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Liu X, Fields R, Schweppe DK, Paulo JA. Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging. Expert Rev Proteomics 2021; 18:795-807. [PMID: 34652972 DOI: 10.1080/14789450.2021.1994390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION Protein phosphorylation is a primary mechanism of signal transduction in cellular systems. Isobaric tagging can be used to investigate alterations in phosphorylation events in sample multiplexing experiments where quantification extends across all conditions. As such, innovations in tandem mass tag methods can facilitate the expansion of the depth and breadth of phosphoproteomic analyses. AREAS COVERED This review discusses the current state of tandem mass tag-centric phosphoproteomics and highlights advances in reagent chemistry, instrumentation, data acquisition, and data analysis. We stress that approaches for phosphoproteomic investigations require high-specificity enrichment, sensitive detection, and accurate phosphorylation site localization. EXPERT OPINION Tandem mass tag-centric phosphoproteomics will continue to be an important conduit for our understanding of signal transduction in living organisms. We anticipate that progress in phosphopeptide enrichment methodologies, enhancements in instrumentation and data acquisition technologies, and further refinements in analytical strategies will be key to the discovery of biologically relevant findings from phosphoproteomics studies.
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Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Rose Fields
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Devin K Schweppe
- Department of Genome Sciences, University of Washington, Seattle, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, USA
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2
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Paulo JA, Schweppe DK. Advances in quantitative high-throughput phosphoproteomics with sample multiplexing. Proteomics 2021; 21:e2000140. [PMID: 33455035 DOI: 10.1002/pmic.202000140] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/18/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023]
Abstract
Eukaryotic protein phosphorylation modulates nearly every major biological process. Phosphorylation regulates protein activity, mediates cellular signal transduction, and manipulates cellular structure. Consequently, the dysregulation of kinase and phosphatase pathways has been linked to a multitude of diseases. Mass spectrometry-based proteomic techniques are increasingly used for the global interrogation of perturbations in phosphorylation-based cellular signaling. Strategies for studying phosphoproteomes require high-specificity enrichment, sensitive detection, and accurate localization of phosphorylation sites with advanced LC-MS/MS techniques and downstream informatics. Sample multiplexing with isobaric tags has also been integral to recent advancements in throughput and sensitivity for phosphoproteomic studies. Each of these facets of phosphoproteomics analysis present distinct challenges and thus opportunities for improvement and innovation. Here, we review current methodologies, explore persistent challenges, and discuss the outlook for isobaric tag-based quantitative phosphoproteomic analysis.
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Affiliation(s)
- Joao A Paulo
- Harvard Medical School, Boston, Massachusetts, USA
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3
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Shteynberg DD, Deutsch EW, Campbell DS, Hoopmann MR, Kusebauch U, Lee D, Mendoza L, Midha MK, Sun Z, Whetton AD, Moritz RL. PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline. J Proteome Res 2019; 18:4262-4272. [PMID: 31290668 PMCID: PMC6898736 DOI: 10.1021/acs.jproteome.9b00205] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Spectral matching sequence database search engines commonly used on mass spectrometry-based proteomics experiments excel at identifying peptide sequence ions, and in addition, possible sequence ions carrying post-translational modifications (PTMs), but most do not provide confidence metrics for the exact localization of those PTMs when several possible sites are available. Localization is absolutely required for downstream molecular cell biology analysis of PTM function in vitro and in vivo. Therefore, we developed PTMProphet, a free and open-source software tool integrated into the Trans-Proteomic Pipeline, which reanalyzes identified spectra from any search engine for which pepXML output is available to provide localization confidence to enable appropriate further characterization of biologic events. Localization of any type of mass modification (e.g., phosphorylation) is supported. PTMProphet applies Bayesian mixture models to compute probabilities for each site/peptide spectrum match where a PTM has been identified. These probabilities can be combined to compute a global false localization rate at any threshold to guide downstream analysis. We describe the PTMProphet tool, its underlying algorithms, and demonstrate its performance on ground-truth synthetic peptide reference data sets, one previously published small data set, one new larger data set, and also on a previously published phosphoenriched data set where the correct sites of modification are unknown. Data have been deposited to ProteomeXchange with identifier PXD013210.
