{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T01:11:02Z","timestamp":1790644262369,"version":"4.1.0"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2017,3,23]],"date-time":"2017-03-23T00:00:00Z","timestamp":1490227200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Netherlands Genomics Initiative","award":["FES0908"],"award-info":[{"award-number":["FES0908"]}]},{"name":"Dutch Government"},{"name":"Netherlands Organization for Scientific Research"},{"name":"Netherlands Proteomics Centre"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,28]]},"DOI":"10.1093\/bib\/bbx031","type":"journal-article","created":{"date-parts":[[2017,2,24]],"date-time":"2017-02-24T20:09:42Z","timestamp":1487966982000},"page":"971-981","source":"Crossref","is-referenced-by-count":63,"title":["Identification of differentially expressed peptides in high-throughput proteomics data"],"prefix":"10.1093","volume":"19","author":[{"given":"Michiel P","family":"van Ooijen","sequence":"first","affiliation":[{"name":"Department of Viroscience, Erasmus MC, CA Rotterdam, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Victor L","family":"Jong","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Research Support, Julius Center, UMC Utrecht, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marinus J C","family":"Eijkemans","sequence":"additional","affiliation":[{"name":"Julius Center for Health Sciences and Primary Care of the University Medical Center Utrecht, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Albert J R","family":"Heck","sequence":"additional","affiliation":[{"name":"Biomolecular Mass Spectrometry and Proteomics, Utrecht University, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arno C","family":"Andeweg","sequence":"additional","affiliation":[{"name":"Department of Viroscience, Erasmus MC, CA Rotterdam, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nadine A","family":"Binai","sequence":"additional","affiliation":[{"name":"Biomolecular Mass Spectrometry Group, Utrecht University, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henk-Jan","family":"van den Ham","sequence":"additional","affiliation":[{"name":"Department of Viroscience, Erasmus MC, CA Rotterdam, Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,3,23]]},"reference":[{"key":"key\n\t\t\t\t20180928113212_bbx031-B1","first-page":"ra46","article-title":"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions","volume":"2","author":"Mayya","year":"2009","journal-title":"Sci Sign"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B2","doi-asserted-by":"crossref","first-page":"1550","DOI":"10.1182\/blood-2007-01-069229","article-title":"Human CD4+CD25+ regulatory T cells: proteome analysis identifies galectin-10 as a novel marker essential for their anergy and suppressive function","volume":"110","author":"Kubach","year":"2007","journal-title":"Blood"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B3","doi-asserted-by":"crossref","first-page":"7535","DOI":"10.1074\/jbc.M110.201236","article-title":"T cell receptor (TCR)-induced tyrosine phosphorylation dynamics identifies THEMIS as a new TCR signalosome component","volume":"286","author":"Brockmeyer","year":"2011","journal-title":"J Biol Chem"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B4","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1074\/mcp.M800139-MCP200","article-title":"Quantitative proteomics reveals GIMAP family proteins 1 and 4 to be differentially regulated during human T helper cell differentiation","volume":"8","author":"Fil\u00e9n","year":"2009","journal-title":"Mol Cell Proteomics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B5","doi-asserted-by":"crossref","first-page":"810","DOI":"10.15252\/msb.20145880","article-title":"Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation","volume":"11","author":"Satpathy","year":"2015","journal-title":"Mol Syst Biol"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B6","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1074\/mcp.M113.034769","article-title":"The one hour yeast proteome","volume":"13","author":"Hebert","year":"2014","journal-title":"Mol Cell Proteomics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B7","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nature13302","article-title":"A draft map of the human proteome","volume":"509","author":"Kim","year":"2014","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B8","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1038\/nature13319","article-title":"Mass-spectrometry-based draft of the human proteome","volume":"509","author":"Wilhelm","year":"2014","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B9","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/j.cels.2016.02.015","article-title":"Plasma proteome profiling to assess human health and disease","volume":"2","author":"Geyer","year":"2016","journal-title":"Cell Syst"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B10","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1146\/annurev-anchem-071213-020216","article-title":"High-Throughput Proteomics","volume":"7","author":"Zhang","year":"2014","journal-title":"Annu Rev Anal Chem"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B11","doi-asserted-by":"crossref","first-page":"1709","DOI":"10.1074\/mcp.M112.024919","article-title":"Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse","volume":"12","author":"Geiger","year":"2013","journal-title":"Mol Cell Proteomics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B12","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1038\/nbt.3418","article-title":"The quantitative and condition-dependent Escherichia coli proteome","volume":"34","author":"Schmidt","year":"2015","journal-title":"Nat Biotechnol"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B13","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1021\/acs.analchem.5b04123","article-title":"Phosphoproteomics in the age of rapid and deep proteome profiling","volume":"88","author":"Riley","year":"2016","journal-title":"Anal