1
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Xie X, Moon PJ, Crossley SWM, Bischoff AJ, He D, Li G, Dao N, Gonzalez-Valero A, Reeves AG, McKenna JM, Elledge SK, Wells JA, Toste FD, Chang CJ. Oxidative cyclization reagents reveal tryptophan cation-π interactions. Nature 2024; 627:680-687. [PMID: 38448587 PMCID: PMC11198740 DOI: 10.1038/s41586-024-07140-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Methods for selective covalent modification of amino acids on proteins can enable a diverse array of applications, spanning probes and modulators of protein function to proteomics1-3. Owing to their high nucleophilicity, cysteine and lysine residues are the most common points of attachment for protein bioconjugation chemistry through acid-base reactivity3,4. Here we report a redox-based strategy for bioconjugation of tryptophan, the rarest amino acid, using oxaziridine reagents that mimic oxidative cyclization reactions in indole-based alkaloid biosynthetic pathways to achieve highly efficient and specific tryptophan labelling. We establish the broad use of this method, termed tryptophan chemical ligation by cyclization (Trp-CLiC), for selectively appending payloads to tryptophan residues on peptides and proteins with reaction rates that rival traditional click reactions and enabling global profiling of hyper-reactive tryptophan sites across whole proteomes. Notably, these reagents reveal a systematic map of tryptophan residues that participate in cation-π interactions, including functional sites that can regulate protein-mediated phase-separation processes.
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Affiliation(s)
- Xiao Xie
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Patrick J Moon
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Steven W M Crossley
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Amanda J Bischoff
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dan He
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gen Li
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Nam Dao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Audrey G Reeves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | | | - Susanna K Elledge
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - F Dean Toste
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
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2
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Hoopes CR, Garcia FJ, Sarkar AM, Kuehl NJ, Barkan DT, Collins NL, Meister GE, Bramhall TR, Hsu CH, Jones MD, Schirle M, Taylor MT. Donor-Acceptor Pyridinium Salts for Photo-Induced Electron-Transfer-Driven Modification of Tryptophan in Peptides, Proteins, and Proteomes Using Visible Light. J Am Chem Soc 2022; 144:6227-6236. [PMID: 35364811 PMCID: PMC10124759 DOI: 10.1021/jacs.1c10536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tryptophan (Trp) plays a variety of critical functional roles in protein biochemistry; however, owing to its low natural frequency and poor nucleophilicity, the design of effective methods for both single protein bioconjugation at Trp as well as for in situ chemoproteomic profiling remains a challenge. Here, we report a method for covalent Trp modification that is suitable for both scenarios by invoking photo-induced electron transfer (PET) as a means of driving efficient reactivity. We have engineered biaryl N-carbamoyl pyridinium salts that possess a donor-acceptor relationship that enables optical triggering with visible light whilst simultaneously attenuating the probe's photo-oxidation potential in order to prevent photodegradation. This probe was assayed against a small bank of eight peptides and proteins, where it was found that micromolar concentrations of the probe and short irradiation times (10-60 min) with violet light enabled efficient reactivity toward surface exposed Trp residues. The carbamate transferring group can be used to transfer useful functional groups to proteins including affinity tags and click handles. DFT calculations and other mechanistic analyses reveal correlations between excited state lifetimes, relative fluorescence quantum yields, and chemical reactivity. Biotinylated and azide-functionalized pyridinium salts were used for Trp profiling in HEK293T lysates and in situ in HEK293T cells using 440 nm LED irradiation. Peptide-level enrichment from live cell labeling experiments identified 290 Trp modifications, with 82% selectivity for Trp modification over other π-amino acids, demonstrating the ability of this method to identify and quantify reactive Trp residues from live cells.
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Affiliation(s)
- Caleb R Hoopes
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Francisco J Garcia
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Akash M Sarkar
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Nicholas J Kuehl
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - David T Barkan
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Nicole L Collins
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
| | - Glenna E Meister
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Taylor R Bramhall
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Chien-Hsiang Hsu
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Michael D Jones
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, Massachusetts 02139, United States
| | - Michael T Taylor
- Department of Chemistry, University of Wyoming, Laramie, Wyoming 82071, United States
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3
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Feng Q, Zhao N, Xia W, Liang C, Dai G, Yang J, Sun J, Liu L, Luo L, Yang J. Integrative proteomics and immunochemistry analysis of the factors in the necrosis and repair in acetaminophen-induced acute liver injury in mice. J Cell Physiol 2018; 234:6561-6581. [PMID: 30417486 DOI: 10.1002/jcp.27397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/17/2018] [Indexed: 12/16/2022]
Abstract
Acetaminophen (APAP) overdose-induced acute liver injury (AILI) is a significant clinical problem worldwide, the hepatotoxicity mechanisms are well elucidated, but the factors involved in the necrosis and repair still remain to be investigated. APAP was injected intraperitoneally in male Institute of Cancer Research (ICR) mice. Quantitative proteome analysis of liver tissues was performed by 2-nitrobenzenesulfenyl tagging, two-dimensional-nano high-performance liquid chromatography separation, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysis. Diffrenetial proteins were verified by the immunochemistry method. 36 and 44 differentially expressed proteins were identified, respectively, at 24 hr after APAP (200 or 300 mg·kg -1 ) administration. The decrease in the mitochondrial protective proteins Prdx6, Prdx3, and Aldh2 accounted for the accumulation of excessive reactive oxygen species (ROS) and aldehydes, impairing mitochondria structure and function. The Gzmf combined with Bax and Apaf-1 jointly contributed to the necrosis. The blockage of Stat3 activation led to the overexpression of unphosphorylated Stat3 and the overproduction of Bax. The overexpression of unphosphorylated Stat3 represented necrosis; the alternation from Stat3 to p-Stat3 in necrotic regions represented hepatocytes from death to renewal. The high expressions of P4hα1, Ncam, α-SMA, and Cygb were involved in the liver repair, they were not only the markers of activated HSC but also represented an intermediate stage of hepatocytes from damage or necrosis to renewal. Our data provided a comprehensive report on the profile and dynamic changes of the liver proteins in AILI; the involvement of Gzmf and the role of Stat3 in necrosis were revealed; and the role of hepatocyte in liver self-repair was well clarified.