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Affiliation(s)
| | | | | | | | | | - Dave Lee
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Luis Mendoza
- Institute for Systems Biology, Seattle, WA, 98008, USA
| | | | - Zhi Sun
- Institute for Systems Biology, Seattle, WA, 98008, USA
| | - Anthony D. Whetton
- Stoller Biomarker Discovery Centre, University of Manchester, Manchester, M13 9PL, UK
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4
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Zhang S, Li X, Fan C, Wu Z, Liu Q. Application of Machine Learning Techniques to Predict Protein Phosphorylation Sites. LETT ORG CHEM 2019. [DOI: 10.2174/1570178615666180907150928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Protein phosphorylation is one of the most important post-translational modifications of proteins.
Almost all processes that regulate the life activities of an organism as well as almost all physiological
and pathological processes are involved in protein phosphorylation. In this paper, we summarize
specific implementation and application of the methods used in protein phosphorylation site prediction
such as the support vector machine algorithm, random forest, Jensen-Shannon divergence combined
with quadratic discriminant analysis, Adaboost algorithm, increment of diversity with quadratic
discriminant analysis, modified CKSAAP algorithm, Bayes classifier combined with phosphorylation
sequences enrichment analysis, least absolute shrinkage and selection operator, stochastic search variable
selection, partial least squares and deep learning. On the basis of this prediction, we use k-nearest
neighbor algorithm with BLOSUM80 matrix method to predict phosphorylation sites. Firstly, we construct
dataset and remove the redundant set of positive and negative samples, that is, removal of protein
sequences with similarity of more than 30%. Next, the proposed method is evaluated by sensitivity
(Sn), specificity (Sp), accuracy (ACC) and Mathew’s correlation coefficient (MCC) these four metrics.
Finally, tenfold cross-validation is employed to evaluate this method. The result, which is verified by
tenfold cross-validation, shows that the average values of Sn, Sp, ACC and MCC of three types of amino
acid (serine, threonine, and tyrosine) are 90.44%, 86.95%, 88.74% and 0.7742, respectively. A
comparison with the predictive performance of PhosphoSVM and Musite reveals that the prediction
performance of the proposed method is better, and it has the advantages of simplicity, practicality and
low time complexity in classification.
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Affiliation(s)
- Shengli Zhang
- School of Mathematics and Statistics, Xidian University, Xi'an 710071, China
| | - Xian Li
- School of Mathematics and Statistics, Xidian University, Xi'an 710071, China
| | - Chengcheng Fan
- School of Mathematics and Statistics, Xidian University, Xi'an 710071, China
| | - Zhehui Wu
- School of Mathematics and Statistics, Xidian University, Xi'an 710071, China
| | - Qian Liu
- Centre for Biostatistics, School of Health Sciences, The University of Manchester, Manchester, M13 9PL, United Kingdom
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5
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An Z, Zhai L, Ying W, Qian X, Gong F, Tan M, Fu Y. PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome. Mol Cell Proteomics 2019; 18:391-405. [PMID: 30420486 PMCID: PMC6356076 DOI: 10.1074/mcp.ra118.000812] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 11/02/2018] [Indexed: 12/27/2022] Open
Abstract
The open (mass tolerant) search of tandem mass spectra of peptides shows great potential in the comprehensive detection of post-translational modifications (PTMs) in shotgun proteomics. However, this search strategy has not been widely used by the community, and one bottleneck of it is the lack of appropriate algorithms for automated and reliable post-processing of the coarse and error-prone search results. Here we present PTMiner, a software tool for confident filtering and localization of modifications (mass shifts) detected in an open search. After mass-shift-grouped false discovery rate (FDR) control of peptide-spectrum matches (PSMs), PTMiner uses an empirical Bayesian method to localize modifications through iterative learning of the prior probabilities of each type of modification occurring on different amino acids. The performance of PTMiner was evaluated on three data sets, including simulated data, chemically synthesized peptide library data and modified-peptide spiked-in proteome data. The results showed that PTMiner can effectively control the PSM FDR and accurately localize the modification sites. At 1% real false localization rate (FLR), PTMiner localized 93%, 84 and 83% of the modification sites in the three data sets, respectively, far higher than two open search engines we used and an extended version of the Ascore localization algorithm. We then used PTMiner to analyze a draft map of human proteome containing 25 million spectra from 30 tissues, and confidently identified over 1.7 million modified PSMs at 1% FDR and 1% FLR, which provided a system-wide view of both known and unknown PTMs in the human proteome.