Chem"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B14","doi-asserted-by":"crossref","first-page":"3444","DOI":"10.1074\/mcp.O113.034181","article-title":"Status of large-scale analysis of post-translational modifications by mass spectrometry","volume":"12","author":"Olsen","year":"2013","journal-title":"Mol Cell Proteomics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B15","doi-asserted-by":"crossref","first-page":"2426","DOI":"10.1074\/mcp.O113.036608","article-title":"Single-step enrichment by Ti4+-IMAC and label-free quantitation enables in-depth monitoring of phosphorylation dynamics with high reproducibility and temporal resolution","volume":"13","author":"de Graaf","year":"2014","journal-title":"Mol Cell Proteomics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B16","doi-asserted-by":"crossref","first-page":"5022","DOI":"10.1128\/JVI.03630-14","article-title":"Host proteome correlates of vaccine-mediated enhanced disease in a mouse model of respiratory syncytial virus infection","volume":"89","author":"van Diepen","year":"2015","journal-title":"J Virol"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B17","doi-asserted-by":"crossref","first-page":"D521","DOI":"10.1093\/nar\/gku1154","article-title":"ProteomeScout: a repository and analysis resource for post-translational modifications and proteins","volume":"43","author":"Matlock","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B18","doi-asserted-by":"crossref","first-page":"D447","DOI":"10.1093\/nar\/gkv1145","article-title":"2016 update of the PRIDE database and its related tools","volume":"44","author":"Vizcaino","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B19","first-page":"gkw1080","article-title":"jPOSTrepo: an international standard data repository for proteomes","volume":"45","author":"Okuda","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B20","doi-asserted-by":"crossref","first-page":"1170","DOI":"10.1002\/pmic.201100515","article-title":"PASSEL: the PeptideAtlas SRMexperiment library","volume":"12","author":"Farrah","year":"2012","journal-title":"Proteomics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B21","first-page":"gkw936","article-title":"The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition","volume":"45","author":"Deutsch","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B22","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1002\/pmic.201400302","article-title":"Making proteomics data accessible and reusable: current state of proteomics databases and repositories","volume":"15","author":"Perez-Riverol","year":"2015","journal-title":"Proteomics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B23","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1074\/mcp.M115.056226","article-title":"An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer","volume":"15","author":"Ruggles","year":"2016","journal-title":"Mol Cell Prot"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B24","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1038\/nmeth.3144","article-title":"Proteogenomics: concepts, applications and computational strategies","volume":"11","author":"Nesvizhskii","year":"2014","journal-title":"Nat Meth"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B25","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.cbpa.2015.10.023","article-title":"Reconciling proteomics with next generation sequencing","volume":"30","author":"Low","year":"2016","journal-title":"Curr Opin Chem Biol"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B26","doi-asserted-by":"crossref","first-page":"2533","DOI":"10.1002\/pmic.201600140","article-title":"Integrating transcriptome and proteome profiling: strategies and applications","volume":"16","author":"Kumar","year":"2016","journal-title":"Proteomics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B27","first-page":"1","article-title":"Clinical implications of recent advances in proteogenomics","volume":"13","author":"Locard-Paulet","year":"2015","journal-title":"Exp Rev Prot"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B28","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1146\/annurev-anchem-071015-041722","article-title":"Proteogenomics: integrating next-generation sequencing and mass spectrometry to characterize human proteomic variation","volume":"9","author":"Sheynkman","year":"2016","journal-title":"Ann Rev Anal Chem"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B29","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1016\/j.celrep.2016.12.016","article-title":"Personalized proteome profiles of healthy and tumor human colon organoids reveal both individual diversity and basic features of colorectal cancer","volume":"18","author":"Cristobal","year":"2017","journal-title":"Cell Rep"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B30","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bib\/bbv084","article-title":"Interpreting functional effects of coding variants: Challenges in proteome-scale prediction, annotation and assessment","volume":"17","author":"Shameer","year":"2016","journal-title":"Brief Bioinform"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B31","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/nature13438","article-title":"Proteogenomic characterization of human colon and rectal cancer","volume":"513","author":"Zhang","year":"2014","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B32","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1016\/j.jprot.2015.09.012","article-title":"Quantitative proteogenomics of human pathogens using DIA-MS","volume":"129","author":"Malmstr\u00f6m","year":"2015","journal-title":"J Proteomics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B33","first-page":"883","article-title":"Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics","volume":"1864","author":"Blein-Nicolas","year":"2016","journal-title":"Biochem Biophys