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Affiliation(s)
- Qin Feng
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,Center for New Drug Pharmacological Research of Lunan Pharmaceutical Group, State Key Laboratory, Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Ningwei Zhao
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.,Shimadzu Biomedical Research Laboratory, Shanghai, China
| | - Wenkai Xia
- Center for New Drug Pharmacological Research of Lunan Pharmaceutical Group, State Key Laboratory, Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - ChengJie Liang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Guoxin Dai
- Center for New Drug Pharmacological Research of Lunan Pharmaceutical Group, State Key Laboratory, Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Jian Yang
- Center for New Drug Pharmacological Research of Lunan Pharmaceutical Group, State Key Laboratory, Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Jingxia Sun
- Center for New Drug Pharmacological Research of Lunan Pharmaceutical Group, State Key Laboratory, Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, China
| | - Lanying Liu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Lan Luo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Jie Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
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4
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Leitner A. A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research. Anal Chim Acta 2018; 1000:2-19. [DOI: 10.1016/j.aca.2017.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
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5
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Huang J, Wang J, Li Q, Zhang Y, Zhang X. Enzyme and Chemical Assisted N-Terminal Blocked Peptides Analysis, ENCHANT, as a Selective Proteomics Approach Complementary to Conventional Shotgun Approach. J Proteome Res 2017; 17:212-221. [DOI: 10.1021/acs.jproteome.7b00521] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jingnan Huang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jie Wang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qingqing Li
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yang Zhang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xumin Zhang
- State Key Laboratory of Genetic
Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
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6
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Hernandez ET, Swaminathan J, Marcotte EM, Anslyn EV. Solution-phase and solid-phase sequential, selective modification of side chains in KDYWEC and KDYWE as models for usage in single-molecule protein sequencing. NEW J CHEM 2017; 41:462-469. [PMID: 28983186 PMCID: PMC5624723 DOI: 10.1039/c6nj02932a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Single-molecule protein sequencing is regarded as a promising new method in the field of proteomics. It potentially offers orders of magnitude improvements in sensitivitiy and throughput for protein detection when compared to mass spectrometry. However, the development of such a technology faces significant barriers, especially in the need to chemically derivatize specific amino-acid types with unique labels. For example, fluorescent dyes would be suitable for single-molecule microscopy or nanopore-based sequencing. These emerging single-molecule protein-sequencing technologies suggests a need to develop an amino acid side chain-selective modification scheme that could target several side chains of interest. Current work for modifying residues focuses mainly on one or two side chains. The need to label many side chains, as recent computational modeling suggests, is required for high protein, sequencing coverage of the human proteome. Herein, we report our stragety for modifying two model peptides KYDWEC and KDYWE containing the most reactive residues, using highly opitmized mass labels in a sequential and selective fashion both using solution-phase and solid-phase chemistries, respectively. This will serve as a step towards a modification scheme appropriate for single-molecule studies.
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Affiliation(s)
- Erik T. Hernandez
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712-1224, USA
| | - Jagannath Swaminathan
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin
| | - Edward M. Marcotte
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin
| | - Eric V. Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712-1224, USA
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7
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Yao Y, Huang J, Cheng K, Pan Y, Qin H, Ye M, Zou H. Specific Enrichment of Peptides with N-Terminal Serine/Threonine by a Solid-Phase Capture-Release Approach for Efficient Proteomics Analysis. Anal Chem 2015; 87:11353-60. [DOI: 10.1021/acs.analchem.5b02711] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yating Yao
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junfeng Huang
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Cheng
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanbo Pan
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongqiang Qin
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Mingliang Ye
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Hanfa Zou
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
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8
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Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
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9
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Kurono S, Kaneko Y, Matsuura S, Niwayama S. Quantification of proteins using (13)C7-labeled and unlabeled iodoacetanilide by nano liquid chromatography/nanoelectrospray ionization and by selected reaction monitoring mass spectrometry. Bioorg Med Chem Lett 2015; 25:1110-6. [PMID: 25619637 DOI: 10.1016/j.bmcl.2014.12.090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/26/2014] [Accepted: 12/29/2014] [Indexed: 10/24/2022]
Abstract
The combination of cysteine-specific modifiers, iodoacetanilide (IAA) and (13)C7-labeled iodoacetanilide ((13)C7-IAA), has been applied to absolute quantification of proteins. The selected reaction monitoring (SRM) with the use of nano liquid chromatography/nanoelectrospray ionization ion trap mass spectrometry (nano LC/nano-ESI-IT-MS) analysis was applied to precise quantification of three commercial proteins. Good correlation was observed between the theoretical ratios and observed ratios for all these proteins both in a simple buffer solution and in a complex protein environment. Due to efficient tagging, this method does not require separate synthesis of isotope-labeled peptides for the SRM studies. Therefore, this method is expected to be a useful tool for proteomics research.
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Affiliation(s)
- Sadamu Kurono
- Laboratory of Molecular Signature Analysis, Division of Health Sciences, Osaka University Graduate School of Medicine, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory Chemicals Division, Wako Pure Chemical Industries, Ltd., 3-1-2 Doshomachi, Chuo-ku, Osaka, Osaka 540-8605, Japan
| | - Yuka Kaneko
- Laboratory of Molecular Signature Analysis, Division of Health Sciences, Osaka University Graduate School of Medicine, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan; Laboratory Chemicals Division, Wako Pure Chemical Industries, Ltd., 3-1-2 Doshomachi, Chuo-ku, Osaka, Osaka 540-8605, Japan
| | - Shuji Matsuura
- Laboratory of Molecular Signature Analysis, Division of Health Sciences, Osaka University Graduate School of Medicine, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Satomi Niwayama
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409-1061, USA; Department of Ophthalmology and Visual Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
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10
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Mesmin C, Domon B. Improvement of the Performance of Targeted LC–MS Assays through Enrichment of Histidine-Containing Peptides. J Proteome Res 2014; 13:6160-8. [DOI: 10.1021/pr5008152] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cédric Mesmin
- Luxembourg Clinical Proteomics
Center, Centre de Recherche Public de la Santé (CRP-Santé), Strassen 1445, Luxembourg
| | - Bruno Domon
- Luxembourg Clinical Proteomics
Center, Centre de Recherche Public de la Santé (CRP-Santé), Strassen 1445, Luxembourg
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11
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Affinity selection of histidine-containing peptides using metal chelate methacrylate monolithic disk for targeted LC–MS/MS approach in high-throughput proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 955-956:42-9. [DOI: 10.1016/j.jchromb.2014.02.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 02/08/2014] [Accepted: 02/12/2014] [Indexed: 11/18/2022]
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12
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Ueda K. Glycoproteomic strategies: From discovery to clinical application of cancer carbohydrate biomarkers. Proteomics Clin Appl 2013; 7:607-17. [PMID: 23640819 DOI: 10.1002/prca.201200123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Carbohydrate antigens are the most frequently and traditionally used biomarkers for cancer, such as CA19-9, CA125, DUPAN-II, AFP-L3, and many others. The diagnostic potential of them was simply based on the cancer-specific alterations of glycan structures on particular glycoproteins in serum/plasma. In spite of the facts that glycosylation disorders are feasible for cancer biomarkers and glycomic analysis technologies to explore them have been rapidly developed, it remains difficult to sensitively screen glycan structure changes on cancer-associated glycoproteins from clinical specimens. Moreover, a lot of additional issues should be appropriately addressed for the clinical application of newly identified glycosylation biomarkers, including analytical throughput, quantitative confirmation of structural changes, and biological explanation for the alterations. In the last decade, significant improvement of mass spectrometric techniques is being made in the aspects of both hardware spec and preanalytical purification procedures for glycoprotein analysis. Here we review potential approaches to perform comprehensive analysis of glycoproteomic biomarker screening from serum/plasma and to realize high-throughput validation of site-specific oligosaccharide variations. The power and problems of mass spectrometric applications on the clinical use of carbohydrate biomarkers are also discussed in this review.
