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Perez JJ, Brady JJ, Broderick A, Horan A, Pedersen K, Wilkins BP. Rapid Quantification of Ammonium Nitrate and Urea Nitrate Using Liquid Chromatography-High-Resolution Orbitrap Mass Spectrometry. Anal Chem 2024; 96:1419-1426. [PMID: 38240047 DOI: 10.1021/acs.analchem.3c03245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Resolution and sensitivity improvements in mass spectrometry technology have enabled renewed attempts at solving challenging analytical issues. One such issue involves the analysis of energetic ionic species. Energetic ionic species make up an important class of chemical materials, and a more robust and versatile analytical platform would provide tremendous value to the analytical community. Initial attempts at quantification of energetic ionic species employed high-resolution time-of-flight measurements with crown ether (CE) complexation and flow injection analysis (FIA). In this investigation, ammonium nitrate (AN) and urea nitrate (UN) in the presence of a crown ether complexation agent were explored by using high-resolution orbitrap mass spectrometry. Product ion scans of these signature complexes reveal positive identification of these energetic ionic species. Finally, quantification was demonstrated for both flow injection and liquid chromatography-mass spectrometry (LC-MS) analysis, suggesting the capability for routine and rapid analysis of these energetic ionic materials.
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Affiliation(s)
- Johnny J Perez
- U.S. Department of Homeland Security, Science & Technology Directorate, Transportation Security Laboratory, William J. Hughes Technical Center, Bldg. 315, Atlantic City, New Jersey 08405, United States
| | - John J Brady
- U.S. Department of Homeland Security, Science & Technology Directorate, Transportation Security Laboratory, William J. Hughes Technical Center, Bldg. 315, Atlantic City, New Jersey 08405, United States
| | - Alicia Broderick
- U.S. Department of Homeland Security, Science & Technology Directorate, Transportation Security Laboratory, William J. Hughes Technical Center, Bldg. 315, Atlantic City, New Jersey 08405, United States
| | - Andrew Horan
- Signature Science, LLC, 2819 Fire Rd. Suite A, Egg Harbor Township, New Jersey 08234, United States
| | - Kevin Pedersen
- Signature Science, LLC, 2819 Fire Rd. Suite A, Egg Harbor Township, New Jersey 08234, United States
| | - Benjamin P Wilkins
- U.S. Department of Homeland Security, Science & Technology Directorate, Transportation Security Laboratory, William J. Hughes Technical Center, Bldg. 315, Atlantic City, New Jersey 08405, United States
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Zhang H, Jia H, Gao Z, Xiang Y, Jiang T, Xu W. Parallel Pseudo-MRM on the “brick” miniature mass spectrometer for high throughput multi-target screening. Talanta 2023; 252:123866. [DOI: 10.1016/j.talanta.2022.123866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022]
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Xu F, Wang W, Ding L, Fang X, Ding CF. Synchronized Reverse Scan Collision Induced Dissociation in Digital Ion Trap Mass Spectrometer for Improving Fragment Ion Detection. Anal Chem 2022; 94:17827-17834. [PMID: 36512629 DOI: 10.1021/acs.analchem.2c03524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Development of fragment ion detection methods is of great importance for mass spectrometer advancement or substance identification. To date, collision induced dissociation (CID) remains the most commonly used ion activation method in MS/MS experiments, and the effectiveness of CID in an ion trap mass spectrometer is limited by low mass cutoff and weak fragmentation yields. Theoretically, controlling the q value is the key to maintain the fragment efficiency and trapping efficiency of MS/MS, thus improving the detection of fragment ion, while currently reported techniques usually require complex circuitry and often produce different CID patterns. In this paper, with the developed synchronized reversed scanning-collision induced dissociation (SRS-CID) technique, we demonstrate its effective improvement in fragment ion detection. The SRS-CID is implemented on a digital ion trap mass spectrometer (DITMS) by reverse scanning the q values during CID process, or specifically, the frequency is increased during the CID process. With the SRS-CID technique, the fragmentation efficiency of precursor ions can be slightly improved. For reserpine analyte, the trapping efficiency for low-mass fragment ions is improved at least 3 times, and for YGGFL, the trapping efficiency for low-mass fragment ions is improved at least 9 times. These experimental results can also be validated by simulations, and the kinetic energy variation plot suggests consecutive fragmentation occurs. In any case, the SRS-CID provides a solution to the low efficiency of fragment ion detection during tandem MS analysis, which will certainly be useful in the future.
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Affiliation(s)
- Fuxing Xu
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Weimin Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Li Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
| | - Xiang Fang
- National Institute of Metrology, Chemical Metrology & Analytical Science Division, Beijing 100029, China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211, China
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Bai Z, Yu R, Zheng T, Sun D, Zhou Y, Tang J, Zhu H, Li G, Niu L, Cui L, Du R, Zhang J, Zhang Y. A Novel Strategy for Unveiling Spatial Distribution Pattern of Gallotannins in Paeonia rockii and Paeonia ostii Based on LC–QTRAP–MS. Metabolites 2022; 12:metabo12040326. [PMID: 35448513 PMCID: PMC9030617 DOI: 10.3390/metabo12040326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Abstract
Gallotannins (GTs) are a series of hydrolyzable tannins with multiple health-promoting effects. In this study, an integrated liquid chromatography tandem mass spectrometry (LC–MS/MS) strategy was developed for unveiling the spatial distribution pattern of GTs in the emerging oilseed crops Paeonia rockii and P. ostii. According to the fragmentation behavior of the representative GT (1,2,3,4,6-penta-O-galloyl-β-D-glucose, PGG), the diagnostic neutral loss (NL) of 170 Da was chosen for the non-targeted screening of GT precursors. Simultaneously, the tandem mass spectrometry spectrum (MS/MS) information was acquired through an enhanced product ion (EPI) scan. Nine major GTs were identified in tree peony. To quantify the targeted GTs in different tissues of tree peony, we established a multiple reaction monitoring (MRM)–enhanced product ion (EPI)-based pseudo-targeted approach under the information-dependent acquisition (IDA) mode. The quantitative results show that the GT compounds were ubiquitous in tree peony plants with diverse structures. The typical GT PGG was mainly distributed in roots, leaves, and petals. This strategy can also be utilized for metabolite characterization and quantification in other substrates.
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Affiliation(s)
- Zhangzhen Bai
- National Engineering Technology Research Center for Oil Peony, College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China; (T.Z.); (D.S.); (Y.Z.); (J.T.); (L.N.)
- Correspondence: (Z.B.); (J.Z.); (Y.Z.); Tel.: +86-029-8708-2632 (J.Z.); +86-029-8708-2878 (Y.Z.)
| | - Rui Yu
- College of Horticulture, China Agricultural University, Beijing 100193, China;
| | - Tiantian Zheng
- National Engineering Technology Research Center for Oil Peony, College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China; (T.Z.); (D.S.); (Y.Z.); (J.T.); (L.N.)
| | - Daoyang Sun
- National Engineering Technology Research Center for Oil Peony, College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China; (T.Z.); (D.S.); (Y.Z.); (J.T.); (L.N.)
| | - Yang Zhou
- National Engineering Technology Research Center for Oil Peony, College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China; (T.Z.); (D.S.); (Y.Z.); (J.T.); (L.N.)
| | - Junman Tang
- National Engineering Technology Research Center for Oil Peony, College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China; (T.Z.); (D.S.); (Y.Z.); (J.T.); (L.N.)
| | - Huili Zhu
- College of Horticulture, Northwest A&F University, Yangling 712100, China;
| | | | - Lixin Niu
- National Engineering Technology Research Center for Oil Peony, College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China; (T.Z.); (D.S.); (Y.Z.); (J.T.); (L.N.)
| | - Lu Cui
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China;
| | - Rui Du
- College of Innovation and experiment, Northwest A&F University, Yangling 712100, China;
| | - Jing Zhang
- College of Horticulture, Northwest A&F University, Yangling 712100, China;
- Correspondence: (Z.B.); (J.Z.); (Y.Z.); Tel.: +86-029-8708-2632 (J.Z.); +86-029-8708-2878 (Y.Z.)
| | - Yanlong Zhang
- National Engineering Technology Research Center for Oil Peony, College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China; (T.Z.); (D.S.); (Y.Z.); (J.T.); (L.N.)
- Correspondence: (Z.B.); (J.Z.); (Y.Z.); Tel.: +86-029-8708-2632 (J.Z.); +86-029-8708-2878 (Y.Z.)
