.50, 1.0, and 10 μg/kg, the average recoveries of azithromycin from pork samples were between 85.8 and 96.5% with a relative standard deviation below 10%. The limit of detection and limit of quantitation were 0.03 and 0.1 μg/kg, respectively. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Authentication of Closely Related Fish and Derived Fish Products Using Tandem Mass Spectrometry and Spectral Library Matching.

PubMed

Nessen, Merel A; van der Zwaan, Dennis J; Grevers, Sander; Dalebout, Hans; Staats, Martijn; Kok, Esther; Palmblad, Magnus

2016-05-11

Proteomics methodology has seen increased application in food authentication, including tandem mass spectrometry of targeted species-specific peptides in raw, processed, or mixed food products. We have previously described an alternative principle that uses untargeted data acquisition and spectral library matching, essentially spectral counting, to compare and identify samples without the need for genomic sequence information in food species populations. Here, we present an interlaboratory comparison demonstrating how a method based on this principle performs in a realistic context. We also increasingly challenge the method by using data from different types of mass spectrometers, by trying to distinguish closely related and commercially important flatfish, and by analyzing heavily contaminated samples. The method was found to be robust in different laboratories, and 94-97% of the analyzed samples were correctly identified, including all processed and contaminated samples.

Evaluation of different hydrophilic stationary phases for the simultaneous determination of iminosugars and other low molecular weight carbohydrates in vegetable extracts by liquid chromatography tandem mass spectrometry.

PubMed

Rodríguez-Sánchez, S; Quintanilla-López, J E; Soria, A C; Sanz, M L

2014-11-01

Iminosugars are considered potential drug candidates for the treatment of several diseases, mainly as a result of their α-glycosidase inhibition properties. A method by hydrophilic interaction liquid chromatography tandem mass spectrometry has been optimized for the first time for the simultaneous determination of complex mixtures of bioactive iminosugars and other low molecular weight carbohydrates (LMWC) in vegetable extracts. Three hydrophilic stationary phases (sulfoalkylbetaine zwitterionic, polyhydroxyethyl aspartamide and ethylene bridge hybrid (BEH) with trifunctionally bonded amide) were compared under both basic and acidic conditions. The best sensitivity (limits of detection between 0.025 and 0.28ngmL -1 ) and overall chromatographic performance in terms of resolution, peak width and analysis time were obtained with the BEH amide column using 0.1% ammonium hydroxide as a mobile phase additive. The optimized method was applied to the analysis of extracts of hyacinth bulbs, buckwheat seeds and mulberry leaves. Iminosugar and other LMWC structures were tentatively assigned by their high resolution daughter ions mass spectra. Several iminosugars such as glycosyl-fagomine in mulberry extract were also described for the first time. Among the extracts analysed, mulberry showed the widest diversity of iminosugars, whereas the highest content of them was found in hyacinth bulb (2.5mgg -1 ) followed by mulberry (1.95 mgg -1 ). Copyright © 2014 Elsevier B.V. All rights reserved.

Quantitative determination of chromium picolinate in animal feeds by solid phase extraction and liquid chromatography-tandem mass spectrometry.

PubMed

Han, Miaomiao; Tian, Ying; Li, Zhen; Chen, Yiqiang; Yang, Wenjun; Zhang, Liying

2017-12-01

Chromium picolinate is one of the important Cr 3+ resources and is widely used in animal production. A convenient, reliable and rapid liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for the quantitative determination of chromium picolinate in animal feeds. Feed samples were extracted with acetonitrile and subsequently cleaned up by solid phase extraction cartridges Supelclean™ LC-18. Chromium picolinate was efficiently separated with a Waters ACQUITY UPLC ® BEH C18 column, ionized with electrospray ion source in positive mode (ESI + ), and quantitatively determined by tandem mass spectrometry in multiple reaction monitoring mode. Standard calibration curve of chromium picolinate in the concentration range from 0.5 to 1000ng/mL was obtained with good linearity correlation coefficient (R 2 =0.9982). Average recoveries ranged from 95.37%∼105.54%, as detected by spiking 0.02∼640mg/kg of chromium picolinate in complete feed, concentrated feed and premix. Intra-day and inter-day coefficient of variation were 0.59%∼6.67% and 2.36%∼6.97%, respectively. The limits of quantitation were 0.02mg/kg, 0.025mg/kg, and 2mg/kg for complete feed, concentrated feed, and premix, respectively. Actual sample analysis indicated that the developed method can be an effective tool to monitoring CrPic content in animal feed. Copyright © 2017. Published by Elsevier B.V.

