Science.gov

Sample records for dissociation tandem mass

  1. 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.

  2. Decoding Split and Pool Combinatorial Libraries with Electron-Transfer Dissociation Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Sarkar, Mohosin; Pascal, Bruce D.; Steckler, Caitlin; Aquino, Claudio; Micalizio, Glenn C.; Kodadek, Thomas; Chalmers, Michael J.

    2013-07-01

    Screening of bead-based split and pool combinatorial chemistry libraries is a powerful approach to aid the discovery of new chemical compounds able to interact with, and modulate the activities of, protein targets of interest. Split and pool synthesis provides for large and well diversified chemical libraries, in this case comprised of oligomers generated from a well-defined starting set. At the end of the synthesis, each bead in the library displays many copies of a unique oligomer sequence. Because the sequence of the oligomer is not known at the time of screening, methods for decoding of the sequence of each screening "hit" are essential. Here we describe an electron-transfer dissociation (ETD) based tandem mass spectrometry approach for the decoding of mass-encoded split and pool libraries. We demonstrate that the newly described "chiral oligomers of pentenoic amides (COPAs)" yield non-sequence-specific product ions upon collisional activated dissociation; however, complete sequence information can be obtained with ETD. To aid in the decoding of libraries from MS and MS/MS data, we have incorporated 79Br/81Br isotope "tags" to differentiate N- and C-terminal product ions. In addition, we have created "Hit-Find," a software program that allows users to generate libraries in silico . The user can then search all possible members of the chemical library for those that fall within a user-defined mass error.

  3. Decoding Split and Pool Combinatorial Libraries with Electron Transfer Dissociation Tandem Mass Spectrometry

    PubMed Central

    Sarkar, Mohosin; Pascal, Bruce D.; Steckler, Caitlin; Aquino, Claudio; Micalizio, Glenn C.; Kodadek, Thomas; Chalmers, Michael J.

    2015-01-01

    Screening of bead-based split and pool combinatorial chemistry libraries is a powerful approach to aid the discovery of new chemical compounds able to interact with, and modulate the activities of, protein targets of interest. Split and pool synthesis provides for large and well diversified chemical libraries, in this case comprised of oligomers generated from a well-defined starting set. At the end of the synthesis, each bead in the library displays many copies of a unique oligomer sequence. Because the sequence of the oligomer is not known at the time of screening, methods for decoding of the sequence of each screening “hit” are essential. Here we describe an electron transfer dissociation (ETD) based tandem mass spectrometry approach for the decoding of mass-encoded split and pool libraries. We demonstrate that the newly described “chiral oligomers of pentenoic amides (COPAs)” yield non-sequence-specific product ions upon collisional activated dissociation; however, complete sequence information can be obtained with ETD. To aid in the decoding of libraries from MS and MS/MS data, we have incorporated 79Br/81Br isotope “tags” to differentiate N- and C-terminal product ions. In addition, we have created “Hit-Find,” a software program that allows users to generate libraries in silico. The user can then search all possible members of the chemical library for those that fall within a user-defined mass error. PMID:23636859

  4. Human embryonic stem cell phosphoproteome revealed by electron transfer dissociation tandem mass spectrometry

    PubMed Central

    Swaney, Danielle L.; Wenger, Craig D.; Thomson, James A.; Coon, Joshua J.

    2009-01-01

    Protein phosphorylation is central to the understanding of cellular signaling, and cellular signaling is suggested to play a major role in the regulation of human embryonic stem (ES) cell pluripotency. Here, we describe the use of conventional tandem mass spectrometry-based sequencing technology—collision-activated dissociation (CAD)—and the more recently developed method electron transfer dissociation (ETD) to characterize the human ES cell phosphoproteome. In total, these experiments resulted in the identification of 11,995 unique phosphopeptides, corresponding to 10,844 nonredundant phosphorylation sites, at a 1% false discovery rate (FDR). Among these phosphorylation sites are 5 localized to 2 pluripotency critical transcription factors—OCT4 and SOX2. From these experiments, we conclude that ETD identifies a larger number of unique phosphopeptides than CAD (8,087 to 3,868), more frequently localizes the phosphorylation site to a specific residue (49.8% compared with 29.6%), and sequences whole classes of phosphopeptides previously unobserved. PMID:19144917

  5. Low-mass ions produced from peptides by high-energy collision-induced dissociation in tandem mass spectrometry.

    PubMed

    Falick, A M; Hines, W M; Medzihradszky, K F; Baldwin, M A; Gibson, B W

    1993-11-01

    High-energy collision-induced dissociation (CID) mass spectrometry provides a rapid and sensitive means for determining the primary sequence of peptides. The low-mass region (below mass 300) of a large number of tandem CID spectra of peptides has been analyzed. This mass region contains several types of informative fragment ions, including dipeptide ions, immonium ions, and other related ions. Useful low-mass ions are also present in negative-ion CID spectra. Immonium ions (general structure [H2N=CH-R](+), where R is the amino acid side chain) and related ions characteristic of specific amino acid residues give information as to the presence or absence of these residues in the peptide being analyzed. Tables of observed immonium and reiated ions for the 20 standard amino acids and for a number of modified amino acids are presented. A database consisting of 228 high-energy CID spectra of peptides has been established, and the frequency of occurrence of various ions indicative of specific ammo acid residues has been determined. Two model computer-aided schemes for analysis of the ammo-acid content of unknown peptides have been developed and tested against the database. PMID:24227532

  6. Collision-induced dissociation pathways of anabolic steroids by electrospray ionization tandem mass spectrometry.

    PubMed

    Guan, Fuyu; Soma, Lawrence R; Luo, Yi; Uboh, Cornelius E; Peterman, Scott

    2006-04-01

    Anabolic steroids are structurally similar compounds, and their product-ion spectra obtained by tandem mass spectrometry under electrospray ionization conditions are quite difficult to interpret because of poly-ring structures and lack of a charge-retaining center in their chemical structures. In the present study, the fragmentation of nine anabolic steroids of interest to the racing industry was investigated by using triple quadrupole mass spectrometer, Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer, and a linear ion trap instrument. With the aid of an expert system software (Mass Frontier version 3.0), accurate mass measurements, and multiple stage tandem mass spectrometric (MS(n)) experiments, fragmentation pathways were elucidated for boldenone, methandrostenolone, tetrahydrogestrinone (THG), trenbolone, normethandrolone and mibolerone. Small differences in the chemical structures of the steroids, such as an additional double-bond or a methyl group, result in significantly different fragmentation pathways. The fragmentation pathways proposed in this paper allow interpretation of major product ions of other anabolic steroids reported by other researchers in a recent publication. The proposed fragmentation pathways are helpful for characterization of new steroids. The approach used in this study for elucidation of the fragmentation pathways is helpful in interpretation of complicated product-ion spectra of other compounds, drugs and their metabolites. PMID:16488153

  7. Targeted Tandem Mass Spectrometry for High-Throughput Comparative Proteomics Employing NanoLC-FTICR MS with External Ion Dissociation

    SciTech Connect

    Kang, Hyuk; Pasa-Tolic, Liljiana; Smith, Richard D.

    2007-05-03

    ABSTRACT-Targeted tandem mass spectrometry (MS/MS) is an attractive proteomic approach that allows selective identification of peptides exhibiting abundance differences between culture conditions and/or diseased states. Herein, we report on a targeted LC-MS/MS capability realized with a 7 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer equipped with a quadrupole interface that provides data-dependent ion selection, accumulation, and dissociation externally to the ICR trap. Identification of a subset of differentially abundant proteins from Shewanella oneidensis grown under suboxic vs. aerobic conditions demonstrates the feasibility of such approach. High mass resolution offered by FTICR and effective on-the-fly elution time correction facilitated accurate selection of targets, while high mass measurement accuracy MS/MS data resulted in unambiguous peptide identifications.

  8. Hydrogen Attachment/Abstraction Dissociation (HAD) of Gas-Phase Peptide Ions for Tandem Mass Spectrometry.

    PubMed

    Takahashi, Hidenori; Sekiya, Sadanori; Nishikaze, Takashi; Kodera, Kei; Iwamoto, Shinichi; Wada, Motoi; Tanaka, Koichi

    2016-04-01

    Dissociation of gas-phase peptide ions through interaction with low-energy hydrogen (H) radical (∼0.15 eV) was observed with a quadrupole ion trap mass spectrometry. The H radical generated by thermal dissociation of H2 molecules passing through a heated tungsten capillary (∼2000 °C) was injected into the ion trap containing target peptide ions. The fragmentation spectrum showed abundant c-/z- and a-/x-type ions, attributable to H attachment/abstraction to/from peptide ion. Because the low-energy neutral H radical initiated the fragmentation, the charge state of the precursor ion was maintained during the dissociation. As a result, precursor ions of any charge state, including singly charged positive and negative ions, could be analyzed for amino acid sequence. The sequence coverage exceeding 90% was obtained for both singly protonated and singly deprotonated substance P peptide. This mass spectrometry also preserved labile post-translational modification bonds. The modification sites of triply phosphorylated peptide (kinase domain of insulin receptor) were identified with the sequence coverage exceeding 80%. PMID:27002918

  9. Determining the Binding Sites of β-Cyclodextrin and Peptides by Electron-Capture Dissociation High Resolution Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Qi, Yulin; Geib, Timon; Volmer, Dietrich A.

    2015-07-01

    Cyclodextrins (CDs) are a group of cyclic oligosaccharides, which readily form inclusion complexes with hydrophobic compounds to increase bioavailability, thus making CDs ideal drug excipients. Recent studies have also shown that CDs exhibit a wide range of protective effects, preventing proteins from aggregation, degradation, and folding. These effects strongly depend on the binding sites on the protein surface. CDs only exhibit weak interactions with amino acids, however; conventional analytical techniques therefore usually fail to reveal the exact location of the binding sites. Moreover, some studies even suggest that CD inclusion complexes are merely electrostatic adducts. Here, electron capture dissociation (ECD) was applied in this proof-of-concept study to examine the exact nature of the CD/peptide complexes, and CD binding sites were unambiguously located for the first time via Fourier-transform ion cyclotron resonance (FTICR) tandem mass spectrometry.

  10. Characterization of an Ion Mobility-Multiplexed Collision Induced Dissociation-Tandem Time-of-Flight Mass Spectrometry Approach

    PubMed Central

    Ibrahim, Yehia M.; Prior, David C.; Baker, Erin S.; Smith, Richard D.; Belov, Mikhail E.

    2010-01-01

    The confidence in peptide (and protein) identifications with ion mobility spectrometry time-of-flight mass spectrometry (IMS-TOFMS) is expected to drastically improve with the addition of information from an efficient ion dissociation step prior to MS detection. High throughput IMS-TOFMS analysis imposes a strong need for multiplexed ion dissociation approaches where multiple precursor ions yield complex sets of fragment ions that are often intermingled with each other in both the drift time and m/z domains. We have developed and evaluated an approach for collision-induced dissociation (CID) using IMS-TOFMS instrument. It has been shown that precursor ions activated inside an rf-device with an axial dc-electric field produce abundant fragment ions which are radially confined with the rf-field and collisionally cooled at an elevated pressure, resulting in high CID efficiencies comparable or higher than those measured in triple-quadrupole instruments. We have also developed an algorithm for deconvoluting these complex multiplexed tandem MS spectra by clustering both the precursor and fragment ions into matching drift time profiles and by utilizing the high mass measurement accuracy achievable with TOFMS. In a single IMS separation from direct infusion of tryptic digest of bovine serum albumin (BSA), we have reliably identified 20 unique peptides using a multiplexed CID approach downstream of the IMS separation. Peptides were identified based upon the correlation between the precursor and fragment drift time profiles and by matching the profile representative masses to those of in silico BSA tryptic peptides and their fragments. The false discovery rate (FDR) of peptide identifications from multiplexed MS/MS spectra was less than 1%. PMID:20596241

  11. Structures of Fluoranthene Reagent Anions Used in Electron Transfer Dissociation and Proton Transfer Reaction Tandem Mass Spectrometry.

    PubMed

    Martens, Jonathan; Berden, Giel; Oomens, Jos

    2016-06-21

    Ion/ion reactions have in recent years seen widespread use in ion activation methods such as electron transfer dissociation (ETD) tandem mass spectrometry (MS/MS) as well as in charge manipulation of highly charged peptides/proteins and their fragments by proton transfer reaction (PTR). These techniques have, in combination, enabled top-down proteomics on limited-resolution benchtop mass spectrometry platforms such as quadrupole ion traps. Anions generated by chemical ionization of fluoranthene are often used for both ETD and PTR reactions; the radical anion of fluoranthene (m/z 202) for ETD and the closed-shell anion resulting from H atom attachment to the radical anion (m/z 203) for PTR. Here we use infrared ion spectroscopy in combination with density functional theory calculations to identify the structures of these reagent anions. We establish that the m/z 203 PTR reagent anion possesses a structure that deviates from what has been suggested previously and provides some insight into the reaction mechanism involved in PTR. PMID:27228406

  12. Top-Down Mass Analysis of Protein Tyrosine Nitration: Comparison of Electron Capture Dissociation with “Slow-Heating” Tandem Mass Spectrometry Methods

    PubMed Central

    2010-01-01

    Tyrosine nitration in proteins is an important post-translational modification (PTM) linked to various pathological conditions. When multiple potential sites of nitration exist, tandem mass spectrometry (MS/MS) methods provide unique tools to locate the nitro-tyrosine(s) precisely. Electron capture dissociation (ECD) is a powerful MS/MS method, different in its mechanisms to the “slow-heating” threshold fragmentation methods, such as collision-induced dissociation (CID) and infrared multiphoton dissociation (IRMPD). Generally, ECD provides more homogeneous cleavage of the protein backbone and preserves labile PTMs. However recent studies in our laboratory demonstrated that ECD of doubly charged nitrated peptides is inhibited by the large electron affinity of the nitro group, while CID efficiency remains unaffected by nitration. Here, we have investigated the efficiency of ECD versus CID and IRMPD for top-down MS/MS analysis of multiply charged intact nitrated protein ions of myoglobin, lysozyme, and cytochrome c in a commercial Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. CID and IRMPD produced more cleavages in the vicinity of the sites of nitration than ECD. However the total number of ECD fragments was greater than those from CID or IRMPD, and many ECD fragments contained the site(s) of nitration. We conclude that ECD can be used in the top-down analysis of nitrated proteins, but precise localization of the sites of nitration may require either of the “slow-heating” methods. PMID:20677807

  13. Differentiation of Regioisomeric Aromatic Ketocarboxylic Acids by Positive Mode Atmospheric Pressure Chemical Ionization Collision-Activated Dissociation Tandem Mass Spectrometry in a Linear Quadrupole Ion Trap Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Amundson, Lucas M.; Owen, Benjamin C.; Gallardo, Vanessa A.; Habicht, Steven C.; Fu, Mingkun; Shea, Ryan C.; Mossman, Allen B.; Kenttämaa, Hilkka I.

    2011-04-01

    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 different collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.

  14. On the dissociation of the naphthalene radical cation: new iPEPICO and tandem mass spectrometry results.

    PubMed

    West, Brandi; Joblin, Christine; Blanchet, Valerie; Bodi, Andras; Sztáray, Bálint; Mayer, Paul M

    2012-11-15

    The dissociation of the naphthalene radical cation has been reinvestigated here by a combination of tandem mass spectrometry and imaging photoelectron photoion coincidence spectroscopy (iPEPICO). Six reactions were explored: (R1) C(10)H(8)(•+) → C(10)H(7)(+) + H (m/z = 127); (R2) C(10)H(8)(•+) → C(8)H(6)(•+) + C(2)H(2) (m/z = 102); (R3) C(10)H(8)(•+) → C(6)H(6)(•+) + C(4)H(2) (m/z = 78); (R4) C(10)H(8)(•+) → C(10)H(6)(•+) + H(2) (m/z = 126); (R5) C(10)H(7)(+) → C(6)H(5)(+) + C(4)H(2) (m/z = 77); (R6) C(10)H(7)(+) → C(10)H(6)(•+) + H (m/z = 126). The E(0) activation energies for the reactions deduced from the present measurements are (in eV) 4.20 ± 0.04 (R1), 4.12 ± 0.05 (R2), 4.27 ± 0.07 (R3), 4.72 ± 0.06 (R4), 3.69 ± 0.26 (R5), and 3.20 ± 0.13 (R6). The corresponding entropies of activation, ΔS(‡)(1000K), derived in the present study are (in J K(-1) mol(-1)) 2 ± 2 (R1), 0 ± 2 (R2), 4 ± 4 (R3), 11 ± 4 (R4), 5 ± 15 (R5), and -19 ± 11 (R6). The derived E(0) value, combined with the previously reported IE of naphthalene (8.1442 eV) results in an enthalpy of formation for the naphthyl cation, Δ(f)H°(0K) = 1148 ± 14 kJ mol(-1)/Δ(f)H°(298K) = 1123 ± 14 kJ mol(-1) (site of dehydrogenation unspecified), slightly lower than the previous estimate by Gotkis and co-workers. The derived E(0) for the second H-loss leads to a Δ(f)H° for ion 7, the cycloprop[a]indene radical cation, of Δ(f)H°(0K) =1457 ± 27 kJ mol(-1)/Δ(f)H°(298K)(C(10)H(6)(+)) = 1432 ± 27 kJ mol(-1). Detailed comparisons are provided with values (experimental and theoretical) available in the literature. PMID:23088182

  15. Conversion of 3-nitrotyrosine to 3-aminotyrosine residues facilitates mapping of tyrosine nitration in proteins by electrospray ionization-tandem mass spectrometry using electron capture dissociation.

    PubMed

    Guo, Jia; Prokai, Laszlo

    2012-12-01

    Protein tyrosine nitration is associated with oxidative stress and various human diseases. Tandem mass spectrometry has been the method of choice for the identification and localization of this posttranslational modification to understand the underlying mechanisms and functional consequences. Due to the electron predator effect of the nitro group limiting fragmentation of the peptide backbone, electron-based dissociation has not been applicable, however, to nitrotyrosine-containing peptides. A straightforward conversion of the nitrotyrosine to the aminotyrosine residues is introduced to address this limitation. When tested with nitrated ubiquitin and human serum albumin as model proteins in top-down and bottom-up approaches, respectively, this chemical derivatization enhanced backbone fragmentation of the corresponding nitroproteins and nitropeptides by electron capture dissociation (ECD). Increased sequence coverage has been obtained by combining in the bottom-up strategy the conversion of nitrotyrosine to aminotyrosine and introducing, in addition to trypsin, a further digesting enzyme of complementary specificity, when protein nitration was mapped by liquid chromatography-electrospray ionization tandem mass spectrometry using both collision-induced dissociation (CID) and ECD. PMID:23280749

  16. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation.

    PubMed

    Rombouts, Ine; Lagrain, Bert; Scherf, Katharina A; Lambrecht, Marlies A; Koehler, Peter; Delcour, Jan A

    2015-01-01

    Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing. PMID:26193081

  17. Hemoglobin variants as models for investigation of dissociation of intact polypeptide chains by ESI tandem mass spectrometry

    SciTech Connect

    Light, K.J.; Loo, J.A.; Edmonds, C.G.; Smith, R.D.

    1991-06-01

    Electrospray ionization mass spectroscopy (ESI-MS) is rapidly becoming a practical biochemical tool for peptide and protein sequence analysis. The utility of ESI-MS is through use of Collisionally Activated Dissociation (ESI-CAD-MS). Human hemoglobin (Hb, {approximately}62 kDa) consists of four polypeptide chains and a prosthetic heme group. There are over 400 Hb variants, characterized by amino acid substitutions in either the alpha or beta polypeptide chains. We investigated ESI-CAD-MS as a tool for rapidly analyzing amino acid substitutions, using eight Hb beta chain variants. The approximate location of the modification can be deduced from comparison of the CAD mass spectra and observance of the mass shifts of the fragment ion containing the substitution. Fragmentation occurs preferentially at the amino terminus of proline residues. For most substitutions, differences in CAD mass spectra were not seen. 2 figs.

  18. Application of matrix calculation 1: Design and adjustment of a tandem mass spectrometer for Collision-Activated Dissociation (CAD)

    NASA Astrophysics Data System (ADS)

    1982-02-01

    A matrix representation of the ion optics of the analyzing stage has been used in a computer model of a tandem mass spectrometer with simultaneous detection for CAD. The matrix algorithm of this model is discussed here as an elegant way of describing the ion optics in a first-order approximation. The accuracy of the calculations is illustrated by comparing calculated and measured adjustments of the instrument under normal experiment conditions. The ion-optical possibilities with respect to transmission, mass resolution influence of several ion optical parameters on the shape and position of the mass focal plane is discussed. The experimental values of mass range, mass resolution and ion transmission agree very well with the calculations. Moreover, the computer model appears to be a useful tool for giving clear insight into the operation of the rather complex ion optics of the instrument. The calculations have been further developed towards higher accuracy, making possible automatic focusing of the mass focal plane onto the detector.

  19. INFRARED SPECTRUM OF POTASSIUM-CATIONIZED TRIETHYLPHOSPHATE GENERATED USING TANDEM MASS SPECTROMETRY AND INFRARED MULTIPLE PHOTON DISSOCIATION

    SciTech Connect

    Gary S. Groenewold; Christopher M. Leavitt; Ryan P. Dain; Jos Oomens; Jeff Steill; van Stipdonk, Michael J.

    2009-09-01

    Tandem mass spectrometry and wavelength selective infrared photodissociation was used to generate an infrared spectrum of gas-phase triethylphosphate cationized by attachment of K+. Prominent absorptions were observed in the region of 900 to 1300 cm-1 that are characteristic of phosphate P=O and P-O-R stretches. The relative positions and intensities of the IR absorptions were reproduced well by density functional theory (DFT) calculations performed using the B3LYP functional and the 6-31+g(d), 6-311+g(d,p) and 6-311++G(3df,2pd) basis sets. Because of good correspondence between experiment and theory for the cation, DFT was then used to generate a theoretical spectrum for neutral triethylphosphate, which in turn accurately reproduces the IR spectrum of the neat liquid when solvent effects are included in the calculations.

  20. Separation and Identification of Isomeric Glycans by Selected Accumulation-Trapped Ion Mobility Spectrometry-Electron Activated Dissociation Tandem Mass Spectrometry.

    PubMed

    Pu, Yi; Ridgeway, Mark E; Glaskin, Rebecca S; Park, Melvin A; Costello, Catherine E; Lin, Cheng

    2016-04-01

    One of the major challenges in structural characterization of oligosaccharides is the presence of many structural isomers in most naturally occurring glycan mixtures. Although ion mobility spectrometry (IMS) has shown great promise in glycan isomer separation, conventional IMS separation occurs on the millisecond time scale, largely restricting its implementation to fast time-of-flight (TOF) analyzers which often lack the capability to perform electron activated dissociation (ExD) tandem MS analysis and the resolving power needed to resolve isobaric fragments. The recent development of trapped ion mobility spectrometry (TIMS) provides a promising new tool that offers high mobility resolution and compatibility with high-performance Fourier transform ion cyclotron resonance (FTICR) mass spectrometers when operated under the selected accumulation-TIMS (SA-TIMS) mode. Here, we present our initial results on the application of SA-TIMS-ExD-FTICR MS to the separation and identification of glycan linkage isomers. PMID:26959868

  1. Classical trajectories and RRKM modeling of collisional excitation and dissociation of benzylammonium and tert-butyl benzylammonium ions in a quadrupole-hexapole-quadrupole tandem mass spectrometer.

    PubMed

    Knyazev, Vadim D; Stein, Stephen E

    2010-03-01

    Collision-induced dissociation of the benzylammonium and the 4-tert-butyl benzylammonium ions was studied experimentally in an electrospray ionization quadrupole-hexapole-quadrupole tandem mass spectrometer. Ion fragmentation efficiencies were determined as functions of the kinetic energy of ions and the collider gas (argon) pressure. A theoretical Monte Carlo model of ion collisional excitation, scattering, and decomposition was developed. The model includes simulation of the trajectories of the parent and the product ions flight through the hexapole collision cell, quasiclassical trajectory modeling of collisional activation and scattering of ions, and Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the parent ion decomposition. The results of modeling demonstrate a general agreement between calculations and experiment. Calculated values of ion fragmentation efficiency are sensitive to initial vibrational excitation of ions, scattering of product ions from the collision cell, and distribution of initial ion velocities orthogonal to the axis of the collision cell. Three critical parameters of the model were adjusted to reproduce the experimental data on the dissociation of the benzylammonium ion: reaction enthalpy and initial internal and translational temperatures of the ions. Subsequent application of the model to decomposition of the t-butyl benzylammonium ion required adjustment of the internal ion temperature only. Energy distribution functions obtained in modeling depend on the average numbers of collisions between the ion and the atoms of the collider gas and, in general, have non-Boltzmann shapes. PMID:20060316

  2. Monte Carlo/RRKM/classical trajectories modeling of collisional excitation and dissociation of n-butylbenzene ion in multipole collision cells of tandem mass spectrometers.

    PubMed

    Knyazev, Vadim D; Stein, Stephen E

    2010-06-10

    The two-channel reaction of collision-induced dissociation (CID) of the n-butylbenzene cation under the conditions of multipole collision cells of tandem mass spectrometers was studied computationally. The results were compared with the experimental data from earlier CID studies. The Monte Carlo method used includes simulation of the trajectories of flight of the parent (n-C(4)H(9)C(6)H(5)(+)) and the product (C(7)H(7)(+) and C(7)H(8)(+)) ions in the electromagnetic field of multipole ion guides and collision cells, classical trajectory modeling of collisional activation and scattering of ions, and RRKM modeling of the parent ion decomposition. Experimental information on the energy dependences of the rates of the n-butylbenzene cation dissociation via two channels was used to create an RRKM model of the reaction. Effects of uncertainties in the critical parameters of the model of the reaction and the collision cells on the results of calculations were evaluated and shown to be minor. The results of modeling demonstrate a good agreement with experiment, providing support for the applied computational method in general and the use of classical trajectory modeling of collisional activation of ions in particular. PMID:20481494

  3. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation

    PubMed Central

    Rombouts, Ine; Lagrain, Bert; Scherf, Katharina A.; Koehler, Peter; Delcour, Jan A.

    2015-01-01

    Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing. PMID:26193081

  4. Molecular formula analysis of fragment ions by isotope-selective collision-induced dissociation tandem mass spectrometry of pharmacologically active compounds.

    PubMed

    Bianco, Giuliana; Buchicchio, Alessandro; Lelario, Filomena; Cataldi, Tommaso R I

    2014-12-01

    The purpose of this work is to explore the mass fragment characterization of commonly used drugs through a novel approach, which involves isotope-selective tandem mass spectrometry (MS/MS). Collision-induced dissociation (CID) was performed with a low-resolution linear ion trap mass spectrometer in positive electrospray ionization. Three pharmacologically active ingredients, i.e. omeprazole, meloxicam and brinzolamide, selected as model compounds in their own formulation, were investigated as a sodiated adduct [C17 H19 N3 O3 S + Na](+) (omeprazole) and as protonated adducts, [C14 H13 N3 O4 S2  + H](+) and [C12 H21 N3 O5 S3  + H](+) , meloxicam and brinzolamide, respectively. Selecting a narrow window of ±0.5 m/z units, precursor ion fragmentation by CID-MS/MS of isotopologues A + 0, A + 1 and A + 2 was found very useful to confirm the chemical formula of product ions, thus aiding the establishment of characteristic fragmentation pathways of all three examined compounds. The correctness of putative molecular formula of product ions was easily demonstrated by exploiting the isotope peak abundance ratios (i.e. IF+0 /IF+1 and IF+0 /IF+2 ) as simple constraints in low-resolution MS instrumentations. PMID:25476951

  5. Improved 6-Plex Tandem Mass Tags Quantification Throughput Using a Linear Ion Trap-High-Energy Collision Induced Dissociation MS(3) Scan.

    PubMed

    Liu, Jane M; Sweredoski, Michael J; Hess, Sonja

    2016-08-01

    The use of tandem mass tags (TMT) as an isobaric labeling strategy is a powerful method for quantitative proteomics, yet its accuracy has traditionally suffered from interference. This interference can be largely overcome by selecting MS(2) fragment precursor ions for high-energy collision induced dissociation (HCD) MS(3) analysis in an Orbitrap scan. While this approach minimizes the interference effect, sensitivity suffers due to the high AGC targets and long acquisition times associated with MS(3) Orbitrap detection. We investigated whether acquiring the MS(3) scan in a linear ion trap with its lower AGC target would increase overall quantification levels with a minimal effect on precision and accuracy. Trypsin-digested proteins from Saccharomyces cerevisiae were tagged with 6-plex TMT reagents. The sample was subjected to replicate analyses using either the Orbitrap or the linear ion trap for the HCD MS(3) scan. HCD MS(3) detection in the linear ion trap vs Orbitrap increased protein identification by 66% with minor loss in precision and accuracy. Thus, the use of a linear ion trap-HCD MS(3) scan during a 6-plex TMT experiment can improve overall identification levels while maintaining the power of multiplexed quantitative analysis. PMID:27377715

  6. Protonation Sites and Dissociation Mechanisms of t-Butylcarbamates in Tandem Mass Spectrometric Assays for Newborn Screening

    PubMed Central

    Spáčil, Zdeněk; Hui, Renjie; Gelb, Michael H.; Tureček, František

    2011-01-01

    Structures of tert-butylcarbamate ions in the gas phase and methanol solution were studied for simple secondary and tertiary carbamates as well as for carbamate-containing products and internal standards for lysosomal enzyme assays used in newborn screening of a α-galactosidase A deficiency (GLA, Fabry disease), mucopolysaccharidosis I (Hurler disease), and mucopolysaccharidosis II (Hunter disease). Protonation of simple t-butylcarbamates can occur at the carbonyl group which is the preferred site in the gas phase. Protonation in methanol solution is more favorable if occurring at the carbamate nitrogen atom. Protonation of more complex t-butylcarbamates occurs at amide and carbamate carbonyl groups, and the ions are stabilized by intramolecular hydrogen bonding which is affected by solvation. Tertiary carbamates containing aminophenol amide groups were calculated to have substantially greater gas-phase basicities than secondary carbamates containing coumarin amide groups. The main diagnostically important ion dissociation by elimination of 2-methylpropene (isobutylene, i-C4H8) and carbon dioxide is shown by experiment and theory to proceed in two steps. Energy-resolved collision-induced dissociation of the Hurler’s disease enzymatic product ion, which is a coumarin-diamine linker-t-butylcarbamate conjugate (3a+), indicated separate energy thresholds for the loss of i-C4H8 and CO2. Computational investigation of the potential energy surface along two presumed reaction pathways indicated kinetic preference for the migration of a t-butyl hydrogen atom to the carbamate carbonyl resulting in the isobutylene loss. The consequent loss of CO2 required further proton migrations that had to overcome energy barriers. PMID:22012676

  7. Identification of Cross-Linked Peptides after Click-Based Enrichment Using Sequential Collision-Induced Dissociation and Electron Transfer Dissociation Tandem Mass Spectrometry

    SciTech Connect

    Chowdhury, Saiful M.; Du, Xiuxia; Tolic, Nikola; Wu, Si; Moore, Ronald J.; Mayer, M. Uljana; Smith, Richard D.; Adkins, Joshua N.

    2009-07-01

    Chemical cross-linking combined with mass spectrometric analysis is emerging as a powerful technique for protein-protein interaction and protein structure elucidation studies.1 Cross-linkers covalently link two interacting proteins, often with chemistries specific to certain amino acid side chains. After enzymatic digestion of the proteins, the resulting cross-linked peptides can be subjected to analysis by LC-MS(/MS) to identify cross-linked species.2,3 For studying protein interactions using chemical cross-linking towards global discovery-based applications, the critical needs are the development of cross-linkers that are highly specific, amenable to LC-MS/MS, and resulting spectra are interpretable by bioinformatics tools to automatically assign cross-linked peptides with high confidence.4-10 As recently mentioned by Aebersold and co-workers, due to the low relative abundances of cross-linking products compared to their unmodified counterparts, enrichment of cross-linked species is also highly desirable to improve the likelihood of unambiguous identification of cross-linked peptides.6 Most of the currently available enrichable cross-linkers are bulky and are not amenable to studying protein-protein interactions in vivo. To discover protein-protein interactions with high confidence, there is a need for chemical cross-linkers that can effectively label protein complexes, utilize mass spectrometry based bottom-up proteomics analysis pipelines and also contains enrichment functionality.