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Li C, Chu S, Tan S, Yin X, Jiang Y, Dai X, Gong X, Fang X, Tian D. Towards Higher Sensitivity of Mass Spectrometry: A Perspective From the Mass Analyzers. Front Chem 2021; 9:813359. [PMID: 34993180 PMCID: PMC8724130 DOI: 10.3389/fchem.2021.813359] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/06/2021] [Indexed: 01/12/2023] Open
Abstract
Mass spectrometry (MS) is one of the most widely used analytical techniques in many fields. Recent developments in chemical and biological researches have drawn much attention to the measurement of substances with low abundances in samples. Continuous efforts have been made consequently to further improve the sensitivity of MS. Modifications on the mass analyzers of mass spectrometers offer a direct, universal and practical way to obtain higher sensitivity. This review provides a comprehensive overview of the latest developments in mass analyzers for the improvement of mass spectrometers' sensitivity, including quadrupole, ion trap, time-of-flight (TOF) and Fourier transform ion cyclotron (FT-ICR), as well as different combinations of these mass analyzers. The advantages and limitations of different mass analyzers and their combinations are compared and discussed. This review provides guidance to the selection of suitable mass spectrometers in chemical and biological analytical applications. It is also beneficial to the development of novel mass spectrometers.
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Affiliation(s)
- Chang Li
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, China
| | - Shiying Chu
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Siyuan Tan
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xinchi Yin
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - You Jiang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xinhua Dai
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xiaoyun Gong
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Xiang Fang
- Technology Innovation Center of Mass Spectrometry for State Market Regulation, Center for Advanced Measurement Science, National Institute of Metrology, Beijing, People’s Republic ofChina
| | - Di Tian
- College of Instrumentation & Electrical Engineering, Jilin University, Changchun, China
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6
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Kang M, Zhang W, Dong L, Ren X, Zhu Y, Wang Z, Liang L, Xue J, Zhang Y, Zhang W, Ouyang Z. On-site testing of multiple drugs of abuse in urine by a miniature dual-LIT mass spectrometer. Anal Chim Acta 2020; 1101:74-80. [PMID: 32029121 DOI: 10.1016/j.aca.2019.12.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 11/27/2022]
Abstract
There is an increasing need for rapid and on-site detection of emerging drugs of abuse. In this work, we developed a method using a miniature dual-LIT (linear ion trap) mass spectrometer recently developed with comprehensive tandem mass spectrometry analysis capability, for qualitative and quantitative analysis of multiple drugs of abuse. Paper-capillary spray cartridges were used with related workflow established to simplify overall analysis procedure. Quantitation of ketamine and methamphetamine was achieved by beam-type collision-induced dissociation on the miniature dual-LIT mass spectrometer and a linear concentration range of 100-5000 ng/mL was obtained. The system has been applied in analysis of real urine samples from individuals addicted to morphine and methamphetamine use. The changes of the ratio of cocaine to its metabolite benzoylecgonine were also explored to estimate the time of cocaine intaking.
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Affiliation(s)
- Manqing Kang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, 100084, Beijing, China
| | - Wanru Zhang
- PURSPEC Technologies, Inc, 33 Shuangqing Road, 100084, Beijing, China
| | - Linpei Dong
- Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, China
| | - Xinxin Ren
- Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, China
| | - Yin Zhu
- Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang Province, 314006, China
| | - Zhenhua Wang
- Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang Province, 314006, China
| | - Lijun Liang
- Public Security Bureau of Jiaxing City, Zhejiang Province, 314000, China
| | - Jinfeng Xue
- Public Security Bureau of Jiaxing City, Zhejiang Province, 314000, China
| | - Yunfeng Zhang
- Institute of Forensic Science, Ministry of Public Security, 100038, Beijing, China.
| | - Wenpeng Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, 100084, Beijing, China; Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA.
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, 100084, Beijing, China; Department of Chemistry, Purdue University, West Lafayette, IN, 47906, USA.
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7
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Xu Z, Jiang T, Xu Q, Zhai Y, Li D, Xu W. Pseudo-Multiple Reaction Monitoring (Pseudo-MRM) Mode on the “Brick” Mass Spectrometer, Using the Grid-SWIFT Waveform. Anal Chem 2019; 91:13838-13846. [DOI: 10.1021/acs.analchem.9b03315] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Zuqiang Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Ting Jiang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Qian Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yanbing Zhai
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Dayu Li
- School of Computer Science and Engineering, Northeastern University, Shenyang, 110819, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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Flowers SA, Lane CS, Karlsson NG. Deciphering Isomers with a Multiple Reaction Monitoring Method for the Complete Detectable O-Glycan Repertoire of the Candidate Therapeutic, Lubricin. Anal Chem 2019; 91:9819-9827. [PMID: 31246420 DOI: 10.1021/acs.analchem.9b01485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Glycosylation is a fundamental post-translational modification, occurring on half of all proteins. Despite its significance, our understanding is limited, in part due to the inherent difficulty in studying these branched, multi-isomer structures. Accessible, detailed, and quantifiable methods for studying glycans, particularly O-glycans, are needed. Here we take a multiple reaction monitoring (MRM) approach to differentiate and relatively quantify all detectable glycans, including isomers, on the heavily O-glycosylated protein lubricin. Lubricin (proteoglycan 4) is essential for lubrication of the joint and eye. Given the therapeutic potential of lubricin, it is essential to understand its O-glycan repertoire in biological and recombinantly produced samples. O-Glycans were released by reductive β-elimination and defined, showing a range of 26 neutral, sulfated, sialylated, and both sulfated and sialylated core 1 (Galβ1-3GalNAcα1-) and core 2 (Galβ1-3(GlcNAcβ1-6)GalNAcα1-) structures. Isomer-specific MRM transitions allowed effective differentiation of neutral glycan isomers as well as sulfated isomeric structures, where the sulfate was retained on the fragment ions. This strategy was not as effective with labile sialylated structures; instead, it was observed that the optimal collision energy for the m/z 290.1 sialic acid B-fragment differed consistently between sialic acid isomers, allowing differentiation between isomers when fragmentation spectra were insufficient. This approach was also effective for purchased Neu5Acα2-3Galβ1-4Glc and Neu5Acα2-6Galβ1-4Glc and for Neu5Acα2-3Galβ1-4GlcNAc and Neu5Acα2-6Galβ1-4GlcNAc linkage isomers with the Neu5Acα2-6 consistently requiring more energy for optimal generation of the m/z 290.1 fragment. Overall, this method provides an effective and easily accessible approach for the quantification and annotation of complex released O-glycan samples.
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Affiliation(s)
- Sarah A Flowers
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Medicinaregatan 9A , 40530 Gothenburg , Sweden.,Department of Neuroscience , Georgetown University , 3970 Reservoir Road NW, New Research Building EP20 , Washington, D.C. , United States
| | - Catherine S Lane
- SCIEX , Phoenix House, Lakeside Drive, Centre Park , Warrington WA1 1RX , United Kingdom
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy , University of Gothenburg , Medicinaregatan 9A , 40530 Gothenburg , Sweden
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Emerging Technologies in Mass Spectrometry-Based DNA Adductomics. High Throughput 2019; 8:ht8020013. [PMID: 31091740 PMCID: PMC6630665 DOI: 10.3390/ht8020013] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/19/2019] [Accepted: 05/09/2019] [Indexed: 12/11/2022] Open
Abstract
The measurement of DNA adducts, the covalent modifications of DNA upon the exposure to the environmental and dietary genotoxicants and endogenously produced electrophiles, provides molecular evidence for DNA damage. With the recent improvements in the sensitivity and scanning speed of mass spectrometry (MS) instrumentation, particularly high-resolution MS, it is now feasible to screen for the totality of DNA damage in the human genome through DNA adductomics approaches. Several MS platforms have been used in DNA adductomic analysis, each of which has its strengths and limitations. The loss of 2′-deoxyribose from the modified nucleoside upon collision-induced dissociation is the main transition feature utilized in the screening of DNA adducts. Several advanced data-dependent and data-independent scanning techniques originated from proteomics and metabolomics have been tailored for DNA adductomics. The field of DNA adductomics is an emerging technology in human exposure assessment. As the analytical technology matures and bioinformatics tools become available for analysis of the MS data, DNA adductomics can advance our understanding about the role of chemical exposures in DNA damage and disease risk.
