{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T20:20:57Z","timestamp":1777666857901,"version":"3.51.4"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Assembling peptides identified from tandem mass spectra into a list of proteins, referred to as protein inference, is an important issue in shotgun proteomics. The objective of protein inference is to find a subset of proteins that are truly present in the sample. Although many methods have been proposed for protein inference, several issues such as peptide degeneracy still remain unsolved.<\/jats:p>\n               <jats:p>Results: In this article, we present a linear programming model for protein inference. In this model, we use a transformation of the joint probability that each peptide\/protein pair is present in the sample as the variable. Then, both the peptide probability and protein probability can be expressed as a formula in terms of the linear combination of these variables. Based on this simple fact, the protein inference problem is formulated as an optimization problem: minimize the number of proteins with non-zero probabilities under the constraint that the difference between the calculated peptide probability and the peptide probability generated from peptide identification algorithms should be less than some threshold. This model addresses the peptide degeneracy issue by forcing some joint probability variables involving degenerate peptides to be zero in a rigorous manner. The corresponding inference algorithm is named as ProteinLP. We test the performance of ProteinLP on six datasets. Experimental results show that our method is competitive with the state-of-the-art protein inference algorithms.<\/jats:p>\n               <jats:p>Availability: The source code of our algorithm is available at: https:\/\/sourceforge.net\/projects\/prolp\/.<\/jats:p>\n               <jats:p>Contact: \u00a0zyhe@dlut.edu.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics Online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts540","type":"journal-article","created":{"date-parts":[[2012,9,7]],"date-time":"2012-09-07T01:09:09Z","timestamp":1346980149000},"page":"2956-2962","source":"Crossref","is-referenced-by-count":20,"title":["A linear programming model for protein inference problem in shotgun proteomics"],"prefix":"10.1093","volume":"28","author":[{"given":"Ting","family":"Huang","sequence":"first","affiliation":[{"name":"School of Software, Dalian University of Technology, Dalian 116621, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zengyou","family":"He","sequence":"additional","affiliation":[{"name":"School of Software, Dalian University of Technology, Dalian 116621, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,9,6]]},"reference":[{"key":"2023012513220411300_bts540-B1","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1089\/cmb.2007.0119","article-title":"Improved ranking functions for protein and modification-site identifications","volume":"15","author":"Bern","year":"2008","journal-title":"J. Comput. Biol."},{"key":"2023012513220411300_bts540-B2","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1038\/nbt1300","article-title":"A high-quality catalog of the drosophila melanogaster proteome","volume":"25","author":"Brunner","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"2023012513220411300_bts540-B3","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1002\/pmic.200300744","article-title":"Unimod: protein modifications for mass spectrometry","volume":"4","author":"David","year":"2004","journal-title":"Proteomics"},{"key":"2023012513220411300_bts540-B4","doi-asserted-by":"crossref","first-page":"3901","DOI":"10.1021\/ac070202e","article-title":"Probability model for assessing proteins assembled from peptides sequences inferred from tandem mass spectrometry data","volume":"79","author":"Feng","year":"2007","journal-title":"Anal. Chem."},{"key":"2023012513220411300_bts540-B5","doi-asserted-by":"crossref","first-page":"12101","DOI":"10.1073\/pnas.0907654107","article-title":"Protein and gene model inference based on statistical modeling in k-partite graphs","volume":"107","author":"Gerster","year":"2010","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012513220411300_bts540-B6","doi-asserted-by":"crossref","first-page":"1786","DOI":"10.1101\/gr.089060.108","article-title":"Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function","volume":"19","author":"Grobei","year":"2009","journal-title":"Genome Res."},{"key":"2023012513220411300_bts540-B7","first-page":"368","article-title":"A partial set covering model for protein mixture identification using mass spectrometry data. IEEE\/ACM Trans","volume":"8","author":"He","year":"2011","journal-title":"Comput. Biol. Bioinform."},{"key":"2023012513220411300_bts540-B8","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1093\/bib\/bbs004","article-title":"Protein inference: a review","volume":"13","author":"Huang","year":"2012","journal-title":"Brief. Bioinform."},{"key":"2023012513220411300_bts540-B9","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1021\/pr0705439","article-title":"Protein identification and peptide expression resolver: harmonizing protein identification with protein expression data","volume":"7","author":"Kearney","year":"2008","journal-title":"J. Proteome Res."},{"key":"2023012513220411300_bts540-B10","doi-asserted-by":"crossref","first-page":"5383","DOI":"10.1021\/ac025747h","article-title":"Empirical statistical model to estimate the accuracy of peptide identifications made by MS\/MS and database search","volume":"74","author":"Keller","year":"2002","journal-title":"Anal. Chem."},{"key":"2023012513220411300_bts540-B11","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1021\/pr070244j","article-title":"The Standard Protein Mix Database: a diverse dataset to assist in the production of improved peptide and protein identification software tools","volume":"7","author":"Klimek","year":"2008","journal-title":"J. Proteome Res."},{"key":"2023012513220411300_bts540-B12","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1038\/msb.2009.54","article-title":"Network-assisted protein identification and data interpretation in shotgun proteomics","volume":"5","author":"Li","year":"2009","journal-title":"Mol. Syst. Biol."},{"key":"2023012513220411300_bts540-B13","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1214\/09-AOAS316","article-title":"A nested mixture model for protein identification using mass spectrometry","volume":"4","author":"Li","year":"2010","journal-title":"Ann. Appl. Stat."