  8. Online coupling of high-resolution chromatography with extreme UV photon activation tandem mass spectrometry: Application to the structural investigation of complex glycans by dissociative photoionization.

    PubMed

    Ropartz, David; Giuliani, Alexandre; Fanuel, Mathieu; Hervé, Cécile; Czjzek, Mirjam; Rogniaux, Hélène

    2016-08-24

    The activation of ions by extreme-energy photons (XUV) produced by a synchrotron radiation beamline is a powerful method for characterizing complex glycans using tandem mass spectrometry (MS). As previously described, this activation method leads to rich fragmentation spectra with many structurally valuable cross-ring cleavages while maintaining labile modifications on the glycan structures. However, until now, the tandem MS event was too long to be compatible with liquid chromatography elution times. In this work, the duty cycle of the activation and detection of fragments was shortened, and the background signal on the spectra was drastically reduced. Both improvements allowed, for the first time, the successful coupling of a UHPLC system to XUV-activated tandem MS. The approach was used to characterize a complex mixture of oligo-porphyrans, which are a class of highly sulfated oligosaccharides, in a fully automated way. Due to an enhanced dynamic range and an increased sensitivity, some hypothetical structures of low abundance have been unequivocally confirmed in this study and others have been revised. Some previously undescribed species of oligo-porphyrans that exhibit lateral branching have been fully resolved. This work contributes to the scarce knowledge of the structure of porphyrans in red algae and pushes the current capacities of XUV-activation tandem MS by demonstrating the possibility of a direct coupling with UHPLC. This study will considerably broaden the applicability and practicality of this method in many fields of analytical biology. PMID:27496992

  9. Identification of epoxide functionalities in protonated monofunctional analytes by using ion/molecule reactions and collision-activated dissociation in different ion trap tandem mass spectrometers.

    PubMed

    Eismin, Ryan J; Fu, Mingkun; Yem, Sonoeun; Widjaja, Fanny; Kenttämaa, Hilkka I

    2012-01-01

    A mass spectrometric method has been delineated for the identification of the epoxide functionalities in unknown monofunctional analytes. This method utilizes gas-phase ion/molecule reactions of protonated analytes with neutral trimethyl borate (TMB) followed by collision-activated dissociation (CAD) in an ion trapping mass spectrometer (tested for a Fourier-transform ion cyclotron resonance and a linear quadrupole ion trap). The ion/molecule reaction involves proton transfer from the protonated analyte to TMB, followed by addition of the analyte to TMB and elimination of methanol. Based on literature, this reaction allows the general identification of oxygen-containing analytes. Vinyl and phenyl epoxides can be differentiated from other oxygen-containing analytes, including other epoxides, based on the loss of a second methanol molecule upon CAD of the addition/methanol elimination product. The only other analytes found to undergo this elimination are some amides but they also lose O = B-R (R = group bound to carbonyl), which allows their identification. On the other hand, other epoxides can be differentiated from vinyl and phenyl epoxides and from other monofunctional analytes based on the loss of (CH(3)O)(2)BOH or formation of protonated (CH(3)O)(2)BOH upon CAD of the addition/methanol elimination product. For propylene oxide and 2,3-dimethyloxirane, the (CH(3)O)(2)BOH fragment is more basic than the hydrocarbon fragment, and the diagnostic ion (CH(3)O)(2)BOH (2) (+) is formed. These reactions involve opening of the epoxide ring. The only other analytes found to undergo (CH(3)O)(2)BOH elimination are carboxylic acids, but they can be differentiated from the rest based on several published ion/molecule reaction methods. Similar results were obtained in the Fourier-transform ion cyclotron resonance and linear quadrupole ion trap mass spectrometer. PMID:22002227

  10. Identification of Epoxide Functionalities in Protonated Monofunctional Analytes by Using Ion/Molecule Reactions and Collision-Activated Dissociation in Different Ion Trap Tandem Mass Spectrometers

    NASA Astrophysics Data System (ADS)

    Eismin, Ryan J.; Fu, Mingkun; Yem, Sonoeun; Widjaja, Fanny; Kenttämaa, Hilkka I.

    2012-01-01

    A mass spectrometric method has been delineated for the identification of the epoxide functionalities in unknown monofunctional analytes. This method utilizes gas-phase ion/molecule reactions of protonated analytes with neutral trimethyl borate (TMB) followed by collision-activated dissociation (CAD) in an ion trapping mass spectrometer (tested for a Fourier-transform ion cyclotron resonance and a linear quadrupole ion trap). The ion/molecule reaction involves proton transfer from the protonated analyte to TMB, followed by addition of the analyte to TMB and elimination of methanol. Based on literature, this reaction allows the general identification of oxygen-containing analytes. Vinyl and phenyl epoxides can be differentiated from other oxygen-containing analytes, including other epoxides, based on the loss of a second methanol molecule upon CAD of the addition/methanol elimination product. The only other analytes found to undergo this elimination are some amides but they also lose O = B-R (R = group bound to carbonyl), which allows their identification. On the other hand, other epoxides can be differentiated from vinyl and phenyl epoxides and from other monofunctional analytes based on the loss of (CH3O)2BOH or formation of protonated (CH3O)2BOH upon CAD of the addition/methanol elimination product. For propylene oxide and 2,3-dimethyloxirane, the (CH3O)2BOH fragment is more basic than the hydrocarbon fragment, and the diagnostic ion (CH3O)2BOH{2/+} is formed. These reactions involve opening of the epoxide ring. The only other analytes found to undergo (CH3O)2BOH elimination are carboxylic acids, but they can be differentiated from the rest based on several published ion/molecule reaction methods. Similar results were obtained in the Fourier-transform ion cyclotron resonance and linear quadrupole ion trap mass spectrometer.

  11. Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching.

    PubMed

    Pai, Pei-Jing; Hu, Yingwei; Lam, Henry

    2016-08-31

    Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a new computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods2008, 5, 873-875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem.2010, 82, 10194-10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. In addition, we further applied our method to reveal, for the first time, the site-specific N-glycosylation profile of recombinant human acetylcholinesterase expressed in HEK293 cells. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis. PMID:27506355

  12. 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...

  13. Tandem-in-space and tandem-in-time mass spectrometry: Triple quadrupoles and quadrupole ion traps

    SciTech Connect

    Johnson, J.V.; Yost, R.A. ); Kelley, P.E.; Bradford, D.C. )

    1990-10-15

    Tandem-in-time and tandem-in-space MS/MS on quadrupole ion trap (ITMS) and triple quadrupole (TQMS) tandem mass spectrometers, respectively, were compared by evaluating the MS/MS daughter spectra, efficiencies of collision-induced dissociation (CID), limits of detection, and dynamic ranges obtained for the methane positive chemical ionization (PCI)-CID of two alkylphosphonates. Although the yield of daughter ions is dependent upon a number of instrumental parameters on both instruments, with judicious selection of parameters the ITMS and TQMS both yielded daughter ions of similar relative abundances. The ITMS had greater efficiencies of fragmentation, collection, and mass selection and transmission of the daughter ions to the detector. With PCI-MS/MS analysis of diisopropyl methylphosphonate standards introduced via capillary gas chromatography, full daughter spectra could be obtained for as little as 15 pg and 1.5 ng injected for the ITMS and the TQMS, respectively.

  14. Fast atom bombardment tandem mass spectrometry of carotenoids

    SciTech Connect

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

    1995-02-01

    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 carotenes 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.

  15. Synthesis and tandem mass spectrometry of chlorinated triacylglycerols.

    PubMed

    Lefsay, Abir M; Guy, Robert D; Chatt, Amares; White, Robert L

    2013-09-01

    The incorporation of 9,10-dichlorooctadecanoyl groups using enzyme-catalyzed acylation and protecting group strategies yielded specific regioisomers of di- and tetrachlorinated triacylglycerols. Hexachloro- and hexabromotriacylglycerols were synthesized by addition of chlorine or bromine to tri-(cis-9-octadecenoyl)glycerol. Upon electrospray ionization and tandem mass spectrometry, the sodium adduct ions of all compounds containing a 9,10-dichlorooctadecanoyl group readily lost two molecules of HCl when subjected to collision-induced dissociation. A mechanism describing sequential HCl losses and the formation of a conjugated diene is proposed for the loss of both vicinal chlorine atoms from an alkyl chain. This characteristic fragmentation behavior and the availability of characterized standards will facilitate the development of quantitative analytical methods for the determination of chlorinated triacylglycerols in lipid mixtures isolated from marine and other biological sources. PMID:23872189

  16. Stability and Degradation of Caffeoylquinic Acids under Different Storage Conditions Studied by High-Performance Liquid Chromatography with Photo Diode Array Detection and High-Performance Liquid Chromatography with Electrospray Ionization Collision-Induced Dissociation Tandem Mass Spectrometry.

    PubMed

    Xue, Meng; Shi, Hang; Zhang, Jiao; Liu, Qing-Quan; Guan, Jun; Zhang, Jia-Yu; Ma, Qun

    2016-01-01

    Caffeoylquinic acids (CQAs) are main constituents in many herbal medicines with various biological and pharmacological effects. However, CQAs will degrade or isomerize when affected by temperature, pH, light, etc. In this study, high-performance liquid chromatography with photodiode array detection (HPLC-PDA) and high-performance liquid chromatography tandem mass spectrometry (HPLC-MS/MS) was utilized to study the stability and degradation of CQAs (three mono-acyl CQAs and four di-acyl CQAs) under various ordinary storage conditions (involving different temperatures, solvents, and light irradiation). The results indicated that the stability of CQAs was mainly affected by temperature and light irradiation, while solvents did not affect it in any obvious way under the conditions studied. Mono-acyl CQAs were generally much more stable than di-acyl CQAs under the same conditions. Meanwhile, the chemical structures of 30 degradation products were also characterized by HPLC-MS(n), inferring that isomerization, methylation, and hydrolysis were three major degradation pathways. The result provides a meaningful clue for the storage conditions of CQAs standard substances and samples. PMID:27455213

  17. Electrospray and tandem mass spectrometry in biochemistry.

    PubMed Central

    Griffiths, W J; Jonsson, A P; Liu, S; Rai, D K; Wang, Y

    2001-01-01

    Over the last 20 years, biological MS has changed out of all recognition. This is primarily due to the development in the 1980s of 'soft ionization' methods that permit the ionization and vaporization of large, polar, and thermally labile biomolecules. These developments in ionization mode have driven the design and manufacture of smaller and cheaper mass analysers, making the mass spectrometer a routine instrument in the biochemistry laboratory today. In the present review the revolutionary 'soft ionization' methods will be discussed with particular reference to electrospray. The mass analysis of ions will be described, and the concept of tandem MS introduced. Where appropriate, examples of the application of MS in biochemistry will be provided. Although the present review will concentrate on the MS of peptides/proteins and lipids, all classes of biomolecules can be analysed, and much excellent work has been done in the fields of carbohydrate and nucleic acid biochemistry. PMID:11311115

  18. Electrospray Ionization Tandem Mass Spectrometry of Ammonium Cationized Polyethers

    NASA Astrophysics Data System (ADS)

    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.

  19. Tandem mass spectrometry for sequencing proanthocyanidins.

    PubMed

    Li, Hui-Jing; Deinzer, Max L

    2007-02-15

    Proanthocyanidins (PAs) are a group of bioflavonoids consisting of oligomers based on catechin monomeric units. These polyphenolic compounds are widely distributed in higher plants and are an integral part of the human diet. A sensitive LC-tandem mass spectrometric (LC/ESI-MS(n)) method in the positive ion mode for sequencing these ubiquitous and highly beneficial antioxidants is described. The hydroxylation patterns and interflavanoid linkage for A- and B-type PAs were determined by fragment ions derived from a retro-Diels-Alder (RDA) fission, heterocyclic ring fission (HRF), a novel benzofuran-forming (BFF) fission described here for the first time, and a quinone methide (QM) fission. The subunit sequence of the PAs was determined by diagnostic ions derived from HRF/RDA fission, HRF/BFF fission, and RDA/HRF fission together with QM fission. A total of 26 PAs were reliably sequenced by the newly established tandem mass spectrometric protocol. It is shown that the protocol based on a combination of these different fragmentation patterns allows for uniquely identifying PA oligomers. PMID:17297981

  20. High-sensitivity mass spectrometry with a tandem accelerator

    SciTech Connect

    Henning, W.

    1983-01-01

    The characteristic features of accelerator mass spectrometry are discussed. A short overview is given of the current status of mass spectrometry with high-energy (MeV/nucleon) heavy-ion accelerators. Emphasis is placed on studies with tandem accelerators and on future mass spectrometry of heavier isotopes with the new generation of higher-voltage tandems.

  1. 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.

  2. Characterization of linear and branched polyacrylates by tandem mass spectrometry.

    PubMed

    Chaicharoen, Kittisak; Polce, Michael J; Singh, Anirudha; Pugh, Coleen; Wesdemiotis, Chrys

    2008-10-01

    The unimolecular degradation of alkali-metal cationized polyacrylates with the repeat unit CH(2)CH(COOR) and a variety of ester pendants has been examined by tandem mass spectrometry. The fragmentation patterns resulting from collisionally activated dissociation depend sensitively on the size of the ester alkyl substituent (R). With small alkyl groups, as in poly(methyl acrylate), lithiated or sodiated oligomers (M) decompose via free-radical chemistry, initiated by random homolytic C-C bond cleavages along the polymer chain. The radical ions formed this way dissociate further by backbiting rearrangements and beta scissions to yield a distribution of terminal fragments with one of the original end groups and internal fragments with 2-3 repeat units. If the ester alkyl group bears three or more carbon atoms, cleavages within the ester moieties become the predominant decomposition channel. This distinct reactivity is observed if R = t-butyl, n-butyl, or the mesogenic group (CH(2))(11)-O-C(6)H(4)-C(6)H(4)-CN. The [M+alkali metal](+) ions of the latter polyacrylates dissociate largely by charge-remote 1,5-H rearrangements that convert COOR to COOH groups by expulsion of 1-alkenes. The acid groups may displace an alcohol unit from a neighboring ester pendant to form a cyclic anhydride, unless hindered by steric effects. Using atom transfer radical polymerization, hyperbranched polyacrylates were prepared carrying ester groups both within and between the branches. Unique alkenes and alcohols are cleaved from ester groups at the branching points, enabling determination of the branching architecture. PMID:18373231

  3. Electron Transfer Dissociation Mass Spectrometry of Hemoglobin on Clinical Samples

    NASA Astrophysics Data System (ADS)

    Coelho Graça, Didia; Lescuyer, Pierre; Clerici, Lorella; Tsybin, Yury O.; Hartmer, Ralf; Meyer, Markus; Samii, Kaveh; Hochstrasser, Denis F.; Scherl, Alexander

    2012-10-01

    A mass spectrometry-based assay combining the specificity of selected reaction monitoring and the protein ion activation capabilities of electron transfer dissociation was developed and employed for the rapid identification of hemoglobin variants from whole blood without previous proteolytic cleavage. The analysis was performed in a robust ion trap mass spectrometer operating at nominal mass accuracy and resolution. Subtle differences in globin sequences, resulting with mass shifts of about one Da, can be unambiguously identified. These results suggest that mass spectrometry analysis of entire proteins using electron transfer dissociation can be employed on clinical samples in a workflow compatible with diagnostic applications.

  4. Tandem mass spectrometry: analysis of complex mixtures

    SciTech Connect

    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 products 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.

  5. Infrared Multiphoton Dissociation of Peptide Cations in a Dual Pressure Linear Ion Trap Mass Spectrometer

    PubMed Central

    Gardner, Myles W.; Smith, Suncerae I.; Ledvina, Aaron R.; Madsen, James A.; Coon, Joshua J.; Schwartz, Jae C.; Stafford, George C.; Brodbelt, Jennifer S.

    2009-01-01

    A dual pressure linear ion trap mass spectrometer was modified to permit infrared multiphoton dissociation (IRMPD) in each of the two cells - the first a high pressure cell operated at nominally 5 × 10-3 Torr and the second a low pressure cell operated at nominally 3 × 10-4 Torr. When IRMPD was performed in the high pressure cell, most peptide ions did not undergo significant photodissociation; however, in the low pressure cell peptide cations were efficiently dissociated with less than 25 ms of IR irradiation regardless of charge state. IRMPD of peptide cations allowed the detection of low m/z product ions including the y1 fragments and immonium ions which are not typically observed by ion trap collision induced dissociation (CID). Photodissociation efficiencies of ~100% and MS/MS (tandem mass spectrometry) efficiencies of greater than 60% were observed for both multiply and singly protonated peptides. In general, higher sequence coverage of peptides was obtained using IRMPD over CID. Further, greater than 90% of the product ion current in the IRMPD mass spectra of doubly charged peptide ions was composed of singly charged product ions compared to the CID mass spectra in which the abundances of the multiply and singly charged product ions were equally divided. Highly charged primary product ions also underwent efficient photodissociation to yield singly charged secondary product ions, thus simplifying the IRMPD product ion mass spectra. PMID:19739654

  6. Structural identification of electron transfer dissociation products in mass spectrometry using infrared ion spectroscopy.

    PubMed

    Martens, Jonathan; Grzetic, Josipa; Berden, Giel; Oomens, Jos

    2016-01-01

    Tandem mass spectrometry occupies a principle place among modern analytical methods and drives many developments in the 'omics' sciences. Electron attachment induced dissociation methods, as alternatives for collision-induced dissociation have profoundly influenced the field of proteomics, enabling among others the top-down sequencing of entire proteins and the analysis of post-translational modifications. The technique, however, produces more complex mass spectra and its radical-driven reaction mechanisms remain incompletely understood. Here we demonstrate the facile structural characterization of electron transfer dissociation generated peptide fragments by infrared ion spectroscopy using the tunable free-electron laser FELIX, aiding the elucidation of the underlying dissociation mechanisms. We apply this method to verify and revise previously proposed product ion structures for an often studied model tryptic peptide, [AlaAlaHisAlaArg+2H](2+). Comparing experiment with theory reveals that structures that would be assigned using only theoretical thermodynamic considerations often do not correspond to the experimentally sampled species. PMID:27277826

  7. Structural identification of electron transfer dissociation products in mass spectrometry using infrared ion spectroscopy

    PubMed Central

    Martens, Jonathan; Grzetic, Josipa; Berden, Giel; Oomens, Jos

    2016-01-01

    Tandem mass spectrometry occupies a principle place among modern analytical methods and drives many developments in the ‘omics' sciences. Electron attachment induced dissociation methods, as alternatives for collision-induced dissociation have profoundly influenced the field of proteomics, enabling among others the top-down sequencing of entire proteins and the analysis of post-translational modifications. The technique, however, produces more complex mass spectra and its radical-driven reaction mechanisms remain incompletely understood. Here we demonstrate the facile structural characterization of electron transfer dissociation generated peptide fragments by infrared ion spectroscopy using the tunable free-electron laser FELIX, aiding the elucidation of the underlying dissociation mechanisms. We apply this method to verify and revise previously proposed product ion structures for an often studied model tryptic peptide, [AlaAlaHisAlaArg+2H]2+. Comparing experiment with theory reveals that structures that would be assigned using only theoretical thermodynamic considerations often do not correspond to the experimentally sampled species. PMID:27277826

  8. Dissociation and Mass Transfer Coefficients for Ammonia Volatilization Models

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Process-based models are being used to predict ammonia emissions from manure sources, but their accuracy has not been fully evaluated for cattle manure. Laboratory trials were conducted to measure the dissociation and mass transfer coefficients for ammonia volatilization from media of buffered ammon...

  9. High-speed tandem mass spectrometric in situ imaging by nanospray desorption electrospray ionization mass spectrometry.

    PubMed

    Lanekoff, Ingela; Burnum-Johnson, Kristin; Thomas, Mathew; Short, Joshua; Carson, James P; Cha, Jeeyeon; Dey, Sudhansu K; Yang, Pengxiang; Prieto Conaway, Maria C; Laskin, Julia

    2013-10-15

    Nanospray desorption electrospray ionization (nano-DESI) combined with tandem mass spectrometry (MS/MS), high-resolution mass analysis of the fragment ions (m/Δm = 17 500 at m/z 200), and rapid spectral acquisition enabled simultaneous imaging and identification of a large number of metabolites and lipids from 92 selected m/z windows (±1 Da) with a spatial resolution of better than 150 μm. Mouse uterine sections of implantation sites on day 6 of pregnancy were analyzed in the ambient environment without any sample pretreatment. MS/MS imaging was performed by scanning the sample under the nano-DESI probe at 10 μm/s, while higher-energy collision-induced dissociation (HCD) spectra were acquired for a targeted inclusion list of 92 m/z values at a rate of ∼6.3 spectra/s. Molecular ions and their corresponding fragments, separated by high-resolution mass analysis, were assigned on the basis of accurate mass measurement. Using this approach, we were able to identify and image both abundant and low-abundance isobaric and isomeric species within each m/z window. MS/MS analysis enabled efficient separation and identification of isomeric and isobaric phospholipids that are difficult to separate in full-scan mode. Furthermore, we identified several metabolites associated with early pregnancy and obtained the first 2D images of these molecules. PMID:24040919

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

    SciTech Connect

    Lanekoff, Ingela T.; Burnum-Johnson, Kristin E.; Thomas, Mathew; Short, Joshua TL; Carson, James P.; Cha, Jeeyeon; Dey, Sudhansu K.; Yang, Pengxiang; Prieto Conaway, Maria C.; Laskin, Julia

    2013-10-15

    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 values 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.

  11. Electrospray tandem mass spectrometric analysis of a dimeric conjugate, salvialeriafone and related compounds

    PubMed Central

    2012-01-01

    Background Electrospray tandem mass spectrometry approach is widely used for the rapid characterization of natural products. This paper describes the gas-phased ESI-MS/MS fragmentation of abietane-type diterpenoids and their novel dimeric conjugate, salvialeriafone (1) using both positive and negative ion electrospray ionization quadropole time-of-flight mass spectrometry (ESI-QqTOF-MS/MS) hybrid instrument. Diterpenoids are widely distributed throughout the plant kingdom and posses interesting biological activities. Results ESI-QqTOF-MS (positive ion mode) of diterpenoids 1–6 under collision-induced dissociation tandem mass spectrometric analysis (CID-MS/MS) showed the characteristic losses of water, carbonmonoxide and propene molecules, while analysis in negative ion mode showed the characteristic losses of water, carbon monoxide, methane molecules and methyl radical. Results demonstrated the differences in the product ions and base peaks due to the differences in the skeleton. A novel dimeric conjugate, salvialeriafone (1) showed characteristic fragmentation pattern and was found to be more prone to form radical ions, as compared to monomeric diterpenoids. The fragmentation pathways of characteristic fragments were proposed with the aid of HRESIMS. Conclusions Extensive tandem mass spectrometric studies of salvialeriafone (1) and related diterpenoids 2–6 were conducted and their characteristic fragments were identified. The knowledge of the fragmentation pattern of these diterpenoids will be useful for the characterization of new dimers of this class of compounds. PMID:23079186

  12. Protonation Sites, Tandem Mass Spectrometry and Computational Calculations of o-Carbonyl Carbazolequinone Derivatives

    PubMed Central

    Martínez-Cifuentes, Maximiliano; Clavijo-Allancan, Graciela; Zuñiga-Hormazabal, Pamela; Aranda, Braulio; Barriga, Andrés; Weiss-López, Boris; Araya-Maturana, Ramiro

    2016-01-01

    A series of a new type of tetracyclic carbazolequinones incorporating a carbonyl group at the ortho position relative to the quinone moiety was synthesized and analyzed by tandem electrospray ionization mass spectrometry (ESI/MS-MS), using Collision-Induced Dissociation (CID) to dissociate the protonated species. Theoretical parameters such as molecular electrostatic potential (MEP), local Fukui functions and local Parr function for electrophilic attack as well as proton affinity (PA) and gas phase basicity (GB), were used to explain the preferred protonation sites. Transition states of some main fragmentation routes were obtained and the energies calculated at density functional theory (DFT) B3LYP level were compared with the obtained by ab initio quadratic configuration interaction with single and double excitation (QCISD). The results are in accordance with the observed distribution of ions. The nature of the substituents in the aromatic ring has a notable impact on the fragmentation routes of the molecules. PMID:27399676

  13. Protonation Sites, Tandem Mass Spectrometry and Computational Calculations of o-Carbonyl Carbazolequinone Derivatives.

    PubMed

    Martínez-Cifuentes, Maximiliano; Clavijo-Allancan, Graciela; Zuñiga-Hormazabal, Pamela; Aranda, Braulio; Barriga, Andrés; Weiss-López, Boris; Araya-Maturana, Ramiro

    2016-01-01

    A series of a new type of tetracyclic carbazolequinones incorporating a carbonyl group at the ortho position relative to the quinone moiety was synthesized and analyzed by tandem electrospray ionization mass spectrometry (ESI/MS-MS), using Collision-Induced Dissociation (CID) to dissociate the protonated species. Theoretical parameters such as molecular electrostatic potential (MEP), local Fukui functions and local Parr function for electrophilic attack as well as proton affinity (PA) and gas phase basicity (GB), were used to explain the preferred protonation sites. Transition states of some main fragmentation routes were obtained and the energies calculated at density functional theory (DFT) B3LYP level were compared with the obtained by ab initio quadratic configuration interaction with single and double excitation (QCISD). The results are in accordance with the observed distribution of ions. The nature of the substituents in the aromatic ring has a notable impact on the fragmentation routes of the molecules. PMID:27399676

  14. Crux: rapid open source protein tandem mass spectrometry analysis.

    PubMed

    McIlwain, Sean; Tamura, Kaipo; Kertesz-Farkas, Attila; Grant, Charles E; Diament, Benjamin; Frewen, Barbara; Howbert, J Jeffry; Hoopmann, Michael R; Käll, Lukas; Eng, Jimmy K; MacCoss, Michael J; Noble, William Stafford

    2014-10-01

    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

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

    SciTech Connect

    Kangas, Lars J.; Metz, Thomas O.; Isaac, Georgis; Schrom, Brian T.; Ginovska-Pangovska, Bojana; Wang, Luning; Tan, Li; Lewis, Robert R.; Miller, John H.

    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 lipids from a subset of lipid classes shows both high sensitivity and specificity.

  16. Electron capture dissociation mass spectrometry of metallo-supramolecular complexes.

    PubMed

    Kaczorowska, Malgorzata A; Hotze, Anna C G; Hannon, Michael J; Cooper, Helen J

    2010-02-01

    The electron capture dissociation (ECD) of metallo-supramolecular dinuclear triple-stranded helicate Fe(2)L(3)(4+) ions was determined by Fourier transform ion cyclotron resonance mass spectrometry. Initial electron capture by the di-iron(II) triple helicate ions produces dinuclear double-stranded complexes analogous to those seen in solution with the monocationic metal centers Cu(I) or Ag(I). The gas-phase fragmentation behavior [ECD, collision-induced dissociation (CID), and infrared multiphoton dissociation (IRMPD)] of the di-iron double-stranded complexes, (i.e., MS(3) of the ECD product) was compared with the ECD, CID, and IRMPD of the Cu(I) and Ag(I) complexes generated from solution. The results suggest that iron-bound dimers may be of the form Fe(I)(2)L(2)(2+) and that ECD by metallo-complexes allows access, in the gas phase, to oxidation states and coordination chemistry that cannot be accessed in solution. PMID:20004114

  17. Liquid chromatographic tandem mass spectrometric determination of five coccidiostats in poultry eggs and feed.

    PubMed

    Mortier, Leen; Daeseleire, Els; Van Peteghem, Carlos

    2005-06-25

    A method is described which permits the quantitative detection of the chemical coccidiostats halofuginone, robenidine, diclazuril, nicarbazin and dimetridazole and its main metabolite 2-hydroxydimetridazole in poultry eggs and feed. Sample preparations were kept very simple and are based upon extraction with an organic solvent. Sample extracts were injected into the liquid chromatography tandem mass spectrometry (LC-MS/MS) system on a C18 column and a gradient elution was performed. Dimetridazole-D3 and diclazuril-bis, a structural analogue of diclazuril, were used as internal standards. Detection was performed on a triple quadrupole mass spectrometer in the selected reaction monitoring mode after ionisation in the positive or negative electrospray ionisation mode. Argon was applied as collision gas for collision induced dissociation. Validation of the methods was performed based on Commission Decision 2002/657/EC [Official Journal of the European Communities L221 (2002) 8]. PMID:15893963

  18. 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

  19. Accelerator mass spectrometry with a coupled tandem-linac system

    SciTech Connect

    Kutschera, W.

    1984-01-01

    A coupled system provides higher energies, which allows one to extend AMS to hitherto untouched mass regions. Another important argument is that the complexity, although bothersome for the operation, increases the selectivity of detecting a particular isotope. The higher-energy argument holds for any heavy-ion accelerator which is capable of delivering higher energy than a tandem. The present use of tandem-linac combinations for AMS, rather than cyclotrons, linacs or combinations of these machines, has mainly to do with the fact that this technique was almost exclusively developed around tandem accelerators. Therefore the tandem-linac combination is a natural extension to higher energies. The use of negative ions has some particular advantages in suppressing background from unwanted elements that do not form stable negative ions (e.g., N, Mg, Ar). On the other hand, this limits the detection of isotopes to elements which do form negative ions. For particular problems it may therefore be advantageous to use a positive-ion machine. What really matters most for choosing one or the other machine is to what extent the entire accelerator system can be operated in a truly quantiative way from the ion source to the detection system. 20 references, 4 figures.

  20. 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. PMID:25303389

  1. Application of Electron Transfer Dissociation Mass Spectrometry in Analyses of Non-enzymatically Glycated Peptides

    SciTech Connect

    Zhang, Qibin; Frolov, Andrej; Tang, Ning; Hoffman, Ralf; van der Goor, Tom; Metz, Thomas O.; Smith, Richard D.

    2007-03-15

    Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in diabetes mellitus research, particularly in the context of development of diabetic complications. The fragmentation behavior of glycated peptides produced from reaction of D-glucose with lysine residues was investigated by electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. It was found that high abundance ions corresponding to various degrees of neutral water losses, as well as furylium ion production, dominate the CID spectra, and that the sequence informative b and y ions were rarely observed when Amadori-modified peptides were fragmented. Contrary to what was observed under CID conditions, ions corresponding to neutral losses of water or furylium ion production were not observed in the ETD spectra. Instead, abundant and almost complete series of c and z type ions were observed regardless of whether the modification site was located in the middle of the sequence or close to the N-terminus, greatly facilitating the peptide sequencing. This study strongly suggests that ETD is a better technique for proteomics studies of non-enzymatically glycated peptides and proteins.