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Macaluso V, Scuderi D, Crestoni ME, Fornarini S, Corinti D, Dalloz E, Martinez-Nunez E, Hase WL, Spezia R. l-Cysteine Modified by S-Sulfation: Consequence on Fragmentation Processes Elucidated by Tandem Mass Spectrometry and Chemical Dynamics Simulations. J Phys Chem A 2019; 123:3685-3696. [DOI: 10.1021/acs.jpca.9b01779] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Veronica Macaluso
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Évry, France
| | - Debora Scuderi
- LCP, Laboratoire de Chimie Physique, Université Paris-Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Simonetta Fornarini
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Davide Corinti
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Enzo Dalloz
- LCP, Laboratoire de Chimie Physique, Université Paris-Sud, Bat. 349, CNRS UMR8000, 15 rue Georges Clemenceau, 91405 Orsay Cedex, France
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza, P.le A. Moro 5, 00185 Roma, Italy
| | - Emilio Martinez-Nunez
- Departamento de Química Física, Facultade de Química, Campus Vida, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - William L. Hase
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Riccardo Spezia
- LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025 Évry, France
- CNRS, Laboratoire de Chimie Théorique, LCT, Sorbonne Université, 4, Place Jussieu, 75252 Paris Cedex 05, France
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11
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Pandeswari PB, Sabareesh V. Middle-down approach: a choice to sequence and characterize proteins/proteomes by mass spectrometry. RSC Adv 2018; 9:313-344. [PMID: 35521579 PMCID: PMC9059502 DOI: 10.1039/c8ra07200k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 12/11/2018] [Indexed: 12/27/2022] Open
Abstract
Owing to rapid growth in the elucidation of genome sequences of various organisms, deducing proteome sequences has become imperative, in order to have an improved understanding of biological processes. Since the traditional Edman method was unsuitable for high-throughput sequencing and also for N-terminus modified proteins, mass spectrometry (MS) based methods, mainly based on soft ionization modes: electrospray ionization and matrix-assisted laser desorption/ionization, began to gain significance. MS based methods were adaptable for high-throughput studies and applicable for sequencing N-terminus blocked proteins/peptides too. Consequently, over the last decade a new discipline called 'proteomics' has emerged, which encompasses the attributes necessary for high-throughput identification of proteins. 'Proteomics' may also be regarded as an offshoot of the classic field, 'biochemistry'. Many protein sequencing and proteomic investigations were successfully accomplished through MS dependent sequence elucidation of 'short proteolytic peptides (typically: 7-20 amino acid residues), which is called the 'shotgun' or 'bottom-up (BU)' approach. While the BU approach continues as a workhorse for proteomics/protein sequencing, attempts to sequence intact proteins without proteolysis, called the 'top-down (TD)' approach started, due to ambiguities in the BU approach, e.g., protein inference problem, identification of proteoforms and the discovery of posttranslational modifications (PTMs). The high-throughput TD approach (TD proteomics) is yet in its infancy. Nevertheless, TD characterization of purified intact proteins has been useful for detecting PTMs. With the hope to overcome the pitfalls of BU and TD strategies, another concept called the 'middle-down (MD)' approach was put forward. Similar to BU, the MD approach also involves proteolysis, but in a restricted manner, to produce 'longer' proteolytic peptides than the ones usually obtained in BU studies, thereby providing better sequence coverage. In this regard, special proteases (OmpT, Sap9, IdeS) have been used, which can cleave proteins to produce longer proteolytic peptides. By reviewing ample evidences currently existing in the literature that is predominantly on PTM characterization of histones and antibodies, herein we highlight salient features of the MD approach. Consequently, we are inclined to claim that the MD concept might have widespread applications in future for various research areas, such as clinical, biopharmaceuticals (including PTM analysis) and even for general/routine characterization of proteins including therapeutic proteins, but not just limited to analysis of histones or antibodies.
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Affiliation(s)
- P Boomathi Pandeswari
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
| | - Varatharajan Sabareesh
- Advanced Centre for Bio Separation Technology (CBST), Vellore Institute of Technology (VIT) Vellore Tamil Nadu 632014 India
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12
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13
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Rzagalinski I, Hainz N, Meier C, Tschernig T, Volmer DA. MALDI Mass Spectral Imaging of Bile Acids Observed as Deprotonated Molecules and Proton-Bound Dimers from Mouse Liver Sections. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:711-722. [PMID: 29417494 PMCID: PMC5889423 DOI: 10.1007/s13361-017-1886-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 12/24/2017] [Accepted: 12/24/2017] [Indexed: 05/07/2023]
Abstract
Bile acids (BAs) play two vital roles in living organisms, as they are involved in (1) the secretion of cholesterol from liver, and (2) the lipid digestion/absorption in the intestine. Abnormal bile acid synthesis or secretion can lead to severe liver disorders. Even though there is extensive literature on the mass spectrometric determination of BAs in biofluids and tissue homogenates, there are no reports on the spatial distribution in the biliary network of the liver. Here, we demonstrate the application of high mass resolution/mass accuracy matrix-assisted laser desorption/ionization (MALDI)-Fourier-transform ion cyclotron resonance (FTICR) to MS imaging (MSI) of BAs at high spatial resolutions (pixel size, 25 μm). The results show chemical heterogeneity of the mouse liver sections with a number of branching biliary and blood ducts. In addition to ion signals from deprotonation of the BA molecules, MALDI-MSI generated several further intense signals at larger m/z for the BAs. These signals were spatially co-localized with the deprotonated molecules and easily misinterpreted as additional products of BA biotransformations. In-depth analysis of accurate mass shifts and additional electrospray ionization and MALDI-FTICR experiments, however, confirmed them as proton-bound dimers. Interestingly, dimers of bile acids, but also unusual mixed dimers of different taurine-conjugated bile acids and free taurine, were identified. Since formation of these complexes will negatively influence signal intensities of the desired [M - H]- ions and significantly complicate mass spectral interpretations, two simple broadband techniques were proposed for non-selective dissociation of dimers that lead to increased signals for the deprotonated BAs. Graphical Abstract ᅟ.
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Affiliation(s)
- Ignacy Rzagalinski
- Institute of Bioanalytical Chemistry, Saarland University, 66123, Saarbrücken, Germany
| | - Nadine Hainz
- Institute of Anatomy and Cell Biology, Saarland University, 66421, Homburg, Germany
| | - Carola Meier
- Institute of Anatomy and Cell Biology, Saarland University, 66421, Homburg, Germany
| | - Thomas Tschernig
- Institute of Anatomy and Cell Biology, Saarland University, 66421, Homburg, Germany
| | - Dietrich A Volmer
- Institute of Bioanalytical Chemistry, Saarland University, 66123, Saarbrücken, Germany.
- Department of Chemistry, Humboldt University of Berlin, 12489, Berlin, Germany.
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14
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Use of phenyl/tetrazolyl-functionalized magnetic microspheres and stable isotope labeled internal standards for significant reduction of matrix effect in determination of nine fluoroquinolones by liquid chromatography-quadrupole linear ion trap mass spectrometry. Anal Bioanal Chem 2017; 410:1709-1724. [PMID: 29285646 DOI: 10.1007/s00216-017-0821-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/28/2017] [Accepted: 12/08/2017] [Indexed: 10/18/2022]
Abstract
In this study, the strategy of unique adsorbent combined with isotope labeled internal standards was used to significantly reduce the matrix effect for the enrichment and analysis of nine fluoroquinolones in a complex sample by liquid chromatography coupled to quadrupole linear ion trap mass spectrometry (LC-QqQLIT-MS/MS). The adsorbent was prepared conveniently by functionalizing Fe3O4@SiO2 microspheres with phenyl and tetrazolyl groups, which could adsorb fluoroquinolones selectively via hydrophobic, electrostatic, and π-π interactions. The established magnetic solid-phase extraction (MSPE) method as well as using stable isotope labeled internal standards in the next MS/MS detection was able to reduce the matrix effect significantly. In the process of LC-QqQLIT-MS/MS analysis, the precursor and product ions of the analytes were monitored quantitatively and qualitatively on a QTrap system equipped simultaneously with the multiple reaction monitoring (MRM) and enhanced product ion (EPI) scan. Subsequently, the enrichment method combined with LC-QqQLIT-MS/MS demonstrated good analytical features in terms of linearity (7.5-100.0 ng mL-1, r > 0.9960), satisfactory recoveries (88.6%-118.3%) with RSDs < 12.0%, LODs = 0.5 μg kg-1 and LOQs = 1.5 μg kg-1 for all tested analytes. Finally, the developed MSPE-LC-QqQLIT-MS/MS method had been successfully applied to real pork samples for food-safety risk monitoring in Ningxia Province, China. Graphical abstract Mechanism of reducing matrix effect through the as-prepared adsorbent.
