1
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Sun Z, Xiao W, Li N, Chang L, Xu P, Li Y. Large-Scale Profiling of Unexpected Tryptic Cleaved Sites at Ubiquitinated Lysines. J Proteome Res 2023; 22:1245-1254. [PMID: 36877145 DOI: 10.1021/acs.jproteome.2c00748] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Trypsin specifically cleaves the C-terminus of lysine and arginine residues but often fails to cleave modified lysines, such as ubiquitination, therefore resulting in the uncleaved K-ε-GG peptides. Therefore, the cleaved ubiquitinated peptide identification was often regarded as false positives and discarded. Interestingly, unexpected cleavage at the K48-linked ubiquitin chain has been reported, suggesting the latent ability of trypsin to cleave ubiquitinated lysine residues. However, it remains unclear whether other trypsin-cleavable ubiquitinated sites are present. In this study, we verified the ability of trypsin in cleaving K6 and K63 besides K48 chains. The uncleaved K-ε-GG peptide was quickly and efficiently generated during trypsin digestion, whereas cleaved ones were produced with much lower efficiency. Then, the K-ε-GG antibody was proved to efficiently enrich the cleaved K-ε-GG peptides and several published large-scale ubiquitylation datasets were re-analyzed to interrogate the cleaved sequence features. In total, more than 2400 cleaved ubiquitinated peptides were identified in the K-ε-GG and UbiSite antibody-based datasets. The frequency of lysine upstream of the cleaved modified K was significantly enriched. The kinetic activity of trypsin in cleaving ubiquitinated peptides was further elucidated. We suggest that the cleaved K-ε-GG sites with high post-translational modification probability (≥0.75) should be considered as true positives in future ubiquitome analyses.
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Affiliation(s)
- Zhen Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing 102206, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, P. R. China
| | - Weidi Xiao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Naikang Li
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing 102206, China.,Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.,Anhui Medical University, Hefei 230032, China.,School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, P. R. China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Institute of Lifeomics, Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing 102206, China.,Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China.,Anhui Medical University, Hefei 230032, China
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2
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Neely BA, Dorfer V, Martens L, Bludau I, Bouwmeester R, Degroeve S, Deutsch EW, Gessulat S, Käll L, Palczynski P, Payne SH, Rehfeldt TG, Schmidt T, Schwämmle V, Uszkoreit J, Vizcaíno JA, Wilhelm M, Palmblad M. Toward an Integrated Machine Learning Model of a Proteomics Experiment. J Proteome Res 2023; 22:681-696. [PMID: 36744821 PMCID: PMC9990124 DOI: 10.1021/acs.jproteome.2c00711] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In recent years machine learning has made extensive progress in modeling many aspects of mass spectrometry data. We brought together proteomics data generators, repository managers, and machine learning experts in a workshop with the goals to evaluate and explore machine learning applications for realistic modeling of data from multidimensional mass spectrometry-based proteomics analysis of any sample or organism. Following this sample-to-data roadmap helped identify knowledge gaps and define needs. Being able to generate bespoke and realistic synthetic data has legitimate and important uses in system suitability, method development, and algorithm benchmarking, while also posing critical ethical questions. The interdisciplinary nature of the workshop informed discussions of what is currently possible and future opportunities and challenges. In the following perspective we summarize these discussions in the hope of conveying our excitement about the potential of machine learning in proteomics and to inspire future research.
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Affiliation(s)
- Benjamin A Neely
- National Institute of Standards and Technology, Charleston, South Carolina 29412, United States
| | - Viktoria Dorfer
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
| | - Isabell Bludau
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | | | - Lukas Käll
- Science for Life Laboratory, KTH - Royal Institute of Technology, 171 21 Solna, Sweden
| | - Pawel Palczynski
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Samuel H Payne
- Department of Biology, Brigham Young University, Provo, Utah 84602, United States
| | - Tobias Greisager Rehfeldt
- Institute for Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
| | | | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Julian Uszkoreit
- Medical Proteome Analysis, Center for Protein Diagnostics (ProDi), Ruhr University Bochum, 44801 Bochum, Germany.,Medizinisches Proteom-Center, Medical Faculty, Ruhr University Bochum, 44801 Bochum, Germany
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich (TUM), 85354 Freising, Germany
| | - Magnus Palmblad
- Leiden University Medical Center, Postbus 9600, 2300 RC Leiden, The Netherlands
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3
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Yu C, Miao R, Ye Z, MacFarlane S, Lu Y, Li J, Yang J, Yan F, Dai L, Chen J. Integrated Proteomics and Transcriptomics Analyses Reveal the Transcriptional Slippage of P3N-PIPO in a Bymovirus. Viruses 2021; 13:1247. [PMID: 34206959 PMCID: PMC8310318 DOI: 10.3390/v13071247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022] Open
Abstract
P3N-PIPO (P3 N-terminal fused with Pretty Interesting Potyviridae ORF), the movement protein of potyviruses, is expressed as a translational fusion with the N-terminus of P3 in potyviruses. As reported in previous studies, P3N-PIPO is expressed via transcriptional slippage at a conserved G2A6 slippery site in the genus Potyvirus. However, it is still unknown whether a similar expression mechanism of P3N-PIPO is used in the other genera of the family Potyviridae. Moreover, due to the extremely low expression level of P3N-PIPO in natural virus-infected plants, the peptides spanning the slippery site which provide direct evidence of the slippage at the protein level, have not been identified yet. In this study, a potato virus X (PVX)-based expression vector was utilized to investigate the expression mechanism of P3N-PIPO. A high expression level of the P3N-PIPO(WT) of turnip mosaic virus (TuMV, genus Potyvirus) was observed based on the PVX expression vector. For the first time, we successfully identified the peptides of P3N-PIPO spanning the slippery site by mass spectrometry. Likewise, the P3N-PIPO(WT) of wheat yellow mosaic virus (WYMV, genus Bymovirus) was also successfully expressed using the PVX expression vector. Integrated proteome and transcriptome analyses revealed that WYMV P3N-PIPO was expressed at the conserved G2A6 site through transcriptional slippage. Moreover, as revealed by mutagenesis analysis, Hexa-adenosine of the G2A6 site was important for the frameshift expression of P3N-PIPO in WYMV. According to our results, the PVX-based expression vector might be used as an excellent tool to study the expression mechanism of P3N-PIPO in Potyviridae. To the best of our knowledge, this is the first experimental evidence for the expression mechanism of P3N-PIPO in the genus Bymovirus, the only genus comprising bipartite virus species in the family Potyviridae.
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Affiliation(s)
- Chulang Yu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China;
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Runpu Miao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Zhuangxin Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Stuart MacFarlane
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK;
| | - Yuwen Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Junmin Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Jian Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Fei Yan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
| | - Liangying Dai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China;
| | - Jianping Chen
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, China;
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (R.M.); (Z.Y.); (Y.L.); (J.L.); (J.Y.); (F.Y.)
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4
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Fu F, Guo Y, Lu X, Zhao P, Zou S, Wang H, Gao R, Pei C. Forensic analysis of soman exposure using characteristic fragment ions from protein adducts. Hum Exp Toxicol 2021; 40:1519-1527. [PMID: 33729033 DOI: 10.1177/09603271211001111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The verification of exposure to nerve agents is a serious challenge, especially in cases of soman (GD) poisoning. Protein adducts are reliable biomarkers, that provide forensic information and evidence during incidents of terrorism or sporadic poisoning. Mass spectrometry, coupled with a proteomics approach, was established for the forensic analysis of GD-based protein adducts. The fragmentation pathways of GD-based protein adducts were investigated for the first time using electrospray ionization tandem mass spectrometry. Three abundant natural loss product ions, [M+2H-54]2+ (loss of two carbon cations), [M+2H-72]2+ (loss of tert-butyl and methyl moieties), and [M+2H-84]2+ (loss of the pinacolyl moieties), were observed in each of the GD-labeled adducts, and the product ions were independent of protein structure and exposure route. A unique mechanism for the formation of product ions involving GD-protein adducts is proposed here. These findings support the development of a simple and precise forensic analysis technique to rapidly verify GD poisoning using these three GD-related product ions.