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Affiliation(s)
- Zhiwu An
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China;; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wantao Ying
- State key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing 102206, China, Beijing Institute of Lifeomics, Beijing 100850, China
| | - Xiaohong Qian
- State key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing 102206, China, Beijing Institute of Lifeomics, Beijing 100850, China
| | - Fuzhou Gong
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China;; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China;.
| | - Yan Fu
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China;; School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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6
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Accurate phosphorylation site localization using phospho-brackets. Anal Chim Acta 2017; 996:38-47. [PMID: 29137706 DOI: 10.1016/j.aca.2017.09.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 11/21/2022]
Abstract
Phosphorylation is one of the most important and widely studied protein post-translational modifications. Tandem mass spectrometry using higher-energy collisional dissociation has evolved into a state-of-the-art analytical platform for both phosphorylation identification and site localization. Tens of thousands of phosphopeptides can now be routinely identified from a single shotgun proteomics study; site localization, however, is much more complicated and many challenges still exist. Here, we report our development of P-bracket using direct experimental evidence of phospho-containing site-determining product ions for accurate site localization without the need for additional FLR control. A P-bracket is defined as a complementary product ion pair that forms a bracket to confine a phosphorylation event to a unique site. P-bracket has been successfully benchmarked with a set of six synthetic phosphopeptides with a single phosphorylation event, a set of 96 synthetic peptides and phosphopeptide reference libraries, and two HeLa phosphopeptide LC-MS/MS (HCD) datasets; Accurate phosphosite localization by P-bracket will greatly enhance identification confidence of phosphopeptides and contribute to structural and functional studies of phosphoproteins.
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7
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Wang X, Xu ML, Li BQ, Zhai HL, Liu JJ, Li SY. Prediction of phosphorylation sites based on Krawtchouk image moments. Proteins 2017; 85:2231-2238. [PMID: 28921635 DOI: 10.1002/prot.25388] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/30/2017] [Accepted: 09/12/2017] [Indexed: 11/05/2022]
Abstract
Protein phosphorylation is one of the most pervasive post-translational modifications and regulates diverse cellular processes in organisms. Under the catalysis of protein kinases, protein phosphorylation usually occurred in the residues serine (S), threonine (T), or tyrosine (Y). In this contribution, we proposed a novel scheme (named KMPhos) for the theoretical prediction of protein phosphorylation sites. First, the numerical matrix was obtained from a protein sequence fragment by replacing the characters of the residues with the chemical descriptors of amino acid molecules to approximately describe the chemical environment of the protein fragment, which was turned to the grayscale image. Then the Krawtchouk image moments were calculated and used to establish the support vector machine models. The accuracies of 10-fold cross validation for the obtained models on the training set are up to 89.7%, 88.6%, and 90.1% for the residues S, Y, and T, respectively. For the independent test set, the prediction accuracies are up to 90.7% (S), 87.8% (T), and 89.3% (Y). The results of ROC and other evaluations are also satisfactory. Compared with several specialized prediction tools, KMPhos provided the higher accuracy and reliability. An available KMPhos package is provided and can be used directly for phosphorylation sites prediction.
