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Levitsky LI, Bubis JA, Gorshkov MV, Tarasova IA. AA_stat: Intelligent profiling of in vivo and in vitro modifications from open search results. J Proteomics 2021; 248:104350. [PMID: 34389500 DOI: 10.1016/j.jprot.2021.104350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/21/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022]
Abstract
Characterization of post-translational modifications is among the most challenging tasks in tandem mass spectrometry-based proteomics which has yet to find an efficient solution. The ultra-tolerant (open) database search attempts to meet this challenge. However, interpretation of the mass shifts observed in open search still requires an effective and automated solution. We have previously introduced the AA_stat tool for analysis of amino acid frequencies at different mass shifts and generation of hypotheses on unaccounted in vitro modifications. Here, we report on the new version of AA_stat, which now complements amino acid frequency statistics with a number of new features: (1) MS/MS-based localization of mass shifts and localization scoring, including shifts which are the sum of modifications; (2) inferring fixed modifications to increase method sensitivity; (3) inferring monoisotopic peak assignment errors and variable modifications based on abundant mass shift localizations to increase the yield of closed search; (4) new mass calibration algorithm to account for partial systematic shifts; (5) interactive integration of all results and a rated list of possible mass shift interpretations. With these options, we improve interpretation of open search results and demonstrate the utility of AA_stat for profiling of abundant and rare amino acid modifications. AA_stat is implemented in Python as an open-source command-line tool available at https://github.com/SimpleNumber/aa_stat. SIGNIFICANCE: Mass spectrometry-based PTM characterization has a long history, yet most of the methods rely on a priori knowledge of modifications of interest and do not provide a whole proteome modification landscape in a blind manner. The open database search is an efficient attempt to address this challenge by identifying peptides with mass shifts corresponding to possible modifications. Then, interpreting these mass shifts is required. Therefore, development of bioinformatics software for post-processing of the open search results, which is capable of detection and accurate annotation of new or unexpected modifications, from characterization of sample preparation efficiency and quality control to discovery of rare post-translational modifications, is of high importance.
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Affiliation(s)
- Lev I Levitsky
- 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
| | - 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
| | - 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
| | - Irina A Tarasova
- 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.
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2
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Cifani P, Li Z, Luo D, Grivainis M, Intlekofer AM, Fenyö D, Kentsis A. Discovery of Protein Modifications Using Differential Tandem Mass Spectrometry Proteomics. J Proteome Res 2021; 20:1835-1848. [PMID: 33749263 PMCID: PMC8341206 DOI: 10.1021/acs.jproteome.0c00638] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recent studies have revealed diverse amino acid, post-translational, and noncanonical modifications of proteins in diverse organisms and tissues. However, their unbiased detection and analysis remain hindered by technical limitations. Here, we present a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics. Termed SAMPEI for spectral alignment-based modified peptide identification, this open-source algorithm is designed for the discovery of functional protein and peptide signaling modifications, without prior knowledge of their identities. Using synthetic standards and controlled chemical labeling experiments, we demonstrate its high specificity and sensitivity for the discovery of substoichiometric protein modifications in complex cellular extracts. SAMPEI mapping of mouse macrophage differentiation revealed diverse post-translational protein modifications, including distinct forms of cysteine itaconatylation. SAMPEI's robust parametrization and versatility are expected to facilitate the discovery of biological modifications of diverse macromolecules. SAMPEI is implemented as a Python package and is available open-source from BioConda and GitHub (https://github.com/FenyoLab/SAMPEI).