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Affiliation(s)
- F Fu
- 535871State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - Y Guo
- 535871State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - X Lu
- 535871State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - P Zhao
- 535871State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - S Zou
- 535871State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - H Wang
- 535871State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - R Gao
- 535871State Key Laboratory of NBC Protection for Civilian, Beijing, China
| | - C Pei
- 535871State Key Laboratory of NBC Protection for Civilian, Beijing, China
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5
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Sun B, Liu Z, Fang X, Wang X, Lai C, Liu L, Xiao C, Jiang Y, Wang F. Improving the performance of proteomic analysis via VAILase cleavage and 193-nm ultraviolet photodissociation. Anal Chim Acta 2021; 1155:338340. [PMID: 33766312 DOI: 10.1016/j.aca.2021.338340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/27/2021] [Accepted: 02/16/2021] [Indexed: 10/22/2022]
Abstract
Further improving the proteomic identification coverage and reliability is still challenging in the mass spectrometry (MS)-based proteomics. Herein, we combine VAILase and trypsin digestion with 193-nm ultraviolet photodissociation (UVPD) and higher-energy collision dissociation (HCD) to improve the performance of bottom-up proteomics. As VAILase exhibits high complementarity to trypsin, the proteome sequence coverage is improved obviously whether with HCD or 193-nm UVPD. The high diversity of fragment ion types produced by UVPD contributes to the improvements of identification reliability for both trypsin- and VAILase-digested peptides with an average XCorr score improvement of 10%.
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Affiliation(s)
- Binwen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Xiang Fang
- National Institute of Metrology, Beijing, 100013, China
| | - Xiaolei Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian, 116023, China
| | - Can Lai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Liu
- School of Life Sciences, Anhui University, 230601, Hefei, Anhui, China
| | - Chunlei Xiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Dalian, 116023, China.
| | - You Jiang
- National Institute of Metrology, Beijing, 100013, China.
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Bubis JA, Gorshkov V, Gorshkov MV, Kjeldsen F. PhosphoShield: Improving Trypsin Digestion of Phosphoproteins by Shielding the Negatively Charged Phosphate Moiety. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2053-2060. [PMID: 32840367 DOI: 10.1021/jasms.0c00171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein phosphorylation is a post-translational modification that is essential to cellular signaling, cellular function, and associated disease progression. Bottom-up proteomics based on enzymatic digestion is the most widely used approach for identifying and quantifying phosphoproteins in complex biological samples. Researchers have largely optimized the experimental conditions for trypsin digestion, and it is now a routine procedure. However, trypsin digestion is impaired by the presence of phosphorylated residues in the protein sequence. This impairment arises from the fact that there are commonly salt bridges between a negatively charged phosphate group and the side chain of protonated arginine or lysine. On average, 55% of all phosphopeptides have their phosphosites located less than three amino acid residues from a cleavage site. Salt bridges reduce the cleavage accessibility for trypsin by masking the basic site chain groups of arginine and lysine. Thus, there are frequent missed cleavages in the vicinity of phosphorylation sites, thereby lessening both the depth of proteome coverage and the quantification accuracy of phosphoproteomics. In this work, we propose a method termed PhosphoShield to mitigate salt bridge formation by adding a digallium complex that exhibits a high binding affinity to the phosphate group. We tested our method using quantitative mass spectrometry analysis of the phosphoproteome of human liver cancer cells (HepG2). PhosphoShield enhances the cleavage frequency of at least 17% of tryptic phosphopeptides having cleavage sites close to the phosphate group.
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Affiliation(s)
- Julia A Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology (State University), 141700 Dolgoprudny, Russia
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
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7
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Rudresha GV, Manjuprasanna VN, Urs AP, Choudhury M, Rajaiah R, Vishwanath BS. Serine protease from Tricosanthus tricuspidata accelerates healing of Echis carinatus venom-induced necrotic wound. Toxicon 2020; 183:1-10. [DOI: 10.1016/j.toxicon.2020.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/11/2020] [Accepted: 05/17/2020] [Indexed: 10/24/2022]
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8
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Schnatbaum K, Solis-Mezarino V, Pokrovsky D, Schäfer F, Nagl D, Hornberger L, Zerweck J, Knaute T, Avramova-Nehmer J, Schutkowski M, Hornung V, Wenschuh H, Völker-Albert MC, Imhof A, Reimer U. New Approaches for Absolute Quantification of Stable-Isotope-Labeled Peptide Standards for Targeted Proteomics Based on a UV Active Tag. Proteomics 2020; 20:e2000007. [PMID: 32267065 DOI: 10.1002/pmic.202000007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Indexed: 01/16/2023]
Abstract
Targeted proteomics depends on the availability of stable isotope labeled (SIL) peptide standards, which for absolute protein quantification need to be absolutely quantified. In the present study, three new approaches for absolute quantification of SIL peptides are developed. All approaches rely on a quantification tag (Qtag) with a specific UV absorption. The Qtag is attached to the peptide during synthesis and is removed by tryptic digestion under standard proteomics workflow conditions. While one quantification method (method A) is designed to allow the fast and economic production of absolutely quantified SIL peptides, two other methods (methods B and C) are developed to enable the straightforward re-quantification of SIL peptides after reconstitution to control and monitor known problems related to peptide solubility, precipitation, and adhesion to vials. All methods yield consistent results when compared to each other and when compared to quantification by amino acid analysis. The precise quantitation methods are used to characterize the in vivo specificity of the H3 specific histone methyltransferase EZH2.
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Affiliation(s)
| | | | - Daniil Pokrovsky
- BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Großhadernerstrasse 9, Planegg-Martinsried, 82152, Germany
| | - Frederike Schäfer
- EpiQMAx GmbH, Großhaderner Str. 9, Planegg-Martinsried, 82152, Germany
| | - Dennis Nagl
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University of Munich, Feodor-Lynen-Straße 25, Munich, 81377, Germany
| | - Lars Hornberger
- JPT Peptide Technologies GmbH, Volmerstrasse 5, Berlin, 12489, Germany
| | - Johannes Zerweck
- JPT Peptide Technologies GmbH, Volmerstrasse 5, Berlin, 12489, Germany
| | - Tobias Knaute
- JPT Peptide Technologies GmbH, Volmerstrasse 5, Berlin, 12489, Germany
| | | | - Mike Schutkowski
- Martin-Luther-Universität Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle, 06120, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-University of Munich, Feodor-Lynen-Straße 25, Munich, 81377, Germany
| | - Holger Wenschuh
- JPT Peptide Technologies GmbH, Volmerstrasse 5, Berlin, 12489, Germany
| | | | - Axel Imhof
- BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University of Munich, Großhadernerstrasse 9, Planegg-Martinsried, 82152, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstrasse 5, Berlin, 12489, Germany
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9
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Fu F, Liu H, Gao R, Zhao P, Lu X, Zhang R, Wang L, Wang H, Pei C. Protein adduct binding properties of tabun-subtype nerve agents after exposure in vitro and in vivo. Toxicol Lett 2020; 321:1-11. [DOI: 10.1016/j.toxlet.2019.12.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 12/09/2019] [Accepted: 12/13/2019] [Indexed: 12/15/2022]
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10
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Choong WK, Chen CT, Wang JH, Sung TY. iHPDM: In Silico Human Proteome Digestion Map with Proteolytic Peptide Analysis and Graphical Visualizations. J Proteome Res 2019; 18:4124-4132. [PMID: 31429573 DOI: 10.1021/acs.jproteome.9b00350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
When conducting proteomics experiments to detect missing proteins and protein isoforms in the human proteome, it is desirable to use a protease that can yield more unique peptides with properties amenable for mass spectrometry analysis. Though trypsin is currently the most widely used protease, some proteins can yield only a limited number of unique peptides by trypsin digestion. Other proteases and multiple proteases have been applied in reported studies to increase the number of identified proteins and protein sequence coverage. To facilitate the selection of proteases, we developed a web-based resource, called in silico Human Proteome Digestion Map (iHPDM), which contains a comprehensive proteolytic peptide database constructed from human proteins, including isoforms, in neXtProt digested by 15 protease combinations of one or two proteases. iHPDM provides convenient functions and graphical visualizations for users to examine and compare the digestion results of different proteases. Notably, it also supports users to input filtering criteria on digested peptides, e.g., peptide length and uniqueness, to select suitable proteases. iHPDM can facilitate protease selection for shotgun proteomics experiments to identify missing proteins, protein isoforms, and single amino acid variant peptides.