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Affiliation(s)
- Xue Wang
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Min Li Xu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Bao Qiong Li
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Hong Lin Zhai
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Jin Jin Liu
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
| | - Shu Yan Li
- College of Chemistry & Chemical Engineering, Lanzhou University, Lanzhou, 730000, People's Republic of China
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8
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Chan CYX, Gritsenko MA, Smith RD, Qian WJ. The current state of the art of quantitative phosphoproteomics and its applications to diabetes research. Expert Rev Proteomics 2016; 13:421-33. [PMID: 26960075 DOI: 10.1586/14789450.2016.1164604] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein phosphorylation is a fundamental regulatory mechanism in many cellular processes and aberrant perturbation of phosphorylation has been implicated in various human diseases. Kinases and their cognate inhibitors have been considered as hotspots for drug development. Therefore, the emerging tools, which enable a system-wide quantitative profiling of phosphoproteome, would offer a powerful impetus in unveiling novel signaling pathways, drug targets and/or biomarkers for diseases of interest. This review highlights recent advances in phosphoproteomics, the current state of the art of the technologies and the challenges and future perspectives of this research area. Finally, some exemplary applications of phosphoproteomics in diabetes research are underscored.
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Affiliation(s)
- Chi Yuet X'avia Chan
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Marina A Gritsenko
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Richard D Smith
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Wei-Jun Qian
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
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9
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Computational Methods in Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 939:63-89. [PMID: 27807744 DOI: 10.1007/978-981-10-1503-8_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This chapter introduces computational methods used in mass spectrometry-based proteomics, including those for addressing the critical problems such as peptide identification and protein inference, peptide and protein quantification, characterization of posttranslational modifications (PTMs), and data-independent acquisitions (DIA). The chapter concludes with emerging applications of proteomic techniques, such as metaproteomics, glycoproteomics, and proteogenomics.
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10
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Abstract
Mass spectrometry-based proteomics provides a powerful tool for large-scale analysis of protein modifications. Statistical and computational analysis of mass spectrometry data is a key step in protein modification identification. This chapter presents common and advanced data analysis strategies for modification identification, including variable modification search, unrestrictive approaches for modification discovery, false discovery rate estimation and control methods, and tools for modification site localization.
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Affiliation(s)
- Yan Fu
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Zhongguancun East Road 55, Beijing, 100190, China.
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11
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Systematic Analysis and Prediction of In Situ Cross Talk of O-GlcNAcylation and Phosphorylation. BIOMED RESEARCH INTERNATIONAL 2015; 2015:279823. [PMID: 26601103 PMCID: PMC4639640 DOI: 10.1155/2015/279823] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 10/01/2015] [Accepted: 10/04/2015] [Indexed: 01/17/2023]
Abstract
Reversible posttranslational modification (PTM) plays a very important role in biological process by changing properties of proteins. As many proteins are multiply modified by PTMs, cross talk of PTMs is becoming an intriguing topic and draws much attention. Currently, lots of evidences suggest that the PTMs work together to accomplish a specific biological function. However, both the general principles and underlying mechanism of PTM crosstalk are elusive. In this study, by using large-scale datasets we performed evolutionary conservation analysis, gene ontology enrichment, motif extraction of proteins with cross talk of O-GlcNAcylation and phosphorylation cooccurring on the same residue. We found that proteins with in situ O-GlcNAc/Phos cross talk were significantly enriched in some specific gene ontology terms and no obvious evolutionary pressure was observed. Moreover, 3 functional motifs associated with O-GlcNAc/Phos sites were extracted. We further used sequence features and GO features to predict O-GlcNAc/Phos cross talk sites based on phosphorylated sites and O-GlcNAcylated sites separately by the use of SVM model. The AUC of classifier based on phosphorylated sites is 0.896 and the other classifier based on GlcNAcylated sites is 0.843. Both classifiers achieved a relatively better performance compared with other existing methods.