  2. Combined infrared multiphoton dissociation and electron capture dissociation with a hollow electron beam in Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Tsybin, Youri O; Witt, Matthias; Baykut, Gökhan; Kjeldsen, Frank; Håkansson, Per

    2003-01-01

    An electron injection system based on an indirectly heated ring-shaped dispenser cathode has been developed and installed in a 7 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. This new hardware design allows high-rate electron capture dissociation (ECD) to be carried out by a hollow electron beam coaxial with the ion cyclotron resonance (ICR) trap. Infrared multiphoton dissociation (IRMPD) can also be performed with an on-axis IR-laser beam passing through a hole at the centre of the dispenser cathode. Electron and photon irradiation times of the order of 100 ms are required for efficient ECD and IRMPD, respectively. As ECD and IRMPD generate fragments of different types (mostly c, z and b, y, respectively), complementary structural information that improves the characterization of peptides and proteins by FTICR mass spectrometry can be obtained. The developed technique enables the consecutive or simultaneous use of the ECD and IRMPD methods within a single FTICR experimental sequence and on the same ensemble of trapped ions in multistage tandem (MS/MS/MS or MS(n)) mass spectrometry. Flexible changing between ECD and IRMPD should present advantages for the analysis of protein digests separated by liquid chromatography prior to FTICRMS. Furthermore, ion activation by either electron or laser irradiation prior to, as well as after, dissociation by IRMPD or ECD increases the efficiency of ion fragmentation, including the w-type fragment ion formation, and improves sequencing of peptides with multiple disulfide bridges. The developed instrumental configuration is essential for combined ECD and IRMPD on FTICR mass spectrometers with limited access into the ICR trap. PMID:12872281

  3. 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

  4. 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

    2016-01-01

    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

  5. Accurate and Efficient Resolution of Overlapping Isotopic Envelopes in Protein Tandem Mass Spectra

    PubMed Central

    Xiao, Kaijie; Yu, Fan; Fang, Houqin; Xue, Bingbing; Liu, Yan; Tian, Zhixin

    2015-01-01

    It has long been an analytical challenge to accurately and efficiently resolve extremely dense overlapping isotopic envelopes (OIEs) in protein tandem mass spectra to confidently identify proteins. Here, we report a computationally efficient method, called OIE_CARE, to resolve OIEs by calculating the relative deviation between the ideal and observed experimental abundance. In the OIE_CARE method, the ideal experimental abundance of a particular overlapping isotopic peak (OIP) is first calculated for all the OIEs sharing this OIP. The relative deviation (RD) of the overall observed experimental abundance of this OIP relative to the summed ideal value is then calculated. The final individual abundance of the OIP for each OIE is the individual ideal experimental abundance multiplied by 1 + RD. Initial studies were performed using higher-energy collisional dissociation tandem mass spectra on myoglobin (with direct infusion) and the intact E. coli proteome (with liquid chromatographic separation). Comprehensive data at the protein and proteome levels, high confidence and good reproducibility were achieved. The resolving method reported here can, in principle, be extended to resolve any envelope-type overlapping data for which the corresponding theoretical reference values are available. PMID:26439836

  6. STRUCTURAL CHARACTERIZATION OF SULFONATED AZO DYES USING LIQUID SECONDARY ION MASS SPECTROMETRY/TANDEM MASS SPECTROMETRY

    EPA Science Inventory

    Eight monosulfonated and disulfonated azo dyes were analyzed using liquid secondary ion mass spectrometry/tandem mass spectrometry, in the negative ion mode, under low-energy conditions (110-150 eV). any structurally characteristic fragment ions were obtained, several of which ha...

  7. 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

  8. 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. PMID:17639579

  9. 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. PMID:15762583

  10. Does deamidation cause protein unfolding? A top-down tandem mass spectrometry study

    PubMed Central

    Soulby, Andrew J; Heal, Jack W; Barrow, Mark P; Roemer, Rudolf A; O'Connor, Peter B

    2015-01-01

    Deamidation is a nonenzymatic post-translational modification of asparagine to aspartic acid or glutamine to glutamic acid, converting an uncharged amino acid to a negatively charged residue. It is plausible that deamidation of asparagine and glutamine residues would result in disruption of a proteins' hydrogen bonding network and thus lead to protein unfolding. To test this hypothesis Calmodulin and B2M were deamidated and analyzed using tandem mass spectrometry on a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS). The gas phase hydrogen bonding networks of deamidated and nondeamidated protein isoforms were probed by varying the infra-red multi-photon dissociation laser power in a linear fashion and plotting the resulting electron capture dissociation fragment intensities as a melting curve at each amino acid residue. Analysis of the unfolding maps highlighted increased fragmentation at lower laser powers localized around heavily deamidated regions of the proteins. In addition fragment intensities were decreased across the rest of the proteins which we propose is because of the formation of salt-bridges strengthening the intramolecular interactions of the central regions. These results were supported by a computational flexibility analysis of the mutant and unmodified proteins, which would suggest that deamidation can affect the global structure of a protein via modification of the hydrogen bonding network near the deamidation site and that top down FTICR-MS is an appropriate technique for studying protein folding. PMID:25653127

  11. Interpretation of tandem mass spectra obtained from cyclic nonribosomal peptides.

    PubMed

    Liu, Wei-Ting; Ng, Julio; Meluzzi, Dario; Bandeira, Nuno; Gutierrez, Marcelino; Simmons, Thomas L; Schultz, Andrew W; Linington, Roger G; Moore, Bradley S; Gerwick, William H; Pevzner, Pavel A; Dorrestein, Pieter C

    2009-06-01

    Natural and non-natural cyclic peptides are a crucial component in drug discovery programs because of their considerable pharmaceutical properties. Cyclosporin, microcystins, and nodularins are all notable pharmacologically important cyclic peptides. Because these biologically active peptides are often biosynthesized nonribosomally, they often contain nonstandard amino acids, thus increasing the complexity of the resulting tandem mass spectrometry data. In addition, because of the cyclic nature, the fragmentation patterns of many of these peptides showed much higher complexity when compared to related counterparts. Therefore, at the present time it is still difficult to annotate cyclic peptides MS/MS spectra. In this current work, an annotation program was developed for the annotation and characterization of tandem mass spectra obtained from cyclic peptides. This program, which we call MS-CPA is available as a web tool (http://lol.ucsd.edu/ms-cpa_v1/Input.py). Using this program, we have successfully annotated the sequence of representative cyclic peptides, such as seglitide, tyrothricin, desmethoxymajusculamide C, dudawalamide A, and cyclomarins, in a rapid manner and also were able to provide the first-pass structure evidence of a newly discovered natural product based on predicted sequence. This compound is not available in sufficient quantities for structural elucidation by other means such as NMR. In addition to the development of this cyclic annotation program, it was observed that some cyclic peptides fragmented in unexpected ways resulting in the scrambling of sequences. In summary, MS-CPA not only provides a platform for rapid confirmation and annotation of tandem mass spectrometry data obtained with cyclic peptides but also enables quantitative analysis of the ion intensities. This program facilitates cyclic peptide analysis, sequencing, and also acts as a useful tool to investigate the uncommon fragmentation phenomena of cyclic peptides and aids the

  12. RScore: a peptide randomicity score for evaluating tandem mass spectra.

    PubMed

    Li, Fuxin; Sun, Wei; Gao, Youhe; Wang, Jue

    2004-01-01

    RScore, a new criterion of randomicity for evaluating tandem mass (MS/MS) spectra, is described. RScore is defined as the relative quality in cross-correlation and matched intensity percentage of a potentially positive peptide to those of other possible candidates for the same spectrum. By utilizing RScore combined with less stringent SEQUEST score filters, the number of true positive peptides can be increased and the number of false positives in datasets from a known protein mixture can be reduced compared with current SEQUEST parameters used alone. This algorithm is simple and adds little overheads to SEQUEST computation. PMID:15282793

  13. A new concept Tandem thermal dissociator/electron impact ion source for RIB generation

    SciTech Connect

    Alton, G.D.; Williams, C.

    1995-12-31

    An innovative thermal dissociation/electron impact ionization positive ion source is presently under design at the Oak Ridge National Laboratory for potential use for generating RIBs at the Holifield Radioactive Ion Beam Facility (HRIBF). Because of the low probability of simultaneously dissociating and efficiently ionizing the individual atomic constituents with conventional, hot-cathode, electron-impact ion sources, the ion beams extracted from these sources often appear as a mixture of several molecular sideband beams. In this way, the intensity of the species of interest is diluted. We have conceived an Ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high efficiency characteristics of an electron impact ionization source. If the concept proves to be a viable option, the source will be used as a complement to the electron beam plasma ion sources already in use at the HRIBF. The design features and principles of operation of the source are described in this article.

  14. Tandem crossed-beam collision-induced dissociation of CO{sub 2}{sup +}

    SciTech Connect

    Chawla, R.; Krishnamurthy, M.; Shukla, A.K.

    1995-12-31

    Angle and energy resolved CID provides valuable information about energy transfer reaction mechanisms and role of excited states in activation and dissociation steps. Recent studies from this laboratory have demonstrated that electronic excitation is a prominent mechanism in low and moderate collision energy CID of certain molecules (acetone, nitromethane) but others (enol acetone, methane, propane, methyl nitrite) dissociate predominantly on the ground state hypersurface. A current focus of this research is angle and energy resolved CID studies of triatomic cations whose potential surfaces are relatively well described. They are a logical bridge between diatomics (which dissociate in a single vibration) and more complex polyatomics (which generally follow RRKM/QET delayed dissociation mechanisms). In the accompanying poster the authors develop a prompt dissociation kinematics model and demonstrate that CID of CS{sub 2}{sup +} is well described by this model. Although the structure and energetics of CO{sub 2}{sup +} are similar to CS{sub 2}{sup +}, the authors find rather different dissociation dynamics for the analogous O{sup +} and CO{sup +} products.

  15. Ion-molecule adduct formation in tandem mass spectrometry.

    PubMed

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

    2016-02-01

    Nowadays most LC-MS methods rely on tandem mass spectrometry not only for quantitation and confirmation of compounds by multiple reaction monitoring (MRM), but also for the identification of unknowns from their product ion spectra. However, gas-phase reactions between charged and neutral species inside the mass analyzer can occur, yielding product ions at m/z values higher than that of the precursor ion, or at m/z values difficult to explain by logical losses, which complicate mass spectral interpretation. In this work, the formation of adduct ions in the mass analyzer was studied using several mass spectrometers with different mass analyzers (ion trap, triple quadrupole, and quadrupole-Orbitrap). Heterocyclic amines (AαC, MeAαC, Trp-P-1, and Trp-P-2), photo-initiators (BP and THBP), and pharmaceuticals (phenacetin and levamisole) were selected as model compounds and infused in LCQ Classic, TSQ Quantum Ultra AM, and Q-Exactive Orbitrap (ThermoFisher Scientific) mass spectrometers using electrospray as ionization method. The generation of ion-molecule adducts depended on the compound and also on the instrument employed. Adducts with neutral organic solvents (methanol and acetonitrile) were only observed in the ion trap instrument (LCQ Classic), because of the ionization source on-axis configuration and the lack of gas-phase barriers, which allowed inertial entrance of the neutrals into the analyzer. Adduct formation (only with water) in the triple quadrupole instruments was less abundant than in the ion trap and quadrupole-Orbitrap mass spectrometers, because of the lower residence time of the reactive product ions in the mass analyzer. The moisture level of the CID and/or damper gas had a great effect in beam-like mass analyzers such as triple quadrupole, but not in trap-like mass analyzers, probably because of the long residence time that allowed adduct formation even with very low concentrations of water inside the mass spectrometer. PMID:26700446

  16. Non-target screening of veterinary drugs using tandem mass spectrometry on SmartMass.

    PubMed

    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. PMID:23532781

  17. 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.

  18. Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments.

    PubMed

    Bazsó, Fanni Laura; Ozohanics, Oliver; Schlosser, Gitta; Ludányi, Krisztina; Vékey, Károly; Drahos, László

    2016-08-01

    The similarity between two tandem mass spectra, which were measured on different instruments, was compared quantitatively using the similarity index (SI), defined as the dot product of the square root of peak intensities in the respective spectra. This function was found to be useful for comparing energy-dependent tandem mass spectra obtained on various instruments. Spectral comparisons show the similarity index in a 2D "heat map", indicating which collision energy combinations result in similar spectra, and how good this agreement is. The results and methodology can be used in the pharma industry to design experiments and equipment well suited for good reproducibility. We suggest that to get good long-term reproducibility, it is best to adjust the collision energy to yield a spectrum very similar to a reference spectrum. It is likely to yield better results than using the same tuning file, which, for example, does not take into account that contamination of the ion source due to extended use may influence instrument tuning. The methodology may be used to characterize energy dependence on various instrument types, to optimize instrumentation, and to study the influence or correlation between various experimental parameters. Graphical Abstract ᅟ. PMID:27206510

  19. Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

    NASA Astrophysics Data System (ADS)

    Bazsó, Fanni Laura; Ozohanics, Oliver; Schlosser, Gitta; Ludányi, Krisztina; Vékey, Károly; Drahos, László

    2016-08-01

    The similarity between two tandem mass spectra, which were measured on different instruments, was compared quantitatively using the similarity index (SI), defined as the dot product of the square root of peak intensities in the respective spectra. This function was found to be useful for comparing energy-dependent tandem mass spectra obtained on various instruments. Spectral comparisons show the similarity index in a 2D "heat map", indicating which collision energy combinations result in similar spectra, and how good this agreement is. The results and methodology can be used in the pharma industry to design experiments and equipment well suited for good reproducibility. We suggest that to get good long-term reproducibility, it is best to adjust the collision energy to yield a spectrum very similar to a reference spectrum. It is likely to yield better results than using the same tuning file, which, for example, does not take into account that contamination of the ion source due to extended use may influence instrument tuning. The methodology may be used to characterize energy dependence on various instrument types, to optimize instrumentation, and to study the influence or correlation between various experimental parameters.

  20. Quantitative Comparison of Tandem Mass Spectra Obtained on Various Instruments

    NASA Astrophysics Data System (ADS)

    Bazsó, Fanni Laura; Ozohanics, Oliver; Schlosser, Gitta; Ludányi, Krisztina; Vékey, Károly; Drahos, László

    2016-05-01

    The similarity between two tandem mass spectra, which were measured on different instruments, was compared quantitatively using the similarity index (SI), defined as the dot product of the square root of peak intensities in the respective spectra. This function was found to be useful for comparing energy-dependent tandem mass spectra obtained on various instruments. Spectral comparisons show the similarity index in a 2D "heat map", indicating which collision energy combinations result in similar spectra, and how good this agreement is. The results and methodology can be used in the pharma industry to design experiments and equipment well suited for good reproducibility. We suggest that to get good long-term reproducibility, it is best to adjust the collision energy to yield a spectrum very similar to a reference spectrum. It is likely to yield better results than using the same tuning file, which, for example, does not take into account that contamination of the ion source due to extended use may influence instrument tuning. The methodology may be used to characterize energy dependence on various instrument types, to optimize instrumentation, and to study the influence or correlation between various experimental parameters.

  1. Electron-Induced Dissociation of Peptides in a Triple Quadrupole Mass Spectrometer Retrofitted with an Electromagnetostatic Cell

    NASA Astrophysics Data System (ADS)

    Voinov, Valery G.; Bennett, Samuel E.; Barofsky, Douglas F.

    2015-05-01

    Dissociation of peptides induced by interaction with (free) electrons (electron-induced dissociation, EID) at electron energies ranging from near 0 to >30 eV was carried out using a radio-frequency-free electromagnetostatic (EMS) cell retrofitted into a triple quadrupole mass spectrometer. The product-ion mass spectra exhibited EID originating from electronically excited even-electron precursor ions, reduced radical cations formed by capture of low-energy electrons, and oxidized radical cations produced by interaction with high-energy electrons. The spectra demonstrate, within the limits of the triple quadrupole's resolving power, that high-energy EID product-ion spectra produced with an EMS cell exhibit essentially the same qualitative structural information, i.e., amino acid side-chain (SC) losses and backbone cleavages, as observed in high-energy EID spectra produced with a Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer. The levels of fragmentation efficiency evident in the product-ion spectra recorded in this study, as was the case for those recorded in earlier studies with FT ICR mass spectrometers, is currently at the margin of analytical utility. Given that this shortcoming can be remedied, EMS cells incorporated into QqQ or QqTOF mass spectrometers could make tandem high-energy EID mass spectrometry more widely accessible for analysis of peptides, small singly charged molecules, pharmaceuticals, and clinical samples.

  2. 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.

  3. Unusual fragmentation of β-linked peptides by ExD tandem Mass Spectrometry

    PubMed Central

    Sargaeva, Nadezda P.; Lin, Cheng; O’Connor, Peter B.

    2015-01-01

    Ion-electron reaction based fragmentation methods (ExD) in tandem mass spectrometry (MS), such as Electron Capture Dissociation (ECD) and Electron Transfer Dissociation (ETD) represent a powerful tool for biological analysis ExD methods have been used to differentiate the presence of the isoaspartate (isoAsp) from the aspartate (Asp) in peptides and proteins. IsoAsp is a β3-type amino acid that has an additional methylene group in the backbone, forming a Cα-Cβ bond within the polypeptide chain. Cleavage of this bond provides specific fragments that allow differentiation of the isomers. The presence of a Cα-Cβ bond within the backbone is unique to β-amino acids, suggesting a similar application of ExD toward the analysis of peptides containing other β-type amino acids. In the current study, ECD and ETD analysis of several β-amino acid containing peptides was performed. It was found that N-Cβ and Cα-Cβ bond cleavages were rare, providing few c and z• type fragments, which was attributed to the instability of the Cβ radical. Instead, the electron capture resulted primarily in the formation of a• and y fragments, representing an alternative fragmentation pathway, likely initiated by the electron capture at a backbone amide nitrogen protonation site within the beta amino acid residues. PMID:21472566

  4. Automated Glycan Sequencing from Tandem Mass Spectra of N-Linked Glycopeptides.

    PubMed

    Yu, Chuan-Yih; Mayampurath, Anoop; Zhu, Rui; Zacharias, Lauren; Song, Ehwang; Wang, Lei; Mechref, Yehia; Tang, Haixu

    2016-06-01

    Mass spectrometry has become a routine experimental tool for proteomic biomarker analysis of human blood samples, partly due to the large availability of informatics tools. As one of the most common protein post-translational modifications (PTMs) in mammals, protein glycosylation has been observed to alter in multiple human diseases and thus may potentially be candidate markers of disease progression. While mass spectrometry instrumentation has seen advancements in capabilities, discovering glycosylation-related markers using existing software is currently not straightforward. Complete characterization of protein glycosylation requires the identification of intact glycopeptides in samples, including identification of the modification site as well as the structure of the attached glycans. In this paper, we present GlycoSeq, an open-source software tool that implements a heuristic iterated glycan sequencing algorithm coupled with prior knowledge for automated elucidation of the glycan structure within a glycopeptide from its collision-induced dissociation tandem mass spectrum. GlycoSeq employs rules of glycosidic linkage as defined by glycan synthetic pathways to eliminate improbable glycan structures and build reasonable glycan trees. We tested the tool on two sets of tandem mass spectra of N-linked glycopeptides cell lines acquired from breast cancer patients. After employing enzymatic specificity within the N-linked glycan synthetic pathway, the sequencing results of GlycoSeq were highly consistent with the manually curated glycan structures. Hence, GlycoSeq is ready to be used for the characterization of glycan structures in glycopeptides from MS/MS analysis. GlycoSeq is released as open source software at https://github.com/chpaul/GlycoSeq/ . PMID:27111718

  5. Desorption electrospray ionisation mass spectrometry and tandem mass spectrometry of low molecular weight synthetic polymers.

    PubMed

    Jackson, Anthony T; Williams, Jonathan P; Scrivens, James H

    2006-01-01

    A range of low molecular weight synthetic polymers has been characterised by means of desorption electrospray ionisation (DESI) combined with both mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Accurate mass experiments were used to aid the structural determination of some of the oligomeric materials. The polymers analysed were poly(ethylene glycol) (PEG), polypropylene glycol (PPG), poly(methyl methacrylate) (PMMA) and poly(alpha-methyl styrene). An application of the technique for characterisation of a polymer used as part of an active ingredient in a pharmaceutical tablet is described. The mass spectra and tandem mass spectra of all of the polymers were obtained in seconds, indicating the sensitivity of the technique. PMID:16912984

  6. Dual-Regge approach to high-energy, low-mass diffraction dissociation

    NASA Astrophysics Data System (ADS)

    Jenkovszky, L. L.; Kuprash, O. E.; Lämsä, J. W.; Magas, V. K.; Orava, R.

    2011-03-01

    A dual-Regge model with a nonlinear proton Regge trajectory in the missing mass (MX2) channel, describing the experimental data on low-mass single diffraction dissociation (SDD), is constructed. Predictions for the LHC energies are given.

  7. Fast-atom bombardment and tandem mass spectrometry of macrolide antibiotics.

    PubMed

    Cerny, R L; Macmillan, D K; Gross, M L; Mallams, A K; Pramanik, B N

    1994-03-01

    Molecular weights of macrolide antibiotics can be determined from either (M + H)(+) or (M + Met)(+), the latter desorbed from alkali metal salt-saturated matrices. The ion chemistry of macrolides, as determined by tandem mass spectrometry (MS/MS), is different for ions produced as metallated than those formed as (M + H)(+) species. An explanation for these differences is the location of the charge. For protonated species, the charge is most likely situated on a functional group with high proton affinity, such as the dimethylamino group of the ammo sugar. The alkali metal ion, however, is bonded to the highly oxygenated aglycone. As a result, the collision-activated dissociation spectra of protonated macrolides are simple with readily identifiable fragment ions in both the high and low mass regions but no fragments in the middle mass range. In contrast, the cationized species give complex spectra with many abundant ions, most of which are located in the high mass range. The complementary nature of the fragmentation of these two species recommends the study of both by MS/MS when determining the structure or confirming the identity of these biomaterials. PMID:24222544

  8. 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). PMID:24849296

  9. Profiling oligosaccharidurias by electrospray tandem mass spectrometry: quantifying reducing oligosaccharides.

    PubMed

    Ramsay, Steven L; Meikle, Peter J; Hopwood, John J; Clements, Peter R

    2005-10-01

    A method to semiquantify urinary oligosaccharides from patients suffering from oligosaccharidurias is presented. 1-Phenyl-3-methyl-5-pyrazolone has been used to derivatize urinary oligosaccharides prior to analysis by electrospray ionization-tandem mass spectrometry (ESI-MS/MS). Disease-specific oligosaccharides were identified for several oligosaccharidurias, including GM1 gangliosidosis, GM2 gangliosidosis, sialic acid storage disease, sialidase/neuraminidase deficiency, galactosialidosis, I-cell disease, fucosidosis, Pompe and Gaucher diseases, and alpha-mannosidosis. The oligosaccharides were referenced against the internal standard, methyl lactose, to produce ratios for comparison with control samples. Elevations in specific urinary oligosaccharides were indicative of lysosomal disease and the defective catabolic enzyme. This method has been adapted to enable assay of large sample numbers and could readily be extended to other oligosaccharidurias and to monitor oligosaccharide levels in patients receiving treatment. It also has immediate potential for incorporation into a newborn screening program. PMID:16111643

  10. Assay for Glycosaminoglycans by Tandem Mass Spectrometry and its Applications

    PubMed Central

    Tomatsu, Shunji; Shimada, Tsutomu; Mason, Robert W; Kelly, Joan; LaMarr, William A; Yasuda, Eriko; Shibata, Yuniko; Futatsumori, Hideyuki; Montaño, Adriana M; Yamaguchi, Seiji; Suzuki, Yasuyuki; Orii, Tadao

    2014-01-01

    Glycosaminoglycans (GAGs) are distributed in the whole body and play a variety of important physiological roles associated with inflammation, growth, coagulation, fibrinolysis, lipolysis, and cell-matrix biology. Accumulation of undegraded GAGs in lysosomes gives rise to a distinct clinical syndrome, mucopolysaccharidoses. Measurement of each specific GAG in a variety of specimens is urgently required to understand GAG interaction with other molecules, physiological status of patients, and prognosis and pathogenesis of the disease. We established a highly sensitive and accurate tandem mass spectrometry (LC-MS/MS) method for measurements of disaccharides derived from four specific GAGs [dermatan sulfate (DS), heparan sulfate (HS), keratan sulfate (KS), and chondroitin sulfate (CS)]. Disaccharides were produced by specific enzyme digestion of each GAG, and quantified by negative ion mode of multiple reaction monitoring. Subclasses of HS and GAGs with identical molecular weights can be separated using a Hypercarbcolumn (2.0 mm×50 mm, 5 μm) with an aectonitrile gradient in ammonium acetate (pH 11.0). We also developed a GAG assay by RapidFire with tandem mass spectrometry (RF-MS/MS). The RF system consists of an integrated solid phase extraction robot that binds and de-salts samples from assay plates and directly injects them into a MS/MS detector, reducing sample processing time to ten seconds. RF-MS/MS consequently yields much faster throughput than conventional LC-MS/MS-based methods. However, the RF system does not have a chromatographic step, and therefore, cannot distinguish GAGs that have identical molecular weights. Both methods can be applied to analysis of dried blood spots, blood, and urine specimens. In this article, we compare the assay methods for GAGs and describe their potential applications. PMID:25068074

  11. 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.…

  12. Analysis of a series of chlorogenic acid isomers using differential ion mobility and tandem mass spectrometry.

    PubMed

    Willems, Jamie L; Khamis, Mona M; Mohammed Saeid, Waleed; Purves, Randy W; Katselis, George; Low, Nicholas H; El-Aneed, Anas

    2016-08-24

    Chlorogenic acids are among the most abundant phenolics found in the human diet. Of these, the mono-caffeoylquinic acids are the predominant phenolics found in fruits, such as apples and pears, and products derived from them. In this research, a comprehensive study of the electrospray ionization (ESI) tandem mass spectrometric (MS/MS) dissociation behavior of the three most common mono-caffeoylquinic acids, namely 5-O-caffeoylquinic acid (5-CQA), 3-O-caffeoylquinic acid (3-CQA) and 4-O-caffeoylquinic acid (4-CQA), were determined using both positive and negative ionization. All proposed structures of the observed product ions were confirmed with second-generation MS(3) experiments. Similarities and differences between the dissociation pathways in the positive and negative ion modes are discussed, confirming the proposed structures and the established MS/MS fingerprints. MS/MS dissociation was primarily driven via the cleavage of the ester bond linking the quinic acid moiety to the caffeic acid moiety within tested molecules. Despite being structural isomers with the same m/z values and dissociation behaviors, the MS/MS data in the negative ion mode was able to differentiate the three isomers based on ion intensity for the major product ions, observed at m/z 191, 179 and 173. This differentiation was consistent among various MS instruments. In addition, ESI coupled with high-field asymmetric waveform ion mobility spectrometry-mass spectrometry (ESI-FAIMS-MS) was employed for the separation of these compounds for the first time. By combining MS/MS data and differential ion mobility, a method for the separation and identification of mono-caffeoylquinic in apple/pear juice samples was developed with a run time of less than 1 min. It is envisaged that this methodology could be used to identify pure juices based on their chlorogenic acid profile (i.e., metabolomics), and could also be used to detect juice-to-juice adulteration (e.g., apple juice addition to pear juice

  13. Improved Isobaric Tandem Mass Tag Quantification by Ion Mobility-Mass Spectrometry

    PubMed Central

    Li, Lingjun

    2014-01-01

    Isobaric tandem mass tags are an attractive alternative to mass difference tags and label free approaches for quantitative proteomics due to the high degree of multiplexing that can be performed with their implementation. A drawback of tandem mass tags are that the co-isolation and co-fragmentation of labeled peptide precursors can result in chimeric MS/MS spectra that can underestimate the fold-change expression of each peptide. Two methods (QuantMode and MS3) have addressed this concern for ion trap and orbitrap instruments, but there is still a need to solve this problem for quadrupole time-of-flight (Q-TOF) instruments. Ion mobility (IM) separations coupled to Q-TOF instruments have the potential to mitigate MS/MS spectra chimeracy since IM-MS has the ability to separate ions based on charge, m/z, and collision cross section (CCS). This work presents results that showcase the power of IM-MS to improve tandem mass tag peptide quantitation accuracy by resolving co-isolated differently charged and same charged peptides prior to MS/MS fragmentation. PMID:24677527

  14. DeconMSn: A Software Tool for accurate parent ion monoisotopic mass determination for tandem mass spectra

    SciTech Connect

    Mayampurath, Anoop M.; Jaitly, Navdeep; Purvine, Samuel O.; Monroe, Matthew E.; Auberry, Kenneth J.; Adkins, Joshua N.; Smith, Richard D.

    2008-04-01

    We present a new software tool for tandem MS analyses that: • accurately calculates the monoisotopic mass and charge of high–resolution parent ions • accurately operates regardless of the mass selected for fragmentation • performs independent of instrument settings • enables optimal selection of search mass tolerance for high mass accuracy experiments • is open source and thus can be tailored to individual needs • incorporates a SVM-based charge detection algorithm for analyzing low resolution tandem MS spectra • creates multiple output data formats (.dta, .MGF) • handles .RAW files and .mzXML formats • compatible with SEQUEST, MASCOT, X!Tandem

  15. Electron Capture Dissociation of Sodium-Adducted Peptides on a Modified Quadrupole/Time-of-Flight Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Voinov, Valery G.; Hoffman, Peter D.; Bennett, Samuel E.; Beckman, Joseph S.; Barofsky, Douglas F.

    2015-12-01

    Electron capture dissociation (ECD), which generally preserves the position of labile post-translational modifications, can be a powerful method for de novo sequencing of proteins and peptides. In this report, ECD product-ion mass spectra of singly and doubly sodiated, nonphosphorylated, and phosphorylated peptides are presented and compared with the ECD mass spectra of their protonated counterparts. ECD of doubly charged, singly sodiated peptides yielded essentially the same sequence information as was produced by the corresponding doubly protonated peptides. The presence of several sodium binding sites on the polypeptide backbone, however, resulted in more complicated spectra. This situation is aggravated by the zwitterionic equilibrium of the free acid peptide precursors. The product-ion spectra of doubly and triply charged peptides possessing two sodium ions were further complicated by the existence of isomers created by the differential distribution of sodium binding sites. Triply charged, phosphorylated precursors containing one sodium, wherein the sodium is attached exclusively to the PO4 group, were found to be as useful for sequence analysis as the fully protonated species. Although sodium adducts are generally minimized during sample preparation, it appears that they can nonetheless provide useful sequence information. Additionally, they enable straightforward identification of a peptide's charge state, even on low-resolution instruments. The experiments were carried out using a radio frequency-free electromagnetostatic cell retrofitted into the collision-induced dissociation (CID) section of a hybrid quadrupole/time-of-flight tandem mass spectrometer.