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Affiliation(s)
- Wai-Kok Choong
- Institute of Information Science , Academia Sinica , Taipei 11529 , Taiwan
| | - Ching-Tai Chen
- Institute of Information Science , Academia Sinica , Taipei 11529 , Taiwan
| | - Jen-Hung Wang
- Institute of Information Science , Academia Sinica , Taipei 11529 , Taiwan
| | - Ting-Yi Sung
- Institute of Information Science , Academia Sinica , Taipei 11529 , Taiwan
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11
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O'Rourke MB, Town SEL, Dalla PV, Bicknell F, Koh Belic N, Violi JP, Steele JR, Padula MP. What is Normalization? The Strategies Employed in Top-Down and Bottom-Up Proteome Analysis Workflows. Proteomes 2019; 7:proteomes7030029. [PMID: 31443461 PMCID: PMC6789750 DOI: 10.3390/proteomes7030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/20/2022] Open
Abstract
The accurate quantification of changes in the abundance of proteins is one of the main applications of proteomics. The maintenance of accuracy can be affected by bias and error that can occur at many points in the experimental process, and normalization strategies are crucial to attempt to overcome this bias and return the sample to its regular biological condition, or normal state. Much work has been published on performing normalization on data post-acquisition with many algorithms and statistical processes available. However, there are many other sources of bias that can occur during experimental design and sample handling that are currently unaddressed. This article aims to cast light on the potential sources of bias and where normalization could be applied to return the sample to its normal state. Throughout we suggest solutions where possible but, in some cases, solutions are not available. Thus, we see this article as a starting point for discussion of the definition of and the issues surrounding the concept of normalization as it applies to the proteomic analysis of biological samples. Specifically, we discuss a wide range of different normalization techniques that can occur at each stage of the sample preparation and analysis process.
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Affiliation(s)
- Matthew B O'Rourke
- Bowel Cancer & Biomarker Lab, Northern Clinical School, Faculty of Medicine and Health, The University of Sydney Lvl 8, Kolling Institute. Royal North Shore Hospital, St. Leonards, NSW 2065, Australia
| | - Stephanie E L Town
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
| | - Penelope V Dalla
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
- Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, The University of Sydney, Glebe 2037, Australia
| | - Fiona Bicknell
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
| | - Naomi Koh Belic
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
| | - Jake P Violi
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
| | - Joel R Steele
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia
| | - Matthew P Padula
- School of Life Sciences and Proteomics Core Facility, Faculty of Science, The University of Technology Sydney, Ultimo 2007, Australia.
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12
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Verification of soman-related nerve agents via detection of phosphonylated adducts from rabbit albumin in vitro and in vivo. Arch Toxicol 2019; 93:1853-1863. [DOI: 10.1007/s00204-019-02485-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 05/15/2019] [Indexed: 12/17/2022]
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13
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Pseudotrypsin: A Little-Known Trypsin Proteoform. Molecules 2018; 23:molecules23102637. [PMID: 30322187 PMCID: PMC6222510 DOI: 10.3390/molecules23102637] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/06/2018] [Accepted: 10/09/2018] [Indexed: 01/06/2023] Open
Abstract
Trypsin is the protease of choice for protein sample digestion in proteomics. The most typical active forms are the single-chain β-trypsin and the two-chain α-trypsin, which is produced by a limited autolysis of β-trypsin. An additional intra-chain split leads to pseudotrypsin (ψ-trypsin) with three chains interconnected by disulfide bonds, which can be isolated from the autolyzate by ion-exchange chromatography. Based on experimental data with artificial substrates, peptides, and protein standards, ψ-trypsin shows altered kinetic properties, thermodynamic stability and cleavage site preference (and partly also cleavage specificity) compared to the above-mentioned proteoforms. In our laboratory, we have analyzed the performance of bovine ψ-trypsin in the digestion of protein samples with a different complexity. It cleaves predominantly at the characteristic trypsin cleavage sites. However, in a comparison with common tryptic digestion, non-specific cleavages occur more frequently (mostly after the aromatic residues of Tyr and Phe) and more missed cleavages are generated. Because of the preferential cleavages after the basic residues and more developed side specificity, which is not expected to occur for the major trypsin forms (but may appear anyway because of their autolysis), ψ-trypsin produces valuable information, which is complementary in part to data based on a strictly specific trypsin digestion and thus can be unnoticed following common proteomics protocols.
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14
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Benadiba M, Serruya R, Maor Y. Bioaccessibility of Shore Magic ® collagen, a low-molecular-weight collagen supplement, in different in vitro barrier models. Heliyon 2018; 4:e00821. [PMID: 30272033 PMCID: PMC6159004 DOI: 10.1016/j.heliyon.2018.e00821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 08/13/2018] [Accepted: 09/20/2018] [Indexed: 11/27/2022] Open
Abstract
Hydrolyzed collagen consists of peptides, which exert important biological functions in different body systems. This study aimed at testing the biological effects of a low molecular weight collagen (LMWC), namely Shore Magic® Collagen (SMC), in a series of in vitro assays and three different in vitro barrier models with translational significance. We also compared SMC's biological activities with its trypsinized form (TSMC). SMC enhanced migration in both epithelial and endothelial cells; and increased the adhesion of epithelial cells, but surprisingly not of endothelial cells. It also diminished the tightness in the gut and blood-brain barriers in vitro while TSMC did not. SMC induced both neurogenesis and BJ epithelial cell proliferation of cells growing below the in vitro barriers. In conclusion, the intact form of SMC shows enhanced bioavailability and efficiency compared with TSMC.
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Affiliation(s)
| | | | - Yehoshua Maor
- Phytor Lab for Drug Development, Hadassah Medical Center Hebrew University Biotechnology Park (JBP), Ein Kerem Campus, Jerusalem 91120, Israel
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15
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Wu Z, Huang J, Huang J, Li Q, Zhang X. Lys-C/Arg-C, a More Specific and Efficient Digestion Approach for Proteomics Studies. Anal Chem 2018; 90:9700-9707. [DOI: 10.1021/acs.analchem.8b02448] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Zhen Wu
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jichang Huang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jingnan Huang
- 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
| | - Xumin Zhang
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
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16
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Kumar M, Joseph SR, Augsburg M, Bogdanova A, Drechsel D, Vastenhouw NL, Buchholz F, Gentzel M, Shevchenko A. MS Western, a Method of Multiplexed Absolute Protein Quantification is a Practical Alternative to Western Blotting. Mol Cell Proteomics 2017; 17:384-396. [PMID: 29192002 DOI: 10.1074/mcp.o117.067082] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 10/12/2017] [Indexed: 12/23/2022] Open
Abstract
Absolute quantification of proteins elucidates the molecular composition, regulation and dynamics of multiprotein assemblies and networks. Here we report on a method termed MS Western that accurately determines the molar abundance of dozens of user-selected proteins at the subfemtomole level in whole cell or tissue lysates without metabolic or chemical labeling and without using specific antibodies. MS Western relies on GeLC-MS/MS and quantifies proteins by in-gel codigestion with an isotopically labeled QconCAT protein chimera composed of concatenated proteotypic peptides. It requires no purification of the chimera and relates the molar abundance of all proteotypic peptides to a single reference protein. In comparative experiments, MS Western outperformed immunofluorescence Western blotting by the protein detection specificity, linear dynamic range and sensitivity of protein quantification. To validate MS Western in an in vivo experiment, we quantified the molar content of zebrafish core histones H2A, H2B, H3 and H4 during ten stages of early embryogenesis. Accurate quantification (CV<10%) corroborated the anticipated histones equimolar stoichiometry and revealed an unexpected trend in their total abundance.