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15
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Patil AA, Chou SW, Chang PY, Lee CW, Cheng CY, Chu ML, Peng WP. High Mass Ion Detection with Charge Detector Coupled to Rectilinear Ion Trap Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1066-1078. [PMID: 27966174 DOI: 10.1007/s13361-016-1548-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/25/2016] [Accepted: 10/28/2016] [Indexed: 06/06/2023]
Abstract
Conventional linear ion trap mass analyzers (LIT-MS) provide high ion capacity and show their MS n ability; however, the detection of high mass ions is still challenging because LIT-MS with secondary electron detectors (SED) cannot detect high mass ions. To detect high mass ions, we coupled a charge detector (CD) to a rectilinear ion trap mass spectrometer (RIT-MS). Immunoglobulin G ions (m/z ~150,000) are measured successfully with controlled ion kinetic energy. In addition, when mass-to-charge (m/z) ratios of singly charged ions exceed 10 kTh, the detection efficiency of CD is found to be greater than that of SED. The CD can be coupled to LIT-MS to extend the detection mass range and provide the potential to perform MS n of high mass ions inside the ion trap. Graphical Abstract ᅟ.
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Affiliation(s)
- Avinash A Patil
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
| | - Szu-Wei Chou
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
- AcroMass technologies Inc., Hukou, Hsinchu, Taiwan, 30352, Republic of China
| | - Pei-Yu Chang
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
| | - Chen-Wei Lee
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China
| | - Chun-Yen Cheng
- AcroMass technologies Inc., Hukou, Hsinchu, Taiwan, 30352, Republic of China
| | - Ming-Lee Chu
- Institute of Physics, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Wen-Ping Peng
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan, 97401, Republic of China.
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16
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Faktor J, Sucha R, Paralova V, Liu Y, Bouchal P. Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues. Proteomics 2017; 17. [DOI: 10.1002/pmic.201600323] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/30/2016] [Accepted: 12/09/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Jakub Faktor
- Regional Centre for Applied Molecular Oncology; Masaryk Memorial Cancer Institute; Brno Czech Republic
| | - Rita Sucha
- Laboratory of Applied Proteome Analyses and Research Center PIGMOD; Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic; Libechov Czech Republic
| | - Vendula Paralova
- Department of Biochemistry, Faculty of Science; Masaryk University; Brno Czech Republic
| | - Yansheng Liu
- Department of Biology, Institute of Molecular Systems Biology; ETH Zurich; Zurich Switzerland
| | - Pavel Bouchal
- Regional Centre for Applied Molecular Oncology; Masaryk Memorial Cancer Institute; Brno Czech Republic
- Department of Biochemistry, Faculty of Science; Masaryk University; Brno Czech Republic
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17
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Huo X, Tang F, Zhang X, Chen J, Zhang Y, Guo C, Wang X. Novel control modes to improve the performance of rectilinear ion trap mass spectrometer with dual pressure chambers. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:105102. [PMID: 27802738 DOI: 10.1063/1.4963711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The rectilinear ion trap (RIT) has gradually become one of the preferred mass analyzers for portable mass spectrometers because of its simple configuration. In order to enhance the performance, including sensitivity, quantitation capability, throughput, and resolution, a novel RIT mass spectrometer with dual pressure chambers was designed and characterized. The studied system constituted a quadrupole linear ion trap (QLIT) in the first chamber and a RIT in the second chamber. Two control modes are hereby proposed: Storage Quadrupole Linear Ion Trap-Rectilinear Ion Trap (SQLIT-RIT) mode, in which the QLIT was used at high pressure for ion storage and isolation, and the RIT was used for analysis; and Analysis Quadrupole Linear Ion Trap-Rectilinear Ion Trap (AQLIT-RIT) mode, in which the QLIT was used for ion storage and cooling. Subsequently, synchronous scanning and analysis were carried out by QLIT and RIT. In SQLIT-RIT mode, signal intensity was improved by a factor of 30; the limit of quantitation was reduced more than tenfold to 50 ng mL-1, and an optimal duty cycle of 96.4% was achieved. In AQLIT-RIT mode, the number of ions coexisting in the RIT was reduced, which weakened the space-charge effect and reduced the mass shift. Furthermore, the mass resolution was enhanced by a factor of 3. The results indicate that the novel control modes achieve satisfactory performance without adding any system complexity, which provides a viable pathway to guarantee good analytical performance in miniaturization of the mass spectrometer.
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Affiliation(s)
- Xinming Huo
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Fei Tang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Xiaohua Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jin Chen
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Yan Zhang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Cheng'an Guo
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Xiaohao Wang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
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18
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Guna M. Extending the Ion Capacity of a Linear Ion Trap Using Nonlinear Radio Frequency Fields. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:2125-2132. [PMID: 26178741 DOI: 10.1007/s13361-015-1227-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 06/23/2015] [Accepted: 06/30/2015] [Indexed: 06/04/2023]
Abstract
Mass selective axial ejection (MSAE) from a low pressure linear ion trap (LIT) is investigated in the presence of added auxiliary nonlinear radio frequency (rf) fields. Nonlinear rf fields allow ions to be ejected with high sensitivity at large excitation amplitudes and reduced deleterious effects of space charge. These permit the operation of the LIT at ion populations considerably larger than the space charge limit usually observed in the absence of the nonlinear fields while maintaining good spectral resolution and mass accuracy. Experimental data show that the greater the strength of the nonlinear field, the less the effects of space charge on mass assignment and peak width. The only deleterious effect is a slight broadening of the mass spectral peaks at the highest values of added nonlinear fields used. Graphical Abstract ᅟ.
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Affiliation(s)
- Mircea Guna
- SCIEX, 71 Four Valley Drive, Concord, Ontario, Canada.
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19
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Jones JW, Pierzchalski K, Yu J, Kane MA. Use of fast HPLC multiple reaction monitoring cubed for endogenous retinoic acid quantification in complex matrices. Anal Chem 2015; 87:3222-30. [PMID: 25704261 DOI: 10.1021/ac504597q] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Retinoic acid (RA), an essential active metabolite of vitamin A, controls numerous physiological processes. In addition to the analytical challenges owing to its geometric isomers, low endogenous abundance, and often localized occurrence, nonspecific interferences observed during liquid chromatography (LC) multiple reaction monitoring (MRM) quantification methods have necessitated lengthy chromatography to obtain accurate quantification free of interferences. We report the development and validation of a fast high performance liquid chromatography (HPLC) multiplexing multiple reaction monitoring cubed (MRM(3)) assay for selective and sensitive quantification of endogenous RA from complex matrices. The fast HPLC separation was achieved using an embedded amide C18 column packed with 2.7 μm fused-core particles which provided baseline resolution of endogenous RA isomers (all-trans-RA, 9-cis-RA, 13-cis-RA, and 9,13-di-cis-RA) and demonstrated significant improvements in chromatographic efficiency compared to porous particle stationary phases. Multiplexing technology further enhanced sample throughput by a factor of 2 by synchronizing parallel HPLC systems to a single mass spectrometer. The fast HPLC multiplexing MRM(3) assay demonstrated enhanced selectivity for endogenous RA quantification in complex matrices and had comparable analytical performance to robust, validated LC-MRM methodology for RA quantification. The quantification of endogenous RA using the described assay was validated on a number of mouse tissues, nonhuman primate tissues, and human plasma samples. The combined integration of fast HPLC, MRM(3), and multiplexing yields an analysis workflow for essential low-abundance endogenous metabolites that has enhanced selectivity in complex matrices and increased throughput that will be useful in efficiently interrogating the biological role of RA in larger study populations.