Simultaneous analysis of ten phytohormones in Sargassum horneri by high-performance liquid chromatography with electrospray ionization tandem mass spectrometry.

PubMed

Li, Yan; Zhou, Chengxu; Yan, Xiaojun; Zhang, Jinrong; Xu, Jilin

2016-05-01

Phytohormones have attracted wide attention due to their important biological functions. However, their detection is still a challenge because of their complex composition, low abundance and diverse sources. In this study, a novel method of high-performance liquid chromatography with electrospray ionization tandem mass spectrometry was developed and validated for the simultaneous determination of ten phytohormones including indole-3-acetic acid, isopentenyladenine, isopentenyl adenosine, trans-zeatin riboside, zeatin, strigolactones, abscisic acid, salicylic acid, gibberellin A3, and jasmonic acid in Sargassum horneri (S. horneri). The phytohormones were extracted from freeze-dried S. horneri with methanol/water/methanoic acid (15:4:1, v/v/v) analyzed on a Hypersil Gold C18 column and detected by electrospray ionization tandem triple quadrupole mass spectrometry in the multiple reaction monitoring mode. The experimental conditions for the extraction and analysis of phytohormones were optimized and validated in terms of reproducibility, linearity, sensitivity, recovery, accuracy, and stability. Distributions of the phytohormones in the stems, blades, and gas bladder of the S. horneri in drift, fixed, and semi-fixed growing states were investigated for the first time. The observed contents of the phytohormones in S. horneri range from not detected to 5066.67 ng/g (fresh weight). Most phytohormones are distributed mainly in the stems of S. horneri in drift and semi-fixed states. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

47 CFR 69.111 - Tandem-switched transport and tandem charge.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Tandem-switched transport and tandem charge. 69... SERVICES (CONTINUED) ACCESS CHARGES Computation of Charges § 69.111 Tandem-switched transport and tandem...-switched transport shall consist of two rate elements, a transmission charge and a tandem switching charge...

Rapid determination of phenolic compounds and alkaloids of carob flour by improved liquid chromatography tandem mass spectrometry.

PubMed

Ortega, Nàdia; Macià, Alba; Romero, Maria-Paz; Trullols, Esther; Morello, Jose-Ramón; Anglès, Neus; Motilva, Maria-Jose

2009-08-26

An improved chromatographic method was developed using ultra-performance liquid chromatography-tandem mass spectrometry to identify and quantify phenolic compounds and alkaloids, theobromine and caffeine, in carob flour samples. The developed method has been validated in terms of speed, sensitivity, selectivity, peak efficiency, linearity, reproducibility, limits of detection, and limits of quantification. The chromatographic method allows the identification and quantification of 20 phenolic compounds, that is, phenolic acids, flavonoids, and their aglycone and glucoside forms, together with the determination of the alkaloids, caffeine and theobromine, at low concentration levels all in a short analysis time of less than 20 min.

Multiplexed bovine milk oligosaccharide analysis with aminoxy tandem mass tags

PubMed Central

Poulsen, Nina Aagaard; Barile, Daniela

2018-01-01

Milk oligosaccharides (OS) are a key factor that influences the infant gut microbial composition, and their importance in promoting healthy infant development and disease prevention is becoming increasingly apparent. Investigating the structures, properties, and sources of these compounds requires a host of complementary analytical techniques. Relative compound quantification by mass spectral analysis of isobarically labeled samples is a relatively new technique that has been used mainly in the proteomics field. Glycomics applications have so far focused on analysis of protein-linked glycans, while analysis of free milk OS has previously been conducted only on analytical standards. In this paper, we extend the use of isobaric glycan tags to the analysis of bovine milk OS by presenting a method for separation of labeled OS on a porous graphitized carbon liquid chromatographic column with subsequent analysis by quadrupole time-of-flight tandem mass spectrometry. Abundances for 15 OS extracted from mature bovine milk were measured, with replicate injections providing coefficients of variation below 15% for most OS. Isobaric labeling improved ionization efficiency for low-abundance, high-molecular weight fucosylated OS, which are known to exist in bovine milk but have been only sporadically reported in the literature. We compared the abundances of four fucosylated OS in milk from Holstein and Jersey cattle and found that three of the compounds were more abundant in Jersey milk, which is in general agreement with a previous study. This novel method represents an advancement in our ability to characterize milk OS and provides the advantages associated with isobaric labeling, including reduced instrumental analysis time and increased analyte ionization efficiency. This improved ability to measure differences in bioactive OS abundances in large datasets will facilitate exploration of OS from all food sources for the purpose of developing health-guiding products for infants