},{"key":"2023012513220411300_bts540-B14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1089\/cmb.2009.0018","article-title":"A Bayesian approach to protein inference problem in shotgun proteomics","volume":"16","author":"Li","year":"2009","journal-title":"J. Comput. Biol."},{"key":"2023012513220411300_bts540-B15","doi-asserted-by":"crossref","first-page":"2018","DOI":"10.1021\/ac701697w","article-title":"Improving protein identification sensitivity by combining MS and MS\/MS information for shotgun proteomics using LTQ-Orbitrap high mass accuracy data","volume":"80","author":"Lu","year":"2008","journal-title":"Anal. Chem."},{"key":"2023012513220411300_bts540-B16","doi-asserted-by":"crossref","first-page":"3872","DOI":"10.1021\/pr900360j","article-title":"IDPicker 2.0: improved protein assembly with high discrimination peptide identification filtering","volume":"8","author":"Ma","year":"2009","journal-title":"J. Proteome Res."},{"key":"2023012513220411300_bts540-B17","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1016\/S1044-0305(02)00352-5","article-title":"Qscore: an algorithm for evaluating sequest database search results","volume":"13","author":"Moore","year":"2002","journal-title":"J. Am. Soc. Mass Spectrom."},{"key":"2023012513220411300_bts540-B18","doi-asserted-by":"crossref","first-page":"4646","DOI":"10.1021\/ac0341261","article-title":"A statistical model for identifying proteins by tandem mass spectrometry","volume":"75","author":"Nesvizhskii","year":"2003","journal-title":"Anal. Chem."},{"key":"2023012513220411300_bts540-B19","doi-asserted-by":"crossref","first-page":"3551","DOI":"10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2","article-title":"Probability-based protein identification by searching sequence databases using mass spectrometry data","volume":"20","author":"Perkins","year":"1999","journal-title":"Electrophoresis"},{"key":"2023012513220411300_bts540-B20","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1074\/mcp.T600049-MCP200","article-title":"EBP: protein identification using multiple tandem mass spectrometry datasets","volume":"6","author":"Price","year":"2007","journal-title":"Mol. Cell. Proteomics"},{"key":"2023012513220411300_bts540-B21","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1038\/nbt0710-647","article-title":"PeptideClassifier for protein inference and targeted quantitative proteomics","volume":"28","author":"Qeli","year":"2010","journal-title":"Nat. Biotechnol."},{"key":"2023012513220411300_bts540-B22","doi-asserted-by":"crossref","first-page":"2955","DOI":"10.1093\/bioinformatics\/btp461","article-title":"Mining gene functional networks to improve mass-spectrometry based protein identification","volume":"25","author":"Ramakrishnan","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012513220411300_bts540-B23","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1093\/bioinformatics\/btp168","article-title":"Integrating shotgun proteomics and mRNA expression data to improve protein identification","volume":"25","author":"Ramakrishnan","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012513220411300_bts540-B24","doi-asserted-by":"crossref","first-page":"1664","DOI":"10.1021\/ac035112y","article-title":"Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases","volume":"76","author":"Sadygov","year":"2004","journal-title":"Anal. Chem."},{"key":"2023012513220411300_bts540-B25","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.1002\/pmic.200900437","article-title":"Scaffold: a bioinformatic tool for validating MS\/MS-based proteomic studies","volume":"10","author":"Searle","year":"2010","journal-title":"Proteomics"},{"key":"2023012513220411300_bts540-B26","doi-asserted-by":"crossref","first-page":"5346","DOI":"10.1021\/pr100594k","article-title":"Efficient marginalization to compute protein posterior probabilities from shotgun mass spectrometry data","volume":"9","author":"Serang","year":"2010","journal-title":"J. Proteome Res."},{"key":"2023012513220411300_bts540-B27","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1093\/bioinformatics\/btm555","article-title":"A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry","volume":"24","author":"Shen","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012513220411300_bts540-B28","doi-asserted-by":"crossref","first-page":"3035","DOI":"10.1002\/pmic.200900370","article-title":"MassSieve: panning MS\/MS peptide data for proteins","volume":"10","author":"Slotta","year":"2010","journal-title":"Proteomics"},{"key":"2023012513220411300_bts540-B29","doi-asserted-by":"crossref","first-page":"M111.012161","DOI":"10.1074\/mcp.M111.012161","article-title":"Direct maximization of protein identifications from tandem mass spectra","volume":"11","author":"Spivak","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"2023012513220411300_bts540-B30","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1021\/pr015504q","article-title":"DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics","volume":"1","author":"Tabb","year":"2002","journal-title":"J. Proteome Res."},{"key":"2023012513220411300_bts540-B31","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1074\/mcp.M400215-MCP200","article-title":"A heuristic method for assigning a false-discovery rate for protein identifications from mascot database search results","volume":"4","author":"Weatherly","year":"2005","journal-title":"Mol. Cell. Proteomics"},{"key":"2023012513220411300_bts540-B32","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1021\/pr049920x","article-title":"DBParser: web-based software for shotgun proteomic data analyses","volume":"3","author":"Yang","year":"2004","journal-title":"J. Proteome Res."},{"key":"2023012513220411300_bts540-B33","doi-asserted-by":"crossref","first-page":"3549","DOI":"10.1021\/pr070230d","article-title":"Proteomic parsimony through bipartite graph analysis improves accuracy and transparency","volume":"6","author":"Zhang","year":"2007","journal-title":"J. Proteome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/22\/2956\/48872105\/bioinformatics_28_22_2956.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/22\/2956\/48872105\/bioinformatics_28_22_2956.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T19:19:55Z","timestamp":1674674395000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/22\/2956\/239773"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,9,6]]},"references-count":33,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2012,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts540","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,11,15]]},"published":{"date-parts":[[2012,9,6]]}}}