{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,17]],"date-time":"2026-01-17T08:07:58Z","timestamp":1768637278695,"version":"3.49.0"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Labeling techniques are being used increasingly to estimate relative protein abundances in quantitative proteomic studies. These techniques require the accurate measurement of correspondingly labeled peptide peak intensities to produce high-quality estimates of differential expression ratios. In mass spectrometers with counting detectors, the measurement noise varies with intensity and consequently accuracy increases with the number of ions detected. Consequently, the relative variability of peptide intensity measurements varies with intensity. This effect must be accounted for when combining information from multiple peptides to estimate relative protein abundance.<\/jats:p>\n               <jats:p>Results: We examined a variety of algorithms that estimate protein differential expression ratios from multiple peptide intensity measurements. Algorithms that account for the variation of measurement error with intensity were found to provide the most accurate estimates of differential abundance. A simple Sum-of-Intensities algorithm provided the best estimates of true protein ratios of all algorithms tested.<\/jats:p>\n               <jats:p>Contact: \u00a0robert.kearney@mcgill.ca<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp610","type":"journal-article","created":{"date-parts":[[2009,11,6]],"date-time":"2009-11-06T02:10:10Z","timestamp":1257473410000},"page":"98-103","source":"Crossref","is-referenced-by-count":58,"title":["Methods for combining peptide intensities to estimate relative protein abundance"],"prefix":"10.1093","volume":"26","author":[{"given":"Brian","family":"Carrillo","sequence":"first","affiliation":[{"name":"1 Department of Biomedical Engineering, McGill University, 2 McGill University and Genome Quebec Innovation Centre Proteomics Platform and 3 Department of Human Genetics, McGill University, Montreal, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Corey","family":"Yanofsky","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, McGill University, 2 McGill University and Genome Quebec Innovation Centre Proteomics Platform and 3 Department of Human Genetics, McGill University, Montreal, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sylvie","family":"Laboissiere","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, McGill University, 2 McGill University and Genome Quebec Innovation Centre Proteomics Platform and 3 Department of Human Genetics, McGill University, Montreal, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert","family":"Nadon","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, McGill University, 2 McGill University and Genome Quebec Innovation Centre Proteomics Platform and 3 Department of Human Genetics, McGill University, Montreal, Canada"},{"name":"1 Department of Biomedical Engineering, McGill University, 2 McGill University and Genome Quebec Innovation Centre Proteomics Platform and 3 Department of Human Genetics, McGill University, Montreal, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robert E.","family":"Kearney","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Engineering, McGill University, 2 McGill University and Genome Quebec Innovation Centre Proteomics Platform and 3 Department of Human Genetics, McGill University, Montreal, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,11,5]]},"reference":[{"key":"2023012507533004500_B1","doi-asserted-by":"crossref","first-page":"3575","DOI":"10.1093\/bioinformatics\/bth446","article-title":"Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum","volume":"20","author":"Anderle","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012507533004500_B2","doi-asserted-by":"crossref","first-page":"2039","DOI":"10.1021\/pr060105m","article-title":"New algorithm for 15N\/14N Quantitation with LC-ESI-MS Using an LTQ-FT Mass Spectrometer","volume":"5","author":"Andreev","year":"2006","journal-title":"J. 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