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Affiliation(s)
- Koji Ueda
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Minato-ku, Tokyo, Japan.
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13
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Kurono S, Kaneko Y, Niwayama S. Quantitative protein analysis using (13)C7-labeled iodoacetanilide and d5-labeled N-ethylmaleimide by nano liquid chromatography/nanoelectrospray ionization ion trap mass spectrometry. Bioorg Med Chem Lett 2013; 23:3111-8. [PMID: 23562245 DOI: 10.1016/j.bmcl.2013.02.112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 02/20/2013] [Accepted: 02/25/2013] [Indexed: 10/27/2022]
Abstract
We have developed a methodology for quantitative analysis and concurrent identification of proteins by the modification of cysteine residues with a combination of iodoacetanilide (IAA, 1) and (13)C7-labeled iodoacetanilide ((13)C7-IAA, 2), or N-ethylmaleimide (NEM, 3) and d5-labeled N-ethylmaleimide (d5-NEM, 4), followed by mass spectrometric analysis using nano liquid chromatography/nanoelectrospray ionization ion trap mass spectrometry (nano LC/nano-ESI-IT-MS). The combinations of these stable isotope-labeled and unlabeled modifiers coupled with LC separation and ESI mass spectrometric analysis allow accurate quantitative analysis and identification of proteins, and therefore are expected to be a useful tool for proteomics research.
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Affiliation(s)
- Sadamu Kurono
- Joint Research Laboratory of Molecular Signature Analysis, Division of Health Sciences, Osaka University Graduate School of Medicine, 1-7 Yamadaoka, Suita, Osaka 565-0871, Japan
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14
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Uen YH, Lin KY, Sun DP, Liao CC, Hsieh MS, Huang YK, Chen YW, Huang PH, Chen WJ, Tai CC, Lee KW, Chen YC, Lin CY. Comparative proteomics, network analysis and post-translational modification identification reveal differential profiles of plasma Con A-bound glycoprotein biomarkers in gastric cancer. J Proteomics 2013; 83:197-213. [PMID: 23541716 DOI: 10.1016/j.jprot.2013.03.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 02/06/2013] [Accepted: 03/10/2013] [Indexed: 12/13/2022]
Abstract
UNLABELLED In the study, we used Con A affinity chromatography, 1-D gel electrophoresis, and nano-LC-MS/MS to screen biomarker candidates in plasma samples obtained from 30 patients with gastric cancer and 30 healthy volunteers. First, we pooled plasma samples matched by age and sex. We identified 17 differentially expressed Con A-bound glycoproteins, including 10 upregulated proteins and 7 downregulated proteins; these differences were significant (Student's t-test, p-value<0.05). Furthermore, 2 of the upregulated proteins displayed expression levels that were increased by 2-fold or more in gastric cancer samples when compared with normal control samples. These proteins included leucine-rich alpha-2-glycoprotein (LRG1) and inter-alpha-trypsin inhibitor heavy chain H3 (ITIH3), and the expression levels were validated by Western blot analysis. Pathway and network analysis of the differentially expressed proteins by Ingenuity Pathway Analysis revealed vital canonical pathways involving acute phase response signaling, the complement system, LXR/RXR activation, hematopoiesis from pluripotent stem cells, and primary immunodeficiency signaling. Our results suggest that Con A-bound LRG1 and ITIH3 may not be practically applicable as a robust biomarker for the early detection of gastric cancer. Additionally, three novel PTMs in ITIH3 were identified and include hexose-N-acetyl-hexosamine at asparagine-(41), trimethylation at aspartic acid-(290), and flavin adenine dinucleotide at histidine-(335). BIOLOGICAL SIGNIFICANCE Our study was to describe a combinatorial approach of Con A affinity chromatography, 1-D SDS-PAGE, and nano-LC/MS/MS that provides a label-free, comparative glycoproteomic quantification strategy for the investigation of glycoprotein profiles in plasma from gastric cancer patients versus healthy volunteers and to identify glycoprotein biomarkers for the early clinical detection of gastric cancer. Three novel PTMs, HexHexNAc, trimethylation and FAD, in Con A-bound ITIH3 were identified and built in molecular modeling. The aspartic acid-(290) trimethylation site was located in a metal ion-dependent adhesion site (MIDAS motif; (290)-DXSXS…T…D-(313)) that may influence important function for binding protein ligands.
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Affiliation(s)
- Yih-Huei Uen
- Superintendent's Office, Chi-Mei Hospital Chiali, Tainan 722, Taiwan
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15
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Watanabe M, Takemasa I, Kawaguchi N, Miyake M, Nishimura N, Matsubara T, Matsuo EI, Sekimoto M, Nagai K, Matsuura N, Monden M, Nishimura O. An application of the 2-nitrobenzenesulfenyl method to proteomic profiling of human colorectal carcinoma: A novel approach for biomarker discovery. Proteomics Clin Appl 2012; 2:925-35. [PMID: 21136890 DOI: 10.1002/prca.200780111] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In the development of novel biomarkers, the proteomic approach is advantageous because using it the cancer-associated proteins can be directly identified. We previously developed a 2-nitrobenzenesulfenyl (NBS) method to improve quantitative proteome analysis. Here, we applied this method to proteomic profiling of colorectal carcinoma (CRC) to identify novel proteins with altered expression in CRC. Each pair of tumor and normal tissue specimens from 12 CRC patients was analyzed, and approximately 5000 NBS-labeled paired peaks were quantified. Peaks with altered signal intensities (>1.5-fold) and occurring frequently in the samples (>70%) were selected, and 128 proteins were identified by MS/MS analyses as differentially expressed proteins in CRC tissues. Many proteins were newly revealed to be CRC related; 30 were reported in earlier studies of CRC. Six proteins that were up-regulated in CRC (ZYX, RAN, RCN1, AHCY, LGALS1, and VIM) were further characterized and validated by Western blot and immunohistochemistry. All six were found to be CRC-localized, either in cancer cells or in stroma cells near the cancer cells. These results indicate that the proteins identified in this study are novel candidates for CRC markers, and that the NBS method is useful in proteome mining to discover novel biomarkers.