Preliminary results of investigations into the use of artificial neural networks for discriminating gas chromatograph mass spectra of remote samples

NASA Technical Reports Server (NTRS)

Geller, Harold A.; Norris, Eugene; Warnock, Archibald, III

1991-01-01

Neural networks trained using mass spectra data from the National Institute of Standards and Technology (NIST) are studied. The investigations also included sample data from the gas chromatograph mass spectrometer (GCMS) instrument aboard the Viking Lander, obtained from the National Space Science Data Center. The work performed to data and the preliminary results from the training and testing of neural networks are described. These preliminary results are presented for the purpose of determining the viability of applying artificial neural networks in discriminating mass spectra samples from remote instrumentation such as the Mars Rover Sample Return Mission and the Cassini Probe.

Determination of nonylphenol ethoxylate metabolites in vegetables and crops by high performance liquid chromatography-tandem mass spectrometry.

PubMed

She, Yongxin; Wang, Jing; Zheng, Yongquan; Cao, Weiqiang; Wang, Rongyan; Dong, Fengshou; Liu, Xingang; Qian, Mingrong; Zhang, Hu; Wu, Liqing

2012-05-01

A method has been developed for the simultaneous determination of the concentration of nonylphenol (4-NP), nonylphenol monoethoxylates (NP1EO) and nonylphenol diethoxylates (NP2EO) in vegetables and crops by liquid chromatography-tandem quadrupole mass spectrometry (HPLC-MS/MS). These target compounds were extracted from vegetable and crop samples with acetonitrile, and then the extracts were cleaned using solid phase extraction with graphitised carbon black tandem primary secondary amine (PSA) cartridges. The MS method enabled highly reliable identification by monitoring the corresponding ammonium adduct [M+NH4](+) in the positive mode for NP1EO and NP2EO, and the deprotonated molecule [M-H](-) in the negative mode for 4-NP. Recoveries for the spiked samples ranged from 65% to 118%. The limit of detection (LOD) of 4-NP, NP1EO and NP2EO was 3, 5 and 0.1μgkg(-1), respectively. This method would be useful for the quick and routine detection of the residues of 4-NP, NP1EO and NP2EO in vegetables and crops. Copyright © 2011 Elsevier Ltd. All rights reserved.

Multi-element analysis of water decoction of medicine food homology plants using inductively coupled plasma-tandem mass spectrometry

NASA Astrophysics Data System (ADS)

Fu, Liang; Shi, Shu-Yun; Chen, Xiao-Qing

2017-07-01

The concentration of twelve trace elements in the water decoction of medicine food homology plants (MFHP) was determined by inductively coupled plasma-tandem mass spectrometry (ICP-MS/MS). Water decoctions of MFHP were analyzed directly using the MS/MS mode after acidification by 1% (v/v) nitric acid. The polyatomic interferences were eliminated by oxygen mass shift, oxygen on-mass, and ammonia mass shift. The accuracy of the method was verified by analysis of standard reference materials. This method was utilized to investigate the water decoction composition of 16 common Chinese MFHPs. The trace elements in the water decoctions of different MFHPs presented significantly different dissolution ratios. The dissolution ratio of V was the lowest (4.21%-14.86%), whereas Zn showed the highest dissolution ratio (24.87%-86.80%). In addition, the dissolution ratio of heavy metallic elements in most MFHP was equal to or was lower than 30%. Therefore, consumption of MHFP decoction could decrease the heavy metal intake associated with MFHP use and reduce the risk of heavy metal poisoning.

Enhancing Accuracy in Molecular Weight Determination of Highly Heterogeneously Glycosylated Proteins by Native Tandem Mass Spectrometry.