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Affiliation(s)
- Mukesh Kumar
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Shai R Joseph
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Martina Augsburg
- §Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Aliona Bogdanova
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - David Drechsel
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Nadine L Vastenhouw
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Frank Buchholz
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany.,§Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany.,¶German Cancer Research Center (DKFZ), Heidelberg and German Cancer Consortium (DKTK) partner site Dresden, 01307 Dresden, Germany.,‖National Center for Tumor Diseases (NCT), University Hospital Carl Gustav Carus, TU Dresden, 01307 Dresden, Germany
| | - Marc Gentzel
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- From the ‡Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany;
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17
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Gonczarowska-Jorge H, Loroch S, Dell'Aica M, Sickmann A, Roos A, Zahedi RP. Quantifying Missing (Phospho)Proteome Regions with the Broad-Specificity Protease Subtilisin. Anal Chem 2017; 89:13137-13145. [PMID: 29136377 DOI: 10.1021/acs.analchem.7b02395] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Despite huge efforts to map the human proteome using mass spectrometry the overall sequence coverage achieved to date is still below 50%. Reasons for missing areas of the proteome comprise protease-resistant domains including the lack/excess of enzymatic cleavage sites, nonunique peptide sequences, impaired peptide ionization/separation and low expression levels. To access novel areas of the proteome the beneficial use of enzymes complementary to trypsin, such as Glu-C, Asp-N, Lys-N, Arg-C, LysargiNase has been reported. Here, we present how the broad-specificity protease subtilisin enables mapping of previously hidden areas of the proteome. We systematically evaluated its digestion efficiency and reproducibility and compared it to the gold standard in the field, trypsin. Notably, subtilisin allows reproducible near-complete digestion of cells lysates in 1-5 min. As expected from its broad specificity the generation of overlapping peptide sequences reduces the number of identified proteins compared to trypsin (8363 vs 6807; 1% protein FDR). However, subtilisin considerably improved the coverage of missing and particularly proline-rich areas of the proteome. Along 14 628 high confidence phosphorylation sites identified in total, only 33% were shared between both enzymes, while 37% were exclusive to subtilisin. Notably, 926 of these were not even accessible by additional in silico digestion with either Asp-N, Arg-C, Glu-C, Lys-C, or Lys-N. Thus, subtilisin might be particularly beneficial for system-wide profiling of post-translational modification sites. Finally, we demonstrate that subtilisin can be used for reporter-ion based in-depth quantification, providing a precision comparable to trypsin-despite broad specificity and fast digestion that may increase technical variance.
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Affiliation(s)
- Humberto Gonczarowska-Jorge
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,CAPES Foundation, Ministry of Education of Brazil, Brasília Distrito Federal 70040-020, Brazil
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany
| | - Margherita Dell'Aica
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum , 44801 Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen , Aberdeen, AB24 3FX, United Kingdom
| | - Andreas Roos
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Newcastle University , Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University , Montreal, Quebec H4A 3T2, Canada.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal, Quebec H3T 1E2, Canada
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18
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Thomas CJ, Cleland TP, Zhang S, Gundberg CM, Vashishth D. Identification and characterization of glycation adducts on osteocalcin. Anal Biochem 2017; 525:46-53. [PMID: 28237256 DOI: 10.1016/j.ab.2017.02.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 02/16/2017] [Accepted: 02/17/2017] [Indexed: 02/07/2023]
Abstract
Osteocalcin is an important extracellular matrix bone protein that contributes to the structural properties of bone through its interactions with hydroxyapatite mineral and with collagen I. This role may be affected by glycation, a labile modification the levels of which has been shown to correlate with bone fragility. Glycation starts with the spontaneous addition of a sugar onto a free amine group on a protein, forming an Amadori product, and then proceeds through several environment-dependent stages resulting in the formation of an advanced glycation end product. Here, we induce the first step of this modification on synthetic osteocalcin, and then use multiple mass spectrometry fragmentation techniques to determine the location of this modification. Collision-induced dissociation resulted in spectra dominated by neutral loss, and was unable to identify Amadori products. Electron-transfer dissociation showed that the Amadori product formed solely on osteocalcin's N-terminus. This suggests that the glycation of osteocalcin is unlikely to interfere with osteocalcin's interaction with hydroxyapatite. Instead, glycation may interfere with its interaction with collagen I or another bone protein, osteopontin. Potentially, the levels of glycated osteocalcin fragments released from bone during bone resorption could be used to assess bone quality, should the N-terminal fragments be targeted.
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Affiliation(s)
- Corinne J Thomas
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Timothy P Cleland
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12182, USA
| | - Sheng Zhang
- Cornell University Biotechnology Resource Center, Cornell University, Ithaca, NY 14853, USA
| | - Caren M Gundberg
- Department of Orthopedics and Rehabilitation, Yale University, New Haven, CT 06520, USA
| | - Deepak Vashishth
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12182, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12182, USA.
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19
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Tailor A, Waddington JC, Meng X, Park BK. Mass Spectrometric and Functional Aspects of Drug–Protein Conjugation. Chem Res Toxicol 2016; 29:1912-1935. [DOI: 10.1021/acs.chemrestox.6b00147] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Arun Tailor
- MRC Center
for Drug Safety
Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Sherrington Building, Ashton Street, Liverpool L69 3GE, United Kingdom
| | - James C. Waddington
- MRC Center
for Drug Safety
Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Sherrington Building, Ashton Street, Liverpool L69 3GE, United Kingdom
| | - Xiaoli Meng
- MRC Center
for Drug Safety
Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Sherrington Building, Ashton Street, Liverpool L69 3GE, United Kingdom
| | - B. Kevin Park
- MRC Center
for Drug Safety
Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Sherrington Building, Ashton Street, Liverpool L69 3GE, United Kingdom
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20
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Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate. Anal Bioanal Chem 2016; 408:1963-73. [PMID: 26804737 DOI: 10.1007/s00216-016-9312-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 12/19/2015] [Accepted: 01/04/2016] [Indexed: 12/21/2022]
Abstract
The ionic detergent sodium deoxycholate (SDC) is compatible with in-solution tryptic digestion and LC-MS/MS-based shotgun proteomics by virtue of being easy to separate from the peptide products via precipitation in acidic buffers. However, it remains unclear whether unique human peptides co-precipitate with SDC during acid treatment of complex biological samples. In this study, we demonstrate for the first time that a large quantity of unique peptides in human blood plasma can be co-precipitated with SDC using an optimized sample preparation method prior to shotgun proteomic analysis. We show that the plasma peptides co-precipitated with SDC can be successfully recovered using a sequential re-solubilization and precipitation procedure, and that this approach is particularly efficient at the extraction of long peptides. Recovery of peptides from the SDC pellet dramatically increased overall proteome coverage (>60 %), thereby improving the identification of low-abundance proteins and enhancing the identification of protein components of membrane-bound organelles. In addition, when we analyzed the physiochemical properties of the co-precipitated peptides, we observed that SDC-based sample preparation improved the identification of mildly hydrophilic/hydrophobic proteins that would otherwise be lost upon discarding the pellet. These data demonstrate that the optimized SDC protocol is superior to sodium dodecyl sulfate (SDS)/urea treatment for identifying plasma biomarkers by shotgun proteomics.
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21
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Šlechtová T, Gilar M, Kalíková K, Tesařová E. Insight into Trypsin Miscleavage: Comparison of Kinetic Constants of Problematic Peptide Sequences. Anal Chem 2015; 87:7636-43. [PMID: 26158323 DOI: 10.1021/acs.analchem.5b00866] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Trypsin, a high fidelity protease, is the most widely used enzyme for protein digestion in proteomic research. Optimal digestion conditions are well-known and so are the expected cleavage products. However, missed cleavage sites are frequently observed when acidic amino acids, aspartic and glutamic acids, are present near the cleavage site. Also, the sequence motifs with successive lysine and/or arginine residues represent a source of missed cleaved sites. In spite of an adverse role of missed cleaved peptides on proteomic research, the digestion kinetics of these problematic sequences is not well-known. In this work, synthetic peptides with various sequence motifs were used as trypsin substrates. Cleavage products were analyzed with reversed-phase high performance liquid chromatography, and the kinetic constants for selected missed cleavage sites were calculated. Relative digestion speed for lysine and arginine sites is compared, including the digestion motifs flanked with aspartic and glutamic acid. Our findings show that DK and DTR motifs are cleaved by trypsin with 3 orders of magnitude lower speed than the arginine site. These motifs are likely to produce missed cleavage peptides in protein tryptic digests even at prolonged digestion times.