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Affiliation(s)
- Makoto Watanabe
- Division of Disease Proteomics, Institute for Protein Research, Osaka University, Osaka, Japan; Life Science Laboratory, Shimadzu Corporation, Kyoto, Japan
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Todorovski T, Fedorova M, Hoffmann R. Identification of isomeric 5-hydroxytryptophan- and oxindolylalanine-containing peptides by mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:453-459. [PMID: 22689620 DOI: 10.1002/jms.2058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Cells continuously produce reactive oxidative species that can modify all cellular components. In proteins, for example, cysteine, methionine, tryptophan (Trp), and tyrosine residues are particularly prone to oxidation. Here, we report two new approaches to distinguish two isomeric oxidation products of Trp residues, i.e. 5-hydroxytryptophan (5-HTP) and oxindolylalanine (Oia) residues, in peptides. First, 2-nitrobenzenesulfenyl chloride, known to derivatize Trp residues in position 2 of the indole ring, was used to label 5-HTP residues. The mass shift of 152.98 m/z units allowed identifying 5-HTP- besides Trp-containing peptides by mass spectrometry, whereas Oia residues were not labeled. Second, fragmentation of the Oia- and 5-HTP-derived immonium ions at m/z 175.08 produced ions characteristic for each residue that allowed their identification even in the presence of y(1) ions at m/z 175.12 derived from peptides with C-terminal arginine residues. The pseudo MS(3) spectra acquired on a quadrupole time-of-flight hybrid mass spectrometer displayed two signals at m/z 130.05 and m/z 132.05 characteristic for Oia-containing peptides and a group of six signals (m/z 103.04, 120.04, 130.04, 133.03, 146.04, and 148.04) for 5-HTP-cointaining peptides. In both cases, the relative signal intensities appeared to be independent of the sequence providing a specific fingerprint of each oxidative modification.
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Affiliation(s)
- Toni Todorovski
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany
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Shimada T, Kuyama H, Sato TA, Tanaka K. Development of iodoacetic acid-based cysteine mass tags: Detection enhancement for cysteine-containing peptide by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anal Biochem 2012; 421:785-7. [DOI: 10.1016/j.ab.2011.12.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/12/2011] [Accepted: 12/02/2011] [Indexed: 01/23/2023]
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18
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Matsubara T, Mita A, Minami K, Hosooka T, Kitazawa S, Takahashi K, Tamori Y, Yokoi N, Watanabe M, Matsuo EI, Nishimura O, Seino S. PGRN is a key adipokine mediating high fat diet-induced insulin resistance and obesity through IL-6 in adipose tissue. Cell Metab 2012; 15:38-50. [PMID: 22225875 DOI: 10.1016/j.cmet.2011.12.002] [Citation(s) in RCA: 198] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 09/23/2011] [Accepted: 12/02/2011] [Indexed: 01/14/2023]
Abstract
Adipose tissue secretes adipokines that mediate insulin resistance, a characteristic feature of obesity and type 2 diabetes. By differential proteome analysis of cellular models of insulin resistance, we identified progranulin (PGRN) as an adipokine induced by TNF-α and dexamethasone. PGRN in blood and adipose tissues was markedly increased in obese mouse models and was normalized with treatment of pioglitazone, an insulin-sensitizing agent. Ablation of PGRN (Grn(-/-)) prevented mice from high fat diet (HFD)-induced insulin resistance, adipocyte hypertrophy, and obesity. Grn deficiency blocked elevation of IL-6, an inflammatory cytokine, induced by HFD in blood and adipose tissues. Insulin resistance induced by chronic administration of PGRN was suppressed by neutralizing IL-6 in vivo. Thus, PGRN is a key adipokine that mediates HFD-induced insulin resistance and obesity through production of IL-6 in adipose tissue, and may be a promising therapeutic target for obesity.
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Affiliation(s)
- Toshiya Matsubara
- Division of Cellular and Molecular Medicine, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
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Hydrazide-functionalized magnetic microspheres for the selective enrichment of digested tryptophan-containing peptides in serum. Talanta 2011; 85:1001-6. [DOI: 10.1016/j.talanta.2011.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 05/03/2011] [Accepted: 05/05/2011] [Indexed: 11/23/2022]
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20
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Wang C, Ye M, Han G, Chen R, Zhang M, Jiang X, Cheng K, Wang F, Zou H. Enrichment of peptides containing consensus sequence by an enzymatic approach for targeted analysis ofproteins. Proteomics 2011; 11:3578-81. [DOI: 10.1002/pmic.201100041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Revised: 05/17/2011] [Accepted: 06/09/2011] [Indexed: 01/25/2023]
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21
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Nutriproteomics: technologies and applications for identification and quantification of biomarkers and ingredients. Proc Nutr Soc 2011; 70:351-64. [DOI: 10.1017/s0029665111000528] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Nutrition refers to the process by which a living organism ingests and digests food and uses the nutrients therein for growth, tissue maintenance and all other functions essential to life. Food components interact with our body at molecular, cellular, organ and system level. Nutrients come in complex mixtures, in which the presence and concentration of single compounds as well as their interactions with other compounds and the food matrix influence their bioavailability and bioefficacy. Traditionally, nutrition research mainly concentrated on supplying nutrients of quality to nourish populations and on preventing specific nutrient deficiencies. More recently, it investigates health-related aspects of individual ingredients or of complete diets, in view of health promotion, performance optimisation, disease prevention and risk assessment. This review focuses on proteins and peptides, their role as nutrients and biomarkers and on the technologies developed for their analysis. In the first part of this review, we provide insights into the way proteins are currently characterised and analysed using classical and emerging proteomic approaches. The scope of the second part is to review major applications of proteomics to nutrition, from characterisation of food proteins and peptides, via investigation of health-related food benefits to understanding disease-related mechanisms.
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Toyama A, Nakagawa H, Matsuda K, Ishikawa N, Kohno N, Daigo Y, Sato TA, Nakamura Y, Ueda K. Deglycosylation and label-free quantitative LC-MALDI MS applied to efficient serum biomarker discovery of lung cancer. Proteome Sci 2011; 9:18. [PMID: 21473792 PMCID: PMC3090313 DOI: 10.1186/1477-5956-9-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 04/08/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Serum is an ideal source of biomarker discovery and proteomic profiling studies are continuously pursued on serum samples. However, serum is featured by high level of protein glycosylations that often cause ionization suppression and confound accurate quantification analysis by mass spectrometry. Here we investigated the effect of N-glycan and sialic acid removal from serum proteins on the performance of label-free quantification results. RESULTS Serum tryptic digests with or without deglycosylation treatment were analyzed by LC-MALDI MS and quantitatively compared on the Expressionist Refiner MS module. As a result, 345 out of 2,984 peaks (11.6%) showed the specific detection or the significantly improved intensities in deglycosylated serum samples (P < 0.01). We then applied this deglycosylation-based sample preparation to the identification of lung cancer biomarkers. In comparison between 10 healthy controls and 20 lung cancer patients, 40 peptides were identified to be differentially presented (P < 0.01). Their quantitative accuracies were further verified by multiple reaction monitoring. The result showed that deglycosylation was needed for the identification of some unique candidates, including previously unreported O-linked glycopeptide of complement component C9. CONCLUSIONS We demonstrated here that sample deglycosylation improves the quantitative performance of shotgun proteomics, which can be effectively applied to any samples with high glycoprotein contents.