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - Zhi Li
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, United States
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - Danmeng Luo
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - Mark Grivainis
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - Andrew M Intlekofer
- Human Oncology & Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
| | - David Fenyö
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, New York 10016, United States
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, New York 10016, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10021, United States
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, and Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, New York 10021, United States
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3
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Dong N, Spencer DM, Quan Q, Le Blanc JCY, Feng J, Li M, Siu KWM, Chu IK. rPTMDetermine: A Fully Automated Methodology for Endogenous Tyrosine Nitration Validation, Site-Localization, and Beyond. Anal Chem 2020; 92:10768-10776. [DOI: 10.1021/acs.analchem.0c02148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Naiping Dong
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Daniel M. Spencer
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Quan Quan
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | | | - Jinwen Feng
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Mengzhu Li
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - K. W. Michael Siu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, Toronto, Ontario M3J 1P3, Canada
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada
| | - Ivan K. Chu
- Department of Chemistry, The University of Hong Kong, Pokfulam, Hong Kong, China
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4
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Degradation of Redox-Sensitive Proteins including Peroxiredoxins and DJ-1 is Promoted by Oxidation-induced Conformational Changes and Ubiquitination. Sci Rep 2016; 6:34432. [PMID: 27703196 PMCID: PMC5050490 DOI: 10.1038/srep34432] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 09/14/2016] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen species (ROS) are key molecules regulating various cellular processes. However, what the cellular targets of ROS are and how their functions are regulated is unclear. This study explored the cellular proteomic changes in response to oxidative stress using H2O2 in dose- and recovery time-dependent ways. We found discernible changes in 76 proteins appearing as 103 spots on 2D-PAGE. Of these, Prxs, DJ-1, UCH-L3 and Rla0 are readily oxidized in response to mild H2O2 stress, and then degraded and active proteins are newly synthesized during recovery. In studies designed to understand the degradation process, multiple cellular modifications of redox-sensitive proteins were identified by peptide sequencing with nanoUPLC-ESI-q-TOF tandem mass spectrometry and the oxidative structural changes of Prx2 explored employing hydrogen/deuterium exchange-mass spectrometry (HDX-MS). We found that hydrogen/deuterium exchange rate increased in C-terminal region of oxidized Prx2, suggesting the exposure of this region to solvent under oxidation. We also found that Lys191 residue in this exposed C-terminal region of oxidized Prx2 is polyubiquitinated and the ubiquitinated Prx2 is readily degraded in proteasome and autophagy. These findings suggest that oxidation-induced ubiquitination and degradation can be a quality control mechanism of oxidized redox-sensitive proteins including Prxs and DJ-1.
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Gianazza E, Parravicini C, Primi R, Miller I, Eberini I. In silico prediction and characterization of protein post-translational modifications. J Proteomics 2015; 134:65-75. [PMID: 26436211 DOI: 10.1016/j.jprot.2015.09.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/17/2015] [Accepted: 09/23/2015] [Indexed: 01/06/2023]
Abstract
This review outlines the computational approaches and procedures for predicting post translational modification (PTM)-induced changes in protein conformation and their influence on protein function(s), the latter being assessed as differential affinity in interaction with either low (ligands for receptors or transporters, substrates for enzymes) or high molecular mass molecules (proteins or nucleic acids in supramolecular assemblies). The scope for an in silico approach is discussed against a summary of the in vitro evidence on the structural and functional outcome of protein PTM.
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Affiliation(s)
- Elisabetta Gianazza
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Gruppo di Studio per la Proteomica e la Struttura delle Proteine, Sezione di Scienze Farmacologiche, Via Balzaretti 9, I-20133 Milan, Italy.