Acta"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B34","doi-asserted-by":"crossref","first-page":"4118","DOI":"10.1021\/acs.jproteome.5b00183","article-title":"Optimization of statistical methods impact on quantitative proteomics data","volume":"14","author":"Pursiheimo","year":"2015","journal-title":"J Proteome Res"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B35","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nbt.1619","article-title":"Analyzing \u2019omics data using hierarchical models","volume":"28","author":"Ji","year":"2010","journal-title":"Nat Biotech"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B36","doi-asserted-by":"crossref","first-page":"1993","DOI":"10.1021\/pr501138h","article-title":"Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics","volume":"14","author":"Webb-Robertson","year":"2015","journal-title":"J Proteome Res"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B37","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1186\/1471-2105-13-S16-S5","article-title":"Normalization and missing value imputation for label-free LC-MS analysis","volume":"13(Suppl 1)","author":"Karpievitch","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B38","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1074\/mcp.M111.015362","article-title":"Super-SILAC allows classification of diffuse large B-cell lymphoma subtypes by their protein expression profiles","volume":"11","author":"Deeb","year":"2012","journal-title":"Mol Cell Proteomics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B39","doi-asserted-by":"crossref","first-page":"731","DOI":"10.1038\/nmeth.3901","article-title":"The Perseus computational platform for comprehensive analysis of (prote)omics data","volume":"13","author":"Tyanova","year":"2016","journal-title":"Nat Methods"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B40","first-page":"79","article-title":"An overview of multiple imputation","author":"Rubin","year":"1988","journal-title":"Proc Surv Res Methods Sect Am Stat Assoc"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B41","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1021\/acs.jproteome.5b00981","article-title":"Accounting for the multiple natures of missing values in label-free quantitative proteomics data sets to compare imputation strategies","volume":"15","author":"Lazar","year":"2016","journal-title":"J. Proteome Res"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B42","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1074\/mcp.R112.025163","article-title":"Tools for label-free peptide quantification","volume":"12","author":"Nahnsen","year":"2013","journal-title":"Mol Cell Prot"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B43","doi-asserted-by":"crossref","first-page":"4099","DOI":"10.1021\/acs.jproteome.5b00568","article-title":"Solution to statistical challenges in proteomics is more statistics, not less","volume":"14","author":"Serang","year":"2015","journal-title":"J Proteome Res"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B44","doi-asserted-by":"crossref","first-page":"2524","DOI":"10.1093\/bioinformatics\/btu305","article-title":"MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments","volume":"30","author":"Choi","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B45","doi-asserted-by":"crossref","first-page":"article3","DOI":"10.2202\/1544-6115.1027","article-title":"Linear models and empirical Bayes methods for assessing differential expression in microarray experiments","volume":"3","author":"Smyth","year":"2004","journal-title":"Stat Appl Genet Mol Biol"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B46","doi-asserted-by":"crossref","first-page":"2946","DOI":"10.1093\/bioinformatics\/btt513","article-title":"NetWeAvers: an R package for integrative biological network analysis with mass spectrometry data","volume":"29","author":"McClellan","year":"2013","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B47","doi-asserted-by":"crossref","first-page":"2741","DOI":"10.1093\/bioinformatics\/btu341","article-title":"Detecting differential protein expression in large-scale population proteomics","volume":"30","author":"Ryu","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B48","doi-asserted-by":"crossref","first-page":"370","DOI":"10.2307\/2344614","article-title":"Generalized linear models","volume":"135","author":"Nelder","year":"1972","journal-title":"J Roy Stat Soc"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B49","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J Roy Statis Soc B"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B50","doi-asserted-by":"crossref","first-page":"1556","DOI":"10.1093\/bioinformatics\/btn217","article-title":"DAnTE: a statistical tool for quantitative analysis of -omics data","volume":"24","author":"Polpitiya","year":"2008","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B51","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v045.i03","article-title":"mice: Multivariate Imputation by Chained Equations in R","volume":"45","author":"Buuren","year":"2011","journal-title":"J Stat Softw"},{"key":"key\n\t\t\t\t20180928113212_bbx031-B52","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1016\/j.dib.2016.01.061","article-title":"Proteome stability analysis of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human colon mucosal biopsies","volume":"6","author":"Bennike","year":"2016","journal-title":"Data Brief"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bib\/article-pdf\/19\/5\/971\/25861117\/bbx031.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,22]],"date-time":"2024-06-22T17:52:33Z","timestamp":1719078753000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/19\/5\/971\/3079005"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3,23]]},"references-count":52,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2017,3,23]]},"published-print":{"date-parts":[[2018,9,28]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbx031","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,9]]},"published":{"date-parts":[[2017,3,23]]}}}