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Affiliation(s)
- Tereza Šlechtová
- †Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague, Czech Republic
| | - Martin Gilar
- ‡Waters Corporation, 34 Maple Street, Milford, Massachusetts 01757, United States
| | - Květa Kalíková
- †Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague, Czech Republic
| | - Eva Tesařová
- †Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 128 43, Prague, Czech Republic
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22
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Borisov OV, Alvarez M, Carroll JA, Brown PW. Sequence Variants and Sequence Variant Analysis in Biotherapeutic Proteins. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1201.ch002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Oleg V. Borisov
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - Melissa Alvarez
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - James A. Carroll
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
| | - Paul W. Brown
- Novavax, Inc., Gaithersburg, Maryland 20878, United States
- Roche Group Member, Genentech, Inc., South San Francisco, California 94080, United States
- Pfizer Worldwide Research & Development, Chesterfield, Missouri 63017, United States
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23
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Duriez E, Trevisiol S, Domon B. Protein Quantification Using a Cleavable Reporter Peptide. J Proteome Res 2014; 14:728-37. [DOI: 10.1021/pr500764e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Elodie Duriez
- Luxembourg Clinical Proteomics Center, CRP-Santé, 1 A-B rue Thomas Edison, Strassen 1445, Luxembourg
| | - Stephane Trevisiol
- Luxembourg Clinical Proteomics Center, CRP-Santé, 1 A-B rue Thomas Edison, Strassen 1445, Luxembourg
| | - Bruno Domon
- Luxembourg Clinical Proteomics Center, CRP-Santé, 1 A-B rue Thomas Edison, Strassen 1445, Luxembourg
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24
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Abstract
Sample preparation has lagged far behind the evolution of instrumentation used in mass-linked protein analysis. Trypsin digestion, for example, still takes a day, as it did 50 years ago, while mass spectral analyses are achieved in seconds. Higher order structure of proteins is frequently modified by varying digestion conditions: shifting the initial points of trypsin cleavage, changing digestion pathways, accelerating peptide bond demasking and altering the distribution of miscleaved products at the completion of proteolysis. Reduction and alkylation are even circumvented in many cases. This review focuses on immobilized enzyme reactor technology as a means to achieve accelerated trypsin digestion by exploiting these phenomena.
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25
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Quantitative proteomics reveals the kinetics of trypsin-catalyzed protein digestion. Anal Bioanal Chem 2014; 406:6247-56. [DOI: 10.1007/s00216-014-8071-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 07/14/2014] [Accepted: 07/25/2014] [Indexed: 11/25/2022]
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26
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Teramoto H, Kojima K. Production of Bombyx mori Silk Fibroin Incorporated with Unnatural Amino Acids. Biomacromolecules 2014; 15:2682-90. [DOI: 10.1021/bm5005349] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hidetoshi Teramoto
- Silk Materials Research
Unit, Genetically
Modified Organisms Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8634, Japan
| | - Katsura Kojima
- Silk Materials Research
Unit, Genetically
Modified Organisms Research Center, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8634, Japan
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27
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Dickhut C, Feldmann I, Lambert J, Zahedi RP. Impact of digestion conditions on phosphoproteomics. J Proteome Res 2014; 13:2761-70. [PMID: 24724590 DOI: 10.1021/pr401181y] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the past few years, the focus of phosphoproteomics has shifted from merely qualitative to quantitative and targeted studies. Tryptic digestion is a critical step that directly affects quantification and that can be impaired by phosphorylation. Therefore, we systematically characterized the digestion efficiency of 19 nonmodified and phosphorylated model peptides. Whereas we quantified a strong reduction of tryptic cleavage within phosphorylated PKA motifs (R)-R-X-pS/pT and also R-X-X-pT sequences, (R)-R-X-pY sequences were almost unaffected. Structural prediction implied the formation of salt bridges between R/K cleavage sites and phosphoamino acids pS/pT as the main reason for impaired tryptic digestion. We evaluated different conditions to optimize the digestion of such "resistant" phosphopeptides, yielding a substantial improvement of digestion efficiency. We performed a quantitative large-scale phosphoproteomic analysis of human platelets to validate our findings in a complex biological sample. Here, increasing trypsin concentrations up to a trypsin to peptide ratio of 1:10 led to a significant gain (i) in the overall number of phosphorylation sites (up to 9%) and (ii) in the intensities of individual phosphopeptides, thereby improving the sensitivity of phosphopeptide quantification. Still, for certain sequences, the negative impact of phosphorylation on digestion efficiency will further complicate the analysis of phosphorylation stoichiometry.
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Affiliation(s)
- Clarissa Dickhut
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund 44227, Germany
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28
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Gershon PD. Cleaved and Missed Sites for Trypsin, Lys-C, and Lys-N Can Be Predicted with High Confidence on the Basis of Sequence Context. J Proteome Res 2013; 13:702-9. [DOI: 10.1021/pr400802z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Paul D. Gershon
- Department of Molecular Biology
and Biochemistry, University of California—Irvine, Irvine, California 92697, United States
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29
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Vandermarliere E, Mueller M, Martens L. Getting intimate with trypsin, the leading protease in proteomics. MASS SPECTROMETRY REVIEWS 2013; 32:453-65. [PMID: 23775586 DOI: 10.1002/mas.21376] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 02/15/2013] [Accepted: 02/15/2013] [Indexed: 05/21/2023]
Abstract
Nowadays, mass spectrometry-based proteomics is carried out primarily in a bottom-up fashion, with peptides obtained after proteolytic digest of a whole proteome lysate as the primary analytes instead of the proteins themselves. This experimental setup crucially relies on a protease to digest an abundant and complex protein mixture into a far more complex peptide mixture. Full knowledge of the working mechanism and specificity of the used proteases is therefore crucial, both for the digestion step itself as well as for the downstream identification and quantification of the (fragmentation) mass spectra acquired for the peptides in the mixture. Targeted protein analysis through selected reaction monitoring, a relative newcomer in the specific field of mass spectrometry-based proteomics, even requires a priori understanding of protease behavior for the proteins of interest. Because of the rapidly increasing popularity of proteomics as an analytical tool in the life sciences, there is now a renewed demand for detailed knowledge on trypsin, the workhorse protease in proteomics. This review addresses this need and provides an overview on the structure and working mechanism of trypsin, followed by a critical analysis of its cleavage behavior, typically simply accepted to occur exclusively yet consistently after Arg and Lys, unless they are followed by a Pro. In this context, shortcomings in our ability to understand and predict the behavior of trypsin will be highlighted, along with the downstream implications. Furthermore, an analysis is carried out on the inherent shortcomings of trypsin with regard to whole proteome analysis, and alternative approaches will be presented that can alleviate these issues. Finally, some reflections on the future of trypsin as the workhorse protease in mass spectrometry-based proteomics will be provided.
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Affiliation(s)
- Elien Vandermarliere
- Department of Medical Protein Research, VIB, B-9000 Ghent, Belgium; Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
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30
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Hong Q, Lebrilla CB, Miyamoto S, Ruhaak LR. Absolute quantitation of immunoglobulin G and its glycoforms using multiple reaction monitoring. Anal Chem 2013; 85:8585-93. [PMID: 23944609 DOI: 10.1021/ac4009995] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Studies aimed toward glycan biomarker discovery have focused on glycan characterization by the global profiling of released glycans. Site-specific glycosylation analysis is less developed but may provide new types of biomarkers with higher sensitivity and specificity. Quantitation of peptide-conjugated glycans directly facilitates the differential analysis of distinct glycoforms associated with specific proteins at distinct sites. We have developed a method using MRM to monitor protein glycosylation normalized to absolute protein concentrations to examine quantitative changes in glycosylation at a site-specific level. This new approach provides information regarding both the absolute amount of protein and the site-specific glycosylation profile and will thus be useful to determine if altered glycosylation profiles in serum/plasma are due to a change in protein glycosylation or a change in protein concentration. The remarkable sensitivity and selectivity of MRM enable the detection of low abundance IgG glycopeptides, even when IgG was digested directly in serum with no cleanup prior to the liquid chromatography. Our results show a low limit of detection of 60 amol and a wide dynamic range of 3 orders magnitude for IgG protein quantitation. The results show that IgG glycopeptides can be analyzed directly from serum (without enrichment) and yield more accurate abundances when normalized to the protein content. This report represents the most comprehensive study so far of the use of multiple reaction monitoring for the quantitation of glycoproteins and their glycosylation patterns in biofluids.
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Affiliation(s)
- Qiuting Hong
- Department of Chemistry, University of California , One Shields Avenue, Davis, California, 95616, United States
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31
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Bond NJ, Shliaha PV, Lilley KS, Gatto L. Improving qualitative and quantitative performance for MS(E)-based label-free proteomics. J Proteome Res 2013; 12:2340-53. [PMID: 23510225 DOI: 10.1021/pr300776t] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Label-free quantitation by data independent methods (for instance MS(E)) is growing in popularity due to the high technical reproducibility of mass spectrometry analysis. The recent introduction of Synapt hybrid instruments capable of incorporating ion mobility separation within mass spectrometry analysis now allows acquisition of high definition MS(E) data (HDMS(E)). HDMS(E) enables deeper proteome coverage and more confident peptide identifications when compared to MS(E), while the latter offers a higher dynamic range for quantitation. We have developed synapter as, a versatile tool to better evaluate the results of data independent acquisitions on Waters instruments. We demonstrate that synapter can be used to combine HDMS(E) and MS(E) data to achieve deeper proteome coverage delivered by HDMS(E) and more accurate quantitation for high intensity peptides, delivered by MS(E). For users who prefer to run samples exclusively in one mode, synapter allows other useful functionality like false discovery rate estimation, filtering on peptide match type and mass error, and filling missing values. Our software integrates with existing tools, thus permitting us to easily combine peptide quantitation information into protein quantitation by a range of different approaches.