| | - Chiara Parravicini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Laboratorio di Biochimica e Biofisica Computazionale, Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia, Via Trentacoste, 2, I-20134 Milan, Italy
| | - Roberto Primi
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Laboratorio di Biochimica e Biofisica Computazionale, Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia, Via Trentacoste, 2, I-20134 Milan, Italy
| | - Ingrid Miller
- Institut für Medizinische Biochemie, Veterinärmedizinische Universität Wien, Veterinärplatz 1, A-1210 Vienna, Austria
| | - Ivano Eberini
- Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Laboratorio di Biochimica e Biofisica Computazionale, Sezione di Biochimica, Biofisica, Fisiologia ed Immunopatologia, Via Trentacoste, 2, I-20134 Milan, Italy
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6
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Computational and statistical methods for high-throughput analysis of post-translational modifications of proteins. J Proteomics 2015. [PMID: 26216596 DOI: 10.1016/j.jprot.2015.07.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The investigation of post-translational modifications (PTMs) represents one of the main research focuses for the study of protein function and cell signaling. Mass spectrometry instrumentation with increasing sensitivity improved protocols for PTM enrichment and recently established pipelines for high-throughput experiments allow large-scale identification and quantification of several PTM types. This review addresses the concurrently emerging challenges for the computational analysis of the resulting data and presents PTM-centered approaches for spectra identification, statistical analysis, multivariate analysis and data interpretation. We furthermore discuss the potential of future developments that will help to gain deep insight into the PTM-ome and its biological role in cells. This article is part of a Special Issue entitled: Computational Proteomics.
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7
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Affiliation(s)
- He Huang
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
| | - Shu Lin
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois 60637, United States
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8
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Na S, Paek E. Software eyes for protein post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:133-147. [PMID: 24889695 DOI: 10.1002/mas.21425] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 07/18/2013] [Accepted: 11/20/2013] [Indexed: 06/03/2023]
Abstract
Post-translational modifications (PTMs) are critical to almost all aspects of complex processes of the cell. Identification of PTMs is one of the biggest challenges for proteomics, and there have been many computational studies for the analysis of PTMs from tandem mass spectrometry (MS/MS). Most early PTM identification studies have been performed by matching MS/MS data to protein databases, using database search tools, but they are prohibitively slow when a large number of PTMs is given as a search parameter. In this article, we present recent developments to search for more types of PTMs and to speed up the search, and discuss many computational issues and solutions in terms of identifying multiply modified peptides or searching for all possible modifications at once in unrestrictive mode. Apart from the most common type of PTMs involving covalent addition of functional groups to proteins, PTMs such as disulfide linkage require dedicated software for the analysis because they may involve cross-linking between two different parts of proteins. Finally, methods for identification of protein disulfide bonds are presented.
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Affiliation(s)
- Seungjin Na
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, 92093; Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, 92093
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9
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Chung C, Emili A, Frey BJ. Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry. Bioinformatics 2013; 29:821-9. [DOI: 10.1093/bioinformatics/btt056] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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10
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Cohen AM, Kostyleva R, Chisholm KA, Pinto DM. Iodination on tyrosine residues during oxidation with sodium periodate in solid phase extraction of N-linked glycopeptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:68-75. [PMID: 22006405 DOI: 10.1007/s13361-011-0262-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 08/30/2011] [Accepted: 09/23/2011] [Indexed: 05/31/2023]
Abstract
Solid-phase extraction of N-linked glycopeptides (SPEG) using hydrazide-modified supports has become a common sample preparation procedure in glycoproteomic experiments. We demonstrate that iodination of tyrosine residues occur in SPEG as a side reaction during an oxidation step with sodium periodate. MS/MS analysis of oxidized bovine serum albumin and carbonic anhydrase digests revealed a characteristic shift of m/z 125.9 on all y and b fragment ions containing the modified tyrosine residues. Selected reaction monitoring (SRM) measurements showed that the peak intensity from of the iodinated peptides increased during the course of oxidation. After an hour of oxidation, SRM analysis revealed that the strongest signal from an iodinated peptide was approximately one-tenth of the intensity of the corresponding unmodified peptide. Iodinated tyrosine residues were also identified in serum samples subjected to SPEG and analyzed by LC-ESI-MS/MS. We recommend assessing this side reaction by including iodotyrosine as a variable modification when performing database searches on SPEG experiments. For SRM-based acquisitions, we encourage the avoidance of tyrosine-containing glycopeptides or, if this is not practical, monitoring transitions that contain the potential modified iodinated tyrosine residue to monitor the presence of the iodinated form of the glycopeptide.