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12
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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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13
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Lee DCH, Jones AR, Hubbard SJ. Computational phosphoproteomics: from identification to localization. Proteomics 2015; 15:950-63. [PMID: 25475148 PMCID: PMC4384807 DOI: 10.1002/pmic.201400372] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/31/2014] [Accepted: 11/26/2014] [Indexed: 01/08/2023]
Abstract
Analysis of the phosphoproteome by MS has become a key technology for the characterization of dynamic regulatory processes in the cell, since kinase and phosphatase action underlie many major biological functions. However, the addition of a phosphate group to a suitable side chain often confounds informatic analysis by generating product ion spectra that are more difficult to interpret (and consequently identify) relative to unmodified peptides. Collectively, these challenges have motivated bioinformaticians to create novel software tools and pipelines to assist in the identification of phosphopeptides in proteomic mixtures, and help pinpoint or "localize" the most likely site of modification in cases where there is ambiguity. Here we review the challenges to be met and the informatics solutions available to address them for phosphoproteomic analysis, as well as highlighting the difficulties associated with using them and the implications for data standards.
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Affiliation(s)
- Dave C H Lee
- Faculty of Life Sciences, University of ManchesterManchester, UK
| | - Andrew R Jones
- Institute of Integrative Biology, University of LiverpoolLiverpool, UK
| | - Simon J Hubbard
- Faculty of Life Sciences, University of ManchesterManchester, UK
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14
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Roux PP, Thibault P. The coming of age of phosphoproteomics--from large data sets to inference of protein functions. Mol Cell Proteomics 2013; 12:3453-64. [PMID: 24037665 DOI: 10.1074/mcp.r113.032862] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Protein phosphorylation is one of the most common post-translational modifications used in signal transduction to control cell growth, proliferation, and survival in response to both intracellular and extracellular stimuli. This modification is finely coordinated by a network of kinases and phosphatases that recognize unique sequence motifs and/or mediate their functions through scaffold and adaptor proteins. Detailed information on the nature of kinase substrates and site-specific phosphoregulation is required in order for one to better understand their pathophysiological roles. Recent advances in affinity chromatography and mass spectrometry (MS) sensitivity have enabled the large-scale identification and profiling of protein phosphorylation, but appropriate follow-up experiments are required in order to ascertain the functional significance of identified phosphorylation sites. In this review, we present meaningful technical details for MS-based phosphoproteomic analyses and describe important considerations for the selection of model systems and the functional characterization of identified phosphorylation sites.
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Affiliation(s)
- Philippe P Roux
- Institute for Research in Immunology and Cancer, Université de Montréal, P.O. Box 6128, Station. Centre-ville, Montréal, Québec H3C 3J7, Canada
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15
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Courcelles M, Bridon G, Lemieux S, Thibault P. Occurrence and Detection of Phosphopeptide Isomers in Large-Scale Phosphoproteomics Experiments. J Proteome Res 2012; 11:3753-65. [DOI: 10.1021/pr300229m] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mathieu Courcelles
- IRIC,
Institute for Research in Immunology and Cancer, ‡Department of Biochemistry, §Department of Chemistry, and ∥Department of
Computer Science and Operational Research, Université de Montréal, P.O. Box 6128,
Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Gaëlle Bridon
- IRIC,
Institute for Research in Immunology and Cancer, ‡Department of Biochemistry, §Department of Chemistry, and ∥Department of
Computer Science and Operational Research, Université de Montréal, P.O. Box 6128,
Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Sébastien Lemieux
- IRIC,
Institute for Research in Immunology and Cancer, ‡Department of Biochemistry, §Department of Chemistry, and ∥Department of
Computer Science and Operational Research, Université de Montréal, P.O. Box 6128,
Station Centre-ville, Montréal, Québec, Canada H3C 3J7
| | - Pierre Thibault
- IRIC,
Institute for Research in Immunology and Cancer, ‡Department of Biochemistry, §Department of Chemistry, and ∥Department of
Computer Science and Operational Research, Université de Montréal, P.O. Box 6128,
Station Centre-ville, Montréal, Québec, Canada H3C 3J7
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16
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Phosphorylation site localization in peptides by MALDI MS/MS and the Mascot Delta Score. Anal Bioanal Chem 2011; 402:249-60. [DOI: 10.1007/s00216-011-5469-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 09/20/2011] [Accepted: 10/03/2011] [Indexed: 10/16/2022]
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17
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Wang F, Song C, Cheng K, Jiang X, Ye M, Zou H. Perspectives of Comprehensive Phosphoproteome Analysis Using Shotgun Strategy. Anal Chem 2011; 83:8078-85. [DOI: 10.1021/ac201833j] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunxia Song