  16. Electron Capture Dissociation of Sodium-Adducted Peptides on a Modified Quadrupole/Time-of-Flight Mass Spectrometer.

    PubMed

    Voinov, Valery G; Hoffman, Peter D; Bennett, Samuel E; Beckman, Joseph S; Barofsky, Douglas F

    2015-12-01

    Electron capture dissociation (ECD), which generally preserves the position of labile post-translational modifications, can be a powerful method for de novo sequencing of proteins and peptides. In this report, ECD product-ion mass spectra of singly and doubly sodiated, nonphosphorylated, and phosphorylated peptides are presented and compared with the ECD mass spectra of their protonated counterparts. ECD of doubly charged, singly sodiated peptides yielded essentially the same sequence information as was produced by the corresponding doubly protonated peptides. The presence of several sodium binding sites on the polypeptide backbone, however, resulted in more complicated spectra. This situation is aggravated by the zwitterionic equilibrium of the free acid peptide precursors. The product-ion spectra of doubly and triply charged peptides possessing two sodium ions were further complicated by the existence of isomers created by the differential distribution of sodium binding sites. Triply charged, phosphorylated precursors containing one sodium, wherein the sodium is attached exclusively to the PO4 group, were found to be as useful for sequence analysis as the fully protonated species. Although sodium adducts are generally minimized during sample preparation, it appears that they can nonetheless provide useful sequence information. Additionally, they enable straightforward identification of a peptide's charge state, even on low-resolution instruments. The experiments were carried out using a radio frequency-free electromagnetostatic cell retrofitted into the collision-induced dissociation (CID) section of a hybrid quadrupole/time-of-flight tandem mass spectrometer. Graphical Abstract ᅟ. PMID:26266643

  17. Sequence analysis of styrenic copolymers by tandem mass spectrometry.

    PubMed

    Yol, Aleer M; Janoski, Jonathan; Quirk, Roderic P; Wesdemiotis, Chrys

    2014-10-01

    Styrene and smaller molar amounts of either m-dimethylsilylstyrene (m-DMSS) or p-dimethylsilylstyrene (p-DMSS) were copolymerized under living anionic polymerization conditions, and the compositions, architectures, and sequences of the resulting copolymers were characterized by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and tandem mass spectrometry (MS(2)). MS analysis revealed that linear copolymer chains containing phenyl-Si(CH3)2H pendants were the major product for both DMSS comonomers. In addition, two-armed architectures with phenyl-Si(CH3)2-benzyl branches were detected as minor products. The comonomer sequence in the linear chains was established by MS(2) experiments on lithiated oligomers, based on the DMSS content of fragments generated by backbone C-C bond scissions and with the help of reference MS(2) spectra obtained from a polystyrene homopolymer and polystyrene end-capped with a p-DMSS block. The MS(2) data provided conclusive evidence that copolymerization of styrene/DMSS mixtures leads to chains with a rather random distribution of the silylated comonomer when m-DMSS is used, but to chains with tapered block structures, with the silylated units near the initiator, when p-DMSS is used. Hence, MS(2) fragmentation patterns permit not only differentiation of the sequences generated in the synthesis, but also the determination of specific comonomer locations along the polymer chain. PMID:25181590

  18. Identification of degradation products of indigoids by tandem mass spectrometry.

    PubMed

    Witkoś, Katarzyna; Lech, Katarzyna; Jarosz, Maciej

    2015-11-01

    The study concerns identification of photodegradation products of indigotin, indirubin and isoindigo. Experimental methodology consists of degradation of standard solutions of indigoids in a solar box and analysis of samples taken at different aging time by using capillary high-performance liquid chromatography coupled with electrospray ionization tandem mass spectrometric and spectrophotometric detectors. Identification of the formed compounds was based on careful interpretation of the electrospray ionization MS/MS spectra. Apart from the well-known degradation products of indigoids: isatin, isatoic anhydride and anthranilic acid, another seven species were also identified, and their proposed structures were confirmed by high-resolution molecular masses measurements; according to the best knowledge of authors, they have not been reported so far. The obtained results formed the basis for postulating mechanism of the process. Moreover, the MRM (Multiple Reaction Monitoring) method was developed for the identification of natural dyes and their degradation products in textiles of historical value. Apart from such colorants as indigotin and flavonoids, also presence of degradation products of indigoids was confirmed. PMID:26505769

  19. Tandem mass spectrometry and infrared spectroscopy as a tool to identify peptide oxidized residues.

    PubMed

    Scuderi, D; Ignasiak, M T; Serfaty, X; de Oliveira, P; Houée Levin, C

    2015-10-21

    The final products obtained by the oxidation of small model peptides containing the thioether function, either methionine or S-methyl cysteine, have been characterized by tandem mass spectrometry and IR Multiple Photon Dissociation (IRMPD) spectroscopy. The modified positions have been clearly identified by the CID-MS(2) fragmentation mass spectra with or without loss of sulfenic acid, as well as by the vibrational signature of the sulfoxide bond at around 1000 cm(-1). The oxidation of the thioether function did not lead to the same products in these model peptides. The sulfoxide and sulfone (to a lesser extent) have been clearly identified as final products of the oxidation of S-methyl-glutathione (GS-Me). Decarboxylation or hydrogen loss are the major oxidation pathways in GS-Me, while they have not been observed in tryptophan-methionine and methionine-tryptophan (Trp-Met and Met-Trp). Interestingly, tryptophan is oxidized in the dipeptide Met-Trp, while that is not the case in the reverse sequence (Trp-Met). PMID:26292724

  20. mMass as a Software Tool for the Annotation of Cyclic Peptide Tandem Mass Spectra

    PubMed Central

    Niedermeyer, Timo H. J.; Strohalm, Martin

    2012-01-01

    Natural or synthetic cyclic peptides often possess pronounced bioactivity. Their mass spectrometric characterization is difficult due to the predominant occurrence of non-proteinogenic monomers and the complex fragmentation patterns observed. Even though several software tools for cyclic peptide tandem mass spectra annotation have been published, these tools are still unable to annotate a majority of the signals observed in experimentally obtained mass spectra. They are thus not suitable for extensive mass spectrometric characterization of these compounds. This lack of advanced and user-friendly software tools has motivated us to extend the fragmentation module of a freely available open-source software, mMass (http://www.mmass.org), to allow for cyclic peptide tandem mass spectra annotation and interpretation. The resulting software has been tested on several cyanobacterial and other naturally occurring peptides. It has been found to be superior to other currently available tools concerning both usability and annotation extensiveness. Thus it is highly useful for accelerating the structure confirmation and elucidation of cyclic as well as linear peptides and depsipeptides. PMID:23028676

  1. 4-HNE Adduct Stability Characterized by Collision-Induced Dissociation and Electron Transfer Dissociation Mass Spectrometry

    PubMed Central

    Fritz, Kristofer S.; Kellersberger, Katherine A.; Gomez, Jose D.; Petersen, Dennis R.

    2012-01-01

    4-hydroxynonenal (4-HNE) alters numerous proteomic and genomic processes. Understanding chemical mechanisms of 4-HNE interactions with biomolecules and their respective stabilities may lead to new discoveries in biomarkers for numerous diseases of oxidative stress. Collision-induced dissociation (CID) and electron transfer dissociation (ETD) MS/MS were utilized to examine the stability of a 4-HNE-Cys Michael adduct. CID conditions resulted in the neutral loss of 4-HNE, also known as a retro-Michael addition reaction (RMA). Consequently, performing ETD fragmentation on this same adduct did not result in RMA. Interestingly, 4-HNE adduct reduction via sodium borohydride (NaBH4) treatment stabilized against the CID induced RMA. In a direct comparison of three forms of 4-HNE adducts, computational modeling revealed sizeable shifts in the shape and orientation of the lowest unoccupied molecular orbital (LUMO) density around the 4-HNE-Cys moiety. These findings demonstrate that ETD MS/MS analysis can be used to improve the detection of 4-HNE-protein modifications by preventing RMA reactions from occurring. PMID:22404378

  2. 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

  3. Axial Imidazole Binding Strengths in Porphyrinoid Cobalt(III) Complexes as Studied by Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Mishra, Ekta; Worlinsky, Jill L.; Gilbert, Thomas M.; Brückner, Christian; Ryzhov, Victor

    2012-06-01

    The Co(II) complexes of twelve meso-tetraaryl-porphyrins, -chlorins, and chlorin analogues containing non-pyrrolic heterocycles were synthesized and converted in situ to the corresponding Co(III) complexes coordinated to one or two imidazoles. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) in conjunction with the energy-variable collision-induced dissociation (CID) technique was used to compare the relative gas-phase binding strength of the axially coordinated imidazoles to the octahedral and square planar Co(III) porphyrinoid complex ions. The observed binding energies of these ligands were rationalized in terms of the effects of porphyrinoid core structure and meso-substitution on the electron density on the central Co(III) centers. Some of these trends were supported by DFT-based computational studies. The study highlights to which extend porphyrins vary from chlorins and chlorin analogues in their coordination abilities and to which extraordinary degree meso-thienyl-substituents influence the electronic structure of porphyrins. The study also defines further the scope and limits CID experiments can be used to interrogate the electronic structures of metalloporphyrin complexes.

  4. Evidence for covalent binding of acyl glucuronides to serum albumin via an imine mechanism as revealed by tandem mass spectrometry.

    PubMed Central

    Ding, A; Ojingwa, J C; McDonagh, A F; Burlingame, A L; Benet, L Z

    1993-01-01

    Acyl glucuronide metabolites of bilirubin and many drugs can react with serum albumin in vivo to form covalent adducts. Such adducts may be responsible for some toxic effects of carboxylic nonsteroidal antiinflammatory agents. The mechanism of formation of the adducts and their chemical structures are unknown. In this paper we describe the use of tandem mass spectrometry to locate binding sites and elucidate the binding mechanism involved in the formation of covalent adducts from tolmetin glucuronide and albumin in vitro. Human serum albumin and excess tolmetin glucuronide were coincubated in the presence of sodium cyanoborohydride to trap imine intermediates. The total protein product was reduced, carboxymethylated, and digested with trypsin. Six tolmetin-containing peptides (indicated by absorbance at 313 nm) were isolated by high-pressure liquid chromatography and analyzed by liquid secondary-ion mass spectrometry and collision-induced dissociation, using a four-sector tandem mass spectrometer. All six peptides contained tolmetin linked covalently via a glucuronic acid to protein lysine groups. Major attachment sites on the protein were Lys-195, -199, and -525; minor sites were identified as Lys-137, -351, and -541. Our results show unambiguously that the glucuronic acid moiety of acyl glucuronides can be retained within the structure when these reactive metabolites bind covalently to proteins, and they suggest that acyl migration followed by Schiff base (imine) formation is a credible mechanism for the generation of covalent adducts in vivo. PMID:8483897

  5. Investigation of silver binding to polyamidoamine (PAMAM) dendrimers by ESI tandem mass spectrometry.

    PubMed

    Mazzitelli, Carolyn L; Brodbelt, Jennifer S

    2006-05-01

    Electrospray ionization tandem mass spectrometry (ESI-MS/MS) was used to probe the binding of silver ions and reduced silver species with polyamidoamine generation 1 amine-terminated (PAMAMG1NH2) and generation 2 hydroxyl-terminated (PAMAMG2OH) dendrimers. At Ag(+)/PAMAMG2OH molar ratios of 1, 2:1 and low abundance 3:1 complexes emerge. Similar results were observed for PAMAMG1NH2. The collisional activated dissociation (CAD) patterns of the dendrimer ions are characterized by losses of amidoamine branches resulting largely from hydrogen migration and cleavage reactions. Ag+/dendrimer complexes are characterized by the loss of a dendrimer branch from the complex, with the silver ion remaining bound to a dendrimer fragment. When the Ag+-bound dendrimer complexes are reduced by hydrazine, low abundance complexes, whose m/z values are consistent with ones containing zerovalent silver species, are observed in the mass spectra. Complexes with three silver atoms are observed in the spectrum containing PAMAMG1NH2, and complexes with four and five silver atoms are observed with PAMAMG2OH. The CAD fragmentation patterns of the complexes formed after the silver reduction are different than those observed for complexes containing one silver ion and are characterized by the ejection of all silver species, possibly as a cluster, leaving the intact dendrimer ion. Experiments with Cu+, Cu2+, and Pt2+ binding to PAMAMG2OH were also done, but reduced metal clusters were not observed in the mass spectra after the addition of hydrazine. PMID:16516486

  6. Quantitative analysis of positional isomers of triacylglycerols via electrospray ionization tandem mass spectrometry of sodiated adducts.

    PubMed

    Herrera, Lisandra Cubero; Potvin, Michael A; Melanson, Jeremy E

    2010-09-01

    Herein we report a reversed-phase high-performance liquid chromatography tandem mass spectrometry (RP-HPLC/MS/MS) method for the analysis of positional isomers of triacylglycerols (TAGs) in vegetable oils. The fragmentation behavior of [M + X](+) ions (X = NH(4), Li, Na or Ag) was studied on a quadrupole-time-of-flight (Q-TOF) mass spectrometer under low-energy collision-induced dissociation (CID) conditions. Mass spectra that were dependent on the X(+) ion and the nature and position of the acyl substituents were observed for four pairs of 'AAB/ABA'-type TAGs, namely PPO/POP, OOP/OPO, LLO/LOL and OOL/OLO (where P is 16:0, palmitic acid; O is 18:1, oleic acid; and L is 18:2, linoleic acid). For the majority of [M + X](+) adducts, the loss of the fatty acid in the outer positions (sn-1 or sn-3) was favored over the loss in the central position (sn-2), which enabled the determination of the fractional abundance of the isomers. Ratios of the intensity of fragment ions at various AAB/ABA compositions produced linear calibration curves with positive slopes, comparable to those obtained traditionally by ESI-MS/MS of [M + NH(4)](+) adducts. The only exceptions were the [M + Ag](+) adducts of the PPO/POP system, which produced calibration curves with negative slopes. Sodium adducts provided the most consistent level of isomeric discrimination for the TAGs studied and also offered the most convenience in that they required no additive to the mobile phase. Therefore, calibration curve data derived from [M + Na](+) adducts were applied to the quantification of TAG regioisomers in sunflower and olive oils. The regiospecific analysis showed that palmitic acid was typically located at positions sn-1 or sn-3, whereas unsaturated fatty acids, oleic and linoleic acids were mostly found at the sn-2 position. PMID:20814981

  7. Native Electrospray and Electron-Capture Dissociation FTICR Mass Spectrometry for Top-Down Studies of Protein Assemblies

    SciTech Connect

    Zhang, Hao; Cui, Weidong; Wen, Jianzhong; Blankenship, Robert E.; Gross, Michael L.

    2011-07-15

    The high sensitivity, extended mass range, and fast data acquisition/processing of mass spectrometry and its coupling with native electrospray ionization (ESI) make the combination complementary to other biophysical methods of protein analysis. Protein assemblies with molecular masses up to MDa are now accessible by this approach. Most current approaches have used quadrupole/time-of-flight tandem mass spectrometry, sometimes coupled with ion mobility, to reveal stoichiometry, shape, and dissociation of protein assemblies. The amino-acid sequence of the subunits, however, still relies heavily on independent bottom-up proteomics. We describe here an approach to study protein assemblies that integrates electron-capture dissociation (ECD), native ESI, and FTICR mass spectrometry (12 T). Flexible regions of assembly subunits of yeast alcohol dehydrogenase (147 kDa), concanavalin A (103 kDa), and photosynthetic Fenna–Matthews–Olson antenna protein complex (140 kDa) can be sequenced by ECD or “activated-ion” ECD. Furthermore, noncovalent metal-binding sites can also be determined for the concanavalin A assembly. Most importantly, the regions that undergo fragmentation, either from one of the termini by ECD or from the middle of a protein, as initiated by CID, correlate well with the B-factor from X-ray crystallography of that protein. This factor is a measure of the extent an atom can move from its coordinated position as a function of temperature or crystal imperfections. The approach provides not only top-down proteomics information of the complex subunits but also structural insights complementary to those obtained by ion mobility.

  8. Differentiation of regioisomeric aromatic ketocarboxylic acids by atmospheric pressure chemical ionization CAD tandem mass spectrometry in a linear quadrupole ion trap mass spectrometer

    SciTech Connect

    Amundson, Lucas M.; Owen, Ben C.; Gallardo, Vanessa A.; Habicht, S. C.; Fu, M.; Shea, R. C.; Mossman, A. B.; Kenttämaa, Hilkka I.

    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 different collision energies. The mechanisms of some of the reactions were examined by H/D exchange reactions and molecular orbital calculations.

  9. Determination of dalcetrapib by liquid chromatography-tandem mass spectrometry.

    PubMed

    Heinig, Katja; Bucheli, Franz; Kuhlmann, Olaf; Zell, Manfred; Pähler, Axel; Zwanziger, Elke; Gross, Günter; Tardio, Joseph; Ishikawa, Tomohiro; Yamashita, Tomoko

    2012-07-01

    The cholesteryl ester transfer protein modulator dalcetrapib is currently under development for the prevention of dyslipidemia and cardiovascular disease. Dalcetrapib, a thioester, is rapidly hydrolyzed in vivo to the corresponding thiophenol which in turn is further oxidized to the dimer and mixed disulfides (where the thiophenol binds to peptides, proteins and other endogenous thiols). These forms co-exist in an oxidation-reduction equilibrium via the thiol and cannot be stabilized without influencing the equilibrium, hence specific determination of individual components, i.e., in order to distinguish between the free thiol, the disulfide dimer and mixed disulfide adducts, was not pursued for routine analysis. The individual forms were quantified collectively as dalcetrapib-thiol (dal-thiol) after reduction under basic conditions with dithiothreitol to break disulfide bonds and derivatization with N-ethylmaleimide to stabilize the free thiol. The S-methyl and S-glucuronide metabolites were determined simultaneously with dal-thiol with no effect from the derivatization procedure. Column-switching liquid chromatography-tandem mass spectrometry provided a simple, fast and robust method for analysis of human and animal plasma and human urine samples. Addition of the surfactant Tween 80 to urine prevented adsorptive compound loss. The lower limits of quantitation (LLOQ) were 5 ng/mL for dal-thiol, and 5 ng/mL for the S-methyl and 50 ng/mL for the S-glucuronide metabolites. Using stable isotope-labeled internal standards, inter- and intra-assay precisions were each <15% (<20% at LLOQ) and accuracy was between 85 and 115%. Recovery was close to 100%, and no significant matrix effect was observed. PMID:22541249

  10. 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).

  11. Low missing mass, single and double diffraction dissociation at the LHC

    SciTech Connect

    Jenkovszky, L. L.; Kuprash, O. E.; Orava, R.; Salii, A.

    2014-12-15

    The cross sections for single and double diffraction dissociation at low missing masses are calculated for the LHC energies on the basis of the dual (Regge) model under the assumption of a dominant contribution of the exchange of the Pomeron Regge pole. The model reproduces the rich resonance structure in the region of low missing masses M{sub x}. Diffractively excited states lie on the nucleon trajectory M{sub x} supplemented with the isolated Roper resonance. Detailed predictions for the squared momentum transfer and missing-mass dependence of the differential and integrated single and double diffraction dissociation in the kinematical range of present and future LHC measurements are given.

  12. Dual-Regge approach to high-energy, low-mass diffraction dissociation

    SciTech Connect

    Jenkovszky, L. L.; Kuprash, O. E.; Laemsae, J. W.; Magas, V. K.; Orava, R.

    2011-03-01

    A dual-Regge model with a nonlinear proton Regge trajectory in the missing mass (M{sub X}{sup 2}) channel, describing the experimental data on low-mass single diffraction dissociation (SDD), is constructed. Predictions for the LHC energies are given.

  13. 10 K Ring Electrode Trap—Tandem Mass Spectrometer for Infrared Spectroscopy of Mass Selected Ions

    NASA Astrophysics Data System (ADS)

    Goebbert, Daniel J.; Meijer, Gerard; Asmis, Knut R.

    2009-03-01

    A novel instrumental setup for measuring infrared photodissociation spectra of buffer gas cooled, mass-selected ions is described and tested. It combines a cryogenically cooled, linear radio frequency ion trap with a tandem mass spectrometer, optimally coupling continuous ion sources to pulsed laser experiments. The use of six independently adjustable DC potentials superimposed over the trapping radio frequency field provides control over the ion distribution within, as well as the kinetic energy distribution of the ions extracted from the ion trap. The scheme allows focusing the ions in space and time, such that they can be optimally irradiated by a pulsed, widely tunable infrared photodissociation laser. Ion intensities are monitored with a time-of-flight mass spectrometer mounted orthogonally to the ion trap axis.

  14. Mass spectrometric and theoretical studies on dissociation of the Ssbnd S bond in the allicin: Homolytic cleavage vs heterolytic cleavage

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang

    2012-08-01

    On the basis of the tandem mass spectrometry (ESI-MS/MS) technique and DFT calculations, an experimental and theoretical investigation has been conducted into the gas-phase dissociation of the S1sbnd S1' bond in the allicin as well as that of the Ssbnd C (S1sbnd C2, S1'sbnd C2') bond. Meanwhile, the influence of protonation, alkali metal ion and electron transfer on the dissociation of the S1sbnd S1' bond has been taken into account. ESI-MS/MS experiments and DFT calculations show that in the neutral allicin, [allicin + Li]+ and [allicin + Na]+, the S1sbnd S1' bond favors homolytic cleavage, while in the allicin radical cation and protonated allicin, the S1sbnd S1' bond prefers heterolytic cleavage. In addition, alkali metal ions can strengthen the S1sbnd S1' bond in the allicin, while protonation or the loss of an electron will weaken the S1sbnd S1' bond.

  15. Enrichment and Analysis of Nonenzymatically Glycated Peptides: Boronate Affinity Chromatography Coupled with Electron-Transfer Dissociation Mass Spectrometry

    SciTech Connect

    Zhang, Qibin; Tang, Ning; Brock, Jonathan W.; Mottaz, Heather M.; Ames, Jennifer M.; Baynes, John; Smith, Richard D.; Metz, Thomas O.

    2007-06-01

    Non-enzymatic glycation of peptides and proteins by D-glucose has important implications in the pathogenesis of diabetes mellitus, particularly in the development of diabetic complications. However, no effective high-throughput methods exist for identifying proteins containing this low abundance post-translational modification in bottom-up proteomic studies. In this report, phenylboronate affinity chromatography was used in a two-step enrichment scheme to selectively isolate first glycated proteins and then glycated, tryptic peptides from human serum glycated in vitro. Enriched peptides were subsequently analyzed by alternating electron transfer dissociation (ETD) and collision induced dissociation (CID) tandem mass spectrometry. It was observed that ETD fragmentation mode resulted in a significantly higher number of glycated peptide identifications (87.6% of all identified peptides) versus CID mode (17.0% of all identified peptides), when utilizing dual glycation enrichment on both the protein and peptide level. This study illustrates that phenylboronate affinity chromatography coupled with LC-MS/MS with ETD as the fragmentation mode is an efficient approach for analyses of glycated proteins and can have broad applications in studies of diabetes mellitus.

  16. Enhanced Methylarginine Characterization by Post-Translational Modification-Specific Targeted Data Acquisition and Electron-Transfer Dissociation Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Hart-Smith, Gene; Low, Jason K. K.; Erce, Melissa A.; Wilkins, Marc R.

    2012-08-01

    When localizing protein post-translational modifications (PTMs) using liquid-chromatography (LC)-tandem mass spectrometry (MS/MS), existing implementations are limited by inefficient selection of PTM-carrying peptides for MS/MS, particularly when PTM site occupancy is sub-stoichiometric. The present contribution describes a method by which peptides carrying specific PTMs of interest—in this study, methylarginines—may be selectively targeted for MS/MS: peptide features are extracted from high mass accuracy single-stage MS data, searched against theoretical PTM-carrying peptide masses, and matching features are subjected to targeted data acquisition LC-MS/MS. Using trypsin digested Saccharomyces cerevisiae Npl3, in which evidence is presented for 18 methylarginine sites—17 of which fall within a glycine-arginine-rich (GAR) domain spanning <120 amino acids—it is shown that this approach outperforms conventional data dependent acquisition (DDA): when applied to a complex protein mixture featuring in vivo methylated Npl3, 95 % more ( P = 0.030) methylarginine-carrying peptides are selected for MS/MS than DDA, leading to an 86 % increase ( P = 0.044) in the number of methylated peptides producing Mascot ion scores ≥20 following electron-transfer dissociation (ETD). Notably, significantly more low abundance arginine methylated peptides (maximum ion intensities <6 × 104 cps) are selected for MS/MS using this approach relative to DDA (50 % more in a digest of purified in vitro methylated Npl3). It is also demonstrated that relative to collision-induced dissociation (CID), ETD facilitates a 586 % increase ( P = 0.016) in average Mascot ion scores of methylarginine-carrying peptides. The present PTM-specific targeted data acquisition approach, though described using methylarginine, is applicable to any ionizable PTM of known mass.

  17. Hydrophilic interaction liquid chromatography-electrospray ionization-tandem mass spectrometry of a complex mixture of native and oxidized phospholipids.

    PubMed

    Losito, I; Facchini, L; Diomede, S; Conte, E; Megli, F M; Cataldi, T R I; Palmisano, F

    2015-11-27

    A mixture of native and oxidized phospholipids (PLs), generated by the soybean lipoxygenase type V-catalyzed partial oxidation of a lipid extract obtained from human platelets, was analyzed by Hydrophilic Interaction Liquid Chromatography-ElectroSpray Ionization-Tandem Mass Spectrometry (HILIC-ESI-MS/MS). The complexity of the resulting mixture was remarkable, considering that the starting lipid extract, containing (as demonstrated in a previous study) about 130 native PLs, was enriched with enzymatically generated hydroperoxylated derivatives and chemically generated hydroxylated forms of PLs bearing polyunsaturated side chains. Nonetheless, the described analytical approach proved to be very powerful; indeed, focusing on phosphatidylcolines (PCs), the most abundant PL class in human platelets, about fifty different native/oxidized species could be identified in a single HILIC-ESI-MS/MS run. Low-energy collision induced dissociation tandem MS (CID-MS/MS) experiments on chromatographically separated species showed single neutral losses of H2O2 and H2O to be typical fragmentation pathways of hydroperoxylated PCs, whereas a single H2O loss was observed for hydroxylated ones. Moreover, diagnostic losses of n-hexanal or n-pentanol were exploited to recognize PCs hydroperoxylated on the last but five carbon atom of a ɷ-6 polyunsaturated side chain. Despite the low resolution of the 3D ion trap mass analyzer used, the described HILIC-ESI-MS/MS approach appears very promising for the identification of oxidized lipids in oxidatively stressed complex biological systems. PMID:26508677

  18. Characterization of oncogene-induced metabolic alterations in hepatic cells by using ultrahigh performance liquid chromatography-tandem mass spectrometry.

    PubMed

    Tang, Zhi; Cao, Tingting; Lin, Shuhai; Fu, Li; Li, Shangfu; Guan, Xin-Yuan; Cai, Zongwei

    2016-05-15

    Elucidation of altered metabolic pathways by using metabolomics may open new avenues for basic research on disease mechanisms and facilitate the development of novel therapeutic strategies. Here, we report the development of ultrahigh performance liquid chromatography-tandem mass spectrometry-based metabolomics platform with capability of measuring both cationic and anionic intermediates in cellular metabolism. The platform was established based on the hydrophobic ion-pairing interaction chromatography coupled with tandem mass spectrometry in multiple reaction monitoring (MRM) mode. The MRM transitions were created and optimized via energy-resolved collision-induced dissociation experiments, serving as an essential reference point for the quantification and identification. For chromatographic separation, application of hydrophobic ion-pairing interaction led to dramatic enhancement on retention of water-soluble metabolites and provision of good peak shapes. Two volatile ion-pairing reagents, namely heptafluorobutyric acid and tributylamine, were used with dedicated C18 columns as complementary separation systems coupled with the MRM analysis, allowing measurement of the metabolites of interest at nanomolar levels. The developed platform was successfully applied to investigate the altered metabolism in hepatic cells with over-expression of an oncogene, thus can provide important information on the rewired metabolism. PMID:26992502

  19. Analysis of triptophenolide and its related compounds from Tripterygium wilfordii Hook.f by electrospray ionization tandem mass spectrometry

    NASA Astrophysics Data System (ADS)

    Li, Rui; Peng, Aihua; He, Chunmei; Wang, Xianhuo; Shi, Jianyou; Chen, Lijuan; Wei, Yuquan

    2008-11-01

    Triptophenolide and its related compounds from Tripterygium wilfordii Hook.f is a kind of diterpenoids which shows anti-inflammatory activity. To study the metabolites of triptophenolide related compounds, the fragmentation mechanisms of them were investigated by using negative electrospray tandem mass spectrometry. With the aid of high resolution of ESI-QTOF-MS/MS, the fragmentation mechanisms of six diterpenoid compounds were systematically investigated. The fragmentation behavior mainly depends on what substituent groups the benzyl C ring bears. If there is a hydroxyl group on the position of C14, loss of CH4 is dominating. However, the successive loss of two CH3 radicals is predominant when the hydroxyl group of O14 is methylated. The lactone ring is prone to be dissociated to loss of CO, CO2 and C2H2O2 molecules. The pericyclic reaction can occur on A ring if there is an active hydrogen resides on C ring. Furthermore, one metabolite of compound A1 was confirmed by cytochrome P450 in vitro and the structure was proposed by tandem mass experiment together with the fragmentation mechanisms of this type of compounds.

  20. Planetary In Situ Sample Analysis with Tandem Two-Step Laser Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Brinckerhoff, W. B.; Getty, S. A.; Cornish, T. J.; Ecelberger, S. A.; Li, X.; Merrill Floyd, M. A.; Arevalo, R.; Elsila, J.; Callahan, M. P.

    2012-12-01

    -) and organic moieties. Second, by focusing a separate "post-ionization" laser pulse just above the sample surface, we can achieve two-step laser mass spectrometry, or L2MS, in the same highly-miniaturized TOF-MS. L2MS enables selective analysis of aromatic organics even in the presence of a complex mineral matrix. Finally, by introducing an ion optical gate in the flight path, we are able to take advantage of the broad focusing capabilities of the "curved field" reflectron at the core of the TOF-MS to achieve pseudo-tandem structural analysis of selected organics. The high-speed gate is used to admit only the molecular ion/s of interest into the reflectron. Diagnostic fragments of the ion/s obtained through metastable decay or active collision-induced dissociation (CID) remain in focus despite having widely variable velocities and masses. As such even molecular isomers with differing fragmentation pathways may be distinguished through a series of pseudo-tandem mass spectra that could be obtained in an automatic process during a mission. The "real-world" benefits of these enhancements are being fully characterized using a set of synthetic and natural standard samples as well as several planetary analogs and meteorites.

  1. Multiphoton dissociation of electrosprayed megadalton-sized DNA ions in a charge-detection mass spectrometer.

    PubMed

    Doussineau, Tristan; Paletto, Pierre; Dugourd, Philippe; Antoine, Rodolphe

    2015-01-01

    Charge detection mass spectrometry in combination with a linear electrostatic ion trap coupled to a continuous wavelength infrared CO2 laser has been used to study the multiphoton dissociation of DNA macromolecular ions. Samples, with masses ranging from 2.23 to 31.5 MDa, include single strand circular M13mp18, double strand circular M13mp18, and double strand linear LambdaPhage DNA fragments. Their activation energies for unimolecular dissociation were determined. Activation energy values slightly increase as a function of the molecular weight. The most important result is the difference between the fragmentations observed for hybridized double-strands and dimers of single strands. PMID:25348472

  2. Structural determination of glycosphingolipids as lithiated adducts by electrospray ionization mass spectrometry using low-energy collisional-activated dissociation on a triple stage quadrupole instrument.

    PubMed

    Hsu, F F; Turk, J

    2001-01-01

    Structural characterization of glycosphingolipids as their lithiated adducts using low-energy collisional-activated dissociation (CAD) tandem mass spectrometry with electrospray ionization (ESI) is described. The tandem mass spectra contain abundant fragment ions reflecting the long chain base (LCB), fatty acid, and the sugar constituent of the molecule and permit unequivocal identification of cerebrosides, di-, trihexosyl ceramides and globosides. The major fragmentation pathways arise from loss of the sugar moiety to yield a lithiated ceramide ion, which undergoes further fragmentation to form multiple fragment ions that confirm the structures of the fatty acid and LCB. The mechanisms for the ion formation and the possible configuration of the fragment ions, resulting from CAD of the lithiated molecular ions ([M + Li]+) of monoglycosylceramides are proposed. The mechanisms were supported by CAD and source CAD tandem mass spectra of various cerebrosides and of their analogous molecules prepared by H-D exchange. Constant neutral loss and precursor ion scannings to identify galactosylceramides with sphingosine or sphinganine LCB subclasses, and with specific N-2-hydroxyl fatty acid subclass in mixtures are also demonstrated. PMID:11142362

  3. A Novel Approach for Untargeted Post-translational Modification Identification Using Integer Linear Optimization and Tandem Mass Spectrometry*

    PubMed Central

    Baliban, Richard C.; DiMaggio, Peter A.; Plazas-Mayorca, Mariana D.; Young, Nicolas L.; Garcia, Benjamin A.; Floudas, Christodoulos A.

    2010-01-01

    A novel algorithm, PILOT_PTM, has been developed for the untargeted identification of post-translational modifications (PTMs) on a template sequence. The algorithm consists of an analysis of an MS/MS spectrum via an integer linear optimization model to output a rank-ordered list of PTMs that best match the experimental data. Each MS/MS spectrum is analyzed by a preprocessing algorithm to reduce spectral noise and label potential complimentary, offset, isotope, and multiply charged peaks. Postprocessing of the rank-ordered list from the integer linear optimization model will resolve fragment mass errors and will reorder the list of PTMs based on the cross-correlation between the experimental and theoretical MS/MS spectrum. PILOT_PTM is instrument-independent, capable of handling multiple fragmentation technologies, and can address the universe of PTMs for every amino acid on the template sequence. The various features of PILOT_PTM are presented, and it is tested on several modified and unmodified data sets including chemically synthesized phosphopeptides, histone H3-(1–50) polypeptides, histone H3-(1–50) tryptic fragments, and peptides generated from proteins extracted from chromatin-enriched fractions. The data sets consist of spectra derived from fragmentation via collision-induced dissociation, electron transfer dissociation, and electron capture dissociation. The capability of PILOT_PTM is then benchmarked using five state-of-the-art methods, InsPecT, Virtual Expert Mass Spectrometrist (VEMS), Modi, Mascot, and X!Tandem. PILOT_PTM demonstrates superior accuracy on both the small and large scale proteome experiments. A protocol is finally developed for the analysis of a complete LC-MS/MS scan using template sequences generated from SEQUEST and is demonstrated on over 270,000 MS/MS spectra collected from a total chromatin digest. PMID:20103568

  4. Ion-retarding lens improves the abundance sensitivity of tandem mass spectrometers

    NASA Technical Reports Server (NTRS)

    Kaiser, K. A.; Stevens, C. M.

    1969-01-01

    Ion-retarding lens which increases the abundance sensitivity of tandem magnetic-analyzer mass spectrometers measures isotopes of low abundance in mass positions adjacent to isotopes of high abundance. The lens increases the abundance sensitivity for isotopes lying farther from high abundance isotopes than the energy cutoff of the lens.

  5. Dissociation and ammonia mass transfer from ammonium solution and dairy cattle manure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Process-based models are being used to predict ammonia (NH**3) emissions from manure sources, but their accuracy has not been fully evaluated for cattle manure. Laboratory trials were conducted to measure the dissociation and mass transfer coefficient for NH**3 volatilization from media of buffered ...