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Affiliation(s)
- Nicholas J Bond
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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32
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 952] [Impact Index Per Article: 86.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Fannes T, Vandermarliere E, Schietgat L, Degroeve S, Martens L, Ramon J. Predicting Tryptic Cleavage from Proteomics Data Using Decision Tree Ensembles. J Proteome Res 2013; 12:2253-9. [DOI: 10.1021/pr4001114] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Thomas Fannes
- Department of Computer Science, Katholieke Universiteit Leuven, Celestijnenlaan 200A,
B-3000, Leuven, Belgium
| | - Elien Vandermarliere
- Department
of Medical Protein
Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Leander Schietgat
- Department of Computer Science, Katholieke Universiteit Leuven, Celestijnenlaan 200A,
B-3000, Leuven, Belgium
| | - Sven Degroeve
- Department
of Medical Protein
Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Lennart Martens
- Department
of Medical Protein
Research, VIB, B-9000 Ghent, Belgium
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Jan Ramon
- Department of Computer Science, Katholieke Universiteit Leuven, Celestijnenlaan 200A,
B-3000, Leuven, Belgium
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Brownridge P, Lawless C, Payapilly AB, Lanthaler K, Holman SW, Harman VM, Grant CM, Beynon RJ, Hubbard SJ. Quantitative analysis of chaperone network throughput in budding yeast. Proteomics 2013; 13:1276-91. [PMID: 23420633 PMCID: PMC3791555 DOI: 10.1002/pmic.201200412] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/29/2012] [Accepted: 11/08/2012] [Indexed: 11/08/2022]
Abstract
The network of molecular chaperones mediates the folding and translocation of the many proteins encoded in the genome of eukaryotic organisms, as well as a response to stress. It has been particularly well characterised in the budding yeast, Saccharomyces cerevisiae, where 63 known chaperones have been annotated and recent affinity purification and MS/MS experiments have helped characterise the attendant network of chaperone targets to a high degree. In this study, we apply our QconCAT methodology to directly quantify the set of yeast chaperones in absolute terms (copies per cell) via SRM MS. Firstly, we compare these to existing quantitative estimates of these yeast proteins, highlighting differences between approaches. Secondly, we cast the results into the context of the chaperone target network and show a distinct relationship between abundance of individual chaperones and their targets. This allows us to characterise the 'throughput' of protein molecules passing through individual chaperones and their groups on a proteome-wide scale in an unstressed model eukaryote for the first time. The results demonstrate specialisations of the chaperone classes, which display different overall workloads, efficiencies and preference for the sub-cellular localisation of their targets. The novel integration of the interactome data with quantification supports re-estimates of the level of protein throughout going through molecular chaperones. Additionally, although chaperones target fewer than 40% of annotated proteins we show that they mediate the folding of the majority of protein molecules (∼62% of the total protein flux in the cell), highlighting their importance.
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Affiliation(s)
- Philip Brownridge
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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35
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Bienvenut WV, Sumpton D, Lilla S, Martinez A, Meinnel T, Giglione C. Influence of various endogenous and artefact modifications on large-scale proteomics analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:443-450. [PMID: 23280976 DOI: 10.1002/rcm.6474] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 11/16/2012] [Accepted: 11/18/2012] [Indexed: 06/01/2023]
Abstract
RATIONALE Some large-scale proteomics studies in which strong cation exchange chromatography has been applied are used to determine proteomes and post-translational modification dynamics. Although such datasets favour the characterisation of thousands of modified peptides, e.g., phosphorylated and N-α-acetylated, a large fraction of the acquired spectra remain unexplained by standard proteomics approaches. Thus, advanced data processing allows characterisation of a significant part of these unassigned spectra. METHODS Our recent investigation of the N-α-acetylation status of plant proteins gave a dataset of choice to investigate further the in-depth characterisation of peptide modifications using Mascot tools associated with relevant validation processes. Such an approach allows to target frequently occurring modifications such as methionine oxidation, phosphorylation or N-α-acetylation, but also the less usual peptide cationisation. Finally, this dataset offers the unique opportunity to determine the overall influence of some of these modifications on the identification score. RESULTS Although methionine oxidation has no influence and tends to favour the characterisation of protein N-terminal peptides, peptide alkalinisation shows an adverse effect on peptide average score. Nevertheless, peptide cationisation appears to favour the characterisation of protein C-terminal peptides with a limited to no direct influence on the identification score. Unexpectedly, our investigation reveals the unfortunate combination of the molecular weight of N-α-acetylation and potassium cation that mimics the mass increment of a phosphorylation group. CONCLUSIONS Since these characterisations rely upon computational treatment associated with statistical validation approaches such as 'False discovery rates' calculation or post-translational modification position validation, our investigation highlights the limitation of such treatment which is biased by the initial searched hypotheses.
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Affiliation(s)
- Willy V Bienvenut
- CNRS, ISV, UPR2355, Bâtiment 23A, 1 avenue de la Terrasse, F-91198, Gif-sur-Yvette Cedex, France.
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Crowdsourcing in proteomics: public resources lead to better experiments. Amino Acids 2013; 44:1129-37. [PMID: 23377569 DOI: 10.1007/s00726-012-1455-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 12/26/2012] [Indexed: 12/19/2022]
Abstract
With the growing interest in the field of proteomics, the amount of publicly available proteome resources has also increased dramatically. This means that there are many useful resources available for almost all aspects of a proteomics experiment. However, it remains vital to use the right resource, for the right purpose, at the right time. This review is therefore meant to aid the reader in obtaining an overview of the available resources and their application, thus providing the necessary background to choose the appropriate resources for the experiment at hand. Many of the resources are also taking advantage of so-called crowdsourcing to maximize the potential of the resource. What this means and how this can improve future experiments will also be discussed. The text roughly follows the steps involved in a proteomics experiment, starting with the planning of the experiment, via the processing of the data and the analysis of the results, to the community-wide sharing of the produced data.
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37
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Boehm ME, Seidler J, Hahn B, Lehmann WD. Site-specific degree of phosphorylation in proteins measured by liquid chromatography-electrospray mass spectrometry. Proteomics 2012; 12:2167-78. [PMID: 22653803 DOI: 10.1002/pmic.201100561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This review focuses on quantitative protein phosphorylation analysis based on coverage of both the phosphorylated and nonphosphorylated forms. In this way, site-specific data on the degree of phosphorylation can be measured, generating the most detailed level of phosphorylation status analysis of proteins. To highlight the experimental challenges in this type of quantitative protein phosphorylation analysis, we discuss the typical workflows for mass spectrometry-based proteomics with a focus on the quantitative analysis of peptide/phosphopeptide ratios. We review workflows for measuring site-specific degrees of phosphorylation including the label-free approach, differential stable isotope labeling of analytes, and methods based on the addition of stable isotope labeled peptide/phosphopeptide pairs as internal standards. The discussion also includes the determination of phosphopeptide isoform abundance data for multiply phosphorylated motifs that contain information about the connectivity of phosphorylation events. The review closes with a prospective on the use of intact stable isotope labeled proteins as internal standards and a summarizing discussion of the typical accuracies of the individual methods.
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Affiliation(s)
- Martin E Boehm
- Molecular Structure Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
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38
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Glatter T, Ludwig C, Ahrné E, Aebersold R, Heck AJR, Schmidt A. Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J Proteome Res 2012; 11:5145-56. [PMID: 23017020 DOI: 10.1021/pr300273g] [Citation(s) in RCA: 233] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The complete and specific proteolytic cleavage of protein samples into peptides is crucial for the success of every shotgun LC-MS/MS experiment. In particular, popular peptide-based label-free and targeted mass spectrometry approaches rely on efficient generation of fully cleaved peptides to ensure accurate and sensitive protein quantification. In contrast to previous studies, we globally and quantitatively assessed the efficiency of different digestion strategies using a yeast cell lysate, label-free quantification, and statistical analysis. Digestion conditions include double tryptic, surfactant-assisted, and tandem-combinatorial Lys-C/trypsin digestion. In comparison to tryptic digests, Lys-C/trypsin digests were found most efficient to yield fully cleaved peptides while reducing the abundance of miscleaved peptides. Subsequent sequence context analysis revealed improved digestion performances of Lys-C/trypsin for miscleaved sequence stretches flanked by charged basic and particulary acidic residues. Furthermore, targeted MS analysis demonstrated a more comprehensive protein cleavage only after Lys-C/trypsin digestion, resulting in a more accurrate absolute protein quantification and extending the number of peptides suitable for SRM assay development. Therefore, we conclude that a serial Lys-C/trypsin digestion is highly attractive for most applications in quantitative MS-based proteomics building on in-solution digestion schemes.