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Affiliation(s)
- Jace W Jones
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, 20 N. Pine Street, Baltimore, Maryland 21201, United States
| | - Keely Pierzchalski
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, 20 N. Pine Street, Baltimore, Maryland 21201, United States
| | - Jianshi Yu
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, 20 N. Pine Street, Baltimore, Maryland 21201, United States
| | - Maureen A Kane
- University of Maryland, School of Pharmacy, Department of Pharmaceutical Sciences, 20 N. Pine Street, Baltimore, Maryland 21201, United States
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20
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Schmidt R, Böhme D, Singer D, Frolov A. Specific tandem mass spectrometric detection of AGE-modified arginine residues in peptides. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:613-624. [PMID: 25800199 DOI: 10.1002/jms.3569] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 12/30/2014] [Accepted: 01/07/2015] [Indexed: 06/04/2023]
Abstract
Glycation is a non-enzymatic reaction of protein amino and guanidino groups with reducing sugars or dicarbonyl products of their oxidative degradation. Modification of arginine residues by dicarbonyls such as glyoxal and methylglyoxal results in formation of advanced glycation end-products (AGEs). In mammals, these modifications impact in diabetes mellitus, uremia, atherosclerosis and ageing. However, due to the low abundance of individual AGE-peptides in enzymatic digests, these species cannot be efficiently detected by LC-ESI-MS-based data-dependent acquisition (DDA) experiments. Here we report an analytical workflow that overcomes this limitation. We describe fragmentation patterns of synthetic AGE-peptides and assignment of modification-specific signals required for unambiguous structure retrieval. Most intense signals were those corresponding to unique fragment ions with m/z 152.1 and 166.1, observed in the tandem mass spectra of peptides, containing glyoxal- and methylglyoxal-derived hydroimidazolone AGEs, respectively. To detect such peptides, specific and sensitive precursor ion scanning methods were established for these signals. Further, these precursor ion scans were incorporated in conventional bottom-up proteomic approach based on data-dependent acquisition (DDA) LC-MS/MS experiments. The method was successfully applied for the analysis of human serum albumin (HSA) and human plasma protein tryptic digest with subsequent structure confirmation by targeted LC-MS/MS (DDA). Altogether 44 hydroimidazolone- and dihydroxyimidazolidine-derived peptides representing 42 AGE-modified proteins were identified in plasma digests obtained from type 2 diabetes mellitus (T2DM) patients.
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Affiliation(s)
- Rico Schmidt
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Center for Biotechnology and Biomedicine (BBZ), Universität Leipzig, Leipzig, Germany
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21
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Mercadante R, Polledri E, Scurati S, Moretto A, Fustinoni S. Identification and Quantification of Metabolites of the Fungicide Tebuconazole in Human Urine. Chem Res Toxicol 2014; 27:1943-9. [DOI: 10.1021/tx500291t] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R. Mercadante
- Department
of Clinical Sciences and Community Health, Università degli Studi di Milano and Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - E. Polledri
- Department
of Clinical Sciences and Community Health, Università degli Studi di Milano and Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - S. Scurati
- AB Sciex, Viale Lombardia,
218, 20861 Brugherio (MB), Italy
| | - A. Moretto
- Department
of Biomedical and Clinical Sciences, Università degli Studi
di Milano, and International Centre for Pesticides and Health Risks
Protection (ICPS), “Luigi Sacco” Hospital, Milan, Italy
| | - S. Fustinoni
- Department
of Clinical Sciences and Community Health, Università degli Studi di Milano and Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
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22
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Wang Y, Zhang X, Zhai Y, Jiang Y, Fang X, Zhou M, Deng Y, Xu W. Mass Selective Ion Transfer and Accumulation in Ion Trap Arrays. Anal Chem 2014; 86:10164-70. [DOI: 10.1021/ac502583b] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yuzhuo Wang
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaohua Zhang
- Department
of Chemistry, FUDAN University, Shanghai 200433, China
| | - Yanbing Zhai
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - You Jiang
- National Institute
of Metrology, Beijing 100013, China
| | - Xiang Fang
- National Institute
of Metrology, Beijing 100013, China
| | - Mingfei Zhou
- Department
of Chemistry, FUDAN University, Shanghai 200433, China
| | - Yulin Deng
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Wei Xu
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
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23
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Wang L, Xu F, Dai X, Fang X, Ding CF. Development and investigation of a mesh-electrode linear ion trap (ME-LIT) mass analyzer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:548-555. [PMID: 24435796 DOI: 10.1007/s13361-013-0803-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/03/2013] [Accepted: 12/03/2013] [Indexed: 06/03/2023]
Abstract
A mesh-electrode linear ion trap (ME-LIT) mass analyzer was developed and its performance was primarily characterized. In conventional linear ion trap mass analyzers, the trapped ions are mass-selected and then ejected in a radial direction by a slot on a trap electrode. The presence of slots can strongly affect the electric field distribution in the ion trapping region and distort the mass analysis performance. To compensate for detrimental electric field effects, the slot is usually designed and fabricated to be as small as possible, and also has very high mechanical accuracy and symmetry. A ME-LIT with several mesh electrodes was built to compensate for the effects caused by slots. Each mesh electrode was fabricated from a plate electrode with a relatively large slot and the slot was covered with a conductive mesh. Our preliminary experimental results show that the ME-LIT could considerably diminish the detrimental electric field effects caused by slots, and increase the mass resolving power and ion detection efficiency. Even with 4-mm-wide slots, a mass resolution in excess of 600 was obtained using the ME-LIT. Mass resolution could be remarkably improved using mesh electrodes in ion traps with asymmetric electrodes. The stability diagram of the ME-LIT was mapped, and highly efficient tandem mass spectrometry was demonstrated. The ME-LIT was qualified as a LIT mass analyzer. The ME-LIT can improve the mass resolution and decrease the requirements of mechanical accuracy and symmetry of slots, so it shows potential for a wide range of practical uses.
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Affiliation(s)
- Liang Wang
- Department of Chemistry and Laser Chemistry Institute, Fudan University, Shanghai, China
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24
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Abstract
Due to their versatility, quadrupole ion traps have become popular mass spectrometers in the growing field of proteomics. High sensitivity, user friendliness and low cost are the key features that have contributed to the success of the technology. However, mass measurement accuracy, resolution and mass range are still not comparable to the analytical performances obtained on other mass spectrometers. In the past 5 years, researchers have tried to overcome these drawbacks, focusing their attention on two different aspects of ion-trap mass spectrometry, development of novel types of ion traps and manipulation of the gas-phase ion chemistry, in order to obtain alternative techniques for tandem mass spectrometry analysis. In the field of trapping devices, improvements in instrumental design have led to the linear ion trap, digital ion trap and orbitrap. Activation methods based on electrons, chemically produced by an anion or from irradiation with an electron beam, have demonstrated their utility in providing complementary sequence information for improving confidence in protein identification.
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25
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Ahmed FE. Utility of mass spectrometry for proteome ana lysis: part I. Conceptual and experimental approaches. Expert Rev Proteomics 2014; 5:841-64. [DOI: 10.1586/14789450.5.6.841] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Kong W, Wen J, Yang Y, Qiu F, Sheng P, Yang M. Simultaneous targeted analysis of five active compounds in licorice by ultra-fast liquid chromatography coupled to hybrid linear-ion trap tandem mass spectrometry. Analyst 2014; 139:1883-94. [DOI: 10.1039/c3an02209a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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27
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Lu M, Campbell JL, Chauhan R, Grapperhaus CA, Chen H. Probing the reactivity and radical nature of oxidized transition metal-thiolate complexes by mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:502-512. [PMID: 23315345 DOI: 10.1007/s13361-012-0537-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 10/11/2012] [Accepted: 10/15/2012] [Indexed: 06/01/2023]
Abstract
Transition metal thiolate complexes such as [PPN](+)[RuL3](-) (PPN = bis(triphenylphosphoranylidene) ammonium and L = diphenylphosphinobenzenethiolate) are known to undergo addition reactions with unsaturated hydrocarbons via the formation of new C-S bonds in solution upon oxidation. The reaction mechanism is proposed to involve metal-stabilized thiyl radical intermediates, a new type of distonic ions such as [RuL3](+) ion in the case of [PPN](+)[RuL3](-). This study presents the reactivity and structure investigation of [RuL3](+) by mass spectrometry (MS) in conjunction with ion/molecule reactions. The addition reactions of [RuL3](+) with alkenes or methyl ketones in the gas phase are indeed observed, in agreement with the proposed mechanism. Such reactivity is also maintained by several fragment ions of [RuL3](+), indicating the preserved thiyl diradical core structure is responsible for the addition reaction. The thiyl radical nature of [RuL3](+) was further verified by the ion/molecule reaction of [RuL3](+) with dimethyl disulfide, in which the characteristic CH3S• transfer occurs, both at atmospheric pressure and also at low pressure (~mTorr). These results provide, for the first time, clear mass spectrometric evidence of the radical nature of [RuL3](+) (i.e., the distonic ion structure of [RuL3](+)), arising from the oxidation of non-innocent thiolate ligands of the complex [PPN](+)[RuL3](-). Similar thiolate complexes, including ReL3 and NiL2, were also examined. Although reactions of oxidized ReL3 or NiL2 with CH3SSCH3 take place at atmospheric pressure, the corresponding reaction did not occur in vacuum. Consistent with these data, the addition of ethylene was not observed either, indicating lower reactivities of [ReL3](+) and [NiL2](+) in comparison to [RuL3](+).