  6. A Novel Two-Stage Tandem Mass Spectrometry Approach and Scoring Scheme for the Identification of O-GlcNAc Modified Peptides

    NASA Astrophysics Data System (ADS)

    Hahne, Hannes; Kuster, Bernhard

    2011-05-01

    The modification of serine and threonine residues in proteins by a single N-acetylglucosamine (O-GlcNAc) residue is an emerging post-translational modification (PTM) with broad biological implications. However, the systematic or large-scale analysis of this PTM is hampered by several factors, including low stoichiometry and the lability of the O-glycosidic bond during tandem mass spectrometry. Using a library of 72 synthetic glycopeptides, we developed a two-stage tandem MS approach consisting of pulsed Q dissociation (PQD) for O-GlcNAc peptide detection and electron transfer dissociation (ETD) for identification and site localization. Based on a set of O-GlcNAc specific fragment ions, we further developed a score (OScore) that discriminates O-GlcNAc peptide spectra from spectra of unmodified peptides with 95% sensitivity and >99% specificity. Integrating the OScore into the two-stage LC-MS/MS approach detected O-GlcNAc peptides in the low fmol range and at 10-fold better sensitivity than a single data-dependent ETD tandem MS experiment.

  7. Strategies in protein sequencing and characterization: multi-enzyme digestion coupled with alternate CID/ETD tandem mass spectrometry.

    PubMed

    Nardiello, Donatella; Palermo, Carmen; Natale, Anna; Quinto, Maurizio; Centonze, Diego

    2015-01-01

    A strategy based on a simultaneous multi-enzyme digestion coupled with electron transfer dissociation (ETD) and collision-induced dissociation (CID) was developed for protein sequencing and characterization, as a valid alternative platform in ion-trap based proteomics. The effect of different proteolytic procedures using chymotrypsin, trypsin, a combination of both, and Lys-C, was carefully evaluated in terms of number of identified peptides, protein coverage, and score distribution. A systematic comparison between CID and ETD is shown for the analysis of peptides originating from the in-solution digestion of standard caseins. The best results were achieved with a trypsin/chymotrypsin mix combined with CID and ETD operating in alternating mode. A post-database search validation of MS/MS dataset was performed, then, the matched peptides were cross checked by the evaluation of ion scores, rank, number of experimental product ions, and their relative abundances in the MS/MS spectrum. By integrated CID/ETD experiments, high quality-spectra have been obtained, thus allowing a confirmation of spectral information and an increase of accuracy in peptide sequence assignments. Overlapping peptides, produced throughout the proteins, reduce the ambiguity in mapping modifications between natural variants and animal species, and allow the characterization of post translational modifications. The advantages of using the enzymatic mix trypsin/chymotrypsin were confirmed by the nanoLC and CID/ETD tandem mass spectrometry of goat milk proteins, previously separated by two-dimensional gel electrophoresis. PMID:25479873

  8. 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.

  9. Characterization of nucleic acids by tandem mass spectrometry - The second decade (2004-2013): From DNA to RNA and modified sequences.

    PubMed

    Schürch, Stefan

    2016-07-01

    Nucleic acids play key roles in the storage and processing of genetic information, as well as in the regulation of cellular processes. Consequently, they represent attractive targets for drugs against gene-related diseases. On the other hand, synthetic oligonucleotide analogues have found application as chemotherapeutic agents targeting cellular DNA and RNA. The development of effective nucleic acid-based chemotherapeutic strategies requires adequate analytical techniques capable of providing detailed information about the nucleotide sequences, the presence of structural modifications, the formation of higher-order structures, as well as the interaction of nucleic acids with other cellular components and chemotherapeutic agents. Due to the impressive technical and methodological developments of the past years, tandem mass spectrometry has evolved to one of the most powerful tools supporting research related to nucleic acids. This review covers the literature of the past decade devoted to the tandem mass spectrometric investigation of nucleic acids, with the main focus on the fundamental mechanistic aspects governing the gas-phase dissociation of DNA, RNA, modified oligonucleotide analogues, and their adducts with metal ions. Additionally, recent findings on the elucidation of nucleic acid higher-order structures by tandem mass spectrometry are reviewed. © 2014 Wiley Periodicals, Inc., Mass Spec Rev 35:483-523, 2016. PMID:25288464

  10. Assigning in vivo carbamylation and acetylation in human lens proteins using tandem mass spectrometry and database searching

    NASA Astrophysics Data System (ADS)

    Park, Zee-Yong; Sadygov, Rovshan; Clark, Judy M.; Clark, John I.; Yates, John R., III

    2007-01-01

    In this paper, we show that ion trap mass spectrometers can differentiate acetylation and carbamylation modifications based on database search results for a lens protein sample. These types of modifications are difficult to distinguish on ion trap instruments because of their lower resolution and mass accuracy. The results were corroborated by using accurate mass information derived from MALDI TOF MS analysis of eluted peptides from a duplicate capillary RPLC separation. Tandem mass spectra of lysine carbamylated peptides were further verified by manual assignments of fragment ions and by the presence of characteristic fragment ions of carbamylated peptides. It was also observed that carbamylated peptides show a strong neutral loss of the carbamyl group in collision induced dissociation (CID), a feature that can be prognostic for carbamylation. In a lens tissue sample of a 67-year-old patient, 12 in vivo carbamylation sites were detected on 7 different lens proteins and 4 lysine acetylation sites were detected on 3 different lens proteins. Among the 12 in vivo carbamylation sites, 9 are novel in vivo carbamylation modification sites. Notably, in vivo carbamylation of [gamma]S crystallin, [beta]A4 crystallin, [beta]B1 crystallin, and [beta]B2 crystallin observed in this study have never been reported before.

  11. Tandem time-of-flight mass spectrometer (TOF-TOF) with a quadratic-field ion mirror

    NASA Astrophysics Data System (ADS)

    Giannakopulos, Anastassios E.; Thomas, Benjamin; Colburn, Alex W.; Reynolds, David J.; Raptakis, Emmanuel N.; Makarov, Alexander A.; Derrick, Peter J.

    2002-05-01

    A tandem time-of-flight (TOF-TOF) mass spectrometer comprised of two ion mirrors is described. The first ion mirror, which is a linear-field, single-stage mirror (MS1) with an intermediate collision cell, has been designed to provide the temporal focus necessary for the second, quadratic-field ion mirror (MS2) to function effectively. Due to the wide energy-range focusing capabilities of the quadratic field employed in the second ion mirror all the fragment ions can be collected in one spectrum without the need to step the reflecting working voltage of the MS2. The size of the active area of the microchannel plate detector used in the preliminary experiments was the limiting factor governing the collection efficiently of fragment ions. The use of the first ion mirror to provide temporal focusing of the precursor ion packet at the first focal point of the quadratic mirror used as the MS2 requires no alteration of the focusing conditions for different masses, in contrast to delayed extraction or postsource pulsed focusing. Precursor ions formed by matrix-assisted laser desorption/ionization were mass-selected with an ion gate located before the collision cell and the fragment ions were mass analyzed using the quadratic-field ion mirror. Experimental results demonstrating effective high-energy collision-induced dissociation of polymer and fullerene molecule-ions are presented.

  12. Benzodiazepines and metabolites from biological fluids by liquid chromatography electrospray tandem mass spectrometry.

    PubMed

    Morris-Kukoski, Cynthia L; Schaff, Jason E; Reda, Louis J

    2012-01-01

    Solid-phase extraction and liquid chromatography-tandem mass spectrometry are invaluable techniques for the determination of benzodiazepines and metabolites in biological matrices. The reason for using tandem mass spectrometry is to increase limits of detection without the need for chemical derivatization. Here we describe a technique for the detection of 26 benzodiazepines and metabolites at a detection limit of approximately 1-2 ng/mL in blood and 1-5 ng/mL in urine when screened using a data-dependent scan method. PMID:22767106

  13. High explosives vapor detection by atmospheric sampling glow discharge ionization/tandem mass spectrometry

    SciTech Connect

    McLuckey, S.A.; Goeringer, D.E.; Asano, K.G.

    1996-02-01

    The combination of atmospheric sampling glow discharge ionization with tandem mass spectrometry for the detection of traces of high explosives is described. Particular emphasis is placed on use of the quadrupole ion trap as the type of tandem mass spectrometer. Atmospheric sampling glow discharge provides a simple, rugged, and efficient means for anion formation while the quadrupole ion trap provides for efficient tandem mass spectrometry. Mass selective ion accumulation and non-specific ion activation methods can be used to overcome deleterious effects arising from ion/ion interactions. Such interactions constitute the major potential technical barrier to the use of the ion trap for real-time monitoring of targeted compounds in uncontrolled and highly variable matrices. Tailored waveforms can be used to effect both mass selective ion accumulation and ion activation. Concatenated tailored waveforms allow for both functions in a single experiment thereby providing the capability for monitoring several targeted species simultaneously. The combination of atmospheric sampling glow discharge ionization with a state-of-the-art analytical quadrupole ion trap is a highly sensitive and specific detector for traces of high explosives. The combination is also small and inexpensive relative to virtually any other form of tandem mass spectrometry. The science and technology underlying the glow discharge/ion trap combination is sufficiently mature to form the basis for an engineering effort to make the detector portable. 85 refs.

  14. Mass fractionation of noble gases in synthetic methane hydrate: Implications for naturally occurring gas hydrate dissociation

    USGS Publications Warehouse

    Hunt, Andrew G.; Stern, Laura; Pohlman, John W.; Ruppel, Carolyn; Moscati, Richard J.; Landis, Gary P.

    2013-01-01

    As a consequence of contemporary or longer term (since 15 ka) climate warming, gas hydrates in some settings may presently be dissociating and releasing methane and other gases to the ocean-atmosphere system. A key challenge in assessing the impact of dissociating gas hydrates on global atmospheric methane is the lack of a technique able to distinguish between methane recently released from gas hydrates and methane emitted from leaky thermogenic reservoirs, shallow sediments (some newly thawed), coal beds, and other sources. Carbon and deuterium stable isotopic fractionation during methane formation provides a first-order constraint on the processes (microbial or thermogenic) of methane generation. However, because gas hydrate formation and dissociation do not cause significant isotopic fractionation, a stable isotope-based hydrate-source determination is not possible. Here, we investigate patterns of mass-dependent noble gas fractionation within the gas hydrate lattice to fingerprint methane released from gas hydrates. Starting with synthetic gas hydrate formed under laboratory conditions, we document complex noble gas fractionation patterns in the gases liberated during dissociation and explore the effects of aging and storage (e.g., in liquid nitrogen), as well as sampling and preservation procedures. The laboratory results confirm a unique noble gas fractionation pattern for gas hydrates, one that shows promise in evaluating modern natural gas seeps for a signature associated with gas hydrate dissociation.

  15. The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search*

    PubMed Central

    Kim, Sangtae; Mischerikow, Nikolai; Bandeira, Nuno; Navarro, J. Daniel; Wich, Louis; Mohammed, Shabaz; Heck, Albert J. R.; Pevzner, Pavel A.

    2010-01-01

    Recent emergence of new mass spectrometry techniques (e.g. electron transfer dissociation, ETD) and improved availability of additional proteases (e.g. Lys-N) for protein digestion in high-throughput experiments raised the challenge of designing new algorithms for interpreting the resulting new types of tandem mass (MS/MS) spectra. Traditional MS/MS database search algorithms such as SEQUEST and Mascot were originally designed for collision induced dissociation (CID) of tryptic peptides and are largely based on expert knowledge about fragmentation of tryptic peptides (rather than machine learning techniques) to design CID-specific scoring functions. As a result, the performance of these algorithms is suboptimal for new mass spectrometry technologies or nontryptic peptides. We recently proposed the generating function approach (MS-GF) for CID spectra of tryptic peptides. In this study, we extend MS-GF to automatically derive scoring parameters from a set of annotated MS/MS spectra of any type (e.g. CID, ETD, etc.), and present a new database search tool MS-GFDB based on MS-GF. We show that MS-GFDB outperforms Mascot for ETD spectra or peptides digested with Lys-N. For example, in the case of ETD spectra, the number of tryptic and Lys-N peptides identified by MS-GFDB increased by a factor of 2.7 and 2.6 as compared with Mascot. Moreover, even following a decade of Mascot developments for analyzing CID spectra of tryptic peptides, MS-GFDB (that is not particularly tailored for CID spectra or tryptic peptides) resulted in 28% increase over Mascot in the number of peptide identifications. Finally, we propose a statistical framework for analyzing multiple spectra from the same precursor (e.g. CID/ETD spectral pairs) and assigning p values to peptide-spectrum-spectrum matches. PMID:20829449

  16. Determination of diarrheic shellfish toxins in mussels by microliquid chromatography-tandem mass spectrometry.

    PubMed

    Draisci, R; Lucentini, L; Giannetti, L; Boria, P; James, K J; Furey, A; Gillman, M; Kelly, S S

    1998-01-01

    A fast, sensitive, and specific procedure for determining toxins that cause diarrheic shellfish poisoning (DSP) using microliquid chromatography coupled with tandem mass spectrometry (micro-LC-MS-MS) is reported. The lipophylic polyether acidic toxins okadaic acid (OA), its isomer dinophysistoxin-2 (DTX-2), the 35-methylokadaic acid dinophysistoxin-1 (DTX-1), and the novel toxin dinophysistoxin-1B (DTX-2B; recently isolated from Irish mussels) were extracted from shellfish tissues with acetone and chromatographed by isocratic elution at 10 microL/min with CH3 CN-H2O, 80 + 20 (v/v), containing 0.1% trifluoroacetic acid, through a C18 reversed-phase column (1.0 mm id). The chromatograph is coupled via an ion spray interface to an atmospheric pressure ionization source. Collision-induced-dissociation (CID) ion mass spectra of the protonated molecule, [M + H]+, at m/z 805 for OA, DTX-2, and DTX-2B and at m/z 819 for DTX-1, were obtained in MS-MS experiments to identify 2 diagnostic fragment ions for each analyte that could be used for selected-reaction-monitoring (SRM) micro-LC-MS-MS analysis. The CID spectrum of DTX-2B confirmed it to be a new OA isomer, like DTX-2. Standard curves obtained by SRM micro-LC-MS-MS were linear (r2 > or = 0.9992) over the range 0.05-1.00 micrograms/mL (i.e., 0.10-2.00 micrograms toxin/g hepatopancreas), and a detection limit of 15 pg/injection was obtained for each DSP toxin. Average recoveries ranged from 95 to 101%, and coefficients of variation ranged from 1.8 to 3.4%. This novel SRM micro-LC-MS-MS method was used to confirm acidic DSP toxins in Irish and Italian toxic mussels. It offers a high degree of specificity because analyte confirmation is based on retention time, molecular weight, structural information obtained from the presence of 2 diagnostic fragments for each analyte, and ion ratios. OA was found in both Irish (< or = 0.7 micrograms/g hepatopancreas) and Italian (< or = 1.5 micrograms/g hepatopancreas) mussels. DTX-1 was

  17. Accurate Mass MS/MS/MS Analysis of Siderophores Ferrioxamine B and E1 by Collision-Induced Dissociation Electrospray Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Sidebottom, Ashley M.; Karty, Jonathan A.; Carlson, Erin E.

    2015-11-01

    Siderophores are bacterially secreted, small molecule iron chelators that facilitate the binding of insoluble iron (III) for reuptake and use in various biological processes. These compounds are classified by their iron (III) binding geometry, as dictated by subunit composition and include groups such as the trihydroxamates (hexadentate ligand) and catecholates (bidentate). Small modifications to the core structure such as acetylation, lipid tail addition, or cyclization, make facile characterization of new siderophores difficult by molecular ion detection alone (MS1). We have expanded upon previous fragmentation-directed studies using electrospray ionization collision-induced dissociation tandem mass spectrometry (ESI-CID-MS/MS/MS) and identified diagnostic MS3 features from the trihydroxamate siderophore class for ferrioxamine B and E1 by accurate mass. Diagnostic features for MS3 include C-C, C-N, amide, and oxime cleavage events with proposed losses of water and -CO from the iron (III) coordination sites. These insights will facilitate the discovery of novel trihydroxamate siderophores from complex sample matrices.

  18. 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…

  19. Combined Dynamic Arrays for Storing and Searching Semi-Ordered Tandem Mass Spectrometry Data

    Technology Transfer Automated Retrieval System (TEKTRAN)

    When performing bioinformatics analysis on tandem mass spectrometry data, there is a computational need to efficiently store and sort these semi-ordered data sets. To solve this problem, a new data structure based on dynamic arrays was designed and implemented in an algorithm that parses semi-order...

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  1. 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...

  2. Selective Chemoprecipitation and Subsequent Release of Tagged Species for the Analysis of Nitropeptides by Liquid Chromatography–Tandem Mass Spectrometry*

    PubMed Central

    Prokai-Tatrai, Katalin; Guo, Jia; Prokai, Laszlo

    2011-01-01

    Tyrosine nitration is a low-abundance post-translational protein modification that requires appropriate enrichment techniques to enable proteomic analyses. We report a simple yet highly specific method to enrich nitropeptides by chemoprecipitation involving only two straightforward chemical modifications of the nitropeptides before capturing the obtained derivatives with a strategically designed solid-phase active ester reagent. Specifically, capping of the aliphatic amines in the peptides is done first by reductive methylation to preserve the charge state of peptides for electrospray ionization mass spectrometric analysis, followed by reduction of nitrotyrosines to the corresponding aminotyrosines. These peptides are then immobilized on the solid-phase active ester reagent, whereas other peptides carrying no free amino groups are separated from the immobilized species by thoroughly washing the beads from which the tagged peptide derivatives can easily be released by acid-catalyzed hydrolysis at room temperature. The benefits of selective enrichment from a matrix of unmodified peptides for liquid chromatography-tandem mass spectrometry are demonstrated on three synthetic nitropeptides that are nitrated fragments of biologically relevant proteins. Identification of several in vitro nitrated human plasma proteins, also implicated under various pathological processes, by database searches from the enriched and tagged tryptic nitropeptides is presented as a practical application. We also show that converting the nitro-group to the small 4-formylbenzoylamido tag does not significantly alter fragmentation properties upon collision-induced dissociation compared with those of the native nitropeptides, and at the same time this derivatization actually improves electron capture dissociation due to conversion of the electron-predator nitro-group to this novel tag. PMID:21540302

  3. 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.

  4. Tandem Mass Spectrometry of Heparan Sulfate Negative Ions: Sulfate Loss Patterns and Chemical Modification Methods for Improvement of Product Ion Profiles

    NASA Astrophysics Data System (ADS)

    Shi, Xiaofeng; Huang, Yu; Mao, Yang; Naimy, Hicham; Zaia, Joseph

    2012-09-01

    Heparan sulfate (HS) is a polysaccharide modified with sulfation, acetylation, and epimerization that enable its binding with protein ligands and regulation of important biological processes. Tandem mass spectrometry has been employed to sequence linear biomolecules e.g., proteins and peptides. However, its application in structural characterization of HS is limited due to the neutral loss of sulfate (SO3) during collisional induced dissociation (CID). In this report, we studied the dissociation patterns of HS disaccharides and demonstrate that the N-sulfate (N-S) bond is especially facile during CID. We identified factors that influence the propensities of such losses from precursor ions and proposed a Free Proton Index (FPI) to help select ions that are able to produce meaningful backbone dissociations. We then investigated the thermodynamics and kinetics of SO3 loss from sulfates that are protonated, deprotonated, and metal-adducted using density functional theory computations. The calculations showed that sulfate loss from a protonated site was much more facile than that from a deprotonated or metal-adducted site. Further, the loss of SO3 from N-sulfate was energetically favored by 3-8 kcal/mol in transition states relative to O-sulfates, making it more prone to this process by a substantial factor. In order to reduce the FPI, representing the number of labile sulfates in HS native chains and oligosaccharides, we developed a series of chemical modifications to selectively replace the N-sulfates of the glucosamine with deuterated acetyl group. These modifications effectively reduced the sulfate density on the HS oligosaccharides and generated considerably more backbone dissociation using on-line LC/tandem MS.

  5. Collisionally activated dissociation and electron capture dissociation of several mass spectrometry-identifiable chemical cross-linkers.

    PubMed

    Chowdhury, Saiful M; Munske, Gerhard R; Tang, Xiaoting; Bruce, James E

    2006-12-15

    One of the challenges in protein interaction studies with chemical cross-linking stems from the complexity of intra-, inter-, and dead-end cross-linked peptide mixtures. We have developed new cross-linkers to study protein-protein interactions with mass spectrometry to improve the ability to deal with this complexity. Even the accurate mass capabilities of FTICR-MS alone cannot unambiguously identify cross-linked peptides from cell-labeling experiments due to the complexity of these mixtures resultant from the enormous number of possible cross-linked species. We have developed novel cross-linkers that have unique fragmentation features in the gas phase. The characteristics of these cross-linkers combined with the accurate mass capability of FTICR-MS can help distinguish cross-linking reaction products and assign protein identities. These cross-linkers that we call protein interaction reporters (PIRs) have been constructed with two reactive groups attached through two bonds that can be preferentially cleaved by low-energy CID of the respective protonated precursor ions. After cleavage of the labile bonds, the middle part of the linker serves as a reporter ion to aid identification of cross-linked peptides. This report highlights three new PIRs with new features that have been developed to improve the efficiency of release of reporter ions. The new cross-linkers reported here were tuned with the addition of an affinity tag, a hydrophilic group, a photocleavable group, and new low-energy MS/MS cleavable bonds. This report presents our investigation of the MSMS fragmentation behavior of selected protonated ions of the new compounds. The comprehensive fragmentation of these PIRs and PIR-labeled cross-linked peptides with low-energy collisions and an example of electron capture dissociation in FTICR-MS is presented. These new cross-linkers will contribute to current systems biology research by allowing acquisition of global or large-scale data on protein

  6. Atmospheric sampling glow discharge ionizataion and triple quadrupole tandem mass spectrometry for explosives vapor detection

    SciTech Connect

    McLuckey, S.A.; Goeringer, D.E.; Asano, K.G.; Hart, K.J.; Glish, G.L.; Grant, B.C.; Chambers, D.M.

    1993-08-01

    The detection and identification of trace vapors of hidden high explosives is an excellent example of a targeted analysis problem. It is desirable to push to ever lower levels the quantity or concentration of explosives material that provides an analytical signal, while at the same time discriminating against all other uninteresting material. The detection system must therefore combine high sensitivity with high specificity. This report describes the philosophy behind the use of atmospheric sampling glow discharge ionization, which is a sensitive, rugged, and convenient means for forming anions from explosives molecules, with tandem mass spectrometry, which provides unparalleled specificity in the identification of explosives-related ions. Forms of tandem mass spectrometry are compared and contrasted to provide a summary of the characteristics to be expected from an explosives detector employing mass spectrometry/mass spectrometry. The instrument developed for the FAA, an atmospheric sampling glow discharge/triple quadrupole mass spectrometer, is described in detail with particular emphasis on the ion source/spectrometer interface and on the capabilities of the spectrometer. Performance characteristics of the system are also described as they pertain to explosives of interest including a description of an automated procedure for the detection and identification of specific explosives. A comparison of various tandem mass spectrometers mated with atmospheric sampling glow discharge is then described and preliminary studies with a vapor preconcentration system provided by the FAA will be described.

  7. Determination of antimigraine compounds rizatriptan, zolmitriptan, naratriptan and sumatriptan in human serum by liquid chromatography/electrospray tandem mass spectrometry.

    PubMed

    Vishwanathan, K; Bartlett, M G; Stewart, J T

    2000-01-01

    Development of a rapid, sensitive and selective method for the determination of antimigraine drugs from human serum is essential for understanding the pharmacokinetics of these drugs when administered concurrently. Solid phase extraction (SPE) using Oasis HLB was used to extract the drugs (sumatriptan, naratriptan, zolmitriptan and rizatriptan) and the internal standard bufotenine from serum. A method based on liquid chromatography/tandem mass spectrometry (LC/MS/MS) was developed and validated to simultaneously quantitate these antimigraine drugs from human serum. The precursor and major product ions of the analytes were monitored on a triple quadrupole mass spectrometer with positive ion electrospray ionization (ESI) in the multiple reaction monitoring (MRM) mode. The base peak in all the analytes is formed by alpha cleavage associated with protonation of the secondary amine. Mechanisms for the formation of the collision-induced dissociation products of these antimigraine compounds are proposed. Linear calibration curves were generated from 1-100 ng/mL with all coefficients of determination greater than 0.99. The inter- and intraday precision (%RSD) were less than 9.3% and accuracy (%error) was less than 9.8% for all components. The limits of detection (LOD) for the method were 250 pg/mL for sumatriptan and 100 pg/mL for the remaining analytes based on a signal-to-noise ratio of 3. PMID:10637423

  8. High Energy Collisions on Tandem Time-of-Flight Mass Spectrometers

    NASA Astrophysics Data System (ADS)

    Cotter, Robert J.

    2013-05-01

    Long before the introduction of matrix-assisted laser desorption/ionization (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 (TOF) 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 TOFs and tandem TOFs, 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.

  9. Tandem Affinity Purification Combined with Mass Spectrometry to Identify Components of Protein Complexes

    PubMed Central

    Kaiser, Peter; Meierhofer, David; Wang, Xiaorong; Huang, Lan

    2011-01-01

    Most biological processes are governed by multiprotein complexes rather than individual proteins. Identification of protein complexes therefore is becoming increasingly important to gain a molecular understanding of cells and organisms. Mass spectrometry–based proteomics combined with affinity-tag-based protein purification is one of the most effective strategies to isolate and identify protein complexes. The development of tandem-affinity purification approaches has revolutionized proteomics experiments. These two-step affinity purification strategies allow rapid, effective purification of protein complexes and, at the same time, minimize background. Identification of even very low-abundant protein complexes with modern sensitive mass spectrometers has become routine. Here, we describe two general strategies for tandem-affinity purification followed by mass spectrometric identification of protein complexes. PMID:18370112

  10. Quantitation of protein post-translational modifications using isobaric tandem mass tags.

    PubMed

    Liang, Hui-Chung; Lahert, Emma; Pike, Ian; Ward, Malcolm

    2015-01-01

    Post-translational modifications (PTMs) of proteins are known to modulate many cellular processes and their qualitative and quantitative evaluation is fundamental for understanding the mechanisms of biological events. Over the past decade, improvements in sample preparation techniques and enrichment strategies, the development of quantitative labeling strategies, the launch of a new generation of mass spectrometers and the creation of bioinformatics tools for the interrogation of ever larger datasets has established MS-based quantitative proteomics as a powerful workflow for global proteomics, PTM analysis and the elucidation of key biological mechanisms. With the advantage of their multiplexing capacity and the flexibility of an ever-growing family of different peptide-reactive groups, isobaric tandem mass tags facilitate quantitative proteomics and PTM experiments and enable higher sample throughput. In this review, we focus on the technical concept and utility of the isobaric tandem mass tag labeling approach to PTM analysis, including phosphorylation, glycosylation and S-nitrosylation. PMID:25697195

  11. Linkage Position and Residue Identification of Disaccharides by Tandem Mass Spectrometry and Linear Discriminant Analysis

    SciTech Connect

    Hui Zhang; Steve M. Brokman; Ning Fang; Nicola L. Pohl; Edward S. Yeung

    2008-03-20

    The discrimination of isomeric disaccharides with different linkage types and different monosaccharide residues--glucose (Glc), galactose (Gal), and mannose (Man) at the non-reducing end - was investigated with tandem mass spectrometry (MS/MS) and linear discriminant analysis (LDA). Conventional matrix-assisted laser desorption/ionization (MALDI)-MS has strong interference peaks from matrix ions in the low mass region (<500 Da). This greatly limits the application of MALDI-MS for the analysis of small molecules such as saccharides. We solved this problem by using LDI with acidic fullerene matrix, which gives a very clean background in the low-mass region. Disaccharides with different linkage types give different tandem mass spectral profiles from various cross-ring fragmentation pathways. Disaccharides with the same linkage type but with three different kinds of monosaccharide residues bear the same fragmentation profiles. However, the relative ratios of the fragment ion intensities were found to be distinctly different among the three disaccharide isomers. By employing statistical tools such as LDA to classify the tandem mass spectra, disaccharide isomers with either different linkages or different monosaccharide residues were successfully classified.

  12. Linkage Position and Residue Identification of Disaccharides by Tandem mass Spectrometry and linear Discriminant Analysis

    SciTech Connect

    Hui Zhang; Steve M. Brokman; Ning Fang; Nicola L. Pohl; Edward S. Yeung

    2008-03-20

    The discrimination of isomeric disaccharides with different linkage types and different monosaccharide residues--glucose (Glc), galactose (Gal), and mannose (Man) at the non-reducing end--was investigated with tandem mass spectrometry (MS/MS) and linear discriminant analysis (LDA). Conventional matrix-assisted laser desorption/ionization (MALDI)-MS has strong interference peaks from matrix ions in the low mass region (<500 Da). This greatly limits the application of MALDI-MS for the analysis of small molecules such as saccharides. We solved this problem by using LDI with acidic fullerene matrix, which gives a very clean background in the low-mass region. Disaccharides with different linkage types give different tandem mass spectral profiles from various cross-ring fragmentation pathways. Disaccharides with the same linkage type but with three different kinds of monosaccharide residues bear the same fragmentation profiles. However, the relative ratios of the fragment ion intensities were found to be distinctly different among the three disaccharide isomers. By employing statistical tools such as LDA to classify the tandem mass spectra, disaccharide isomers with either different linkages or different monosaccharide residues were successfully classified.

  13. A tandem mass spectrometric study of bile acids: interpretation of fragmentation pathways and differentiation of steroid isomers.

    PubMed

    Qiao, Xue; Ye, Min; Liu, Chun-fang; Yang, Wen-zhi; Miao, Wen-juan; Dong, Jing; Guo, De-an

    2012-02-01

    Bile acids are steroids with a pentanoic acid substituent at C-17. They are the terminal products of cholesterol excretion, and play critical physiological roles in human and animals. Bile acids are easy to detect but difficult to identify by using mass spectrometry due to their poly-ring structure and various hydroxylation patterns. In this study, fragmentation pathways of 18 free and conjugated bile acids were interpreted by using tandem mass spectrometry. The analyses were conducted on ion trap and triple quadrupole mass spectrometers. Upon collision-induced dissociation, the conjugated bile acids could cleave into glycine or taurine related fragments, together with the steroid skeleton. Fragmentations of free bile acids were further elucidated, especially by atmospheric pressure chemical ionization mass spectrometry in positive ion mode. Aside from universally observed neutral losses, eliminations occurred on bile acid carbon rings were proposed for the first time. Moreover, four isomeric 5β-cholanic acid hydroxyl derivatives (3α,6α-, 3α,7β-, 3α,7α-, and 3α,12α-) were differentiated using electrospray ionization in negative ion mode: 3α,7β-OH substituent inclined to eliminate H(2)O and CH(2)O(2) groups; 3α,6α-OH substituent preferred neutral loss of two H(2)O molecules; 3α,12α-OH substituent apt to lose the carboxyl in the form of CO(2) molecule; and 3α,7α-OH substituent exhibited no further fragmentation after dehydration. This study provided specific interpretation for mass spectra of bile acids. The results could contribute to bile acid analyses, especially in clinical assays and metabonomic studies. PMID:22133544

  14. Effect of nuclear mass on carrier-envelope-phase-controlled electron localization in dissociating molecules

    NASA Astrophysics Data System (ADS)

    Xu, Han; Xu, Tian-Yu; He, Feng; Kielpinski, D.; Sang, R. T.; Litvinyuk, I. V.

    2014-04-01

    We explore the effect of nuclear mass on the laser-driven electron localization process. We dissociate a mixed H2 and D2 target with intense, carrier-envelope-phase (CEP) stable 6 fs laser pulses and detect the products in a reaction microscope. We observe a very strong CEP-dependent asymmetry in proton and deuteron emission for low dissociation energy channels. This asymmetry is stronger for H2 than for D2. We also observe a large CEP offset between the asymmetry spectra for H2 and D2. Our theoretical simulations, based on a one-dimensional two-channel model, agree very well with the asymmetry spectra, but fail to account properly for the phase difference between the two isotopes.