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Affiliation(s)
- Atsuhiko Toyama
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Tsurumiku-Suehirocho1-7-22, Yokohama, Japan.
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Huang YQ, Liu JQ, Gong H, Yang J, Li Y, Feng YQ. Use of isotope mass probes for metabolic analysis of the jasmonate biosynthetic pathway. Analyst 2011; 136:1515-22. [DOI: 10.1039/c0an00736f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Uto H, Kanmura S, Takami Y, Tsubouchi H. Clinical proteomics for liver disease: a promising approach for discovery of novel biomarkers. Proteome Sci 2010; 8:70. [PMID: 21192835 PMCID: PMC3023778 DOI: 10.1186/1477-5956-8-70] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 12/31/2010] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer and advanced hepatic fibrosis is a major risk factor for HCC. Hepatic fibrosis including liver cirrhosis and HCC are mainly induced by persistent hepatitis B or C virus infection, with approximately 500 million people infected with hepatitis B or C virus worldwide. Furthermore, the number of patients with non-alcoholic fatty liver disease (NAFLD) has recently increased and NAFLD can progress to cirrhosis and HCC. These chronic liver diseases are major causes of morbidity and mortality, and the identification of non-invasive biomarkers is important for early diagnosis. Recent advancements in quantitative and large-scale proteomic methods could be used to optimize the clinical application of biomarkers. Early diagnosis of HCC and assessment of the stage of hepatic fibrosis or NAFLD can also contribute to more effective therapeutic interventions and an improve prognosis. Furthermore, advancements of proteomic techniques contribute not only to the discovery of clinically useful biomarkers, but also in clarifying the molecular mechanisms of disease pathogenesis by using body fluids, such as serum, and tissue samples and cultured cells. In this review, we report recent advances in quantitative proteomics and several findings focused on liver diseases, including HCC, NAFLD, hepatic fibrosis and hepatitis B or C virus infections.
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Affiliation(s)
- Hirofumi Uto
- Department of Digestive and Lifestyle-related Diseases, Health Research Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, 890-8544, Japan.
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Roeser J, Bischoff R, Bruins AP, Permentier HP. Oxidative protein labeling in mass-spectrometry-based proteomics. Anal Bioanal Chem 2010; 397:3441-55. [PMID: 20155254 PMCID: PMC2911539 DOI: 10.1007/s00216-010-3471-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/11/2010] [Accepted: 01/12/2010] [Indexed: 01/07/2023]
Abstract
Oxidation of proteins and peptides is a common phenomenon, and can be employed as a labeling technique for mass-spectrometry-based proteomics. Nonspecific oxidative labeling methods can modify almost any amino acid residue in a protein or only surface-exposed regions. Specific agents may label reactive functional groups in amino acids, primarily cysteine, methionine, tyrosine, and tryptophan. Nonspecific radical intermediates (reactive oxygen, nitrogen, or halogen species) can be produced by chemical, photochemical, electrochemical, or enzymatic methods. More targeted oxidation can be achieved by chemical reagents but also by direct electrochemical oxidation, which opens the way to instrumental labeling methods. Oxidative labeling of amino acids in the context of liquid chromatography(LC)-mass spectrometry (MS) based proteomics allows for differential LC separation, improved MS ionization, and label-specific fragmentation and detection. Oxidation of proteins can create new reactive groups which are useful for secondary, more conventional derivatization reactions with, e.g., fluorescent labels. This review summarizes reactions of oxidizing agents with peptides and proteins, the corresponding methodologies and instrumentation, and the major, innovative applications of oxidative protein labeling described in selected literature from the last decade.
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Affiliation(s)
- Julien Roeser
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Andries P. Bruins
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hjalmar P. Permentier
- Analytical Biochemistry and Mass Spectrometry Core Facility, Department of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Takami Y, Uto H, Tamai T, Sato Y, Ishida YI, Morinaga H, Sakakibara Y, Moriuchi A, Oketani M, Ido A, Nakajima T, Okanoue T, Tsubouchi H. Identification of a novel biomarker for oxidative stress induced by hydrogen peroxide in primary human hepatocytes using the 2-nitrobenzenesulfenyl chloride isotope labeling method. Hepatol Res 2010; 40:438-45. [PMID: 20236361 DOI: 10.1111/j.1872-034x.2009.00615.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
AIM Oxidative stress is involved in the progression of non-alcoholic steatohepatitis (NASH). However, there are few biomarkers that are easily measured and accurately reflect the disease states. The aim of this study was to identify novel oxidative stress markers using the 2-nitrobenzenesulfenyl (NBS) stable isotope labeling method and to examine the clinical utility of these diagnostic markers for NASH. METHODS Proteins extracted from phosphate buffered saline- and hydrogen peroxide-loaded human primary hepatocyte were labeled with the [(12)C]- and [(13)C]-NBS reagents, respectively. Pairs of peaks with 6-Da differences in which the [(13)C]-NBS labeling was more intense than the [(12)C]-NBS labeling were detected by MALDI-TOF/MS and identified by MS/MS ion searching. RESULTS Four pairs of peaks, m/z 1705-1711, m/z 1783-1789, m/z 1902-1908 and m/z 2790-2796, were identified as cytochrome c oxidase VIb (COX6B), liver carboxylesterase 1 (CES1), carbamoyl-phosphate synthase 1 (CPS1) and superoxide dismutase (MnSOD), respectively. Furthermore, serum MnSOD protein levels were significantly higher in NASH patients than in simple steatosis (SS) patients. The serum MnSOD levels tended to increase in parallel with the stage of fibrosis. CONCLUSION The NBS labeling technique was useful to identify biomarkers. Serum MnSOD may be a useful biomarker that can distinguish between SS and NASH.