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Affiliation(s)
- Mei Lu
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
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28
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Flowers SA, Ali L, Lane CS, Olin M, Karlsson NG. Selected reaction monitoring to differentiate and relatively quantitate isomers of sulfated and unsulfated core 1 O-glycans from salivary MUC7 protein in rheumatoid arthritis. Mol Cell Proteomics 2013; 12:921-31. [PMID: 23457413 DOI: 10.1074/mcp.m113.028878] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Rheumatoid arthritis is a common and debilitating systemic inflammatory condition affecting up to 1% of the world's population. This study aimed to investigate the immunological significance of O-glycans in chronic arthritis at a local and systemic level. O-Glycans released from synovial glycoproteins during acute and chronic arthritic conditions were compared and immune-reactive glycans identified. The sulfated core 1 O-glycan (Galβ1-3GalNAcol) was immune reactive, showing a different isomeric profile in the two conditions. From acute reactive arthritis, three isomers could be sequenced, but in patients with chronic rheumatoid arthritis, only a single 3-Gal sulfate-linked isomer could be identified. The systemic significance of this glycan epitope was investigated using the salivary mucin MUC7 in patients with rheumatoid arthritis and normal controls. To analyze this low abundance glycan, a selected reaction monitoring (SRM) method was developed to differentiate and relatively quantitate the core 1 O-glycan and the sulfated core 1 O-glycan Gal- and GalNAc-linked isomers. The acquisition of highly sensitive full scan linear ion trap MS/MS spectra in addition to quantitative SRM data allowed the 3- and 6-linked Gal isomers to be differentiated. The method was used to relatively quantitate the core 1 glycans from MUC7 to identify any systemic changes in this carbohydrate epitope. A statistically significant increase in sulfation was identified in salivary MUC7 from rheumatoid arthritis patients. This suggests a potential role for this epitope in chronic inflammation. This study was able to develop an SRM approach to specifically identify and relatively quantitate sulfated core 1 isomers and the unsulfated structure. The expansion of this method may afford an avenue for the high throughput investigation of O-glycans.
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Affiliation(s)
- Sarah A Flowers
- Department of Medical Biochemistry, Institute of Biomedicine, University of Gothenburg, Medicinaregatan 9A, 405 30, Gothenburg, Sweden
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29
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Rocco M, Lomaglio T, Loperte A, Satriani A. Metapontum Forest Reserve: Salt Stress Responses in <i>Pinus halepensis</i>. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.43a086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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30
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Gallien S, Duriez E, Crone C, Kellmann M, Moehring T, Domon B. Targeted proteomic quantification on quadrupole-orbitrap mass spectrometer. Mol Cell Proteomics 2012; 11:1709-23. [PMID: 22962056 DOI: 10.1074/mcp.o112.019802] [Citation(s) in RCA: 368] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
There is an immediate need for improved methods to systematically and precisely quantify large sets of peptides in complex biological samples. To date protein quantification in biological samples has been routinely performed on triple quadrupole instruments operated in selected reaction monitoring mode (SRM), and two major challenges remain. Firstly, the number of peptides to be included in one survey experiment needs to be increased to routinely reach several hundreds, and secondly, the degree of selectivity should be improved so as to reliably discriminate the targeted analytes from background interferences. High resolution and accurate mass (HR/AM) analysis on the recently developed Q-Exactive mass spectrometer can potentially address these issues. This instrument presents a unique configuration: it is constituted of an orbitrap mass analyzer equipped with a quadrupole mass filter as the front-end for precursor ion mass selection. This configuration enables new quantitative methods based on HR/AM measurements, including targeted analysis in MS mode (single ion monitoring) and in MS/MS mode (parallel reaction monitoring). The ability of the quadrupole to select a restricted m/z range allows one to overcome the dynamic range limitations associated with trapping devices, and the MS/MS mode provides an additional stage of selectivity. When applied to targeted protein quantification in urine samples and benchmarked with the reference SRM technique, the quadrupole-orbitrap instrument exhibits similar or better performance in terms of selectivity, dynamic range, and sensitivity. This high performance is further enhanced by leveraging the multiplexing capability of the instrument to design novel acquisition methods and apply them to large targeted proteomic studies for the first time, as demonstrated on 770 tryptic yeast peptides analyzed in one 60-min experiment. The increased quality of quadrupole-orbitrap data has the potential to improve existing protein quantification methods in complex samples and address the pressing demand of systems biology or biomarker evaluation studies.
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Affiliation(s)
- Sebastien Gallien
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, L-1445 Strassen, Luxembourg
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31
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Campbell JL, Le Blanc JCY, Schneider BB. Probing Electrospray Ionization Dynamics Using Differential Mobility Spectrometry: The Curious Case of 4-Aminobenzoic Acid. Anal Chem 2012; 84:7857-64. [DOI: 10.1021/ac301529w] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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32
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Huang C, Guo B, Wang X, Li J, Zhu W, Chen B, Ouyang S, Yao S. A generic approach for expanding homolog-targeted residue screening of sulfonamides using a fast matrix separation and class-specific fragmentation-dependent acquisition with a hybrid quadrupole-linear ion trap mass spectrometer. Anal Chim Acta 2012; 737:83-98. [DOI: 10.1016/j.aca.2012.05.041] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Revised: 05/13/2012] [Accepted: 05/19/2012] [Indexed: 10/28/2022]
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33
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Zhang K, Wong JW, Yang P, Hayward DG, Sakuma T, Zou Y, Schreiber A, Borton C, Nguyen TV, Kaushik B, Oulkar D. Protocol for an electrospray ionization tandem mass spectral product ion library: development and application for identification of 240 pesticides in foods. Anal Chem 2012; 84:5677-84. [PMID: 22686274 DOI: 10.1021/ac300844d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modern determination techniques for pesticides must yield identification quickly with high confidence for timely enforcement of tolerances. A protocol for the collection of liquid chromatography (LC) electrospray ionization (ESI)-quadruple linear ion trap (Q-LIT) mass spectrometry (MS) library spectra was developed. Following the protocol, an enhanced product ion (EPI) library of 240 pesticides was developed by use of spectra collected from two laboratories. A LC-Q-LIT-MS workflow using scheduled multiple reaction monitoring (sMRM) survey scan, information-dependent acquisition (IDA) triggered collection of EPI spectra, and library search was developed and tested to identify the 240 target pesticides in one single LC-Q-LIT MS analysis. By use of LC retention time, one sMRM survey scan transition, and a library search, 75-87% of the 240 pesticides were identified in a single LC/MS analysis at fortified concentrations of 10 ng/g in 18 different foods. A conventional approach with LC-MS/MS using two MRM transitions produced the same identifications and comparable quantitative results with the same incurred foods as the LC-Q-LIT using EPI library search, finding 1.2-49 ng/g of either carbaryl, carbendazim, fenbuconazole, propiconazole, or pyridaben in peaches; carbendazim, imazalil, terbutryn, and thiabendazole in oranges; terbutryn in salmon; and azoxystrobin in ginseng. Incurred broccoli, cabbage, and kale were screened with the same EPI library using three LC-Q-LIT and a LC-quadruple time-of-flight (Q-TOF) instruments. The library search identified azoxystrobin, cyprodinil, fludioxinil, imidacloprid, metalaxyl, spinosyn A, D, and J, amd spirotetramat with each instrument. The approach has a broad application in LC-MS/MS type targeted screening in food analysis.
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Affiliation(s)
- Kai Zhang
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland 20740, United States.