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Kai Cheng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xinning Jiang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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Palumbo AM, Smith SA, Kalcic CL, Dantus M, Stemmer PM, Reid GE. Tandem mass spectrometry strategies for phosphoproteome analysis. MASS SPECTROMETRY REVIEWS 2011; 30:600-25. [PMID: 21294150 DOI: 10.1002/mas.20310] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Protein phosphorylation is involved in nearly all essential biochemical pathways and the deregulation of phosphorylation events has been associated with the onset of numerous diseases. A multitude of tandem mass spectrometry (MS/MS) and multistage MS/MS (i.e., MS(n) ) strategies have been developed in recent years and have been applied toward comprehensive phosphoproteomic analysis, based on the interrogation of proteolytically derived phosphopeptides. However, the utility of each of these MS/MS and MS(n) approaches for phosphopeptide identification and characterization, including phosphorylation site localization, is critically dependant on the properties of the precursor ion (e.g., polarity and charge state), the specific ion activation method that is employed, and the underlying gas-phase ion chemistries, mechanisms and other factors that influence the gas-phase fragmentation behavior of phosphopeptide ions. This review therefore provides an overview of recent studies aimed at developing an improved understanding of these issues, and highlights the advantages and limitations of both established (e.g., CID) and newly maturing (e.g., ECD, ETD, photodissociation, etc.) yet complementary, ion activation techniques. This understanding is expected to facilitate the continued refinement of existing MS/MS strategies, and the development of novel MS/MS techniques for phosphopeptide analysis, with great promise in providing new insights into the role of protein phosphorylation on normal biological function, and in the onset and progression of disease. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:600-625, 2011.
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Affiliation(s)
- Amanda M Palumbo
- Department of Chemistry, Michigan State University, East Lansing, USA
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19
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Xu H, Schaniel C, Lemischka IR, Ma'ayan A. Toward a complete in silico, multi-layered embryonic stem cell regulatory network. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:708-33. [PMID: 20890967 DOI: 10.1002/wsbm.93] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Recent efforts in systematically profiling embryonic stem (ES) cells have yielded a wealth of high-throughput data. Complementarily, emerging databases and computational tools facilitate ES cell studies and further pave the way toward the in silico reconstruction of regulatory networks encompassing multiple molecular layers. Here, we briefly survey databases, algorithms, and software tools used to organize and analyze high-throughput experimental data collected to study mammalian cellular systems with a focus on ES cells. The vision of using heterogeneous data to reconstruct a complete multi-layered ES cell regulatory network is discussed. This review also provides an accompanying manually extracted dataset of different types of regulatory interactions from low-throughput experimental ES cell studies available at http://amp.pharm.mssm.edu/iscmid/literature.
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Affiliation(s)
- Huilei Xu
- Department of Gene and Cell Medicine and The Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, NY 10029, USA
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Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B. Confident phosphorylation site localization using the Mascot Delta Score. Mol Cell Proteomics 2010; 10:M110.003830. [PMID: 21057138 DOI: 10.1074/mcp.m110.003830] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Large scale phosphorylation analysis is more and more getting into focus of proteomic research. Although it is now possible to identify thousands of phosphorylated peptides in a biological system, confident site localization remains challenging. Here we validate the Mascot Delta Score (MD-score) as a simple method that achieves similar sensitivity and specificity for phosphosite localization as the published Ascore, which is mainly used in conjunction with Sequest. The MD-score was evaluated using liquid chromatography-tandem MS data of 180 individually synthesized phosphopeptides with precisely known phosphorylation sites. We tested the MD-score for a wide range of commonly available fragmentation methods and found it to be applicable throughout with high statistical significance. However, the different fragmentation techniques differ strongly in their ability to localize phosphorylation sites. At 1% false localization rate, the highest number of correctly assigned phosphopeptides was achieved by higher energy collision induced dissociation in combination with an Orbitrap mass analyzer followed very closely by low resolution ion trap spectra obtained after electron transfer dissociation. Both these methods are significantly better than low resolution spectra acquired after collision induced dissociation and multi stage activation. Score thresholds determined from simple calibration functions for each fragmentation method were stable over replicate analyses of the phosphopeptide set. The MD-score outperforms the Ascore for tyrosine phosphorylated peptides and we further show that the ability to call sites correctly increases with increasing distance of two candidate sites within a peptide sequence. The MD-score does not require complex computational steps which makes it attractive in terms of practical utility. We provide all mass spectra and the synthetic peptides to the community so that the development of present and future localization software can be benchmarked and any laboratory can determine MD-scores and localization probabilities for their individual analytical set up.