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Affiliation(s)
- Alejandro M Cohen
- National Research Council, Institute for Marine Biosciences, 1411 Oxford St., Halifax, Nova Scotia, Canada
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11
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Na S, Bandeira N, Paek E. Fast multi-blind modification search through tandem mass spectrometry. Mol Cell Proteomics 2011; 11:M111.010199. [PMID: 22186716 DOI: 10.1074/mcp.m111.010199] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
With great biological interest in post-translational modifications (PTMs), various approaches have been introduced to identify PTMs using MS/MS. Recent developments for PTM identification have focused on an unrestrictive approach that searches MS/MS spectra for all known and possibly even unknown types of PTMs at once. However, the resulting expanded search space requires much longer search time and also increases the number of false positives (incorrect identifications) and false negatives (missed true identifications), thus creating a bottleneck in high throughput analysis. Here we introduce MODa, a novel "multi-blind" spectral alignment algorithm that allows for fast unrestrictive PTM searches with no limitation on the number of modifications per peptide while featuring over an order of magnitude speedup in relation to existing approaches. We demonstrate the sensitivity of MODa on human shotgun proteomics data where it reveals multiple mutations, a wide range of modifications (including glycosylation), and evidence for several putative novel modifications. Based on the reported findings, we argue that the efficiency and sensitivity of MODa make it the first unrestrictive search tool with the potential to fully replace conventional restrictive identification of proteomics mass spectrometry data.
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Affiliation(s)
- Seungjin Na
- Division of Computer Science and Engineering, Hanyang University, Seoul 133-791, Korea
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12
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Kil YJ, Becker C, Sandoval W, Goldberg D, Bern M. Preview: a program for surveying shotgun proteomics tandem mass spectrometry data. Anal Chem 2011; 83:5259-67. [PMID: 21619057 DOI: 10.1021/ac200609a] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Database search programs for peptide identification by tandem mass spectrometry ask their users to set various parameters, including precursor and fragment mass tolerances, digestion specificity, and allowed types of modifications. Even proteomics experts with detailed knowledge of their samples may find it difficult to make these choices without significant investigation, and poor choices can lead to missed identifications and misleading results. Here we describe a program called Preview that analyzes a set of mass spectra for mass errors, digestion specificity, and known and unknown modifications, thereby facilitating parameter selection. Moreover, Preview optionally recalibrates mass over charge measurements, leading to further improvement in identification results. In a study of Bruton's tyrosine kinase, we find that the use of Preview improved the number of confidently identified mass spectra and phosphorylation sites by about 50%.
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Affiliation(s)
- Yong J Kil
- Palo Alto Research Center, 3333 Coyote Hill Road, Palo Alto, California 94304, USA
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13
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Ning Z, Zhou H, Wang F, Abu-Farha M, Figeys D. Analytical Aspects of Proteomics: 2009–2010. Anal Chem 2011; 83:4407-26. [DOI: 10.1021/ac200857t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Hu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Fangjun Wang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China 116023
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14
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Chung C, Liu J, Emili A, Frey BJ. Computational refinement of post-translational modifications predicted from tandem mass spectrometry. ACTA ACUST UNITED AC 2011; 27:797-806. [PMID: 21258065 PMCID: PMC3051323 DOI: 10.1093/bioinformatics/btr017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Motivation: A post-translational modification (PTM) is a chemical modification of a protein that occurs naturally. Many of these modifications, such as phosphorylation, are known to play pivotal roles in the regulation of protein function. Henceforth, PTM perturbations have been linked to diverse diseases like Parkinson's, Alzheimer's, diabetes and cancer. To discover PTMs on a genome-wide scale, there is a recent surge of interest in analyzing tandem mass spectrometry