PubMed

Wang, Guanbo; de Jong, Rob N; van den Bremer, Ewald T J; Parren, Paul W H I; Heck, Albert J R

2017-05-02

The determination of molecular weights (MWs) of heavily glycosylated proteins is seriously hampered by the physicochemical characteristics and heterogeneity of the attached carbohydrates. Glycosylation impacts protein migration during sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE) and size-exclusion chromatography (SEC) analysis. Standard electrospray ionization (ESI)-mass spectrometry does not provide a direct solution as this approach is hindered by extensive interference of ion signals caused by closely spaced charge states of broadly distributed glycoforms. Here, we introduce a native tandem MS-based approach, enabling charge-state resolution and charge assignment of protein ions including those that escape mass analysis under standard MS conditions. Using this method, we determined the MW of two model glycoproteins, the extra-cellular domains of the highly and heterogeneously glycosylated proteins CD38 and epidermal growth factor receptor (EGFR), as well as the overall MW and binding stoichiometries of these proteins in complex with a specific antibody.

Determination of fluspirilene in human plasma by liquid chromatography-tandem mass spectrometry with electrospray ionisation.

PubMed

Swart, K J; Sutherland, F C; van Essen, G H; Hundt, H K; Hundt, A F

1998-12-18

An ultra-sensitive method for the determination of fluspirilene in plasma was established, using high-performance liquid chromatographic separation with tandem mass spectrometric detection. The samples were extracted with hexane/isoamyl alcohol, separated on a Phenomenex Luna C18 5 mu 150 x 2.1 mm column with a mobile phase consisting of methanol-water-acetic acid (600:400:1) at a flow-rate of 0.3 ml/min. Detection was achieved by a Finnigan Matt mass spectrometer (LCQ) at unit resolution in full scan mode scanning the product ion spectrum from m/z 130-500 and monitoring the transition of the protonated molecular ion at m/z 476.2, to the sum of the largest product ions m/z 371, 342 and 274 (MS-MS). Electrospray ionisation was used for ion production. The mean recovery for fluspirilene was 90% with a lower limit of quantification of 21.50 pg/ml using 1 ml plasma for extraction. This is the first chromatographic method described for the determination of fluspirilene in plasma that is accurate and sensitive enough to be used in pharmacokinetic studies.

The Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra.

PubMed

Shilov, Ignat V; Seymour, Sean L; Patel, Alpesh A; Loboda, Alex; Tang, Wilfred H; Keating, Sean P; Hunter, Christie L; Nuwaysir, Lydia M; Schaeffer, Daniel A

2007-09-01

The Paragon Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented. Sequence Temperature Values are computed using a sequence tag algorithm, allowing the degree of implication by an MS/MS spectrum of each region of a database to be determined on a continuum. Counter to conventional approaches, features such as modifications, substitutions, and cleavage events are modeled with probabilities rather than by discrete user-controlled settings to consider or not consider a feature. The use of feature probabilities in conjunction with Sequence Temperature Values allows for a very large increase in the effective search space with only a very small increase in the actual number of hypotheses that must be scored. The algorithm has a new kind of user interface that removes the user expertise requirement, presenting control settings in the language of the laboratory that are translated to optimal algorithmic settings. To validate this new algorithm, a comparison with Mascot is presented for a series of analogous searches to explore the relative impact of increasing search space probed with Mascot by relaxing the tryptic digestion conformance requirements from trypsin to semitrypsin to no enzyme and with the Paragon Algorithm using its Rapid mode and Thorough mode with and without tryptic specificity. Although they performed similarly for small search space, dramatic differences were observed in large search space. With the Paragon Algorithm, hundreds of biological and artifact modifications, all possible substitutions, and all levels of conformance to the expected digestion pattern can be searched in a single search step, yet the typical cost in search time is only 2-5 times that of conventional small search space. Despite this large increase in effective search space, there is no drastic loss of discrimination that typically accompanies the exploration of large search space.

[Simultaneous determination of nine estrogens in eel by ultrafast liquid chromatography-tandem mass spectrometry with isotope dilution technique and solid-phase extraction].