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Affiliation(s)
- Yoichiro Takami
- Department of Digestive and Lifestyle-related Disease, Health Research, Human and Environmental Sciences, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima
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KANAZAWA M, ANYOJI H, TU HK, NAGASHIMI U, OGIWARA A. Quantitative Proteomic Analysis System: i-OPAL. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2010. [DOI: 10.2477/jccj.h2117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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28
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Synthesis of 13C7-labeled iodoacetanilide and application to quantitative analysis of peptides and a protein by isotope differential mass spectrometry. Bioorg Med Chem Lett 2009; 19:5698-702. [DOI: 10.1016/j.bmcl.2009.08.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Revised: 08/02/2009] [Accepted: 08/04/2009] [Indexed: 12/21/2022]
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29
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Matsuo EI, Watanabe M, Kuyama H, Nishimura O. A new strategy for protein biomarker discovery utilizing 2-nitrobenzenesulfenyl (NBS) reagent and its applications to clinical samples. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:2607-14. [DOI: 10.1016/j.jchromb.2009.05.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 04/06/2009] [Accepted: 05/24/2009] [Indexed: 12/11/2022]
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Okamura N, Masuda T, Gotoh A, Shirakawa T, Terao S, Kaneko N, Suganuma K, Watanabe M, Matsubara T, Seto R, Matsumoto J, Kawakami M, Yamamori M, Nakamura T, Yagami T, Sakaeda T, Fujisawa M, Nishimura O, Okumura K. Quantitative proteomic analysis to discover potential diagnostic markers and therapeutic targets in human renal cell carcinoma. Proteomics 2008; 8:3194-203. [DOI: 10.1002/pmic.200700619] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Quantitative proteomics as a new piece of the systems biology puzzle. J Proteomics 2008; 71:357-67. [PMID: 18640294 DOI: 10.1016/j.jprot.2008.07.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 06/30/2008] [Accepted: 07/02/2008] [Indexed: 12/19/2022]
Abstract
The definition of the role of each gene product in its cellular context is of outstanding importance in the post-genomics era. Recent technological innovations have driven research in proteomics from single protein characterization to global approaches, aiming to achieve a comprehensive qualitative and quantitative description of complex molecular mechanisms. In this review, we discuss the methodology of quantitative proteomics as it applies to the analysis of complex biological model systems. A special attention will be given to model systems that are suitable for functional genomic studies, where the potential of quantitative proteomics can be effectively demonstrated.
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Fojta M, Billová S, Havran L, Pivoňková H, Černocká H, Horáková P, Paleček E. Osmium Tetroxide, 2,2′-Bipyridine: Electroactive Marker for Probing Accessibility of Tryptophan Residues in Proteins. Anal Chem 2008; 80:4598-605. [DOI: 10.1021/ac800527u] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miroslav Fojta
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Sabina Billová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Luděk Havran
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Hana Pivoňková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Hana Černocká
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petra Horáková
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic, and Department of Functional Genomics and Proteomics, Institute of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Froelich JM, Reid GE. The origin and control of ex vivo oxidative peptide modifications prior to mass spectrometry analysis. Proteomics 2008; 8:1334-45. [PMID: 18306178 DOI: 10.1002/pmic.200700792] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The origin and control of ex vivo sample handling related oxidative modifications of methionine-, S-alkyl cysteine-, and tryptophan-containing peptides obtained from typical "in-solution" or "in-gel" proteolytic digestion strategies, have been examined by capillary HPLC and MS/MS. The origin of increased oxidation levels were found to be predominantly associated with the extensive ex vivo sample handling steps required for gel electrophoresis and/or in-gel proteolytic digestion of proteins prior to analysis by MS. Conditions for deliberately controlling the oxidation state (both oxidation and reduction) of these peptides, as well as for those containing cysteine, have been evaluated using a series of model synthetic peptides and standard tryptic protein digests. Essentially complete oxidation of methionine- and S-alkyl cysteine-containing peptides was achieved by reaction with 30% hydrogen peroxide/5% acetic acid at room temperature for 30 min. Under these conditions, cysteine was also converted to cysteic acid, while only limited oxidation of tryptophan to oxindolylalanine, and methionine and S-alkyl cysteine sulfoxides to their respective sulfones, were observed. Efficient reduction of methionine- and S-alkyl cysteine sulfoxide-containing peptides was achieved by reaction in 1 M dimethylsulfide/10 M hydrochloric acid at room temperature for 10 and 45 min, respectively. None of the reduction conditions evaluated were found to result in the reduction of oxindolylalanine, cysteic acid, or methionine sulfone.
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Affiliation(s)
- Jennifer M Froelich
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
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Sun MC, Chen CD, Huang YS, Wu ZS, Ho YP. Matrix-assisted laser desorption/ionization-MS-based relative quantification of peptides and proteins using iodoacetamide and N-methyliodoacetamide as labeling reagents. J Sep Sci 2008; 31:538-47. [PMID: 18210377 DOI: 10.1002/jssc.200700440] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The use of iodoacetamide (IAA) and N-methyliodoacetamide (MIAA) as labeling agents for the relative measurements of proteins using MALDI-MS is described herein. These reagents, which alkylate the thiol groups of cysteine residues in proteins, were introduced during the alkylation step of a common protein denaturation and digestion process. This approach is simpler and cheaper than those involving isotope labeling agents. The labeling agents described herein displayed good dynamic ranges and correlation coefficients for protein quantification analyses when the proteins were treated through either in-solution or in-gel digestion. The best dynamic ranges (in the molar ratio) for proteins lysozyme, transferrin, and BSA (in-solution digestion) are 0.1-10, 0.1-8, and 0.1-8, respectively. The corresponding correlation coefficients are greater than 0.99. The IAA/MIAA labeling is a useful method for the relative quantification of peptides and digested proteins when the chromatographic isotope effect is not a major concern.
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Affiliation(s)
- Mei-Chuan Sun
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan, ROC
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35
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Experimental and computational approaches to quantitative proteomics: Status quo and outlook. J Proteomics 2008; 71:19-33. [DOI: 10.1016/j.jprot.2007.12.001] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 12/14/2007] [Accepted: 12/18/2007] [Indexed: 01/11/2023]
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36
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Yeo WS, Lee SJ, Lee JR, Kim KP. Nitrosative protein tyrosine modifications: biochemistry and functional significance. BMB Rep 2008; 41:194-203. [DOI: 10.5483/bmbrep.2008.41.3.194] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Jiang X, Ye M, Zou H. Technologies and methods for sample pretreatment in efficient proteome and peptidome analysis. Proteomics 2008; 8:686-705. [DOI: 10.1002/pmic.200700617] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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38
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Gevaert K, Van Damme P, Ghesquière B, Impens F, Martens L, Helsens K, Vandekerckhove J. A la carte proteomics with an emphasis on gel-free techniques. Proteomics 2007; 7:2698-718. [PMID: 17640001 DOI: 10.1002/pmic.200700114] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Since the introduction of the proteome term somewhat more than a decade ago the field of proteomics witnessed a rapid growth mainly fueled by instrumental analytical improvements. Of particular notice is the advent of a diverse set of gel-free proteomics techniques. In this review, we discuss several of these gel-free techniques both for monitoring protein concentration changes and protein modifications, in particular protein phosphorylation, glycosylation, and protein processing. Furthermore, different approaches for (multiplexed) gel-free proteome analysis are discussed.
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Affiliation(s)
- Kris Gevaert
- Department of Medical Protein Research, VIB, Ghent, Belgium.
