{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,5]],"date-time":"2026-02-05T23:12:16Z","timestamp":1770333136662,"version":"3.49.0"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We present an approach to statistically pinpoint differentially expressed proteins that have quantitation values near the quantitation threshold and are not identified in all replicates (marginal cases). Our method uses a Bayesian strategy to combine parametric statistics with an empirical distribution built from the reproducibility quality of the technical replicates.<\/jats:p>\n               <jats:p>Availability:The software is freely available for academic use at http:\/\/pcarvalho.com\/patternlab.<\/jats:p>\n               <jats:p>Contact: \u00a0paulo@pcarvalho.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq632","type":"journal-article","created":{"date-parts":[[2010,11,13]],"date-time":"2010-11-13T01:20:02Z","timestamp":1289611202000},"page":"275-276","source":"Crossref","is-referenced-by-count":32,"title":["Analyzing marginal cases in differential shotgun proteomics"],"prefix":"10.1093","volume":"27","author":[{"given":"Paulo C.","family":"Carvalho","sequence":"first","affiliation":[{"name":"1 Center for Technological Development in Health, 2Department of Physiology and Pharmacodynamics, Laboratory of Toxinology, 3Department of Biochemistry and Molecular Biology, Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Rio de Janeiro, Brazil, 4Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA, 5Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil and 6Computer Science Department, University of California, Los Angeles, CA 90024, USA"},{"name":"1 Center for Technological Development in Health, 2Department of Physiology and Pharmacodynamics, Laboratory of Toxinology, 3Department of Biochemistry and Molecular Biology, Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Rio de Janeiro, Brazil, 4Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA, 5Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil and 6Computer Science Department, University of California, Los Angeles, CA 90024, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juliana S. G.","family":"Fischer","sequence":"additional","affiliation":[{"name":"1 Center for Technological Development in Health, 2Department of Physiology and Pharmacodynamics, Laboratory of Toxinology, 3Department of Biochemistry and Molecular Biology, Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Rio de Janeiro, Brazil, 4Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA, 5Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil and 6Computer Science Department, University of California, Los Angeles, CA 90024, USA"},{"name":"1 Center for Technological Development in Health, 2Department of Physiology and Pharmacodynamics, Laboratory of Toxinology, 3Department of Biochemistry and Molecular Biology, Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Rio de Janeiro, Brazil, 4Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA, 5Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil and 6Computer Science Department, University of California, Los Angeles, CA 90024, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonas","family":"Perales","sequence":"additional","affiliation":[{"name":"1 Center for Technological Development in Health, 2Department of Physiology and Pharmacodynamics, Laboratory of Toxinology, 3Department of Biochemistry and Molecular Biology, Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Rio de Janeiro, Brazil, 4Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA, 5Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil and 6Computer Science Department, University of California, Los Angeles, CA 90024, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John R.","family":"Yates","sequence":"additional","affiliation":[{"name":"1 Center for Technological Development in Health, 2Department of Physiology and Pharmacodynamics, Laboratory of Toxinology, 3Department of Biochemistry and Molecular Biology, Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Rio de Janeiro, Brazil, 4Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA, 5Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil and 6Computer Science Department, University of California, Los Angeles, CA 90024, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valmir C.","family":"Barbosa","sequence":"additional","affiliation":[{"name":"1 Center for Technological Development in Health, 2Department of Physiology and Pharmacodynamics, Laboratory of Toxinology, 3Department of Biochemistry and Molecular Biology, Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Rio de Janeiro, Brazil, 4Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA, 5Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil and 6Computer Science Department, University of California, Los Angeles, CA 90024, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elias","family":"Bareinboim","sequence":"additional","affiliation":[{"name":"1 Center for Technological Development in Health, 2Department of Physiology and Pharmacodynamics, Laboratory of Toxinology, 3Department of Biochemistry and Molecular Biology, Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Rio de Janeiro, Brazil, 4Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA, 5Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil and 6Computer Science Department, University of California, Los Angeles, CA 90024, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2010,11,11]]},"reference":[{"key":"2023012512181245900_B1","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1186\/1471-2105-9-316","article-title":"PatternLab for proteomics: a tool for differential shotgun proteomics","volume":"9","author":"Carvalho","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023012512181245900_B2","doi-asserted-by":"crossref","DOI":"10.1002\/0471250953.bi1313s30","article-title":"Analyzing shotgun proteomic data with PatternLab for proteomics","author":"Carvalho","year":"2010","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"2023012512181245900_B3","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1016\/j.jprot.2010.01.003","article-title":"Dynamic proteomic overview of glioblastoma cells (A172) exposed to perillyl alcohol","volume":"73","author":"Fischer","year":"2010","journal-title":"J. Proteomics"},{"key":"2023012512181245900_B4","doi-asserted-by":"crossref","first-page":"4193","DOI":"10.1021\/ac0498563","article-title":"A model for random sampling and estimation of relative protein abundance in shotgun proteomics","volume":"76","author":"Liu","year":"2004","journal-title":"Anal. Chem."},{"key":"2023012512181245900_B5","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/85686","article-title":"Large-scale analysis of the yeast proteome by multidimensional protein identification technology","volume":"19","author":"Washburn","year":"2001","journal-title":"Nat. Biotechnol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/2\/275\/48870168\/bioinformatics_27_2_275.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/2\/275\/48870168\/bioinformatics_27_2_275.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:57:06Z","timestamp":1674658626000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/2\/275\/285110"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,11,11]]},"references-count":5,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2011,1,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btq632","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,1,15]]},"published":{"date-parts":[[2010,11,11]]}}}