PubMed

Chen, Xiaohong; Yao, Shanshan; Li, Xiaoping; Zhao, Yonggang; Jin, Micong

2012-11-01

Developing a rapid and sensitive analytical method based on ultrafast liquid chromatography-tandem mass spectrometry (UFLC-MS/MS) with solid-phase extraction (SPE) for the simultaneous determination of nine estrogens (dienestrol, diethylstilbestrol, estrone, hexestrol, 17-alpha-estradiol, 17-beta-estradiol, estriol, 17alpha-ethinylestradiol and estradiol valerate) in eel. After the sample was extracted by acetonitrile and cleaned by Waters Oasis HLB solid-phase extraction cartridge, the UFLC separation was performed on a Shim-pack XR-ODS II column (100 mm x 2.0 mm, 2.2 microm) with a linear gradient elution program of methanol solution containing 0.04% ammonia (v/v) and 0.04% ammonia aqueous solution (v/v) as the mobile phase. Electrospray ionization was applied and operated in the negative multiple reaction monitoring (MRM) mode. The quantitation was used by isotope internal standard dilution technique. The results showed that the limits of quantitation (LOQs, S/N(10) were in the range of 0.07-0.4 microg/kg, the calibration curves were in good linearities for the nine analytes in the range of 0.5-50.0 microg/L with the correlative coefficients (r2) more than 0.998, the recoveries were between 81.0% and 110.0% with the relative standard deviations (RSDs) of 1.92%-8.24%. Additional, the mass spectra characterization of the nine estrogens was discussed and the fragmentation pathways were speculated. The developed method is rapid, sensitive, specific and reproducible, and adapts not only to the simultaneous determination of the nine trace estrogens including the epimer of 17-alpha-estradiol and 17-beta-estradiol but also to the identified detection in other fish tissues.

Quantitation of iothalamate in urine and plasma using liquid chromatography electrospray tandem mass spectrometry (HPLC-ESI-MS/MS).

PubMed

Molinaro, Ross J; Ritchie, James C

2010-01-01

The following chapter describes a method to measure iothalamate in plasma and urine samples using high performance liquid chromatography combined with electrospray positive ionization tandem mass spectrometry (HPLC-ESI-MS/MS). Methanol and water are spiked with the internal standard (IS) iohexol. Iothalamate is isolated from plasma after IS spiked methanol extraction and from urine by IS spiked water addition and quick-spin filtration. The plasma extractions are dried under a stream of nitrogen. The residue is reconstituted in ammonium acetate-formic acid-water. The reconstituted plasma and filtered urine are injected into the HPLC-ESI-MS/MS. Iothalamate and iohexol show similar retention times in plasma and urine. Quantification of iothalamate in the samples is made by multiple reaction monitoring using the hydrogen adduct mass transitions, from a five-point calibration curve.

Tissue spray ionization mass spectrometry for rapid recognition of human lung squamous cell carcinoma

NASA Astrophysics Data System (ADS)

Wei, Yiping; Chen, Liru; Zhou, Wei; Chingin, Konstantin; Ouyang, Yongzhong; Zhu, Tenggao; Wen, Hua; Ding, Jianhua; Xu, Jianjun; Chen, Huanwen

2015-05-01

Tissue spray ionization mass spectrometry (TSI-MS) directly on small tissue samples has been shown to provide highly specific molecular information. In this study, we apply this method to the analysis of 38 pairs of human lung squamous cell carcinoma tissue (cancer) and adjacent normal lung tissue (normal). The main components of pulmonary surfactants, dipalmitoyl phosphatidylcholine (DPPC, m/z 757.47), phosphatidylcholine (POPC, m/z 782.52), oleoyl phosphatidylcholine (DOPC, m/z 808.49), and arachidonic acid stearoyl phosphatidylcholine (SAPC, m/z 832.43), were identified using high-resolution tandem mass spectrometry. Monte Carlo sampling partial least squares linear discriminant analysis (PLS-LDA) was used to distinguish full-mass-range mass spectra of cancer samples from the mass spectra of normal tissues. With 5 principal components and 30 - 40 Monte Carlo samplings, the accuracy of cancer identification in matched tissue samples reached 94.42%. Classification of a tissue sample required less than 1 min, which is much faster than the analysis of frozen sections. The rapid, in situ diagnosis with minimal sample consumption provided by TSI-MS is advantageous for surgeons. TSI-MS allows them to make more informed decisions during surgery.