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39
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Zhang J, Zhang L, Zhou Y, Guo YL. A novel pyrimidine-based stable-isotope labeling reagent and its application to quantitative analysis using matrix-assisted laser desorption/ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:1514-21. [PMID: 17618528 DOI: 10.1002/jms.1260] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
As an extension of our previous work, a novel pyrimidine-based stable-isotope labeling reagent, [d(0)]-/[d(6)]-4,6-dimethoxy-2-(methylsulfonyl)pyrimidine (DMMSP), was developed for comparative quantification of proteins by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Our one-step labeling strategy combines several desirable properties such as cysteine-specific labeling, signal amplification and direct analysis with minimum sample handling. All these features not only allow easy interpretation for protein identification and quantification but also ensure rapid and sensitive progression to MS analysis. Using cysteine, Cys-containing peptide, and lysozyme digest as model samples, the labeling methodology was established and the following pilot application for quantitative analysis was accomplished with high confidence, accuracy, efficiency, and reproducibility. The application of DMMSP-labeling strategy is expected to provide a powerful new tool for comparative proteome research, especially for the analysis of low-abundance proteins.
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Affiliation(s)
- Jing Zhang
- Shanghai Mass Spectrometry Center, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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40
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Abstract
Creating protein profiles of tissues and tissue fluids, which contain secreted proteins and peptides released from various cells, is critical for biomarker discovery as well as drug and vaccine target selection. It is extremely difficult to obtain pure samples from tissues or tissue fluids, however, and identification of complex protein mixtures is still a challenge for mass spectrometry analysis. Here, we summarize recent advances in techniques for extracting proteins from tissues for mass spectrometry profiling and imaging. We also introduce a novel technique using a capillary ultrafiltration (CUF) probe to enable in vivo collection of proteins from the tissue microenvironment. The CUF probe technique is compared with existing sampling techniques, including perfusion, saline wash, fine-needle aspiration and microdialysis. In this review, we also highlight quantitative mass spectrometric proteomic approaches with, and without, stable-isotope labels. Advances in quantitative proteomics will significantly improve protein profiling of tissue and tissue fluid samples collected by CUF probes.
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Affiliation(s)
- Shi Yang
- The Burnham Institute for Medical Research, Proteomics Facility, La Jolla, CA 92037, USA.
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41
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Ivakhno S, Kornelyuk A. Quantitative proteomics and its applications for systems biology. BIOCHEMISTRY (MOSCOW) 2007; 71:1060-72. [PMID: 17125453 DOI: 10.1134/s0006297906100026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Here we discuss the current state of research in the rapidly growing field of quantitative proteomics and its applications to systems biology. Quantitative proteomics can be successfully used for characterizing alterations in protein abundance, finding novel protein-protein and protein-peptide interactions, investigating formation of large macromolecular complexes, and elucidating temporal changes in organellar protein composition and phosphorylation in signal transduction cascades. Further, quantitative proteomics can directly compare activation of entire signaling networks in response to individual stimuli and discover critical differences in their circuits that account for alterations of cell response. Maturation of proteomic bioinformatics applications and continuous improvements in proteomics and related genomics and transcriptomics technologies now allows us to investigate cellular mechanisms at the integrative system level.
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Affiliation(s)
- S Ivakhno
- University of Edinburgh, School of Informatics, Edinburgh, EH8 9LE, Scotland, UK.
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42
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Leitner A, Lindner W. Chemistry meets proteomics: the use of chemical tagging reactions for MS-based proteomics. Proteomics 2007; 6:5418-34. [PMID: 16972287 DOI: 10.1002/pmic.200600255] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
As proteomics matures from a purely descriptive to a function-oriented discipline of the life sciences, there is strong demand for novel methodologies that increase the depth of information that can be obtained from proteomic studies. MS has long played a central role for protein identification and characterization, often in combination with dedicated chemical modification reactions. Today, chemistry is helping to advance the field of proteomics in numerous ways. In this review, we focus on those methodologies that have a significant impact for the large-scale study of proteins and peptides. This includes approaches that allow the introduction of affinity tags for the enrichment of subclasses of peptides or proteins and strategies for in vitro stable isotope labeling for quantification purposes, among others. Particular attention is given to the study of PTMs where recent advancements have been promising, but many interesting targets are not yet being addressed.
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Affiliation(s)
- Alexander Leitner
- Department of Analytical Chemistry and Food Chemistry, University of Vienna, Vienna, Austria.
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43
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Tsumoto H, Murata C, Miyata N, Kohda K, Taguchi R. Efficient identification and quantification of proteins using isotope-coded 1-(6-methylnicotinoyloxy)succinimides by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2007; 21:3815-3824. [PMID: 17972273 DOI: 10.1002/rcm.3279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We describe a convenient and useful method for the identification and relative quantification of proteins using light and heavy reagents, 1-(6-methylnicotinoyloxy)succinimides (6-CH(3)-Nic-NHS and 6-CD(3)-Nic-NHS, respectively). This method is based on the chemical derivatization of amino groups of tryptic peptides with these reagents, i.e., the basic moiety of the reagents thus incorporated into both the N-terminal amino group and the epsilon-amino group of the lysine residue would improve the ionization efficiency of tryptic peptides. An increase in protein sequence coverage is achieved by derivatization with these reagents or by combination of mass values before and after derivatization. Since a combination of 6-CH(3)-Nic-NHS and d(3)-labeled reagent (6-CD(3)-Nic-NHS) generates a 3 Da mass difference per reaction site, the d(3)-labeled reagent shifts the mass values of d(0)-labeled peptides according to the number of reactive amino groups in the peptides. In the case of tryptic peptides, the mass values of C-terminal arginine and lysine peptides are shifted by 3 and 6 Da, respectively. Further, the 3 Da mass difference between 6-CH(3)-Nic-NHS and 6-CD(3)-Nic-NHS offers a means for the relative quantification of protein by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
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Affiliation(s)
- Hiroki Tsumoto
- Research Institute of Pharmaceutical Sciences, Musashino University, Shinmachi Nishitokyo-shi, Tokyo 202-8585, Japan
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44
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Synthesis of D-labeled naphthyliodoacetamide and application to quantitative peptide analysis by isotope differential mass spectrometry. Bioorg Med Chem Lett 2006; 16:6054-7. [DOI: 10.1016/j.bmcl.2006.08.112] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2006] [Revised: 08/28/2006] [Accepted: 08/29/2006] [Indexed: 11/19/2022]
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45
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Nordhoff E, Lehrach H. Identification and characterization of DNA-binding proteins by mass spectrometry. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2006; 104:111-95. [PMID: 17290821 DOI: 10.1007/10_2006_037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry is the most sensitive and specific analytical technique available for protein identification and quantification. Over the past 10 years, by the use of mass spectrometric techniques hundreds of previously unknown proteins have been identified as DNA-binding proteins that are involved in the regulation of gene expression, replication, or DNA repair. Beyond this task, the applications of mass spectrometry cover all aspects from sequence and modification analysis to protein structure, dynamics, and interactions. In particular, two new, complementary ionization techniques have made this possible: matrix-assisted laser desorption/ionization and electrospray ionization. Their combination with different mass-over-charge analyzers and ion fragmentation techniques, as well as specific enzymatic or chemical reactions and other analytical techniques, has led to the development of a broad repertoire of mass spectrometric methods that are now available for the identification and detailed characterization of DNA-binding proteins. These techniques, how they work, what their requirements and limitations are, and selected examples that document their performance are described and discussed in this chapter.