data, and several unrestrictive (so-called ‘blind’) PTM search methods have been reported. However, these approaches are subject to noise in mass measurements and in the predicted modification site (amino acid position) within peptides, which can result in false PTM assignments. Results: To address these issues, we devised a machine learning algorithm, PTMClust, that can be applied to the output of blind PTM search methods to improve prediction quality, by suppressing noise in the data and clustering peptides with the same underlying modification to form PTM groups. We show that our technique outperforms two standard clustering algorithms on a simulated dataset. Additionally, we show that our algorithm significantly improves sensitivity and specificity when applied to the output of three different blind PTM search engines, SIMS, InsPecT and MODmap. Additionally, PTMClust markedly outperforms another PTM refinement algorithm, PTMFinder. We demonstrate that our technique is able to reduce false PTM assignments, improve overall detection coverage and facilitate novel PTM discovery, including terminus modifications. We applied our technique to a large-scale yeast MS/MS proteome profiling dataset and found numerous known and novel PTMs. Accurately identifying modifications in protein sequences is a critical first step for PTM profiling, and thus our approach may benefit routine proteomic analysis. Availability: Our algorithm is implemented in Matlab and is freely available for academic use. The software is available online from http://genes.toronto.edu. Supplementary Information:Supplementary data are available at Bioinformatics online. Contact:frey@psi.utoronto.ca
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Affiliation(s)
- Clement Chung
- Department of Computer Science, University of Toronto, Toronto, Canada
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15
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Abstract
Methods for predicting protein post-translational modifications have been developed extensively. In this chapter, we review major post-translational modification prediction strategies, with a particular focus on statistical and machine learning approaches. We present the workflow of the methods and summarize the advantages and disadvantages of the methods.
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Affiliation(s)
- Chunmei Liu
- Department of Systems and Computer Science, Howard University, Washington, DC, USA.
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16
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Jeong J, Jung Y, Na S, Jeong J, Lee E, Kim MS, Choi S, Shin DH, Paek E, Lee HY, Lee KJ. Novel oxidative modifications in redox-active cysteine residues. Mol Cell Proteomics 2010; 10:M110.000513. [PMID: 21148632 DOI: 10.1074/mcp.m110.000513] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Redox-active cysteine, a highly reactive sulfhydryl, is one of the major targets of ROS. Formation of disulfide bonds and other oxidative derivatives of cysteine including sulfenic, sulfinic, and sulfonic acids, regulates the biological function of various proteins. We identified novel low-abundant cysteine modifications in cellular GAPDH purified on 2-dimensional gel electrophoresis (2D-PAGE) by employing selectively excluded mass screening analysis for nano ultraperformance liquid chromatography-electrospray-quadrupole-time of flight tandem mass spectrometry, in conjunction with MODi and MODmap algorithm. We observed unexpected mass shifts (Δm=-16, -34, +64, +87, and +103 Da) at redox-active cysteine residue in cellular GAPDH purified on 2D-PAGE, in oxidized NDP kinase A, peroxiredoxin 6, and in various mitochondrial proteins. Mass differences of -16, -34, and +64 Da are presumed to reflect the conversion of cysteine to serine, dehydroalanine (DHA), and Cys-SO2-SH respectively. To determine the plausible pathways to the formation of these products, we prepared model compounds and examined the hydrolysis and hydration of thiosulfonate (Cys-S-SO2-Cys) either to DHA (Δm=-34 Da) or serine along with Cys-SO2-SH (Δm=+64 Da). We also detected acrylamide adducts of sulfenic and sulfinic acids (+87 and +103 Da). These findings suggest that oxidations take place at redox-active cysteine residues in cellular proteins, with the formation of thiosulfonate, Cys-SO2-SH, and DHA, and conversion of cysteine to serine, in addition to sulfenic, sulfinic and sulfonic acids of reactive cysteine.
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Affiliation(s)
- Jaeho Jeong
- The Center for Cell Signaling & Drug Discovery Research, College of Pharmacy, Division of Life & Pharmaceutical Sciences, Department of Bioinspired Science, Ewha Womans University, Seoul, Korea 120-750
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