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Savitski MM, Scholten A, Sweetman G, Mathieson T, Bantscheff M. Evaluation of Data Analysis Strategies for Improved Mass Spectrometry-Based Phosphoproteomics. Anal Chem 2010; 82:9843-9. [DOI: 10.1021/ac102083q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
| | - Arjen Scholten
- Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Toby Mathieson
- Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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22
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Palmisano G, Thingholm TE. Strategies for quantitation of phosphoproteomic data. Expert Rev Proteomics 2010; 7:439-56. [PMID: 20536313 DOI: 10.1586/epr.10.19] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Recent developments in phosphoproteomic sample-preparation techniques and sensitive mass spectrometry instrumentation have led to large-scale identifications of phosphoproteins and phosphorylation sites from highly complex samples. This has facilitated the implementation of different quantitation strategies in order to study the biological role of protein phosphorylation during disease progression, differentiation or during external stimulation of a cellular system. In this article, a brief summary of the most popular strategies for phosphoproteomic studies is given; however, the main focus will be on different quantitation strategies. Methods for metabolic labeling, chemical modification and label-free quantitation and their applicability or inapplicability in phosphoproteomic studies are discussed.
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Affiliation(s)
- Giuseppe Palmisano
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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Ozlu N, Akten B, Timm W, Haseley N, Steen H, Steen JA. Phosphoproteomics. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 2:255-276. [DOI: 10.1002/wsbm.41] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Nurhan Ozlu
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Bikem Akten
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Children's Hospital Boston, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Wiebke Timm
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Children's Hospital Boston, Boston, MA, USA
| | - Nathan Haseley
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- Department of Biological Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Hanno Steen
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Children's Hospital Boston, Boston, MA, USA
| | - Judith A.J. Steen
- Proteomics Center at Children's Hospital Boston, Boston, MA, USA
- F.M. Kirby Neurobiology Center, Children's Hospital Boston, Boston, MA 02115, USA
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
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Bailey CM, Sweet SMM, Cunningham DL, Zeller M, Heath JK, Cooper HJ. SLoMo: automated site localization of modifications from ETD/ECD mass spectra. J Proteome Res 2009; 8:1965-71. [PMID: 19275241 DOI: 10.1021/pr800917p] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recently, software has become available to automate localization of phosphorylation sites from CID data and to assign associated confidence scores. We present an algorithm, SLoMo (Site Localization of Modifications), which extends this capability to ETD/ECD mass spectra. Furthermore, SLoMo caters for both high and low resolution data and allows for site-localization of any UniMod post-translational modification. SLoMo accepts input data from a variety of formats (e.g., Sequest, OMSSA). We validate SLoMo with high and low resolution ETD, ECD, and CID data.