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Kim YJ, Zaidi-Ainouch Z, Gallien S, Domon B. Mass spectrometry–based detection and quantification of plasma glycoproteins using selective reaction monitoring. Nat Protoc 2012; 7:859-71. [DOI: 10.1038/nprot.2012.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Zgoła-Grześkowiak A, Grześkowiak T. The use of a triple quadrupole linear ion trap mass spectrometer with electrospray ionisation for fragmentation studies of selected antifungal drugs. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3049-3055. [PMID: 21953959 DOI: 10.1002/rcm.5188] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Fragmentation studies of three antifungal drugs, clotrimazole, fluconazole and clioquinol ,were performed. A triple quadrupole linear ion trap mass spectrometer was used for this purpose. This type of equipment enables MS(3) spectra to be obtained which lead to better understanding of fragmentation pathways. Nevertheless, it is rarely used for fragmentation studies. The results obtained here for the antifungal drugs gave further insight into fragmentation pathways of clotrimazole and fluconazole. Moreover, fragmentation of clioquinol was investigated which had not been presented before.
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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Guna M, Londry FA. Tandem Ion Trap Design with Enhanced Mass Analysis Capabilities for Large Populations of Ions. Anal Chem 2011; 83:6363-7. [DOI: 10.1021/ac201285n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mircea Guna
- AB SCIEX, 71 Four Valley Drive, Concord, Ontario, Canada
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Abstract
The metabolome is composed of a vast number of small-molecule metabolites that exhibit a diversity of physical and chemical properties and exist over a wide dynamic range in biological samples. Multiple analytical techniques, used in a complementary manner, are required to achieve high coverage of the metabolome. MS is playing a central role in metabolomics research. Herein, we present a brief overview of the MS-based technologies employed for high-throughput metabolomics. These technologies range from chromatography-MS techniques, such as GC-MS and LC-MS, to chromatography-free techniques, such as direct infusion, matrix-assisted and matrix-free laser desorption/ionization, imaging and some new ambient ionization approaches. Chemoinformatics and bioinformatics tools are widely available to facilitate successful metabolomics studies by turning the complex metabolomics data into biological information through streamlined data processing, analysis and interpretation.
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Gallien S, Duriez E, Domon B. Selected reaction monitoring applied to proteomics. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:298-312. [PMID: 21394846 DOI: 10.1002/jms.1895] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Selected reaction monitoring (SRM) performed on triple quadrupole mass spectrometers has been the reference quantitative technique to analyze small molecules for several decades. It is now emerging in proteomics as the ideal tool to complement shotgun qualitative studies; targeted SRM quantitative analysis offers high selectivity, sensitivity and a wide dynamic range. However, SRM applied to proteomics presents singularities that distinguish it from small molecules analysis. This review is an overview of SRM technology and describes the specificities and the technical aspects of proteomics experiments. Ongoing developments aiming at increasing multiplexing capabilities of SRM are discussed; they dramatically improve its throughput and extend its field of application to directed or supervised discovery experiments.
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Affiliation(s)
- Sebastien Gallien
- Luxembourg Clinical Proteomics center (LCP), Centre de Recherche Public de la Santé, 1 B rue Thomas Edison, L-1445 Strassen, Luxembourg
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40
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Belov ME, Prasad S, Prior DC, Danielson WF, Weitz K, Ibrahim YM, Smith RD. Pulsed multiple reaction monitoring approach to enhancing sensitivity of a tandem quadrupole mass spectrometer. Anal Chem 2011; 83:2162-71. [PMID: 21344863 DOI: 10.1021/ac103006b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Liquid chromatography (LC)-triple quadrupole mass spectrometers operating in a multiple reaction monitoring (MRM) mode are increasingly used for quantitative analysis of low-abundance analytes in highly complex biochemical matrixes. After development and selection of optimum MRM transitions, sensitivity and data quality limitations are largely related to mass spectral peak interferences from sample or matrix constituents and statistical limitations at low number of ions reaching the detector. Herein, we report on a new approach to enhancing MRM sensitivity by converting the continuous stream of ions from the ion source into a pulsed ion beam through the use of an ion funnel trap (IFT). Evaluation of the pulsed MRM approach was performed with a tryptic digest of Shewanella oneidensis strain MR-1 spiked with several model peptides. The sensitivity improvement observed with the IFT coupled in to the triple quadrupole instrument is based on several unique features. First, ion accumulation radio frequency (rf) ion trap facilitates improved droplet desolvation, which is manifested in the reduced background ion noise at the detector. Second, signal amplitude for a given transition is enhanced because of an order-of-magnitude increase in the ion charge density compared to a continuous mode of operation. Third, signal detection at the full duty cycle is obtained, as the trap use eliminates dead times between transitions, which are inevitable with continuous ion streams. In comparison with the conventional approach, the pulsed MRM signals showed 5-fold enhanced peak amplitude and 2-3-fold reduced chemical background, resulting in an improvement in the limit of detection (LOD) by a factor of ∼4-8.
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Affiliation(s)
- Mikhail E Belov
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States.
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41
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Williamson NA, Reilly C, Tan CT, Ramarathinam SH, Jones A, Hunter CL, Rooney FR, Purcell AW. A novel strategy for the targeted analysis of protein and peptide metabolites. Proteomics 2010; 11:183-92. [PMID: 21204246 DOI: 10.1002/pmic.201000474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 10/12/2010] [Accepted: 10/14/2010] [Indexed: 11/12/2022]
Abstract
In many biological applications such as epitope discovery or drug metabolism studies, the detection of naturally processed exogenous proteins (e.g. vaccines or peptide therapeutics) and their metabolites is frequently complicated by the presence of a complex endogenous mixture of closely related or even identical compounds. We describe a method that incorporates stable isotope labelling of the protein of interest, allowing the selective screening of the intact molecule and all metabolites using a modified precursor ion scan. This method involves monitoring the low-molecular-weight fragment ions produced during MS/MS that distinguish isotopically labelled peptides from related endogenous compounds. All isotopically labelled peptides can be selected using this method. The technique makes no assumptions about the processed or post-translational state of the peptide, and hence can selectively screen out modified peptides that would otherwise be missed by single reaction monitoring approaches. This method does not replace single reaction monitoring or regular precursor scanning techniques; instead, it is a method that can be used when the assumptions required for the former two techniques cannot be predicted. The potential for this technique to be used in metabolism and pharmacokinetic experiments is discussed with specific examples looking at the metabolism of α-synuclein in serum and the brain.
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Affiliation(s)
- Nicholas A Williamson
- Department of Biochemistry and Molecular Biology, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia.
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Kim J, Minkler PE, Salomon RG, Anderson VE, Hoppel CL. Cardiolipin: characterization of distinct oxidized molecular species. J Lipid Res 2010; 52:125-35. [PMID: 20858593 DOI: 10.1194/jlr.m010520] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cardiolipin (CL) is a phospholipid predominantly found in the mitochondrial inner membrane and is associated structurally with individual complexes of the electron transport chain (ETC). Because the ETC is the major mitochondrial reactive oxygen species (ROS)-generating site, the proximity to the ETC and bisallylic methylenes of the PUFA chains of CL make it a likely target of ROS in the mitochondrial inner membrane. Oxidized cellular CL products, uniquely derived from ROS-induced autoxidation, could serve as biomarkers for the presence of the ROS and could help in the understanding of the mechanism of oxidative stress. Because major CL species have four unsaturated acyl chains, whereas other phospholipids usually have only one in the sn-2 position, characterization of oxidized CL is highly challenging. In the current study, we exposed CL, under aerobic conditions, to singlet oxygen (¹O₂), the radical initiator 2,2'-azobis(2-methylpropionamidine) dihydrochloride, or room air, and the oxidized CL species were characterized by HPLC-tandem mass spectrometry (MS/MS). Our reverse-phase ion-pair HPLC-MS/MS method can characterize the major and minor oxidized CL species by detecting distinctive fragment ions associated with specific oxidized species. The HPLC-MS/MS results show that monohydroperoxides and bis monohydroperoxides were generated under all three conditions. However, significant amounts of CL dihydroperoxides were produced only by ¹O₂-mediated oxidation. These products were barely detectable from radical oxidation either in a liposome bilayer or in thin film. These observations are only possible due to the chromatographic separation of the different oxidized species.