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Affiliation(s)
- Eckhard Nordhoff
- Department Lehrach, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
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46
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Kurono S, Kurono T, Komori N, Niwayama S, Matsumoto H. Quantitative proteome analysis using D-labeled N-ethylmaleimide and 13C-labeled iodoacetanilide by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Bioorg Med Chem 2006; 14:8197-209. [PMID: 17049249 PMCID: PMC1876768 DOI: 10.1016/j.bmc.2006.09.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Revised: 09/12/2006] [Accepted: 09/12/2006] [Indexed: 11/16/2022]
Abstract
A new methodology for quantitative analysis of proteins is described, applying stable-isotope labeling by small organic molecules combined with one- or two-dimensional electrophoresis and MALDI-TOF-MS, also allowing concurrent protein identification by peptide mass fingerprinting. Our method eliminates fundamental problems in other existing isotope-tagging methods requiring liquid chromatography and MS/MS, such as isotope effects, fragmentation, and solubility. It is also anticipated to be more practical and accessible than those LC-dependent methods.
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47
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Bublitz R, Kreusch S, Ditze G, Schulze M, Cumme GA, Fischer C, Winter A, Hoppe H, Rhode H. Robust protein quantitation in chromatographic fractions using MALDI-MS of tryptic peptides. Proteomics 2006; 6:3909-17. [PMID: 16739130 DOI: 10.1002/pmic.200500747] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A method is introduced to evaluate protein concentrations using the height sum of all MALDI-MS peaks that unambiguously match theoretic tryptic peptide masses of the protein sought after. The method uses native chromatographic protein fractionation prior to digestion but does not require any depletion, labeling, derivatization, or preparation of a compound similar to the analyte. All peak heights of tryptic peptides are normalized with the peak height of a unique standard peptide added to the MALDI-MS samples. The sum of normalized peak heights, S(n), or the normalized mean peak height, M(n), reflects the concentration of the respective protein. For fractions containing various proteins, S(n) and M(n) can be used to compare concentrations of a protein between different fractions. For fractions with one predominating protein, they can be used to estimate concentration ratios between fractions, or to quantify the fractional protein concentration after calibration with pure protein solutions. Initial native fractionation retains the possibility to apply all conventional analytic procedures. Moreover, it renders the method relatively robust to MS mass accuracy. The method was validated with albumin, transferrin, alpha1-antitrypsin, and immunoglobulin G within highly complex chromatographic fractions of pathological and normal sera, which contained the respective intact native protein in dominating as well as minor concentrations. The correlation found between S(n) and the protein concentration as determined with ELISA showed that the method can be applied to select markers for distinguishing between normal and pathological serum samples.
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Affiliation(s)
- Renate Bublitz
- Institute of Biochemistry I, Medical Faculty, Friedrich Schiller University, D-07740 Jena, Germany
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48
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Matsuo EI, Toda C, Watanabe M, Ojima N, Izumi S, Tanaka K, Tsunasawa S, Nishimura O. Selective detection of 2-nitrobenzenesulfenyl-labeled peptides by matrix-assisted laser desorption/ionization-time of flight mass spectrometry using a novel matrix. Proteomics 2006; 6:2042-9. [PMID: 16521152 DOI: 10.1002/pmic.200500575] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The 2-nitrobenzenesulfenyl (NBS) method, which is useful for quantitative proteome analysis, is based on stable isotope labeling of tryptophan residues with NBS chloride ((12)C(6)-NBSCl or (13)C(6)-NBSCl). We found that 3-hydroxy-4-nitrobenzoic acid (3H4NBA) is a more suitable matrix than 2,5-dihydroxybenzoic acid (DHB) for detecting NBS-labeled peptides by MALDI-quadrupole IT (QIT)-TOF MS . Furthermore, NBS-labeled peptides were selectively ionized and detected in a mixture of NBS-labeled and unlabeled peptides. Labeled paired peaks were easily detected without enrichment, nonpaired labeled peaks were clearly distinguished from unlabeled contaminating peptides, and nitrotyrosine-containing peptides were also selectively detected on the 3H4NBA matrix, while by-product-peaks arising from nitrobenzene moieties were suppressed. The use of 3H4NBA as a comatrix with CHCA improved the sensitivity of detection while substantially retaining the selectivity of 3H4NBA. The 3H4NBA matrix offers great advantages in terms of simplicity, sensitivity, and usability when used for the NBS method and for MALDI-TOF MS analysis applied to compounds having a nitrobenzene ring.
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Affiliation(s)
- Ei-Ichi Matsuo
- Life Science Laboratory, Shimadzu Corporation, Nakagyo-ku, Kyoto, Japan
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49
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Abstract
The field of proteomics is built on technologies to analyze large numbers of proteins--ideally the entire proteome--in the same experiment. Mass spectrometry (MS) has been successfully used to characterize proteins in complex mixtures, but results so far have largely been qualitative. Two recently developed methodologies offer the opportunity to obtain quantitative proteomic information. Comparing the signals from the same peptide under different conditions yields a rough estimate of relative protein abundance between two proteomes. Alternatively, and more accurately, peptides are labeled with stable isotopes, introducing a predictable mass difference between peptides from two experimental conditions. Stable isotope labels can be incorporated 'post-harvest', by chemical approaches or in live cells through metabolic incorporation. This isotopic handle facilitates direct quantification from the mass spectra. Using these quantitative approaches, precise functional information as well as temporal changes in the proteome can be captured by MS.
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Affiliation(s)
- Shao-En Ong
- The Broad Institute of MIT and Harvard, 320 Bent Street, Cambridge, Massachusetts 02141, USA.
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50
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Li C, Gawandi V, Protos A, Phillips RS, Amster IJ. A matrix-assisted laser desorption/ionization compatible reagent for tagging tryptophan residues. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2006; 12:213-21. [PMID: 17057278 DOI: 10.1255/ejms.814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Chemical tagging of amino acids is an important tool in proteomics analysis, and has been used to introduce isotope labels and mass defect labels into proteolytic peptides by derivatization of cysteine or lysine residues. Here, we present a new reagent with chemical specificity for tryptophan residues. Previously, 2-nitrobenzenesulfenyl chloride has been used as a highly specific reagent for labeling tryptophan residues. We show that this tag undergoes UV dissociation during matrix assisted laser desorption/ionization (MALDI). The multiplicity of photofragments increases the difficulty of characterizing the derivatization products. To overcome this problem, we have synthesized a new reagent, 2-(trifluoromethyl)benzenesulfenyl chloride, which is shown to react quantitatively with tryptophan in peptides and proteins. Most significantly, it exhibits high photostability in MALDI-Fourier transform mass spectrometry analyses.
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Affiliation(s)
- Chunyan Li
- Department of Chemistry, University of Georgia, Athens, Georgia 30602, USA
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