  15. Mass spectrometric determination of the dissociation energy of the AuMg diatomic molecule

    NASA Astrophysics Data System (ADS)

    Balducci, G.; Ciccioli, A.; Gigli, G.; Kudin, L. S.

    2003-02-01

    The dissociation energy of the intermetallic molecule AuMg was for the first time determined by the Knudsen-effusion mass spectrometry technique. Partial pressures of Au(g), Mg(g), AuMg(g) and Au 2(g) species produced under equilibrium vaporization of an appropriate alloy were monitored in the temperature range 1870-2333 K. The collected data were analyzed by the second- and third-law methods for the gaseous equilibria AuMg(g)=Au(g) + Mg(g) and AuMg(g) + Au(g)=Au 2(g) + Mg(g). The selected value for the dissociation energy of AuMg at 0 K is D0∘(AuMg)= 175.4±2.7 kJ/mol.

  16. Quality control for building libraries from electrospray ionization tandem mass spectra.

    PubMed

    Yang, Xiaoyu; Neta, Pedatsur; Stein, Stephen E

    2014-07-01

    Electrospray ionization (ESI) tandem mass spectrometry coupled with liquid chromatography is a routine technique for identifying and quantifying compounds in complex mixtures. The identification step can be aided by matching acquired tandem mass spectra (MS(2)) against reference library spectra as is routine for electron ionization (EI) spectra from gas chromatography/mass spectrometry (GC/MS). However, unlike the latter spectra, ESI MS(2) spectra are likely to originate from various precursor ions for a given target molecule and may be acquired at varying energies and resolutions and have characteristic noise signatures, requiring processing methods very different from EI to obtain complete and high quality reference spectra for individual analytes. This paper presents procedures developed for creating a tandem mass spectral library that addresses these factors. Library building begins by acquiring MS(2) spectra for all major MS(1) peaks in an infusion run, followed by assigning MS(2) spectra to clusters and creating a consensus spectrum for each. Intensity-based constraints for cluster membership were developed, as well as peak testing to recognize and eliminate suspect peaks and reduce noise. Consensus spectra were then examined by a human evaluator using a number of criteria, including a fraction of annotated peaks and consistency of spectra for a given ion at different energies. These methods have been developed and used to build a library from >9000 compounds, yielding 230,000 spectra. PMID:24896981

  17. Spectral probabilities of top-down tandem mass spectra

    SciTech Connect

    Liu, Xiaowen; Segar, Matthew W.; Li, Shuai Cheng; Kim, Sangtae

    2014-01-24

    In mass spectrometry (MS)-based proteomics, accurate estimation of statistical signicance of peptide and protein identications is desired for determining whether they are actually correct. Probabilistic models, such as the generating function method, have been successfully applied to compute statistical signicance of peptide-spectrum matches (PSMs) in bottom-up MS, but it is limited to PSMs of short peptides without post-translational modications (PTMs). Recently, top-down MS has be- come available in many laboratories, which often identies intact proteins with PTMs. In this paper, we propose an extended generating function (EGF) method for accurately computing statistical signicance of protein- spectrum matches (PrSMs) with PTMs.

  18. Single amino acid sequence polymorphisms in rat cardiac troponin revealed by top-down tandem mass spectrometry.

    PubMed

    Sancho Solis, Raquel; Ge, Ying; Walker, Jeffery W

    2008-01-01

    Heterotrimeric cardiac troponin (cTn) is a critical component of the thin filament regulatory complex in cardiac muscle. Two of the three subunits, cTnI and cTnT, are subject to post-translational modifications such as proteolysis and phosphorylation, but linking modification patterns to function remains a major challenge. To obtain a global view of the biochemical state of cTn in native tissue, we performed high resolution top-down mass spectrometry of cTn heterotrimers from healthy adult rat hearts. cTn heterotrimers were affinity purified, desalted and then directly subjected to mass spectrometry using a 7 Tesla Thermo LTQ-FT-ICR instrument equipped with an ESI source. Molecular ions for N-terminally processed and acetylated cTnI and cTnT were readily detected as were other post-translationally modified forms of these proteins. cTnI was phosphorylated with a distribution of un-, mono- and bisphosphorylated forms of 41 +/- 3%, 46 +/- 1%, 13 +/- 3%, respectively. cTnT was predominantly monophosphorylated and partially proteolyzed at the Glu(29)-Pro(30) peptide bond. Also observed in high resolution spectra were 'shadow' peaks of similar intensity to 'parent' peaks exhibiting masses of cTnI+16 Da and cTnT+128 Da, subsequently shown by tandem mass spectrometry (MS/MS) to be single amino acid polymorphisms. Intact and protease-digested cTn subunits were fragmented by electron capture dissociation or collision activated dissociation to localize an Ala/Ser polymorphism at residue 7 of cTnI. Similar analysis of cTnT localized an additional Gln within a three residue alternative splice site beginning at residue 192. Besides being able to provide unique insights into the global state of post-translational modification of cTn subunits, high resolution top-down mass spectrometry readily revealed naturally occurring single amino acid sequence variants including a genetic polymorphism at residue 7 in cTnI, and an alternative splice isoform that affects a putative hinge region

  19. Large Scale Discovery and De Novo-Assisted Sequencing of Cationic Antimicrobial Peptides (CAMPs) by Microparticle Capture and Electron-Transfer Dissociation (ETD) Mass Spectrometry.

    PubMed

    Juba, Melanie L; Russo, Paul S; Devine, Megan; Barksdale, Stephanie; Rodriguez, Carlos; Vliet, Kent A; Schnur, Joel M; van Hoek, Monique L; Bishop, Barney M

    2015-10-01

    The identification and sequencing of novel cationic antimicrobial peptides (CAMPs) have proven challenging due to the limitations associated with traditional proteomics methods and difficulties sequencing peptides present in complex biomolecular mixtures. We present here a process for large-scale identification and de novo-assisted sequencing of newly discovered CAMPs using microparticle capture followed by tandem mass spectrometry equipped with electron-transfer dissociation (ETD). This process was initially evaluated and verified using known CAMPs with varying physicochemical properties. The effective parameters were then applied in the analysis of a complex mixture of peptides harvested from American alligator plasma using custom-made (Bioprospector) functionalized hydrogel particles. Here, we report the successful sequencing process for CAMPs that has led to the identification of 340 unique peptides and the discovery of five novel CAMPs from American alligator plasma. PMID:26327436

  20. Infrared irradiation in the collision cell of a hybrid tandem quadrupole/time-of-flight mass spectrometer for declustering and cleaning of nanoelectrosprayed protein complex ions.

    PubMed

    El-Faramawy, Ayman; Guo, Yuzhu; Verkerk, Udo H; Thomson, Bruce A; Siu, K W Michael

    2010-12-01

    Herein we report the performance of a hybrid quadrupole time-of-flight tandem mass spectrometer with an improved designed for coaxial infrared laser introduction for the characterization and dissociation of large protein complex ions and their aggregates formed under nanoelectrospray ionization. The major improvement from the original design (Raspopov, S. A.; El-Faramawy, A.; Thomson, B. A.; Siu, K. W. M. Anal. Chem. 2006, 78, 4572-4577) involves the use of a hollow silica waveguide and physical isolation of the infrared laser. Large model protein complex ions and their aggregates examined include alcohol dehydrogenase, avidin, GroEL, and others. Gentle heating of these complexes with the infrared laser facilitated declustering and resulted in better resolved mass spectral peaks and more accurate molecular-weight measurements. PMID:21062028

  1. Ion mobility tandem mass spectrometry enhances performance of bottom-up proteomics.

    PubMed

    Helm, Dominic; Vissers, Johannes P C; Hughes, Christopher J; Hahne, Hannes; Ruprecht, Benjamin; Pachl, Fiona; Grzyb, Arkadiusz; Richardson, Keith; Wildgoose, Jason; Maier, Stefan K; Marx, Harald; Wilhelm, Mathias; Becher, Isabelle; Lemeer, Simone; Bantscheff, Marcus; Langridge, James I; Kuster, Bernhard

    2014-12-01

    One of the limiting factors in determining the sensitivity of tandem mass spectrometry using hybrid quadrupole orthogonal acceleration time-of-flight instruments is the duty cycle of the orthogonal ion injection system. As a consequence, only a fraction of the generated fragment ion beam is collected by the time-of-flight analyzer. Here we describe a method utilizing postfragmentation ion mobility spectrometry of peptide fragment ions in conjunction with mobility time synchronized orthogonal ion injection leading to a substantially improved duty cycle and a concomitant improvement in sensitivity of up to 10-fold for bottom-up proteomic experiments. This enabled the identification of 7500 human proteins within 1 day and 8600 phosphorylation sites within 5 h of LC-MS/MS time. The method also proved powerful for multiplexed quantification experiments using tandem mass tags exemplified by the chemoproteomic interaction analysis of histone deacetylases with Trichostatin A. PMID:25106551

  2. Ion Mobility Tandem Mass Spectrometry Enhances Performance of Bottom-up Proteomics

    PubMed Central

    Helm, Dominic; Vissers, Johannes P. C.; Hughes, Christopher J.; Hahne, Hannes; Ruprecht, Benjamin; Pachl, Fiona; Grzyb, Arkadiusz; Richardson, Keith; Wildgoose, Jason; Maier, Stefan K.; Marx, Harald; Wilhelm, Mathias; Becher, Isabelle; Lemeer, Simone; Bantscheff, Marcus; Langridge, James I.; Kuster, Bernhard

    2014-01-01

    One of the limiting factors in determining the sensitivity of tandem mass spectrometry using hybrid quadrupole orthogonal acceleration time-of-flight instruments is the duty cycle of the orthogonal ion injection system. As a consequence, only a fraction of the generated fragment ion beam is collected by the time-of-flight analyzer. Here we describe a method utilizing postfragmentation ion mobility spectrometry of peptide fragment ions in conjunction with mobility time synchronized orthogonal ion injection leading to a substantially improved duty cycle and a concomitant improvement in sensitivity of up to 10-fold for bottom-up proteomic experiments. This enabled the identification of 7500 human proteins within 1 day and 8600 phosphorylation sites within 5 h of LC-MS/MS time. The method also proved powerful for multiplexed quantification experiments using tandem mass tags exemplified by the chemoproteomic interaction analysis of histone deacetylases with Trichostatin A. PMID:25106551

  3. A review of statistical methods for protein identification using tandem mass spectrometry

    PubMed Central

    Serang, Oliver; Noble, William

    2012-01-01

    Tandem mass spectrometry has emerged as a powerful tool for the characterization of complex protein samples, an increasingly important problem in biology. The effort to efficiently and accurately perform inference on data from tandem mass spectrometry experiments has resulted in several statistical methods. We use a common framework to describe the predominant methods and discuss them in detail. These methods are classified using the following categories: set cover methods, iterative methods, and Bayesian methods. For each method, we analyze and evaluate the outcome and methodology of published comparisons to other methods; we use this comparison to comment on the qualities and weaknesses, as well as the overall utility, of all methods. We discuss the similarities between these methods and suggest directions for the field that would help unify these similar assumptions in a more rigorous manner and help enable efficient and reliable protein inference. PMID:22833779

  4. 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

  5. Evaluation and optimization of electron capture dissociation efficiency in fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    McFarland, Melinda A; Chalmers, Michael J; Quinn, John P; Hendrickson, Christopher L; Marshall, Alan G

    2005-07-01

    Electron capture dissociation (ECD) efficiency has typically been lower than for other dissociation techniques. Here we characterize experimental factors that limit ECD and seek to improve its efficiency. Efficiency of precursor to product ion conversion was measured for a range of peptide (approximately 15% efficiency) and protein (approximately 33% efficiency) ions of differing sizes and charge states. Conversion of precursor ions to products depends on electron irradiation period and maximizes at approximately 5-30 ms. The optimal irradiation period scales inversely with charge state. We demonstrate that reflection of electrons through the ICR cell is more efficient and robust than a single pass, because electrons can cool to the optimal energy for capture, which allows for a wide range of initial electron energy. Further, efficient ECD with reflected electrons requires only a short (approximately 500 micros) irradiation period followed by an appropriate delay for cooling and interaction. Reflection of the electron beam results in electrons trapped in or near the ICR cell and thus requires a brief (approximately 50 micros) purge for successful mass spectral acquisition. Further electron irradiation of refractory precursor ions did not result in further dissociation. Possibly the ion cloud and electron beam are misaligned radially, or the electron beam diameter may be smaller than that of the ion cloud such that remaining precursor ions do not overlap with the electron beam. Several ion manipulation techniques and use of a large, movable dispenser cathode reduce the possibility that misalignment of the ion and electron beams limits ECD efficiency. PMID:15914017

  6. A review of clinical diagnostic applications of liquid chromatography-tandem mass spectrometry.

    PubMed

    Shushan, Bori

    2010-01-01

    Liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) technology is emerging as a complementary method to traditional methodology used for clinical applications. Enhanced specificity and high-throughput capabilities are providing significant benefits to clinical diagnostic laboratories conducting routine analyses. This technology is expected to expand rapidly as scientists focus on more complicated challenges that can be solved efficiently by adding LC/MS/MS to their arsenal of techniques. PMID:20949635

  7. Erratum: Erratum to: Axial Imidazole Binding Strengths in Porphyrinoid Cobalt(III) Complexes as Studied by Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Mishra, Ekta; Worlinsky, Jill L.; Gilbert, Thomas M.; Brückner, Christian; Ryzhov, Victor

    2012-08-01

    The Co(II) complexes of twelve meso-tetraaryl-porphyrins, -chlorins, and chlorin analogues containing non-pyrrolic heterocycles were synthesized and converted in situ to the corresponding Co(III) complexes coordinated to one or two imidazoles. Electrospray ionization tandem mass spectrometry (ESI-MS/MS) in conjunction with the energy-variable collision-induced dissociation (CID) technique was used to compare the relative gas-phase binding strength of the axially coordinated imidazoles to the octahedral and square planar Co(III) porphyrinoid complex ions. The observed binding energies of these ligands were rationalized in terms of the effects of porphyrinoid core structure and meso-substitution on the electron density on the central Co(III) centers. Some of these trends were supported by DFT-based computational studies. The study highlights to which extend porphyrins vary from chlorins and chlorin analogues in their coordination abilities and to which extraordinary degree meso-thienyl-substituents influence the electronic structure of porphyrins. The study also defines further the scope and limits CID experiments can be used to interrogate the electronic structures of metalloporphyrin complexes.

  8. Typing of Blood-Group Antigens on Neutral Oligosaccharides by Negative-Ion Electrospray Ionization Tandem Mass Spectrometry

    PubMed Central

    Zhang, Hongtao; Zhang, Shuang; Tao, Guanjun; Zhang, Yibing; Mulloy, Barbara; Zhan, Xiaobei; Chai, Wengang

    2013-01-01

    Blood-group antigens, such as those containing fucose and bearing the ABO(H)- and Lewis-type determinants expressed on the carbohydrate chains of glycoproteins and glycolipids, and also on unconjugated free oligosaccharides in human milk and other secretions, are associated with various biological functions. We have previously shown the utility of negative-ion electrospay ionization tandem mass spectrometry with collision-induced dissociation (ESI-CID-MS/MS) for typing of Lewis (Le) determinants, e.g. Lea, Lex, Leb, and Ley on neutral and sialylated oligosaccharide chains. In the present report we extended the strategy to characterization of blood-group A-, B- and H-determinants on type 1 and type 2, and also on type 4 globoside chains to provide a high sensitivity method for typing of all the major blood-group antigens, including the A, B, H, Lea, Lex, Leb, and Ley determinants, present in oligosaccharides. Using the principles established we identified two minor unknown oligosaccharide components present in the products of enzymatic synthesis by bacterial fermentation. We also demonstrated that the unique fragmentations derived from the D- and 0,2A-type cleavages observed in ESI-CID-MS/MS, which are important for assigning blood-group and chain types, only occur under the negative-ion conditions for reducing sugars but not for reduced alditols or under positive-ion conditions. PMID:23692402

  9. Accelerated solvent extraction and liquid chromatography-tandem mass spectrometry quantitation of corticosteroid residues in bovine liver.

    PubMed

    Draisci, R; Marchiafava, C; Palleschi, L; Cammarata, P; Cavalli, S

    2001-04-01

    A new method for the rapid extraction and unequivocal confirmation of two highly potent fluorinated synthetic corticosteroids, dexamethasone and its beta-epimer betamethasone, in bovine liver was developed. Flumethasone was used as internal standard. An extraction procedure using an accelerated solvent extraction system was employed for the isolation of the analytes in liver samples. The procedure was highly automated, including defatting and extraction steps, sequentially carried out under 1.0 x 10(4) kPa in about 35 min. The extracts were then directly analysed by tandem mass spectrometry with on-line liquid chromatography. The analytes were ionised in a heated nebulizer interface operating in the negative ion mode where the molecular related ions [M-H-CH2O]- were generated for each analyte, at m/z 361 for betamethasone and dexamethasone and at m/z 379 for flumethasone. They served as precursor ions for collision-induced dissociation and three diagnostic product ions for the drugs were identified to carry out analyte confirmation by selected reaction monitoring. Assessment of recovery, specificity and precision for betamethasone, dexamethasone and flumethasone proved the method suitable for confirmatory purposes. The limit of quantification of betamethasone and dexamethasone in liver tissue was 1.0 microg/kg. PMID:11334334

  10. Fast multi-blind modification search through tandem mass spectrometry.

    PubMed

    Na, Seungjin; Bandeira, Nuno; Paek, Eunok

    2012-04-01

    With great biological interest in post-translational modifications (PTMs), various approaches have been introduced to identify PTMs using MS/MS. Recent developments for PTM identification have focused on an unrestrictive approach that searches MS/MS spectra for all known and possibly even unknown types of PTMs at once. However, the resulting expanded search space requires much longer search time and also increases the number of false positives (incorrect identifications) and false negatives (missed true identifications), thus creating a bottleneck in high throughput analysis. Here we introduce MODa, a novel "multi-blind" spectral alignment algorithm that allows for fast unrestrictive PTM searches with no limitation on the number of modifications per peptide while featuring over an order of magnitude speedup in relation to existing approaches. We demonstrate the sensitivity of MODa on human shotgun proteomics data where it reveals multiple mutations, a wide range of modifications (including glycosylation), and evidence for several putative novel modifications. Based on the reported findings, we argue that the efficiency and sensitivity of MODa make it the first unrestrictive search tool with the potential to fully replace conventional restrictive identification of proteomics mass spectrometry data. PMID:22186716

  11. Characterization of oligodeoxynucleotides by electron detachment dissociation fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Yang, Jiong; Mo, Jingjie; Adamson, Julie T; Håkansson, Kristina

    2005-03-15

    Electron detachment dissociation (EDD), recently introduced by Zubarev and co-workers for the dissociation of multiply charged biomolecular anions via a radical ion intermediate, has been shown to be analogous to electron capture dissociation (ECD) in several respects, including more random peptide fragmentation and retention of labile posttranslational modifications. We have previously demonstrated unique fragmentation behavior in ECD compared to vibrational excitation for oligodeoxynucleotide cations. However, that approach is limited by the poor sensitivity for oligonucleotide ionization in positive ion mode. Here, we show implementation of EDD on a commercial Fourier transform ion cyclotron resonance mass spectrometer utilizing two different configurations: a heated filament electron source and an indirectly heated hollow dispenser cathode electron source. The dispenser cathode configuration provides higher EDD efficiency and additional fragmentation channels for hexamer oligodeoxynucleotides. As in ECD, even-electron d/w ion series dominate the spectra, but we also detect numerous a/z (both even-electron and radical species), (a/z - B), c/x, (c/x - B), and (d/w - B) ions with minimal nucleobase loss from the precursor ions. In contrast to previous high-energy collision-activated dissociation (CAD) and ion trap CAD of radical oligonucleotide anions, we only observe minimum sugar cross-ring cleavage, possibly due to the short time scale of EDD, which limits secondary fragmentation. Thus, EDD provides fragmentation similar to ECD for oligodeoxynucleotides but at enhanced sensitivity. Finally, we show that noncovalent bonding in a DNA duplex can be preserved following EDD, illustrating another analogy with ECD. We believe the latter finding implies EDD has promise for characterization of nucleic acid structure and folding. PMID:15762599

  12. MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra

    PubMed Central

    2015-01-01

    Systematic analysis and interpretation of the large number of tandem mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck in discovery-driven research. MS/MS mass spectral libraries are small compared to all known small molecule structures and are often not freely available. MS2Analyzer was therefore developed to enable user-defined searches of thousands of spectra for mass spectral features such as neutral losses, m/z differences, and product and precursor ions from MS/MS spectra in MSP/MGF files. The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/. As the reference query set, 147 literature-reported neutral losses and their corresponding substructures were collected. This set was tested for accuracy of linking neutral loss analysis to substructure annotations using 19 329 accurate mass tandem mass spectra of structurally known compounds from the NIST11 MS/MS library. Validation studies showed that 92.1 ± 6.4% of 13 typical neutral losses such as acetylations, cysteine conjugates, or glycosylations are correct annotating the associated substructures, while the absence of mass spectra features does not necessarily imply the absence of such substructures. Use of this tool has been successfully demonstrated for complex lipids in microalgae. PMID:25263576

  13. Electrospray Ionization Tandem Mass Spectrometry (ESI-MS/MS)-Based Shotgun Lipidomics

    SciTech Connect

    Mezengie, Giorgis I.

    2011-01-11

    In the past decade, many new strategies for mass spectrometry (MS)-based analyses of lipids have been developed. Lipidomics is one of the most promising research fields to emerge as a result of these advances in MS. Currently, mass spectrometric analysis of lipids involves two complementary approaches: direct infusion (shotgun lipidomics) and liquid chromatography coupled to MS. In this chapter, I will demonstrate the approach of shotgun lipidomics using electrospray ionization tandem MS for the analysis of lipid molecular species directly from crude biological extracts of tissue or fluids.

  14. Rapid electron capture dissociation of mass-selectively accumulated oligodeoxynucleotide dications

    NASA Astrophysics Data System (ADS)

    Schultz, Kristin N.; Håkansson, Kristina

    2004-05-01

    We have performed extended characterization of the fragmentation patterns of oligodeoxynucleotide dications following electron capture dissociation (ECD) utilizing improved instrumentation. Our current results from a 9.4 T Fourier transform ion cyclotron resonance mass spectrometer equipped with mass-selective external ion accumulation and an indirectly heated dispenser cathode electron source demonstrate much richer fragmentation than from a previous 7 T instrument with a directly heated filament electron source. We propose the previous absence of backbone product ions from purine-containing oligonucleotides is a result of intramolecular hydrogen bonding, preventing product ions from separating. Similar behavior is observed at non-optimized ECD conditions with the current instrumentation. However, infrared laser heating of the resulting charge-reduced radical species results in extensive backbone fragmentation (different from infrared multiphoton dissociation) of the oligonucleotide dA6, demonstrating potential for ECD to characterize nucleic acid secondary structure. Under more optimized conditions, rich fragmentation, mostly in terms of w, (a/z-B), and (c/x-B) products, is observed for dA6, dC6, dG5, and d(GCATGC) following ECD only, allowing complete sequencing in several cases. The current ECD spectra contain some doubly charged products, indicating that populations of gas-phase oligodeoxynucleotide dications are zwitterionic.

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

    SciTech Connect

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

    2005-01-01

    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 methods 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.

  16. N, N-Dimethyl Leucines as Novel Isobaric Tandem Mass Tags for Quantitative Proteomics and Peptidomics

    PubMed Central

    Xiang, Feng; Ye, Hui; Chen, Ruibing; Fu, Qiang; Li, Lingjun

    2010-01-01

    Herein we describe the development and application of a set of novel N, N-dimethyl leucine (DiLeu) 4-plex isobaric tandem mass (MS2) tagging reagents with high quantitation efficacy and greatly reduced cost for neuropeptide and protein analysis. DiLeu reagents serve as attractive alternatives for isobaric tag for relative and absolute quantitation (iTRAQ) and tandem mass tags (TMTs) due to their synthetic simplicity, labeling efficiency and improved fragmentation efficiency. DiLeu reagent resembles the general structure of a tandem mass tag in that it contains an amine reactive group (triazine ester) targeting the N-terminus and ε-amino group of the lysine side-chain of a peptide, a balance group, and a reporter group. A mass shift of m/z 145.1 is observed for each incorporated label. Intense a1 reporter ions at m/z 115.1, 116.1, 117.1, and 118.1 are observed for all pooled samples upon MS2. All labeling reagents are readily synthesized from commercially available chemicals with greatly reduced cost. Labels 117 and 118 can be synthesized in one step and labels 115 and 116 can be synthesized in two steps. Both DiLeu and iTRAQ reagents show comparable protein sequence coverage (~43%) and quantitation accuracy (<15%) for tryptically digested protein samples. Furthermore, enhanced fragmentation of DiLeu labeling reagents offers greater confidence in protein identification and neuropeptide sequencing from complex neuroendocrine tissue extracts from a marine model organism, Callinectes sapidus. PMID:20218596

  17. 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. PMID:23159734

  18. Study of acetylation on Ser/Thr/Tyr/Lys, and trimethylation on Lys using electrospray tandem mass spectrometry

    NASA Astrophysics Data System (ADS)

    Li, Yan; Ball, Haydn L.

    2009-03-01

    Post-translational modifications (PTM) corresponding to a gain in mass of 42 Da are of increasing interest. It has been widely recognized that acetylation and trimethylation on Lys regulates gene transcription and silencing. In addition, it was recently discovered that acetylation of Ser and Thr residues on a signaling kinase can block its activation. In this paper, three series of model peptides were chemically synthesized to generate comparative MS data. Electrospray collision-induced dissociation tandem mass spectrometry was used to characterize the fragmentation pattern of acetylation on Ser, Thr, and Tyr residues. In separate experiments, the fragmentation pattern and efficiency were studied for acetylation and trimethylation on Lys. Our results confirmed those previously reported, that a characteristic immonium ion at m/z 126 corresponds to an acetylated Lys, and we further differentiated acetylation from trimethylation by their effects on peptide fragmentation efficiency. With the same primary sequence, a trimethylated peptide requires higher energy to fragment compared to the acetylated analogue. For peptides containing acetylated Ser, the y-60 and b-60 ions are commonly observed when the acetylation site is at, or close to, the C-terminus or N-terminus of the daughter ion, respectively; for acetylated Thr, in addition to y-60 and b-60 ions, y-42 ions are usually dominant. The loss of 42 Da and 60 Da can correspond to the loss of CH2CO through deacetylation and CH3COOH through [beta]-elimination, respectively. Meanwhile, loss of 42 Da and 18 Da individually can also contribute to the loss of 60 Da. When peptide containing acetylated Tyr/Lys is fragmented, the acetyl group remains attached to their respective side-chains. The fragmentation pattern was similar whether the acetylation site was close to C-terminus or N-terminus of the peptide. This study provides a better understanding of the MSMS fragmentation character of peptides with acetylation on Ser, Thr

  19. Simultaneous Determination and Pharmacokinetic Study of Protocatechuic Aldehyde and Its Major Active Metabolite Protocatechuic Acid in Rat Plasma by Liquid Chromatography-Tandem Mass Spectrometry.

    PubMed

    Wang, Xiangyang; Yan, Kaijing; Ma, Xiaohui; Li, Wei; Chu, Yang; Guo, Jiahua; Li, Shuming; Zhou, Shuiping; Zhu, Yonghong; Liu, Changxiao

    2016-05-01

    A very simple and selective high-performance liquid chromatography electrospray ionization tandem mass spectrometry (LC-MS-MS) method was developed for simultaneous determination and pharmacokinetic study of protocatechuic aldehyde (PAL) and its active metabolite protocatechuic acid (PCA). The method involves a simple liquid-liquid extraction with ethyl acetate. The separation was performed on a Hypersil GOLD C18column (2.1 × 150 mm, 3.0 µm; particle, Thermo, USA) with isocratic elution using a mobile phase consisted of methanol and water (containing 0.1% formic acid) at a flow rate of 0.2 mL/min. The detection of target compounds was done by using low-energy collision dissociation tandem mass spectrometry (CID-MS-MS) using the selective reaction monitoring scan mode. The method was linear for all analytes over the investigated range for all correlation coefficients greater than 0.9950. The lower limits of quantification were 2.0 ng/mL for PAL and PCA. The intra- and interday precisions (relative standard deviation, RSD %) were <6.84 and 5.54%, and the accuracy (relative error, RE %) was between -2.85 and 0.74% (n= 6). The developed method was applied to study the pharmacokinetics of PAL and its major active metabolite PCA in rat plasma after oral and intravenous administration of PAL. PMID:26969682

  20. Combined infrared multiphoton dissociation and electron-capture dissociation using co-linear and overlapping beams in Fourier transform ion cyclotron resonance mass spectrometry.

    PubMed

    Mihalca, Romulus; van der Burgt, Yuri E M; McDonnell, Liam A; Duursma, Marc; Cerjak, Iliya; Heck, Albert J R; Heeren, Ron M A

    2006-01-01

    A novel set-up for Fourier transform ion cyclotron resonance mass spectrometry (FTICR) is reported for simultaneous infrared multiphoton dissociation (IRMPD) and electron-capture dissociation (ECD). An unmodified electron gun ensures complete, on-axis overlap between the electron and the photon beams. The instrumentation, design and implementation of this novel approach are described. In this configuration the IR beam is directed into the ICR cell using a pneumatically actuated mirror inserted into the ion-optical path. Concept validation was made using different combinations of IRMPD and ECD irradiation events on two standard peptides. The ability to perform efficient IRMPD, ECD and especially simultaneous IRMPD and ECD using lower irradiation times is demonstrated. The increase in primary sequence coverage, with the combined IRMPD and ECD set-up, also increases the confidence in peptide and protein assignments. PMID:16705647

  1. Identification of GABAC Receptor Protein Homeostasis Network Components from Three Tandem Mass Spectrometry Proteomics Approaches

    PubMed Central

    Wang, Ya-Juan; Han, Dong-Yun; Tabib, Tracy; Yates, John R.; Mu, Ting-Wei

    2013-01-01

    Gamma-amino butyric acid type C (GABAC) receptors inhibit neuronal firing primarily in retina. Maintenance of GABAC receptor protein homeostasis in cells is essential for its function. However, a systematic study of GABAC receptor protein homeostasis (proteostasis) network components is absent. Here, co-immunoprecipitation of human GABAC-ρ1 receptor complexes was performed in HEK293 cells overexpressing ρ1 receptors. To enhance the coverage and reliability of identified proteins, immunoisolated ρ1 receptor complexes were subjected to three tandem mass spectrometry (MS)-based proteomic analyses: namely, gel-based tandem MS (GeLC-MS/MS), solution-based tandem MS (SoLC-MS/MS), and multidimensional protein identification technology (MudPIT). From the 107 identified proteins, we assembled GABAC-ρ1 receptor proteostasis network components, including proteins with protein folding, degradation, and trafficking functions. We studied representative individual ρ1 receptor interacting proteins, including calnexin, a lectin chaperone that facilitates glycoprotein folding, and LMAN1, a glycoprotein trafficking receptor, and global effectors that regulate protein folding in cells based on bioinformatics analysis, including HSF1, a master regulator of the heat shock response, and XBP1, a key transcription factor of the unfolded protein response. Manipulating selected GABAC receptor proteostasis network components is a promising strategy to regulate GABAC receptor folding, trafficking, degradation and thus function to ameliorate related retinal diseases. PMID:24079818

  2. Quantitative profiling of bacteriocins present in dairy-free probiotic preparations of Lactobacillus acidophilus by nanoliquid chromatography-tandem mass spectrometry.