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Affiliation(s)
- Timo Glatter
- Proteomics Core Facility, Biozentrum, Basel University, Basel, Switzerland
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39
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Brownridge PJ, Harman VM, Simpson DM, Beynon RJ. Absolute multiplexed protein quantification using QconCAT technology. Methods Mol Biol 2012; 893:267-93. [PMID: 22665307 DOI: 10.1007/978-1-61779-885-6_18] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In addition to protein identification, protein quantification is becoming a key output of proteomic experiments. Although relative quantification techniques are more commonplace and central to discovery proteomics, most assays require absolute quantification. The growth in systems biology has also increased the demand for absolute protein abundance values for input into models. QconCATs are created by concatenating peptide sequences taken from the target proteins into artificial proteins. The QconCAT acts as a source of internal standards and enables parallel absolute quantification of multiple proteins. QconCATs are typically applied in targeted proteomic workflows and so benefit from the greater sensitivity and wider dynamic range of these approaches. In this chapter, we discuss the design, construction, expression, and deployment of a QconCAT and the resulting experiments required for multiplex absolute quantification.
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Affiliation(s)
- Philip J Brownridge
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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40
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Lawless C, Hubbard SJ. Prediction of missed proteolytic cleavages for the selection of surrogate peptides for quantitative proteomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:449-56. [PMID: 22804685 DOI: 10.1089/omi.2011.0156] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Quantitative proteomics experiments are usually performed using proteolytic peptides as surrogates for their parent proteins, inferring protein amounts from peptide-level quantitation. This process is frequently dependent on complete digestion of the parent protein to its limit peptides so that their signal is truly representative. Unfortunately, proteolysis is often incomplete, and missed cleavage peptides are frequently produced that are unlikely to be optimal surrogates for quantitation, particularly for label-mediated approaches seeking to derive absolute values. We have generated a predictive computational tool that is able to predict which candidate proteolytic peptide bonds are likely to be missed by the standard enzyme trypsin. Our cross-validated prediction tool uses support vector machines and achieves high accuracy in excess of 0.94 precision (PPV), with attendant high sensitivity of 0.79, across multiple proteomes. We believe this is a useful tool for selecting candidate quantotypic peptides, seeking to minimize likely loss owing to missed cleavage, which will be a boon for quantitative proteomic pipelines as well as other areas of proteomics. Our results are discussed in the context of recent results examining the kinetics of missed cleavages in proteomic digestion protocols, and show agreement with observed experimental trends. The software has been made available at http://king.smith.man.ac.uk/mcpred .
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Affiliation(s)
- Craig Lawless
- Faculty of Life Sciences, The University of Manchester, Manchester, UK
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41
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Munday DC, Surtees R, Emmott E, Dove BK, Digard P, Barr JN, Whitehouse A, Matthews D, Hiscox JA. Using SILAC and quantitative proteomics to investigate the interactions between viral and host proteomes. Proteomics 2012; 12:666-72. [PMID: 22246955 DOI: 10.1002/pmic.201100488] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/28/2011] [Accepted: 11/02/2011] [Indexed: 02/05/2023]
Abstract
Viruses continue to pose some of the greatest threats to human and animal health, and food security worldwide. Therefore, new approaches are required to increase our understanding of virus-host cell interactions and subsequently design more effective therapeutic countermeasures. Quantitative proteomics based on stable isotope labeling by amino acids in cell culture (SILAC), coupled to LC-MS/MS and bioinformatic analysis, is providing an excellent resource for studying host cell proteomes and can readily be applied for the study of virus infection. Here, we review this approach and discuss how virus-host cell interactions can best be studied, what is realistically feasible, and the potential limitations. For example, sub-cellular fractionation can reduce sample complexity for LC-MS/MS, increase data return and provide information regarding protein trafficking between different cellular compartments. The key to successful quantitative proteomics combines good experimental design and appropriate sample preparation with statistical analysis and validation of the MS data through the use of independent techniques and functional analysis. The annotation of the human genome and the increasing availability of biological reagents such as antibodies, provide the optimum parameters for studying viruses that infect humans, in human cell lines. SILAC-based quantitative proteomics can also be used to study the interactome of viral proteins with the host cell. Coupling proteomic studies with global transcriptomic and RNA depletion experiments will provide great insights into the complexity of the infection process, and potentially reveal new antiviral targets.
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Affiliation(s)
- Diane C Munday
- Faculty of Biological Sciences, and Astbury Centre for StructuralMolecular Biology, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK.
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42
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Bienvenut WV, Sumpton D, Martinez A, Lilla S, Espagne C, Meinnel T, Giglione C. Comparative large scale characterization of plant versus mammal proteins reveals similar and idiosyncratic N-α-acetylation features. Mol Cell Proteomics 2012; 11:M111.015131. [PMID: 22223895 DOI: 10.1074/mcp.m111.015131] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
N-terminal modifications play a major role in the fate of proteins in terms of activity, stability, or subcellular compartmentalization. Such modifications remain poorly described and badly characterized in proteomic studies, and only a few comparison studies among organisms have been made available so far. Recent advances in the field now allow the enrichment and selection of N-terminal peptides in the course of proteome-wide mass spectrometry analyses. These targeted approaches unravel as a result the extent and nature of the protein N-terminal modifications. Here, we aimed at studying such modifications in the model plant Arabidopsis thaliana to compare these results with those obtained from a human sample analyzed in parallel. We applied large scale analysis to compile robust conclusions on both data sets. Our data show strong convergence of the characterized modifications especially for protein N-terminal methionine excision, co-translational N-α-acetylation, or N-myristoylation between animal and plant kingdoms. Because of the convergence of both the substrates and the N-α-acetylation machinery, it was possible to identify the N-acetyltransferases involved in such modifications for a small number of model plants. Finally, a high proportion of nuclear-encoded chloroplast proteins feature post-translational N-α-acetylation of the mature protein after removal of the transit peptide. Unlike animals, plants feature in a dedicated pathway for post-translational acetylation of organelle-targeted proteins. The corresponding machinery is yet to be discovered.
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Affiliation(s)
- Willy V Bienvenut
- CNRS, Centre de Recherche de Gif, Institut des Sciences du Végétal, F-91198 Gif-sur-Yvette cedex, France
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43
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Fornelli L, Schmid AW, Grasso L, Vogel H, Tsybin YO. Deamidation and transamidation of substance P by tissue transglutaminase revealed by electron-capture dissociation fourier transform mass spectrometry. Chemistry 2010; 17:486-97. [PMID: 21207565 DOI: 10.1002/chem.201002483] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2010] [Indexed: 11/07/2022]
Abstract
Tissue transglutaminase (tTGase) catalyzes both deamidation and transamidation of peptides and proteins by using a peptidyl glutamine as primary substrate. A precise consensus sequence for the enzyme is unknown and the ratio between deamidated and transamidated (or cross-linked) reaction products is highly substrate-dependent. Due to its overlapping body distribution with tTGase and ease of manipulation with tandem mass spectrometry, we used the neuropeptide substance P as a model to investigate the associated enzymatic kinetics and reaction products. Online liquid-chromatography Fourier-transform ion-cyclotron-resonance mass spectrometry (FT-ICR MS) combined with electron-capture dissociation (ECD) was employed to study the tTGase-induced modifications of substance P. A particular strength of ECD for peptide-enzyme reaction product monitoring is its ability to distinguish isomeric amino acids, for example, Glu and iso-Glu, by signature product ions. Our studies show that the primary reaction observed is deamidation, with the two consecutive glutamine residues converted sequentially into glutamate: first Gln(5) , and subsequently Gln(6) . We then applied ECD FT-ICR MS to identify the transamidation site on an enzymatically cross-linked peptide, which turned out to correspond to Gln(5) . Three populations of substance-P dimers were detected that differed by the number of deamidated Gln residues. The higher reactivity of Gln(5) over Gln(6) was further confirmed by cross-linking SP with monodansylcadaverine (MDC). Overall, our approach described herein is of a general importance for mapping both enzymatically induced post-translational protein modifications and cross-linking. Finally, in vitro Ca-signaling assays revealed that the main tTGase reaction product, the singly deamidated SP (RPKPEQFFGLM-NH(2) ), has increased agonist potency towards its natural receptor, thus confirming the biologically relevant role of deamidation.