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Affiliation(s)
- Junhwan Kim
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
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Gao H, Deng S, Obach RS. A Simple Liquid Chromatography-Tandem Mass Spectrometry Method to Determine Relative Plasma Exposures of Drug Metabolites across Species for Metabolite Safety Assessments. Drug Metab Dispos 2010; 38:2147-56. [DOI: 10.1124/dmd.110.034637] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Abstract
The current status of de novo sequencing of peptides by MS/MS is reviewed with focus on collision cell MS/MS spectra. The relation between peptide structure and observed fragment ion series is discussed and the exhaustive extraction of sequence information from CID spectra of protonated peptide ions is described. The partial redundancy of the extracted sequence information and a high mass accuracy are recognized as key parameters for dependable de novo sequencing by MS. In addition, the benefits of special techniques enhancing the generation of long uninterrupted fragment ion series for de novo peptide sequencing are highlighted. Among these are terminal (18)O labeling, MS(n) of sodiated peptide ions, N-terminal derivatization, the use of special proteases, and time-delayed fragmentation. The emerging electron transfer dissociation technique and the recent progress of MALDI techniques for intact protein sequencing are covered. Finally, the integration of bioinformatic tools into peptide de novo sequencing is demonstrated.
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Affiliation(s)
- Joerg Seidler
- Molecular Structure Analysis, German Cancer Research Center, Heidelberg, Germany
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45
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Kenny DJ, Worthington KR, Hoyes JB. Scanwave: a new approach to enhancing spectral data on a tandem quadrupole mass spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1061-1069. [PMID: 20304673 DOI: 10.1016/j.jasms.2010.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Revised: 02/01/2010] [Accepted: 02/06/2010] [Indexed: 05/29/2023]
Abstract
A new type of mass analyzer is described, which allows low-resolution axial ion ejection to be obtained from a traveling wave based, stacked ring collision cell. Linking this ejection temporally with the scanning of the second quadrupole of a tandem quadrupole mass spectrometer provides an improvement in sampling duty cycle, which results in significant signal intensity improvements for scanning acquisitions such as product ion spectra. A near 100% storage efficiency is enabled by a split cell design, which allows ion fragmentation and accumulation to be performed in one section of the collision cell whilst previously accumulated ions are simultaneously ejected from the rear of the cell. These characteristics combine to give an m/z-dependent signal gain of 7-20x over a conventional scanning quadrupole for a 1000 Th scan. The ability to swap very rapidly from a non-enhanced mode of operation to an enhanced mode whilst retaining the existing sensitivity, speed, and functionality of a conventional tandem quadrupole mass spectrometer is also described.
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Affiliation(s)
- Daniel J Kenny
- Waters Corporation, MS Technologies Centre, Wythenshawe, Manchester, United Kingdom.
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46
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García-Galán MJ, Villagrasa M, Díaz-Cruz MS, Barceló D. LC-QqLIT MS analysis of nine sulfonamides and one of their acetylated metabolites in the Llobregat River basin. Quantitative determination and qualitative evaluation by IDA experiments. Anal Bioanal Chem 2010; 397:1325-34. [PMID: 20306259 DOI: 10.1007/s00216-010-3630-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 02/26/2010] [Accepted: 03/01/2010] [Indexed: 11/29/2022]
Abstract
Robust instrumental analytical chemistry and the subsequent development of improved analytical methodologies and extraction procedures have enabled the detection at environmental levels of new emerging contaminants, for example pharmaceuticals. The objective of this study was to explore the potential of liquid chromatography-tandem quadrupole-linear ion trap (LC-QqLIT MS) for quantitative determination of nine sulfonamides (SAs) and one acetylated metabolite in surface water from the Llobregat River and one of its main tributaries, the Anoia River, in Catalonia (Spain). A total of 21 samples were taken in three sampling campaigns. Recoveries ranging from 26% to 123% were calculated for the SAs studied, and method limits of detection (MLODs) achieved were in the range 0.05-0.2 ng L(-1). Through the different campaigns, concentrations ranged from 0.74 ng L(-1) (sulfamethizole) to 2,482 ng L(-1) (sulfamethazine) in the Llobregat River, and from 0.27 ng L(-1) (sulfamethizole) to 168 ng L(-1) (sulfamethoxazole) in the Anoia River. Sulfamethoxazole and sulfapyridine were the two SAs most frequently detected (80% and 71% respectively). N(4)-acetylsulfamethazine was detected in both rivers, but with different frequencies (4% of the samples from the Anoia River and 43% of those from the Llobregat River). Information-dependent acquisition (IDA) experiments were also developed in order to obtain enhanced product-ion spectra in surface water samples.
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Affiliation(s)
- M Jesús García-Galán
- Department Environmental Chemistry, Institute of Environmental Diagnostic and Water Studies (IDAEA), Spanish Council of Scientific Research (CSIC), Jordi Girona 18-26, 08034 Barcelona, Spain
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47
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Walther TC, Olsen JV, Mann M. Yeast expression proteomics by high-resolution mass spectrometry. Methods Enzymol 2010; 470:259-80. [PMID: 20946814 DOI: 10.1016/s0076-6879(10)70011-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Comprehensive analysis of yeast as a model system requires to reliably determine its composition. Systematic approaches to globally determine the abundance of RNAs have existed for more than a decade and measurements of mRNAs are widely used as proxies for detecting changes in protein abundance. In contrast, methodologies to globally quantitate proteins are only recently becoming available. Such experiments are essential as proteins mediate the majority of biological processes and their abundance does not always correlate well with changes in gene expression. Particularly translational and post-translational controls contribute majorly to regulation of protein abundance, for example in heat shock stress response. The development of new sample preparation methods, high-resolution mass spectrometry and novel bioinfomatic tools close this gap and allow the global quantitation of the yeast proteome under different conditions. Here, we provide background information on proteomics by mass-spectrometry and describe the practice of a comprehensive yeast proteome analysis.
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Affiliation(s)
- Tobias C Walther
- Organelle Architecture and Dynamics, Max Planck Institute of Biochemistry, Martinsried, Germany
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48
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Griffiths WJ, Sjövall J. Bile acids: analysis in biological fluids and tissues. J Lipid Res 2010; 51:23-41. [PMID: 20008121 PMCID: PMC2789783 DOI: 10.1194/jlr.r001941-jlr200] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 09/10/2009] [Indexed: 01/15/2023] Open
Abstract
The formation of bile acids/bile alcohols is of major importance for the maintenance of cholesterol homeostasis. Besides their functions in lipid absorption, bile acids/bile alcohols are regulatory molecules for a number of metabolic processes. Their effects are structure-dependent, and numerous metabolic conversions result in a complex mixture of biologically active and inactive forms. Advanced methods are required to characterize and quantify individual bile acids in these mixtures. A combination of such analyses with analyses of the proteome will be required for a better understanding of mechanisms of action and nature of endogenous ligands. Mass spectrometry is the basic detection technique for effluents from chromatographic columns. Capillary liquid chromatography-mass spectrometry with electrospray ionization provides the highest sensitivity in metabolome analysis. Classical gas chromatography-mass spectrometry is less sensitive but offers extensive structure-dependent fragmentation increasing the specificity in analyses of isobaric isomers of unconjugated bile acids. Depending on the nature of the bile acid/bile alcohol mixture and the range of concentration of individuals, different sample preparation sequences, from simple extractions to group separations and derivatizations, are applicable. We review the methods currently available for the analysis of bile acids in biological fluids and tissues, with emphasis on the combination of liquid and gas phase chromatography with mass spectrometry.
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Affiliation(s)
- William J. Griffiths
- Institute of Mass Spectrometry, School of Medicine, Grove Building Swansea University Singleton Park Swansea SA2 8PP United Kingdom
| | - Jan Sjövall
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet SE-17177 Stockholm Sweden
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50
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Fortin T, Salvador A, Charrier JP, Lenz C, Bettsworth F, Lacoux X, Choquet-Kastylevsky G, Lemoine J. Multiple Reaction Monitoring Cubed for Protein Quantification at the Low Nanogram/Milliliter Level in Nondepleted Human Serum. Anal Chem 2009; 81:9343-52. [DOI: 10.1021/ac901447h] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- T. Fortin
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - A. Salvador
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - J. P. Charrier
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - C. Lenz
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - F. Bettsworth
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - X. Lacoux
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - G. Choquet-Kastylevsky
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
| | - J. Lemoine
- R&D Proteomique, bioMérieux SA, Marcy l’Etoile, France, UMR 5180 Sciences Analytiques, Université de Lyon, Lyon1, France, and PSM Support, Applied Biosystems, Darmstadt, Germany
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