    PubMed

    Nandakumar, Renu; Talapatra, Kesh

    2014-01-01

    Bacteriocins are a heterogeneous group of ribosomally synthesized peptides or proteins with antimicrobial activity, produced predominantly by lactic acid bacteria, with potential applications as biopreservatives and probiotics. We describe here a novel strategy based on a bottom-up, shotgun proteomic approach using nanoliquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) with multiple fragmentation techniques for the quantitative profiling of bacteriocins present in the probiotic preparations of Lactobacillus acidophilus. A direct LC-MS/MS analysis with alternate collision-induced dissociation, high-energy collision dissociation, and electron-transfer dissociation fragmentation following a filter-assisted size-exclusion sample prefractionation has resulted in the identification of peptides belonging to 37 bacteriocins or related proteins. Peptides from lactacin F, helveticin J, lysin, avicin A, acidocin M, curvaticin FS47, and carocin D were predominant. The process of freeze drying under vacuum was observed to affect both the diversity and abundance of bacteriocins. Data acquisition using alternating complementary peptide fragmentation modes, especially electron-transfer dissociation, has significantly enhanced the peptide sequence coverage and number of bacteriocin peptides identified. Multi-enzyme proteolytic digestion was observed to increase the sample complexity and dynamic range, lowering the chances of detection of low-abundant bacteriocin peptides by LC-MS/MS. An analytical platform integrating size exclusion prefractionation, nanoLC-MS/MS analysis with multiple fragmentation techniques, and data-dependent decision tree-driven bioinformatic data analysis is novel in bacteriocin research and suitable for the comprehensive bioanalysis of diverse, low-abundant bacteriocins in complex samples. PMID:24565320

  3. The simultaneous determination of hydrophobicity and dissociation constant by liquid chromatography-mass spectrometry.

    PubMed

    Wiczling, P; Struck-Lewicka, W; Kubik, L; Siluk, D; Markuszewski, M J; Kaliszan, R

    2014-06-01

    Convenient methods for testing drug candidates' lipophilicity and acidity are highly requested in modern pharmaceutical research and drug development strategies. Reversed-phase high-performance liquid chromatography (RP HPLC) might be particularly useful for the determination of both dissociation constant and the (pH-dependent) partition coefficient related parameters, applicable in high-throughput analysis of multi-component mixtures. The general theory of combined pH/organic modifier gradient has recently provided equations relating gradient retention time and pH of the mobile phase. The purpose of this work was to facilitate the identification of analytes in this technique by its transfer to RP HPLC coupled with time-of-flight mass spectrometry with electrospray ionization source (ESI-TOF-MS). The accuracy of the proposed methodology was assessed by analyzing a set of known drugs. The ammonium formate, ammonium acetate or ammonium bicarbonate buffers were used to control pH during chromatographic analysis. In result, the pKa and hydrophobicity parameters were determined and the accuracy of the estimated values was assessed by comparing them with literature data. The gradient RP HPLC coupled with ESI-TOF-MS methods allowed for the rapid determination of dissociation constant and hydrophobicity and was shown to be especially applicable for complex mixtures. The use of ESI-TOF-MS detection allowed to achieve the medium-throughput screening rate (100 compounds/day) and provided a simple approach to assess pharmacokinetically important physicochemical properties of drugs. PMID:24598171

  4. Characterization of neurohistone variants and post-translational modifications by electron capture dissociation mass spectrometry

    NASA Astrophysics Data System (ADS)

    Garcia, Benjamin A.; Siuti, Nertila; Thomas, C. Eric; Mizzen, Craig A.; Kelleher, Neil L.

    2007-01-01

    Post-translational modifications (PTMs) of histones are intimately involved in chromatin structure and thus have roles in cellular processes through their impact on gene activation or repression. At the forefront in histone PTM analysis are mass spectrometry-based techniques, which have capabilities to produce improved views of processes affected by chromatin remodeling via histone modifications. In this report, we take the first mass spectrometric look at histone variant expression and post-translational modifications from histones isolated from rat brain tissue. Analyses of whole rat brain identified specific histone H2A and H2B gene family members and several H4 and H3 post-translational modification sites by electron capture dissociation (ECD) mass spectrometry. We subsequently compared these results to selected rat brain regions. Major differences in the expression profiles of H2A and H2B gene family members or in the post-translational modifications on histone H4 were not observed from the different brain regions using a Top Down approach. However, "Middle Down" mass spectrometry facilitating improved characterization of the histone H3 tail (1-50 residues), revealed an enrichment of trimethylation on Lys9 from cerebellum tissue compared to H3 extracted from whole brain, cerebral cortex or hypothalamus tissue. We forward this study in honor of Professor Donald F. Hunt, whose pioneering efforts in protein and PTM analyses have spawned new eras and numerous careers, many exemplified in this special issue.

  5. High-throughput multiclass method for antibiotic residue analysis by liquid chromatography-tandem mass spectrometry.

    PubMed

    Chico, J; Rúbies, A; Centrich, F; Companyó, R; Prat, M D; Granados, M

    2008-12-12

    A simple and rapid method has been developed for the residue analysis of 39 antibiotics (tetracyclines, quinolones, penicillins, sulfonamides and macrolides) in foodstuffs of animal origin. The method combines an effective extraction technique, which uses water-methanol as extracting solvent, with ultra-high-pressure liquid chromatography-tandem mass spectrometry, allowing both confirmation and quantification in a single chromatographic run. The multiresidue method has been validated in chicken muscle matrix according to European Union Decision 2002/657/EC. It has been implemented as a routine method in a Public Health Laboratory, instead of the five plates test and LC methods previously used. PMID:18992888

  6. Tandem mass spectrometric fragmentation patterns of known and new steviol glycosides with structure proposals.

    PubMed

    Zimmermann, Benno F

    2011-06-15

    Stevia rebaudiana contains several steviol glycosides that have a sweet flavor. They are up to 450 times sweeter than sucrose, but some have an undesirable aftertaste. Up to 2010, ten different steviol glycosides have been described from the leaves or purified extracts of S. rebaudiana. In this paper, the tandem mass spectrometric fragmentation patterns of these ten compounds are compiled, along with a scheme for structural elucidation. This scheme is then applied to 12 steviol glycosides that have not yet been described. The proposed structures of five steviol glycosides have been confirmed by other authors. PMID:21594932

  7. 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.

  8. Improving quantitative precision and throughput by reducing calibrator use in liquid chromatography-tandem mass spectrometry.

    PubMed

    Rule, Geoffrey S; Rockwood, Alan L

    2016-05-01

    To improve efficiency in our mass spectrometry laboratories we have made efforts to reduce the number of calibration standards utilized for quantitation over time. We often analyze three or more batches of 96 samples per day, on a single instrument, for a number of assays. With a conventional calibration scheme at six concentration levels this amounts to more than 5000 calibration points per year. Modern LC-tandem mass spectrometric instrumentation is extremely rugged however, and isotopically labelled internal standards are widely available. This made us consider whether alternative calibration strategies could be utilized to reduce the number of calibration standards analyzed while still retaining high precision and accurate quantitation. Here we demonstrate how, by utilizing a single calibration point in each sample batch, and using the resulting response factor (RF) to update an existing, historical response factor (HRF), we are able to obtain improved precision over a conventional multipoint calibration approach, as judged by quality control samples. The laboratory component of this study was conducted with an existing LC tandem mass spectrometric method for three androgen analytes in our production laboratory. Using examples from both simulated and laboratory data we illustrate several aspects of our single point alternative calibration strategy and compare it with a conventional, multipoint calibration approach. We conclude that both the cost and burden of preparing multiple calibration standards with every batch of samples can be reduced while at the same time maintaining, or even improving, analytical quality. PMID:27086099

  9. Gas Chromatography/Atmospheric Pressure Chemical Ionization Tandem Mass Spectrometry for Fingerprinting the Macondo Oil Spill.

    PubMed

    Lobodin, Vladislav V; Maksimova, Ekaterina V; Rodgers, Ryan P

    2016-07-01

    We report the first application of a new mass spectrometry technique (gas chromatography combined to atmospheric pressure chemical ionization tandem mass spectrometry, GC/APCI-MS/MS) for fingerprinting a crude oil and environmental samples from the largest accidental marine oil spill in history (the Macondo oil spill, the Gulf of Mexico, 2010). The fingerprinting of the oil spill is based on a trace analysis of petroleum biomarkers (steranes, diasteranes, and pentacyclic triterpanes) naturally occurring in crude oil. GC/APCI enables soft ionization of petroleum compounds that form abundant molecular ions without (or little) fragmentation. The ability to operate the instrument simultaneously in several tandem mass spectrometry (MS/MS) modes (e.g., full scan, product ion scan, reaction monitoring) significantly improves structural information content and sensitivity of analysis. For fingerprinting the oil spill, we constructed diagrams and conducted correlation studies that measure the similarity between environmental samples and enable us to differentiate the Macondo oil spill from other sources. PMID:27281271

  10. [Microchip-based reversed-phase liquid chromatography-tandem mass spectrometry platform for protein analysis].

    PubMed

    Liang, Yu; Wu, Ci; Dai, Zhongpeng; Liang, Zuocheng; Liang, Zhen; Zhang, Lihua; Zhang, Yukui

    2011-06-01

    Due to the high throughput and high sensitivity, the hyphenation of microchip-based high performance liquid chromatography with tandem mass spectrometry has been paid much attention. In our recent work, with poly (lauryl methacrylate-co-trimethylolpropane trimethacrylate) monolithic materials prepared in microchannels as trap and separation columns, conventional micro-liquid chromatography pumps and valves for fluidic control, and a small-bore open-tube capillary attached to the outlet channel as chip-mass spectrometer (MS) interface, the microchip-based reversed-phase liquid chromatography-tandem mass spectrometry (RPLC-MS/MS) platform was established, and applied for the identification of proteins. By such platform, 100 ng digest of bovine serum albumin (BSA) was successfully analyzed with the sequence coverages as 39.37%, 37.89% and 34.10% (with the relative standard deviation (RSD) of 7.3%) in three runs, separately. To evaluate the chip-to-chip reproducibility, BSA was identified by such platform with the microchips from different batches containing trap column, separation column and chip-MS interface. The obtained sequence coverage and the number of peptides identified were comparable. All these results showed high sensitivity and good reproducibility of such platform, demonstrating the great potential for rapid protein analysis. PMID:22032155

  11. 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. PMID:19939702

  12. Scandium analysis in silicon-containing minerals by inductively coupled plasma tandem mass spectrometry

    NASA Astrophysics Data System (ADS)

    Whitty-Léveillé, Laurence; Drouin, Elisabeth; Constantin, Marc; Bazin, Claude; Larivière, Dominic

    2016-04-01

    This article reports on the development of a new method for the accurate and precise determination of the amount of scandium, Sc, in silicon-containing minerals, based on the use of tandem quadrupole inductively coupled plasma mass spectrometry (ICP-MS/MS). The tandem quadrupole instrument enables new mass filtering configurations, which can reduce polyatomic interferences during the determination of Sc in mineral matrices. He and O2 were used and compared as collision and reaction gases for the removal of interferences at m/z 45 and 61. Using helium gas was ineffective to overcome all of the spectral interferences observed at m/z 45 and particularly for Si-based interferences. However, conversion of Sc+ ions into ScO+ ions (after bombardment with O2 in the octopole reaction system coupled with the use of the instrument in MS/MS mass-shift mode) provided interference-free conditions and sufficiently low limits of detection, down to 3 ng L- 1, to accurately detect Sc. The accuracy of the proposed methodology was assessed by analyzing five different reference materials (BX-N, OKA-2, NIM-L, SY-3 and GH).

  13. Application of dual tree complex wavelet transform in tandem mass spectrometry.

    PubMed

    Murugesan, Selvaraaju; Tay, David B H; Cooke, Ira; Faou, Pierre

    2015-08-01

    Mass Spectrometry (MS) is a widely used technique in molecular biology for high throughput identification and sequencing of peptides (and proteins). Tandem mass spectrometry (MS/MS) is a specialised mass spectrometry technique whereby the sequence of peptides can be determined. Preprocessing of the MS/MS data is indispensable before performing any statistical analysis on the data. In this work, preprocessing of MS/MS data is proposed based on the Dual Tree Complex Wavelet Transform (DTCWT) using almost symmetric Hilbert pair of wavelets. After the preprocessing step, the identification of peptides is done using the database search approach. The performance of the proposed preprocessing technique is evaluated by comparing its performance against Discrete Wavelet Transform (DWT) and Stationary Wavelet Transform (SWT). The preprocessing performed using DTCWT identified more peptides compared to DWT and SWT. PMID:26004826

  14. Analysis of acetamiprid in vegetables using gas chromatography-tandem mass spectrometry.

    PubMed

    Mateu-Sánchez, Manuel; Moreno, Mercedes; Arrebola, F Javier; Martínez Vidal, José Luis

    2003-05-01

    A new analytical method has been validated for determining the insecticide acetamiprid in vegetables using gas chromatography (OC) and different mass spectrometric detection techniques, such as full-scan mass spectrometry (MS), and tandem mass spectrometry (MS/MS). For this purpose, a previous extraction of the vegetable sample was carried out with ethyl acetate. In GC-MS/MS, the lowest detectable concentration was 0.001 mg kg(-1), the average recovery rates at various fortification levels (0.015 and 0.030 mg kg(-1)) ranged between 82.4 and 85.7% and the relative standard deviations were lower than 12.2% in all cases. PMID:12769368

  15. A novel “correlated ion and neutral time of flight” method: Event-by-event detection of neutral and charged fragments in collision induced dissociation of mass selected ions

    SciTech Connect

    Teyssier, C.; Fillol, R.; Abdoul-Carime, H.; Farizon, B.; Farizon, M.

    2014-01-15

    A new tandem mass spectrometry (MS/MS) method based on time of flight measurements performed on an event-by-event detection technique is presented. This “correlated ion and neutral time of flight” method allows to explore Collision Induced Dissociation (CID) fragmentation processes by directly identifying not only all ions and neutral fragments produced but also their arrival time correlations within each single fragmentation event from a dissociating molecular ion. This constitutes a new step in the characterization of molecular ions. The method will be illustrated here for a prototypical case involving CID of protonated water clusters H{sup +}(H{sub 2}O){sub n=1–5} upon collisions with argon atoms.

  16. Multiphoton Dissociation of Electrosprayed MegaDalton-Sized DNA Ions in a Charge-Detection Mass Spectrometer

    NASA Astrophysics Data System (ADS)

    Doussineau, Tristan; Paletto, Pierre; Dugourd, Philippe; Antoine, Rodolphe

    2015-01-01

    Charge detection mass spectrometry in combination with a linear electrostatic ion trap coupled to a continuous wavelength infrared CO2 laser has been used to study the multiphoton dissociation of DNA macromolecular ions. Samples, with masses ranging from 2.23 to 31.5 MDa, include single strand circular M13mp18, double strand circular M13mp18, and double strand linear LambdaPhage DNA fragments. Their activation energies for unimolecular dissociation were determined. Activation energy values slightly increase as a function of the molecular weight. The most important result is the difference between the fragmentations observed for hybridized double-strands and dimers of single strands.

  17. Structural Characterization of Anticancer Drug Paclitaxel and Its Metabolites Using Ion Mobility Mass Spectrometry and Tandem Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Lee, Hong Hee; Hong, Areum; Cho, Yunju; Kim, Sunghwan; Kim, Won Jong; Kim, Hugh I.

    2016-02-01

    Paclitaxel (PTX) is a popular anticancer drug used in the treatment of various types of cancers. PTX is metabolized in the human liver by cytochrome P450 to two structural isomers, 3'- p-hydroxypaclitaxel (3 p-OHP) and 6α-hydroxypaclitaxel (6α-OHP). Analyzing PTX and its two metabolites, 3 p-OHP and 6α-OHP, is crucial for understanding general pharmacokinetics, drug activity, and drug resistance. In this study, electrospray ionization ion mobility mass spectrometry (ESI-IM-MS) and collision induced dissociation (CID) are utilized for the identification and characterization of PTX and its metabolites. Ion mobility distributions of 3 p-OHP and 6α-OHP indicate that hydroxylation of PTX at different sites yields distinct gas phase structures. Addition of monovalent alkali metal and silver metal cations enhances the distinct dissociation patterns of these structural isomers. The differences observed in the CID patterns of metalated PTX and its two metabolites are investigated further by evaluating their gas-phase structures. Density functional theory calculations suggest that the observed structural changes and dissociation pathways are the result of the interactions between the metal cation and the hydroxyl substituents in PTX metabolites.

  18. 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.

  19. 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.

  20. iPE-MMR: An integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data

    PubMed Central

    Jung, Hee-Jung; Purvine, Samuel O.; Kim, Hokeun; Petyuk, Vladislav A.; Hyung, Seok-Won; Monroe, Matthew E.; Mun, Dong-Gi; Kim, Kyong-Chul; Park, Jong-Moon; Kim, Su-Jin; Tolic, Nikola; Slysz, Gordon W.; Moore, Ronald J.; Zhao, Rui; Adkins, Joshua N.; Anderson, Gordon A.; Lee, Hookeun; Camp, David G.; Yu, Myeong-Hee; Smith, Richard D.; Lee, Sang-Won

    2010-01-01

    Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, “integrated Post-Experiment Monoisotopic Mass Refinement” (iPE-MMR), integrates steps: 1) generation of refined MS/MS data by DeconMSn; 2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR; 3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion including multiple charge states, in an MS scan, to determine precursor mass. By combining these methods, iPE-MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data. PMID:20863060

  1. 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

  2. Positive and negative tandem mass spectrometric fingerprints of lipids from the halophilic Archaea Haloarcula marismortuis⃞

    PubMed Central

    de Souza, Lauro M.; Müller-Santos, Marcelo; Iacomini, Marcello; Gorin, Philip A. J.; Sassaki, Guilherme L.

    2009-01-01

    Lipids from the extremely halophilic Archaea, Haloarcula marismortui, contain abundant phytanyl diether phospholipids, namely archaetidic acid (AA), archaetidylglycerol (AG), archaetidylglycerosulfate (AGS), with mainly archaetidylglycerophosphate methyl ester (AGP-Me). These were accompanied by a triglycosyl archaeol (TGA), lacking characteristic sulfate groups. Tandem-mass spectrometry was employed to provide fingerprints for identifying these known lipids, as well as small amounts of unsaturated phospholipids. These contained 3 and 6 double bonds in their archaeol moiety, suggested by negative tandem-MS of intact phospholipids, as indicated by differences between their pseudo-molecular ion and specific fragment ions designated as π2. The core ether lipids were confirmed by electrospray ionization mass spectrometry (ESI-MS) as 2,3-di-O-phytanyl-sn-glycerol (C20, C20), which gave rise to a precursor-ion at m/z 660 [M+Li]+, and its fragment ion at m/z 379 [M+Li]+, consistent with mono-O-phytanyl-glycerol. Furthermore, lithiated ions at m/z 654 (MS1), 379 (MS2) and m/z 648 (MS1), 373 (MS2), combined with 1H/13C NMR chemical shifts at δ 5.31-121.6 (C2/2′-H2/2′), 5.08-124.9 (C6/6′-H6/6′) and 5.10-126.0 (10/10′-H10/10′) confirmed the presence of unsaturated homologs of archaeol. We carried out a comprehensive study on the lipids present in cells of H. marismortui. We used positive and negative ESI-MS with tandem-MS, which served as a fingerprint analysis for identifying the majority of component lipids. PMID:19258281

  3. Screening of newborn infants for cholestatic hepatobiliary disease with tandem mass spectrometry

    PubMed Central

    Mushtaq, Imran; Logan, Stuart; Morris, Michael; Johnson, Andrew W; Wade, Angie M; Kelly, Deirdre; Clayton, Peter T

    1999-01-01

    Objective To assess the feasibility of screening for cholestatic hepatobiliary disease and extrahepatic biliary atresia by using tandem mass spectrometry to measure conjugated bile acids in dried blood spots obtained from newborn infants at 7-10 days of age for the Guthrie test. Setting Three tertiary referral clinics and regional neonatal screening laboratories. Design Unused blood spots from the Guthrie test were retrieved for infants presenting with cholestatic hepatobiliary disease and from the two cards stored on either side of each card from an index child. Concentrations of conjugated bile acids measured by tandem mass spectrometry in the two groups were compared. Main outcome measures Concentrations of glycodihydroxycholanoates, glycotrihydroxycholanoates, taurodihydroxycholanoates, and taurotrihydroxycholanoates. Receiver operator curves were plotted to determine which parameter (or combination of parameters) would best predict the cases of cholestatic hepatobiliary disease and extrahepatic biliary atresia. The sensitivity and specificity at a selection of cut off values for each bile acid species and for total bile acid concentrations for the detection of the two conditions were calculated. Results 218 children with cholestatic hepatobiliary disease were eligible for inclusion in the study. Two children without a final diagnosis and five who presented at <14 days of age were excluded. Usable blood spots were obtained from 177 index children and 708 comparison children. Mean concentrations of all four bile acid species were significantly raised in children with cholestatic hepatobiliary disease and extrahepatic biliary atresia compared with the unaffected children (P<0.0001). Of 177 children with cholestatic hepatobiliary disease, 104 (59%) had a total bile acid concentration >33 μmol/l (97.5th centile value for comparison group). Of the 61 with extrahepatic biliary atresia, 47 (77%) had total bile acid concentrations >33

  4. Effect of D-allose on prostate cancer cell lines: phospholipid profiling by nanoflow liquid chromatography-tandem mass spectrometry.

    PubMed

    Jeong, Rae Ung; Lim, Sangsoo; Kim, Myoung Ok; Moon, Myeong Hee

    2011-08-01

    D-Allose, a rare, naturally occurring monosaccharide, is known to exert anti-proliferative effects on cancer cells. The effects of D-allose on the cellular membranes of hormone-refractory prostate cancer cell line (DU145), hormone-sensitive prostate cancer cell line (LNCaP), and normal prostate epithelial cells (PrEC) were studied at the molecular level by phospholipid (PL) profiling using a shotgun lipidomic method. The molecular structures of 85 PL species including 23 phosphatidylcholines, 12 phosphatidylethanolamines (PEs), 11 phosphatidylserines (PSs), 16 phosphatidylinositols, 9 phosphatidic acids (PAs), and 14 phosphatidylglycerols (PGs) were identified by data-dependent collision-induced dissociation of nanoflow liquid chromatography-tandem mass spectrometry, and the PL amounts were quantified. The addition of D-allose to prostate cancer cell lines during their growth phases had negligible or decreased effects on the relative regulation of PL species, but several new PS molecules (two for DU145 and three for LNCaP) emerged. In contrast, experiments on the PrEC cell line revealed that some high abundant species (14:0/14:0-PE, 16:2/16:0-PG, and 20:6/18:1-PA) showed significant increases in concentration. These findings support a mechanism for the anti-proliferative effect of D-allose on prostate cancer cell lines that involves the induction of programmed cell death since PS molecules are known to induce apoptosis. Principal component analysis was carried out to examine differences in PL distributions among the three cell lines promoted by D-allose. PMID:21633842

  5. Investigations of the Mechanism of the "Proline Effect" in Tandem Mass Spectrometry Experiments: The "Pipecolic Acid Effect"

    NASA Astrophysics Data System (ADS)

    Raulfs, Mary Disa M.; Breci, Linda; Bernier, Matthew; Hamdy, Omar M.; Janiga, Ashley; Wysocki, Vicki; Poutsma, John C.

    2014-10-01

    The fragmentation behavior of a set of model peptides containing proline, its four-membered ring analog azetidine-2-carboxylic acid (Aze), its six-membered ring analog pipecolic acid (Pip), an acyclic secondary amine residue N-methyl-alanine (NMeA), and the D stereoisomers of Pro and Pip has been determined using collision-induced dissociation in ESI-tandem mass spectrometers. Experimental results for AAXAA, AVXLG, AAAXA, AGXGA, and AXPAA peptides are presented, where X represents Pro, Aze, Pip, or NMeA. Aze- and Pro-containing peptides fragment according to the well-established "proline effect" through selective cleavage of the amide bond N-terminal to the Aze/Pro residue to give yn + ions. In contrast, Pip- and NMA-fragment through a different mechanism, the "pipecolic acid effect," selectively at the amide bond C-terminal to the Pip/NMA residue to give bn + ions. Calculations of the relative basicities of various sites in model peptide molecules containing Aze, Pro, Pip, or NMeA indicate that whereas the "proline effect' can in part be rationalized by the increased basicity of the prolyl-amide site, the "pipecolic acid effect" cannot be justified through the basicity of the residue. Rather, the increased flexibility of the Pip and NMeA residues allow for conformations of the peptide for which transfer of the mobile proton to the amide site C-terminal to the Pip/NMeA becomes energetically favorable. This argument is supported by the differing results obtained for AAPAA versus AA(D-Pro)AA, a result that can best be explained by steric effects. Fragmentation of pentapeptides containing both Pro and Pip indicate that the "pipecolic acid effect" is stronger than the "proline effect."

  6. Hybrid quadrupole mass filter/quadrupole ion trap/time-of-flight-mass spectrometer for infrared multiple photon dissociation spectroscopy of mass-selected ions

    SciTech Connect

    Gulyuz, Kerim; Stedwell, Corey N.; Wang Da; Polfer, Nick C.

    2011-05-15

    We present a laboratory-constructed mass spectrometer optimized for recording infrared multiple photon dissociation (IRMPD) spectra of mass-selected ions using a benchtop tunable infrared optical parametric oscillator/amplifier (OPO/A). The instrument is equipped with two ionization sources, an electrospray ionization source, as well as an electron ionization source for troubleshooting. This hybrid mass spectrometer is composed of a quadrupole mass filter for mass selection, a reduced pressure ({approx}10{sup -5} Torr) quadrupole ion trap (QIT) for OPO irradiation, and a reflectron time-of-flight drift tube for detecting the remaining precursor and photofragment ions. A helium gas pulse is introduced into the QIT to temporarily increase the pressure and hence enhance the trapping efficiency of axially injected ions. After a brief pump-down delay, the compact ion cloud is subjected to the focused output from the continuous wave OPO. In a recent study, we implemented this setup in the study of protonated tryptophan, TrpH{sup +}, as well as collision-induced dissociation products of this protonated amino acid [W. K. Mino, Jr., K. Gulyuz, D. Wang, C. N. Stedwell, and N. C. Polfer, J. Phys. Chem. Lett. 2, 299 (2011)]. Here, we give a more detailed account on the figures of merit of such IRMPD experiments. The appreciable photodissociation yields in these measurements demonstrate that IRMPD spectroscopy of covalently bound ions can be routinely carried out using benchtop OPO setups.

  7. Analysis of alcohols, as dimethylglycine esters, by electrospray ionization tandem mass spectrometry.

    PubMed

    Johnson, D W

    2001-03-01

    Dimethylglycine (DMG) esters are new derivatives for the rapid, sensitive and selective analysis of primary and secondary alcohols, in complex mixtures, by electrospray ionization tandem mass spectrometry (ESI-MS/MS). Their development was inspired by the use of the complementary dimethylaminoethyl esters for the trace, rapid analysis of fatty acids. DMG esters are simply prepared by heating a dichloromethane solution of the imidazolide of dimethylglycine, containing triethylamine, and an alcohol. DMG esters of long-chain fatty alcohols, isoprenoidal alcohols and hydroxy-acids are analysed by electrospray ionization tandem mass spectrometry with a precursor ion of m/z 104 scan. Diols, glyceryl esters, glyceryl ethers and some sterols are analysed by a neutral loss of 103 Da scan. Trimethylglycine (TMG) ester iodides, prepared by alkylation of DMG esters with methyl iodide, are more sensitive derivatives for molecules containing secondary alcohol groups, such as cholesterol and gibberellic acid. They are analysed by a precursor ion of m/z 118 scan. DMG or TMG derivatives were shown to be at least comparable and sometimes an order of magnitude more sensitive than N-methylpyridyl ether derivatives for ESI-MS/MS analysis of the different classes of alcohols. Applications of these derivatives for the diagnosis of inherited disorders and the analysis of natural products are presented. PMID:11312519

  8. Ultra performance liquid chromatography tandem mass spectrometry performance evaluation for analysis of antibiotics in natural waters.

    PubMed

    Tamtam, Fatima; Mercier, Fabien; Eurin, Joëlle; Chevreuil, Marc; Le Bot, Barbara

    2009-03-01

    An ultra performance liquid chromatography electrospray tandem mass spectrometry (UPLC/MS/MS) method was developed and validated for the determination of 17 antibiotics in natural waters in one single extraction and chromatographic procedure. Gradient separation conditions were optimised for 17 compounds belonging to five different antibiotic groups: quinolones (oxolinic acid, nalidixic acid, pipemidic acid, flumequine), fluoroquinolones (enoxacin, ciprofloxacin, norfloxacin, ofloxacin, enrofloxacin, sarafloxacin, danofloxacin, difloxacin, lomefloxacin), sulphonamides (sulphamethoxazole, sulphamethazine), nitro-imidazole (ornidazole) and diaminopyrimidine (trimethoprim). The separation of all compounds, obtained using a 1.7 microm particle size column (100 mm x 2.1 mm), was achieved within 10 min time. Water samples were adjusted to pH 7 and extracted using Oasis hydrophilic-lipophilic balance (HLB) solid phase extraction cartridges. After elution with methanol and concentration, extracts were injected in a C18 column (Acquity UPLC BEH C18) and detected by tandem mass spectrometry. Average recovery from 100 ng L(-1) fortified samples was higher than 70% for most of the compounds, with relative standard deviations below 20%. Performances of the method (recoveries, detection limit, quantification limit and relative standard deviation) and matrix effects were studied, and results obtained showed that method was suitable for routine analysis of antibiotics in surface water. Samples analysis from Seine River (France) confirmed the interest of antibiotic contamination evaluation in that area. PMID:19148627

  9. 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). PMID:27154569

  10. Screening newborns for metabolic disorders based on targeted metabolomics using tandem mass spectrometry

    PubMed Central

    2015-01-01

    The main purpose of newborn screening is to diagnose genetic, metabolic, and other inherited disorders, at their earliest to start treatment before the clinical manifestations become evident. Understanding and tracing the biochemical data obtained from tandem mass spectrometry is vital for early diagnosis of metabolic diseases associated with such disorders. Accordingly, it is important to focus on the entire diagnostic process, including differential and confirmatory diagnostic options, and the major factors that influence the results of biochemical analysis. Compared to regular biochemical testing, this is a complex process carried out by a medical physician specialist. It is comprised of an integrated program requiring multidisciplinary approach such as, pediatric specialist, expert scientist, clinical laboratory technician, and nutritionist. Tandem mass spectrometry is a powerful tool to improve screening of newborns for diverse metabolic diseases. It is likely to be used to analyze other treatable disorders or significantly improve existing newborn tests to allow broad scale and precise testing. This new era of various screening programs, new treatments, and the availability of detection technology will prove to be beneficial for the future generations. PMID:26512346

  11. 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

  12. Screening newborns for metabolic disorders based on targeted metabolomics using tandem mass spectrometry.

    PubMed

    Yoon, Hye-Ran

    2015-09-01

    The main purpose of newborn screening is to diagnose genetic, metabolic, and other inherited disorders, at their earliest to start treatment before the clinical manifestations become evident. Understanding and tracing the biochemical data obtained from tandem mass spectrometry is vital for early diagnosis of metabolic diseases associated with such disorders. Accordingly, it is important to focus on the entire diagnostic process, including differential and confirmatory diagnostic options, and the major factors that influence the results of biochemical analysis. Compared to regular biochemical testing, this is a complex process carried out by a medical physician specialist. It is comprised of an integrated program requiring multidisciplinary approach such as, pediatric specialist, expert scientist, clinical laboratory technician, and nutritionist. Tandem mass spectrometry is a powerful tool to improve screening of newborns for diverse metabolic diseases. It is likely to be used to analyze other treatable disorders or significantly improve existing newborn tests to allow broad scale and precise testing. This new era of various screening programs, new treatments, and the availability of detection technology will prove to be beneficial for the future generations. PMID:26512346

  13. Determination of bromate in drinking water by ultraperformance liquid chromatography-tandem mass spectrometry.

    PubMed

    Alsohaimi, Ibrahim Hotan; Alothman, Zeid Abdullah; Khan, Mohammad Rizwan; Abdalla, Mohammad Abulhassan; Busquets, Rosa; Alomary, Ahmad Khodran

    2012-10-01

    Bromate is a byproduct formed as a result of disinfection of bromide-containing source water with ozone or hypochlorite. The International Agency for Research on Cancer has recognized bromate as a possible human carcinogen, thus it is essential to determine in drinking water. Present work highlights a development of sensitive and fast analytical method for bromate determination in drinking water by using ultraperformance liquid chromatography-tandem mass spectrometry. The quality parameters of the developed method were established, obtaining very low limit of detection (0.01 ng/mL), repeatability and reproducibility have been found to be less than 3% in terms of relative standard deviation when analyzing a bromate standard at 0.05 μg/mL with 0.4 min analysis time. Developed method was applied for the analysis of metropolitan and bottled water from Saudi Arabia; 22 samples have been analyzed. Bromate was detected in the metropolitan water samples (from desalinization source) at concentrations ranging between 3.43 and 75.04 ng/mL and in the bottled water samples at concentrations ranging between 2.07 and 21.90 ng/mL. Moreover, in comparison to established analytical methods such as liquid chromatography-tandem mass spectrometry, the proposed method was found to be very sensitive, selective and rapid for the routine analysis of bromate at low level in drinking water. PMID:22815069

  14. [Determination of azaspiracid-1 in shellfishes by liquid chromatography with tandem mass spectrometry].