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Affiliation(s)
- Luca Fornelli
- Biomolecular Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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44
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Zhang X, Højrup P. Cyclization of the N-Terminal X-Asn-Gly Motif during Sample Preparation for Bottom-Up Proteomics. Anal Chem 2010; 82:8680-5. [DOI: 10.1021/ac1019478] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xumin Zhang
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Peter Højrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
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45
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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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46
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Perdivara I, Deterding LJ, Przybylski M, Tomer KB. Mass spectrometric identification of oxidative modifications of tryptophan residues in proteins: chemical artifact or post-translational modification? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1114-7. [PMID: 20219394 PMCID: PMC2900464 DOI: 10.1016/j.jasms.2010.02.016] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 02/01/2010] [Accepted: 02/05/2010] [Indexed: 05/08/2023]
Abstract
Oxidative modification of tryptophan to kynurenine (KYN) and N-formyl kynurenine (NFK) has been described in mitochondrial proteins associated with redox metabolism, and in human cataract lenses. To a large extent, however, previously reported identifications of these modifications were performed using peptide mass fingerprinting and/or tandem-MS data of proteins separated by gel electrophoresis. To date, it is uncertain whether NFK and KYN may represent sample handling artifacts or exclusively post-translational events. To address the problem of the origin of tryptophan oxidation, we characterized several antibodies by liquid chromatography-tandem mass spectrometry, with and without the use of electrophoretic separation of heavy and light chains. Antibodies are not normally expected to undergo oxidative modifications, however, several tryptophan (Trp) residues on both heavy and light chains were found extensively modified to both doubly oxidized Trp and KYN following SDS-PAGE separation and in-gel digestion. In contrast, those residues were observed as non-modified upon in-solution digestion. These results indicate that Trp oxidation may occur as an artifact in proteins separated by SDS-PAGE, and their presence should be carefully interpreted, especially when gel electrophoretic separation methods are employed.
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Affiliation(s)
- Irina Perdivara
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
- Laboratory of Analytical Chemistry and Biopolymer Structure Analysis, University of Konstanz, 78457 Konstanz, Germany
| | - Leesa J. Deterding
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Michael Przybylski
- Laboratory of Analytical Chemistry and Biopolymer Structure Analysis, University of Konstanz, 78457 Konstanz, Germany
- Address reprint requests to: Dr. Kenneth B. Tomer, Laboratory of Structural Biology, National Institutes of Environmental Health Sciences, Phone: +1 919 541 1966, Fax: +1 919 541 0220, . Professor Dr. Michael Przybylski, Department of Chemistry, University of Konstanz, Phone:++49-7531-882249, Fax: ++49-7531-3097,
| | - Kenneth B. Tomer
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
- Address reprint requests to: Dr. Kenneth B. Tomer, Laboratory of Structural Biology, National Institutes of Environmental Health Sciences, Phone: +1 919 541 1966, Fax: +1 919 541 0220, . Professor Dr. Michael Przybylski, Department of Chemistry, University of Konstanz, Phone:++49-7531-882249, Fax: ++49-7531-3097,
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Bogunovic B, Srinivasan P, Ueda Y, Tomita Y, Maric M. Comparative quantitative mass spectrometry analysis of MHC class II-associated peptides reveals a role of GILT in formation of self-peptide repertoire. PLoS One 2010; 5:e10599. [PMID: 20485683 PMCID: PMC2868880 DOI: 10.1371/journal.pone.0010599] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 04/15/2010] [Indexed: 12/22/2022] Open
Abstract
Gamma interferon Inducible Lysosomal Thiol reductase (GILT) is a unique lysosomal reductase that reduces disulfide bonds of endocytosed proteins. Lack of GILT clearly decreases CD4 T cell-antigen specific responses against some epitopes of antigens containing disulfide bonds, but not to proteins with few or no disulfide bridges. Hence, global impact of GILT on antigen presentation is currently not well understood. We used Nano-LC-ESI-MS/MS to investigate how GILT affects diversity of self-peptides presented by MHC class II molecules. Surprisingly, the repertoire of self-peptides in the absence of GILT does not appear to be significantly different, as only few peptide species (∼2%) were found to be the unique indicators of GILT's presence or absence. In the absence of GILT about thirty peptide species (∼5%) were found either uniquely or fourteen to hundred fold more abundantly expressed than in the presence of GILT. Our data indicate that GILT has limited yet unexpected effect on self-peptide species presented by MHC class II antigens.
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Affiliation(s)
- Branka Bogunovic
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D. C., United States of America
| | - Priya Srinivasan
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D. C., United States of America
| | - Yumi Ueda
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, D. C., United States of America
| | - York Tomita
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, Washington, D. C., United States of America
| | - Maja Maric
- Department of Microbiology and Immunology, Georgetown University School of Medicine, Washington, D. C., United States of America
- * E-mail:
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XU CM, ZHANG JY, LIU H, SUN HC, ZHU YP, XIE HW. Advance of Peptide Detectability Prediction on Mass Spectrometry Platform in Proteomics. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1016/s1872-2040(09)60023-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cuervo P, Domont GB, De Jesus JB. Proteomics of trypanosomatids of human medical importance. J Proteomics 2010; 73:845-67. [PMID: 20056176 DOI: 10.1016/j.jprot.2009.12.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2009] [Accepted: 12/18/2009] [Indexed: 12/31/2022]
Abstract
Leishmania spp., Trypanosoma cruzi, and Trypanosoma brucei are protozoan parasites that cause a spectrum of fatal human diseases around the world. Recent completion of the genomic sequencing of these parasites has enormous relevance to the study of their biology and the pathogenesis of the diseases they cause because it opens the door to high-throughput proteomic technologies. This review encompasses studies using diverse proteomic approaches with these organisms to describe and catalogue global protein profiles, reveal changes in protein expression during development, elucidate the subcellular localisation of gene products, and evaluate host-parasite interactions.
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Affiliation(s)
- Patricia Cuervo
- Laboratorio de Pesquisa em Leishmaniose, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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Rehulková H, Marchetti-Deschmann M, Pittenauer E, Allmaier G, Rehulka P. Improved identification of hordeins by cysteine alkylation with 2-bromoethylamine, SDS-PAGE and subsequent in-gel tryptic digestion. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:1613-1621. [PMID: 19787686 DOI: 10.1002/jms.1675] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Proteomic-based description of varieties of barley (Hordeum vulgare L.) is a very important task especially in the food and brewing industry. This study is focused on major storage proteins in barley--hordeins--as a group of proteins soluble in alcohol/water mixtures that shows up significant changes in proteomic profiles for different varieties of barley. Unusual amino acid composition of hordeins with low numbers of lysine and arginine in combination with high content of proline and glutamine complicates their identification in a common proteomic workflow, because tryptic digestion produces just a few peptides amenable for successful mass spectrometric analysis. To increase the number of cleavage sites, in this work, cysteines in hordeins were chemically modified with 2-bromoethylamine (BEA) for their conversion into aminoethylcysteines. These mimic lysine residues and are recognized by trypsin as potential cleavage sites (if not followed by a proline residue) on the C-terminal side of the modified cysteine. Small extent of side reactions (towards histidine, N-terminus of the peptide, methionine, and also here the newly discovered reaction towards aminoethylcysteine) during modification with BEA could be observed after a longer period of reaction but this did not hinder the analysis when optimal conditions were used. Application of trypsin for in-gel digestion of hordeins, previously modified chemically with BEA, provided a higher number of short peptides and their subsequent mass spectrometric analysis resulted in an improved identification of hordeins. This approach can also be used for the analysis of other similar protein groups (e.g. gliadins in wheat) or other cysteines containing proteins having a low number of lysine and arginine residues in their primary structure.
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Affiliation(s)
- Helena Rehulková
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic, v.v.i., Veverí 97, 602 00 Brno, Czech Republic
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