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Affiliation(s)
- Christopher M Bailey
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom
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Feng J, Garrett WM, Naiman DQ, Cooper B. Correlation of Multiple Peptide Mass Spectra for Phosphoprotein Identification. J Proteome Res 2009; 8:5396-405. [DOI: 10.1021/pr900596u] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Jian Feng
- Department of Applied Mathematics and Statistics, The Johns Hopkins University, Baltimore, Maryland 21218, Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, Maryland 20705, and Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705
| | - Wesley M. Garrett
- Department of Applied Mathematics and Statistics, The Johns Hopkins University, Baltimore, Maryland 21218, Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, Maryland 20705, and Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705
| | - Daniel Q. Naiman
- Department of Applied Mathematics and Statistics, The Johns Hopkins University, Baltimore, Maryland 21218, Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, Maryland 20705, and Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705
| | - Bret Cooper
- Department of Applied Mathematics and Statistics, The Johns Hopkins University, Baltimore, Maryland 21218, Animal Biosciences and Biotechnology Laboratory, USDA-ARS, Beltsville, Maryland 20705, and Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705
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Boersema PJ, Mohammed S, Heck AJR. Phosphopeptide fragmentation and analysis by mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:861-878. [PMID: 19504542 DOI: 10.1002/jms.1599] [Citation(s) in RCA: 284] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Reversible phosphorylation is a key event in many biological processes and is therefore a much studied phenomenon. The mass spectrometric (MS) analysis of phosphorylation is challenged by the substoichiometric levels of phosphorylation and the lability of the phosphate group in collision-induced dissociation (CID). Here, we review the fragmentation behaviour of phosphorylated peptides in MS and discuss several MS approaches that have been developed to improve and facilitate the analysis of phosphorylated peptides. CID of phosphopeptides typically results in spectra dominated by a neutral loss of the phosphate group. Several proposed mechanisms for this neutral loss and several factors affecting the extent at which this occurs are discussed. Approaches are described to interpret such neutral loss-dominated spectra to identify the phosphopeptide and localize the phosphorylation site. Methods using additional activation, such as MS(3) and multistage activation (MSA), have been designed to generate more sequence-informative fragments from the ion produced by the neutral loss. The characteristics and benefits of these methods are reviewed together with approaches using phosphopeptide derivatization or specific MS scan modes. Additionally, electron-driven dissociation methods by electron capture dissociation (ECD) or electron transfer dissociation (ETD) and their application in phosphopeptide analysis are evaluated. Finally, these techniques are put into perspective for their use in large-scale phosphoproteomics studies.
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Affiliation(s)
- Paul J Boersema
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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27
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Sweet SMM, Bailey CM, Cunningham DL, Heath JK, Cooper HJ. Large scale localization of protein phosphorylation by use of electron capture dissociation mass spectrometry. Mol Cell Proteomics 2009; 8:904-12. [PMID: 19131326 PMCID: PMC2689766 DOI: 10.1074/mcp.m800451-mcp200] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Revised: 12/19/2008] [Indexed: 01/06/2023] Open
Abstract
We used on-line electron capture dissociation (ECD) for the large scale identification and localization of sites of phosphorylation. Each FT-ICR ECD event was paired with a linear ion trap collision-induced dissociation (CID) event, allowing a direct comparison of the relative merits of ECD and CID for phosphopeptide identification and site localization. Linear ion trap CID was shown to be most efficient for phosphopeptide identification, whereas FT-ICR ECD was superior for localization of sites of phosphorylation. The combination of confident CID and ECD identification and confident CID and ECD localization is particularly valuable in cases where a phosphopeptide is identified just once within a phosphoproteomics experiment.
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Affiliation(s)
- Steve M M Sweet
- Cancer Research UK Growth Factor Group, College of Life and Environmental Sciences, Universityof Birmingham, Edgbaston, Birmingham B152TT, United Kingdom
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28
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Palumbo AM, Reid GE. Evaluation of Gas-Phase Rearrangement and Competing Fragmentation Reactions on Protein Phosphorylation Site Assignment Using Collision Induced Dissociation-MS/MS and MS3. Anal Chem 2008; 80:9735-47. [DOI: 10.1021/ac801768s] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amanda M. Palumbo
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gavin E. Reid
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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29
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Han G, Ye M, Zou H. Development of phosphopeptide enrichment techniques for phosphoproteome analysis. Analyst 2008; 133:1128-38. [DOI: 10.1039/b806775a] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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