    PubMed

    Yao, Jianhua; Tan, Zhijun; Zhou, Deqing; Guo, Mengmeng; Xing, Lihong; Yang, Shouguo

    2010-04-01

    A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the determination of azaspiracid-1 (AZA1) in shellfishes was described. After being extracted using methanol and water (80:20, v/v), the extract was cleaned-up by solid phase extraction (SPE) of MAX column, then determined by using a reversed-phase high performance liquid chromatography (HPLC) isocratic program coupled with tandem mass spectrometry in selected reaction monitoring mode (SRM). And the extract was eluted with acetonitrile-water (80:20, v/v) on an Atlantis dC18 column (150 mm x 4.6 mm, 5.0 microm) with mobile phase containing 50 mmol/L formic acid and 2 mmol/L ammonium formate. The detection limit was 11.00 pg/g. The calibration curve was linear (R2 = 0.998 1) in the range of 48.85-2 442 ng/L. The average recoveries of the shellfish tissue extract at three spiked levels (36.64, 73.27, 146.54 pg/g) were from 75.8% to 82.5% (n = 6). The relative standard derivations (RSDs) were less than 10%. The 112 shellfish samples from the local markets of Dalian, Qingdao, Guangzhou were detected by the method, and AZA1 was detected in some samples from Dalian and Guangzhou. The results showed that the method is simple, rapid, sensitive and suitable for the detection of AZA1 in shellfishes. PMID:20712117

  15. Triacylglycerol profile in cocoa liquors using MALDI-TOF and LC-ESI tandem mass spectrometry.

    PubMed

    Bono, Luca; Seraglia, Roberta; Roverso, Marco; Di Carro, Marina; Magi, Emanuele

    2014-09-01

    Triacylglycerols are responsible for chocolate's peculiar melting behavior: the type and position of fatty acids on the glycerol molecule strongly affect the melting range of cocoa butter. For this reason, the characterization of triglyceride composition in cocoa products is particularly important. In this work, triacylglycerols extracted from cocoa liquor samples were analyzed by matrix-assisted laser desorption/ionization time-of-flight (TOF) and electrospray ionization tandem mass spectrometry (MS/MS) coupled to liquid chromatography. Extracted samples were initially analyzed by direct injection in MS to obtain information on triglyceride molecular weights; relevant MS parameters were optimized, and the possible formation of the adducts [M + Na](+) and [M + NH(4)](+) was studied. Tandem mass experiments (both with triple quadrupole and TOF/TOF) were performed to study the fragmentation pathways (in particular, the loss of palmitic, stearic and oleic acid) and identify the triacylglycerols in cocoa liquors. Some signals of the spectra obtained with both MS techniques could indicate the presence of diacylglycerols in the cocoa extract, but different experimental evidences demonstrated that they were generated by the in-source fragmentation of triglycerides. A nonaqueous reversed-phase chromatographic separation was also developed and used to support the identification of the analytes; nine triacylglycerols were recognized in the cocoa liquor extracts. The three different batches of Ecuador cocoa liquor did not show significant differences in the triacylglycerol profile. PMID:25230186

  16. Determination of biogenic amines in beer and wine by capillary electrophoresis-tandem mass spectrometry.

    PubMed

    Daniel, Daniela; Dos Santos, Vagner Bezerra; Vidal, Denis Tadeu Rajh; do Lago, Claudimir Lucio

    2015-10-16

    A capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) method for the simultaneous assessment of nine biogenic amines (spermine, spermidine, putrescine, cadaverine, histamine, phenylethylamine, tryptamine, tyramine, and urocanic acid) in commercial samples of beer and wine is introduced. The samples were submitted to a simple clean-up step with poly(vinylpolypyrrolidone) followed by filtration. Electrophoretic separation in a polyvinyl alcohol (PVA)-coated capillary using 0.5 mol L(-1) acetic acid (pH 2.5) as background electrolyte and detection by electrospray-tandem mass spectrometry was employed. The range of the correlation coefficients of the calibration curves of the analyzed compounds was 0.996-0.999, and the limits of detection and limits of quantification were in the range of 1-2 μg L(-1) and 3-8 μg L(-1), respectively. The recovery values for samples spiked at three concentration levels (0.2, 0.5, and 1.0 mg L(-1)) ranged from 87 to 113% with standard deviation not greater than 5.8%. The use of a PVA-coated silica capillary allows suppressing the electroosmotic flow and, consequently, increasing of the separation efficiency. The method was successfully used to determine biogenic amines in commercial samples of beer and wine. PMID:26362807

  17. Quantitative analysis of tivantinib in rat plasma using ultra performance liquid chromatography with tandem mass spectrometry.

    PubMed

    Bai, Yan-Li; Yuan, Hong-Chang; Zhang, Dong-Tao; Liu, Yuan; Zhang, Yin

    2016-07-15

    In this work, a simple, sensitive and fast ultra performance liquid chromatography with tandem mass spectrometry (UPLC-MS/MS) method was developed and validated for the quantitative determination of tivantinib in rat plasma. Plasma samples were processed with a protein precipitation. The separation was achieved by an Acquity UPLC BEH C18 (2.1mm×50mm, 1.7μm) column with a gradient mobile phase consisting of 0.1% formic acid in water and acetonitrile. Detection was carried out using positive-ion electrospray tandem mass spectrometry via multiple reaction monitoring (MRM). The validated method had an excellent linearity in the range of 1.0-100ng/mL (r(2)>0.9967) with a lower limit of quantification (1.0ng/mL). The extraction recovery was in the range of 79.4-84.2% for tivantinib and 80.3% for carbamazepine (internal standard, IS). The intra- and inter-day precision was below 8.9% and accuracy was from -7.2% to 9.5%. No notable matrix effect and astaticism was observed for tivantinib. The method has been successfully applied to a pharmacokinetic study of tivantinib in rats for the first time, which provides the basis for the further development and application of tivantinib. PMID:27179187

  18. Determination of ecliptasaponin A in rat plasma and tissues by liquid chromatography-tandem mass spectrometry.

    PubMed

    Zhao, Jing; Liu, Erwei; Han, Lifeng; Wang, Linlin; Zhang, Yi; Wang, Tao; Fang, Shiming; Gao, Xiumei

    2016-06-01

    A sensitive, rapid and specific high-performance liquid chromatography tandem mass spectrometry method (HPLC-MS/MS) was developed to determine ecliptasaponin A in rat plasma and tissues after oral administration. Ginsenoside Rg1 was used as the internal standard (IS). The plasma and tissues samples were prepared by liquid-liquid extraction with ethyl acetate and separated on an Eclipse Plus C18 column (2.1 mm × 150 mm, 5 µm) at a flow rate of 0.4 mL/min using acetonitrile and water (containing 0.05% acetic acid) as the mobile phase. The tandem mass detection was carried out with eletrospray ionization in negative mode. Quantification was performed by using multiple reaction monitoring (MRM), which monitored the fragmentation of m/z 633.4→587.2 for ecliptasaponin A and m/z 859.4→637.4 for the IS. The calibration curves obtained were linear in different matrices, and the lower limit of quantification (LLOQ) achieved was 0.5 ng/mL both for rat plasma and tissues. The intra- and inter-day precisions were below 15%. This method was successfully applied to pharmacokinetic study of ecliptasaponin A in rat plasma and tissues after oral administration. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26378987

  19. Quantification of galactosylsphingosine in the twitcher mouse using electrospray ionization-tandem mass spectrometry.

    PubMed

    Whitfield, P D; Sharp, P C; Taylor, R; Meikle, P

    2001-12-01

    Globoid cell leukodystrophy (Krabbe disease) is an autosomal recessive inherited neurodegenerative disorder caused by the deficiency of the lysosomal enzyme beta-galactosylceramidase. The pathogenesis of the disorder has been proposed to arise from the accumulation of the cytotoxic metabolite galactosylsphingosine (psychosine). The twitcher mouse is a naturally occurring murine model of globoid cell leukodystrophy. We have developed a rapid, sensitive, and specific mass spectrometric method for determining the galactosylsphingosine concentration in the tissues of twitcher mice. Galactosylsphingosine is extracted from the tissues in methanol, isolated using strong cation-exchange and C18 solid-phase extraction chromatography, and then directly analyzed using electrospray ionization-tandem mass spectrometry. A lactosylsphingosine internal standard has been employed for quantification. The assay demonstrated significant accumulation of galactosylsphingosine in the brain, spinal cord, and kidney of twitcher mice. It is anticipated that this method may be of use in the monitoring of experimental therapies for globoid cell leukodystrophy. PMID:11734583

  20. 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. PMID:27452180

  1. Tandem mass spectrometric analysis of glyphosate, glufosinate, aminomethylphosphonic acid and methylphosphinicopropionic acid.

    PubMed

    Goodwin, Lee; Startin, James R; Goodall, David M; Keely, Brendan J

    2003-01-01

    A detailed MS(n) study of glyphosate, glufosinate and their main metabolites, aminomethylphosphonic acid and methylphosphinicopropionic acid, using an ion trap mass spectrometer, was performed. The analytes show good response in negative ion electrospray mass spectrometry (ES-MS) as [M-H](-) ions. Tandem-MS spectra reveal a wealth of structurally specific ions, allowing characterisation of the fragmentation pathways of the four analytes in their native form for the first time. The ions formed at each stage of fragmentation reveal ions common to each analyte, such as phosphinate, as well as analyte specific transitions. Simplex optimisation allows optimum trapping and fragmentation parameters to be determined leading to improved response for particular transitions and transition sequences, and revealing previously unseen ions. PMID:12717770

  2. 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. PMID:27060508

  3. Structural characterization of major soyasaponins in traditional cultivars of Fagioli di Sarconi beans investigated by high-resolution tandem mass spectrometry.

    PubMed

    Bianco, Giuliana; Buchicchio, Alessandro; Cataldi, Tommaso R I

    2015-08-01

    Major soyasaponins, i.e., soyasaponins I, V, βg, and αg from traditional Fagioli di Sarconi beans (Phaseolus vulgaris L., ecotype Tabacchino), were analyzed by reversed-phase liquid chromatography-mass spectrometry (MS) using high-resolution Fourier transform ion cyclotron resonance (FTICR) MS on electrospray ionization in positive-ion mode. Fagioli di Sarconi beans are protected by the European Union [Commission Regulation (EC) No 1263/96] with the mark PGI (for "Protected Geographical Indication"), and are cultivated in Basilicata (southern Italy). Protonated adducts of soyasaponins I, V, βg, and αg were observed at m/z 943.5262, 959.5213, 1069.5583, and 1085.5534, respectively. Gas-phase dissociation of soyasaponins by infrared multiphoton dissociation FTICR MS was performed using a CO2 laser source at a wavelength of 10.6 μm. Most of the fragment ions were identified unambiguously by using the high-resolution and accurate mass value provided by the FTICR mass spectrometer. All soyasaponins exhibit a sequential and neutral loss of sugar moieties at relatively short irradiation times (i.e., less than 50 ms). When the pulse length was increased, a more pronounced fragmentation occurred, with several signals in the lower part of the mass spectrum. In the case of soyasaponins βg and αg, the occurrence of the conjugated product ion at m/z 127.0389 ([C6H6O3 + H](+), 2,3-dihydro-2,5-dihydroxy-6-methyl-4H-pyran-4-one) was evidenced. Coupling reversed-phase liquid chromatography with high-performance FTICR MS in combination with infrared multiphoton dissociation tandem MS proved to be very promising for the structural characterization of soyasaponins, and is also suitable for the rapid and accurate structural investigation of other saponins. Graphical Abstract Representative Infrared Multiphoton Dissociation (IRMPD)-FTICR MS spectra of main group B saponins in Fagioli di Sarconi beans. PMID:26065561

  4. Functional group composition of ambient and source organic aerosols determined by tandem mass spectrometry

    NASA Astrophysics Data System (ADS)

    Dron, J.; El Haddad, I.; Temime-Roussel, B.; Jaffrezo, J.-L.; Wortham, H.; Marchand, N.

    2010-04-01

    The functional group composition of various organic aerosols (OA) is being investigated using a recently developed analytical approach based on atmospheric pressure chemical ionisation-tandem mass spectrometry (APCI-MS/MS). The determinations of the three functional groups' contents are performed quantitatively by neutral loss (carboxylic and carbonyl groups) and precursor ion (nitro groups) scanning modes of a tandem mass spectrometer. Major organic aerosol sources are studied: vehicular emission and wood combustion for primary aerosol sources; and a secondary organic aerosol (SOA) produced through photo-oxidation of o-xylene. The results reveal significant differences in the functional group contents of these source aerosols. The laboratory generated SOA is dominated by carbonyls while carboxylics are preponderate in the wood combustion particles. On the other hand, vehicular emissions are characterised by a strong nitro content. The total amount of the three functional groups accounted for 1.7% (vehicular) to 13.5% (o-xylene photo-oxidation) of the organic carbon. The diagnostic functional group ratios are then used to tentatively differentiate sources of particles collected in an urban background environment located in an Alpine valley (Chamonix, France) during a strong winter pollution event. The three functional groups under study account for a total functionalisation rate of 2.2 to 3.8% of the organic carbon in this ambient aerosol, which is also dominated by carboxylic moieties. In this particular case study of a deep alpine valley during winter, we show that the nitro- and carbonyl-to-carboxylic diagnostic ratios can be a useful tool to distinguish the sources. In these conditions, the total OA concentrations are highly dominated by wood combustion OA. This result is confirmed by an organic markers source apportionment approach which assesses a wood burning organic carbon contribution of about 60%. Finally, examples of functional group mass spectra of all

  5. The dissociation kinetics of NO on Rh(111) as studied by temperature programmed static secondary ion mass spectrometry and desorption

    NASA Astrophysics Data System (ADS)

    Borg, H. J.; Reijerse, J. F. C.-J. M.; van Santen, R. A.; Niemantsverdriet, J. W.

    1994-12-01

    Temperature programmed static secondary ion mass spectrometry (TPSSIMS) and temperature programmed desorption (TPD) have been used to study the kinetics of adsorption, dissociation, and desorption of NO on Rh(111). At 100 K, NO adsorption is molecular and proceeds via mobile precursor state kinetics with a high initial sticking probability. SSIMS indicates the presence of two distinct NO adsorption states, indicative of threefold adsorption at low coverage, and occupation of bridge sites at higher coverages. Three characteristic coverage regimes appear with respect to NO dissociation. At low coverages θNO<0.25 ML, NO dissociates completely at temperatures between 275 and 340 K. If we neglect lateral interactions and assume pure first order dissociation kinetics, we find effective values for the activation barrier and preexponential factor of 40±6 kJ/mol and 106±1 s-1 for the dissociation of 0.15-0.20 ML NO. However, if we assume that a NO molecule needs an ensemble of three to four vacant sites in order to dissociate, the preexponential factor and activation energy are ˜1011 s-1 and 65 kJ/mol, in better agreement with transition state theory expectations. The Nads and Oads dissociation products desorb as N2 and O2, respectively, with desorption parameters Edes=118±10 kJ/mol and νdes=1010.1±1.0 s-1 for N2 in the zero coverage limit. At higher coverages, the desorption kinetics of N2 is strongly influenced by the presence of coadsorbed oxygen. In the medium coverage range 0.25<θNO<0.50 ML, part of the NO desorbs molecularly, with an estimated desorption barrier of 113±10 kJ/mol and a preexponential of 1013.5±1.0 s-1. Dissociation of NO becomes progressively inhibited due to site blocking, the onset shifting from 275 K at 0.25 ML to 400 K, coinciding with the NO desorption temperature, at a coverage of 0.50 ML. The accumulation of nitrogen and oxygen atoms on the highly covered surface causes a destabilization of the nitrogen atoms, which results in an

  6. Analysis of Non-Enzymatically Glycated Peptides: Neutral-Loss Triggered MS3 Versus Multi-Stage Activation Tandem Mass Spectrometry

    SciTech Connect

    Zhang, Qibin; Petyuk, Vladislav A.; Schepmoes, Athena A.; Orton, Daniel J.; Monroe, Matthew E.; Yang, Feng; Smith, Richard D.; Metz, Thomas O.

    2008-10-15

    Non-enzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. While electron transfer dissociation (ETD) has been shown to outperform collision-induced dissociation (CID) in sequencing glycated peptides by tandem mass spectrometry, ETD instrumentation is not yet available in all laboratories. In this study, we evaluated different advanced CID techniques (i.e., neutral-loss triggered MS3 and multi-stage activation) during LC-MSn analyses of Amadori-modified peptides enriched from human serum glycated in vitro. During neutral-loss triggered MS3 experiments, MS3 scans triggered by neutral-losses of 3 H2O or 3 H2O + HCHO produced similar results in terms of glycated peptide identifications. However, neutral losses of 3 H2O resulted in significantly more glycated peptide identifications during multi-stage activation experiments. Overall, the multi-stage activation approach produced more glycated peptide identifications, while the neutral-loss triggered MS3 approach resulted in much higher specificity. Both techniques offer a viable alternative to ETD for identifying glycated peptides when that method is unavailable.

  7. Method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation in conjunction with mass spectrometric analysis

    DOEpatents

    Laskin, Julia [Richland, WA; Futrell, Jean H [Richland, WA

    2008-04-29

    The invention relates to a method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation (SID) in conjunction with mass spectrometric analysis. Results demonstrate formation of a wide distribution of structure-specific fragments having wide sequence coverage useful for sequencing and identifying the complex molecules.

  8. Direct analysis by electrospray ionization tandem mass spectrometry of mixtures of phosphatidyldiacylglycerols from Lactobacillus.

    PubMed

    Cabrera, G M; Murga, M L; de Valdez, G F; Seldes, A M

    2000-12-01

    Electrospray ionization followed by collision-induced dissociation in a quadrupole ion trap mass spectrometer of mixtures of deprotonated phosphatidyldiacylglycerols afforded a group of three diagnostic ions of convenient abundance for each phosphatidyldiacylglycerol (PG) present in the mixture. Thus, it was possible to determine unmistakably the identity and substitution positions (sn-1 or sn-2) for both acyl groups of each PG present in the mixture. The method also allows the study of isomeric mixtures of PG and mixtures containing minor amounts of some PG from crude extracts of Lactobacillus acidophillus. The present results improve those of previous studies using fast atom bombardment and electrospray ionization tanden mass spectrometry, in which it was reported that it was possible to differentiate the identity and position of the sn-2 acyl substituent only by the presence of one ion, with variable abundance. PMID:11180636

  9. 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.

  10. 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.

  11. Clustering and Filtering Tandem Mass Spectra Acquired in Data-Independent Mode

    NASA Astrophysics Data System (ADS)

    Pak, Huisong; Nikitin, Frederic; Gluck, Florent; Lisacek, Frederique; Scherl, Alexander; Muller, Markus

    2013-12-01

    Data-independent mass spectrometry activates all ion species isolated within a given mass-to-charge window ( m/z) regardless of their abundance. This acquisition strategy overcomes the traditional data-dependent ion selection boosting data reproducibility and sensitivity. However, several tandem mass (MS/MS) spectra of the same precursor ion are acquired during chromatographic elution resulting in large data redundancy. Also, the significant number of chimeric spectra and the absence of accurate precursor ion masses hamper peptide identification. Here, we describe an algorithm to preprocess data-independent MS/MS spectra by filtering out noise peaks and clustering the spectra according to both the chromatographic elution profiles and the spectral similarity. In addition, we developed an approach to estimate the m/z value of precursor ions from clustered MS/MS spectra in order to improve database search performance. Data acquired using a small 3 m/z units precursor mass window and multiple injections to cover a m/z range of 400-1400 was processed with our algorithm. It showed an improvement in the number of both peptide and protein identifications by 8 % while reducing the number of submitted spectra by 18 % and the number of peaks by 55 %. We conclude that our clustering method is a valid approach for data analysis of these data-independent fragmentation spectra. The software including the source code is available for the scientific community.

  12. MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra

    PubMed Central

    2014-01-01

    Today’s highly accurate spectra provided by modern tandem mass spectrometers offer considerable advantages for the analysis of proteomic samples of increased complexity. Among other factors, the quantity of reliably identified peptides is considerably influenced by the peptide identification algorithm. While most widely used search engines were developed when high-resolution mass spectrometry data were not readily available for fragment ion masses, we have designed a scoring algorithm particularly suitable for high mass accuracy. Our algorithm, MS Amanda, is generally applicable to HCD, ETD, and CID fragmentation type data. The algorithm confidently explains more spectra at the same false discovery rate than Mascot or SEQUEST on examined high mass accuracy data sets, with excellent overlap and identical peptide sequence identification for most spectra also explained by Mascot or SEQUEST. MS Amanda, available at http://ms.imp.ac.at/?goto=msamanda, is provided free of charge both as standalone version for integration into custom workflows and as a plugin for the Proteome Discoverer platform. PMID:24909410

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

    PubMed

    Horlacher, Oliver; Lisacek, Frederique; Müller, Markus

    2016-03-01

    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. PMID:26653734

  14. Accurate mass determination of short-lived isotopes by a tandem Penning-trap mass spectrometer

    SciTech Connect

    Stolzenberg, H.; Becker, S.; Bollen, G.; Kern, F.; Kluge, H.; Otto, T.; Savard, G.; Schweikhard, L. ); Audi, G. ); Moore, R.B. ); The ISOLDE Collaboration

    1990-12-17

    A mass spectrometer consisting of two Penning traps has been set up for short-lived isotopes at the on-line mass separator ISOLDE at CERN. The ion beam is collected and cooled in the first trap. After delivery to the second trap, high-accuracy direct mass measurements are made by determining the cyclotron frequency of the stored ions. Measurements have been performed for {sup 118}Cs--{sup 137}Cs. A resolving power of over 10{sup 6} and an accuracy of 1.4{times}10{sup {minus}7} have been achieved, corresponding to about 20 keV.

  15. Differentiation of Linear and Cyclic Polymer Architectures by MALDI Tandem Mass Spectrometry (MALDI-MS2)

    NASA Astrophysics Data System (ADS)

    Yol, Aleer M.; Dabney, David E.; Wang, Shih-Fan; Laurent, Boyd A.; Foster, Mark D.; Quirk, Roderic P.; Grayson, Scott M.; Wesdemiotis, Chrys

    2013-01-01

    [M + Ag]+ ions from cyclic and linear polystyrenes and polybutadienes, formed by matrix-assisted laser desorption ionization (MALDI), give rise to significantly different fragmentation patterns in tandem mass spectrometry (MS2) experiments. In both cases, fragmentation starts with homolytic cleavage at the weakest bond, usually a C-C bond, to generate two radicals. From linear structures, the separated radicals depolymerize extensively by monomer losses and backbiting rearrangements, leading to low-mass radical ions and much less abundant medium- and high-mass closed-shell fragments that contain one of the original end groups, along with internal fragments. With cyclic structures, depolymerization is less efficient, as it can readily be terminated by intramolecular H-atom transfer between the still interconnected radical sites (disproportionation). These differences in fragmentation reactivity result in substantially different fragment ion distributions in the MS2 spectra. Simple inspection of the relative intensities of low- versus high-mass fragments permits conclusive determination of the macromolecular architecture, while full spectral interpretation reveals the individual end groups of linear polymers or the identity of the linker used to form the cyclic polymer.

  16. 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. PMID:27054915

  17. Determination of ethylglucuronide in oral fluid by ultra-performance liquid chromatography- tandem mass spectrometry.

    PubMed

    Hegstad, S; Johnsen, L; Mørland, J; Christophersen, A S

    2009-05-01

    An ultra-performance liquid chromatography-tandem mass spectrometry method has been developed and validated for the determination of ethylglucuronide (EtG) in oral fluid. Sample clean-up was achieved by solid-phase extraction with a Hyper-SEP SAX column. Negative ionization was performed in the multiple reaction monitoring mode. Two transitions were monitored for the analyte and one for the internal standard EtG-d(5). The calibration range was 4.4-222 ng/mL. The recovery of the analyte ranged from 86 to 99%, and the between-assay precisions ranged from 5 to 9% RSD. The limit of quantification was found to be 4.4 ng/mL. The concentration of EtG in oral fluid collected 2-14 h after a moderate alcohol intake varied from 13.3 to 57.7 ng/mL. PMID:19470222

  18. Characterization of protein N-glycosylation by tandem mass spectrometry using complementary fragmentation techniques

    PubMed Central

    Ford, Kristina L.; Zeng, Wei; Heazlewood, Joshua L.; Bacic, Antony

    2015-01-01

    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. We have used three common fragmentation techniques, namely CID, HCD, 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. PMID:26379696

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

    NASA Astrophysics Data System (ADS)

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

    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 shortcoming 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 database searches. Our MS-GappedDictionary algorithm (based on Gapped Spectral Dictionaries) enables proteogenomics applications that are prohibitively time consuming with existing approaches. We further introduce gapped tags that have advantages over the conventional peptide sequence tags in filtration-based MS/MS database searches.

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

    PubMed

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

    2009-11-01

    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

  1. Determination of prostaglandin analogs in cosmetic products by high performance liquid chromatography with tandem mass spectrometry.

    PubMed

    Wittenberg, James B; Zhou, Wanlong; Wang, Perry G; Krynitsky, Alexander J

    2014-09-12

    A method was developed and validated for the determination of 16 prostaglandin analogs in cosmetic products. The QuEChERS (Quick, Easy, Cheap, Efficient, Rugged, Safe) liquid-liquid extraction method, typically used for pesticide residue analysis, was utilized as the sample preparation technique. The prostaglandin analogs were chromatographically separated and quantified using high performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS). Thirty-one cosmetic products were surveyed, and 13 products were determined to contain a prostaglandin analog with amounts ranging from 27.4 to 297μg/g. The calculated concentrations for the cosmetic products were in a similar range when compared to the concentrations of three different prostaglandin analog-containing prescription products. PMID:25085824

  2. 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

  3. A comparison of salivary testosterone measurement using immunoassays and tandem mass spectrometry.

    PubMed

    Welker, Keith M; Lassetter, Bethany; Brandes, Cassandra M; Prasad, Smrithi; Koop, Dennis R; Mehta, Pranjal H

    2016-09-01

    Enzyme immunoassays (EIAs) are widely used to measure salivary testosterone. However, little is known about how accurately different EIAs assess testosterone, partially because estimates across various EIAs differ considerably. We compared testosterone concentrations across EIAs of three commonly used manufacturers (DRG International, Salimetrics, and IBL International) to liquid chromatography tandem mass spectrometry (LC-MS/MS). Relative to EIAs from Salimetrics and IBL International, EIAs supplied by DRG International provided the closest approximation to LC-MS/MS testosterone concentrations, followed closely by EIAs from Salimetrics, and then IBL. Additionally, EIAs tended to inflate estimates of lower testosterone concentrations in women. Examining our results and comparing them to existing data revealed that testosterone EIAs had decreased linear correspondence with LC-MS/MS in comparison to cortisol EIAs. Overall, this paper provides researchers with information to better measure testosterone in their research and more accurately compare testosterone measurements across different methods. PMID:27295182

  4. Characterization of protein N-glycosylation by tandem mass spectrometry using complementary fragmentation techniques

    DOE PAGESBeta

    Ford, Kristina L.; Zeng, Wei; Heazlewood, Joshua L.; Bacic, Antony

    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

  5. Characterization of protein N-glycosylation by tandem mass spectrometry using complementary fragmentation techniques

    SciTech Connect

    Ford, Kristina L.; Zeng, Wei; Heazlewood, Joshua L.; Bacic, Antony

    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, 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.

  6. Tandem mass spectrometry of herbicide residues in lipid-rich tissue.

    PubMed

    Headley, J V; Peru, K M; Arts, M T

    1995-12-01

    A tandem mass spectrometry procedure, originally developed for bacterial biofilms was adapted for the identification of herbicide residues in lipid-rich tissue of amphipods collected from microcosms in a prairie wetland. For this application, the amounts of tissue employed (less than 1 mg wet weight), and detection of target analytes at picogram levels, were similar to the values reported for bacterial biofilms. Described is an application of the technique for the identification of residues of the herbicide S-2,3,3-trichloroallyl diisopropyl thiocarbamate (triallate; trade name Avadex-BW). For amphipods collected from microcosms exposed to the herbicide 2-[4-(2,4-dichlorophenoxy)phenoxy]propionic acid methyl ester (diclofop-methyl, trade name Hoe Grass), there were detectable levels of only the hydrolysis product, diclofop acid, in the lipid-rich tissue. Other transformation products reported for bacterial biofilms were not observed in the amphipods. PMID:8633778

  7. An accurate and efficient algorithm for Peptide and ptm identification by tandem mass spectrometry.

    PubMed

    Ning, Kang; Ng, Hoong Kee; Leong, Hon Wai

    2007-01-01

    Peptide identification by tandem mass spectrometry (MS/MS) is one of the most important problems in proteomics. Recent advances in high throughput MS/MS experiments result in huge amount of spectra. Unfortunately, identification of these spectra is relatively slow, and the accuracies of current algorithms are not high with the presence of noises and post-translational modifications (PTMs). In this paper, we strive to achieve high accuracy and efficiency for peptide identification problem, with special concern on identification of peptides with PTMs. This paper expands our previous work on PepSOM with the introduction of two accurate modified scoring functions: Slambda for peptide identification and Slambda* for identification of peptides with PTMs. Experiments showed that our algorithm is both fast and accurate for peptide identification. Experiments on spectra with simulated and real PTMs confirmed that our algorithm is accurate for identifying PTMs. PMID:18546510

  8. Rapid and multi-level characterization of trastuzumab using sheathless capillary electrophoresis-tandem mass spectrometry

    PubMed Central

    Gahoual, Rabah; Burr, Alicia; Busnel, Jean-Marc; Kuhn, Lauriane; Hammann, Phillipe; Beck, Alain; François, Yannis-Nicolas; Leize-Wagner, Emmanuelle

    2013-01-01

    Monoclonal antibodies (mAbs) are highly complex proteins that display a wide range of microheterogeneity that requires multiple analytical methods for full structure assessment and quality control. As a consequence, the characterization of mAbs on different levels is particularly product - and time - consuming. This work presents the characterization of trastuzumab sequence using sheathless capillary electrophoresis (referred as CESI) – tandem mass spectrometry (CESI-MS/MS). Using this bottom-up proteomic-like approach, CESI-MS/MS provided 100% sequence coverage for both heavy and light chain via peptide fragment fingerprinting (PFF) identification. The result was accomplished in a single shot, corresponding to the analysis of 100 fmoles of digest. The same analysis also enabled precise characterization of the post-translational hot spots of trastuzumab, used as a representative widely marketed therapeutic mAb, including the structural confirmation of the five major N-glycoforms. PMID:23563524

  9. Stimulation of Slack K(+) Channels Alters Mass at the Plasma Membrane by Triggering Dissociation of a Phosphatase-Regulatory Complex.

    PubMed

    Fleming, Matthew R; Brown, Maile R; Kronengold, Jack; Zhang, Yalan; Jenkins, David P; Barcia, Gulia; Nabbout, Rima; Bausch, Anne E; Ruth, Peter; Lukowski, Robert; Navaratnam, Dhasakumar S; Kaczmarek, Leonard K

    2016-08-30

    Human mutations in the cytoplasmic C-terminal domain of Slack sodium-activated potassium (KNa) channels result in childhood epilepsy with severe intellectual disability. Slack currents can be increased by pharmacological activators or by phosphorylation of a Slack C-terminal residue by protein kinase C. Using an optical biosensor assay, we find that Slack channel stimulation in neurons or transfected cells produces loss of mass near the plasma membrane. Slack mutants associated with intellectual disability fail to trigger any change in mass. The loss of mass results from the dissociation of the protein phosphatase 1 (PP1) targeting protein, Phactr-1, from the channel. Phactr1 dissociation is specific to wild-type Slack channels and is not observed when related potassium channels are stimulated. Our findings suggest that Slack channels are coupled to cytoplasmic signaling pathways and that dysregulation of this coupling may trigger the aberrant intellectual development associated with specific childhood epilepsies. PMID:27545877

  10. 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