{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T03:20:47Z","timestamp":1776914447663,"version":"3.51.2"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Isobaric labelling techniques such as iTRAQ and TMT are popular methods for relative protein abundance estimation in proteomic studies. However, measurements are assessed at the peptide spectrum level and exhibit substantial heterogeneity per protein. Hence, clever summarization strategies are required to infer protein ratios. So far, current methods rely exclusively on quantitative values, while additional information on peptides is available, yet it is not considered in these methods.<\/jats:p>\n               <jats:p>Methods: We present iPQF (isobaric Protein Quantification based on Features) as a novel peptide-to-protein summarization method, which integrates peptide spectra characteristics as well as quantitative values for protein ratio estimation. We investigate diverse features characterizing spectra reliability and reveal significant correlations to ratio accuracy in spectra. As a result, we developed a feature-based weighting of peptide spectra.<\/jats:p>\n               <jats:p>Results: A performance evaluation of iPQF in comparison to nine different protein ratio inference methods is conducted on five published MS2 and MS3 datasets with predefined ground truth. We demonstrate the benefit of using peptide feature information to improve protein ratio estimation. Compared to purely quantitative approaches, our proposed strategy achieves increased accuracy by addressing peptide spectra reliability.<\/jats:p>\n               <jats:p>Availability and implementation: The iPQF algorithm is available within the established R\/Bioconductor package MSnbase (version\u2009\u2265\u20091.17.8).<\/jats:p>\n               <jats:p>Contact: \u00a0renardB@rki.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv675","type":"journal-article","created":{"date-parts":[[2015,11,21]],"date-time":"2015-11-21T02:29:46Z","timestamp":1448072986000},"page":"1040-1047","source":"Crossref","is-referenced-by-count":19,"title":["iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification"],"prefix":"10.1093","volume":"32","author":[{"given":"Martina","family":"Fischer","sequence":"first","affiliation":[{"name":"Research Group Bioinformatics (NG 4), Robert Koch Institute, 13353 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bernhard Y.","family":"Renard","sequence":"additional","affiliation":[{"name":"Research Group Bioinformatics (NG 4), Robert Koch Institute, 13353 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,11,20]]},"reference":[{"key":"2023020111560595900_btv675-B1","doi-asserted-by":"crossref","first-page":"1702","DOI":"10.1074\/mcp.M800029-MCP200","article-title":"Robust and sensitive iTRAQ quantification on an LTQ Orbitrap mass spectrometer","volume":"7","author":"Bantscheff","year":"2008","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020111560595900_btv675-B2","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/1471-2105-13-34","article-title":"PPINGUIN: Peptide profiling guided identification of proteins improves quantitation of iTRAQ ratios","volume":"13","author":"Bauer","year":"2012","journal-title":"BMC Bioinform."},{"key":"2023020111560595900_btv675-B3","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/1471-2105-8-214","article-title":"Precise protein quantification based on peptide quantification using iTRAQ","volume":"8","author":"Boehm","year":"2007","journal-title":"BMC Bioinform."},{"key":"2023020111560595900_btv675-B4","doi-asserted-by":"crossref","first-page":"2758","DOI":"10.1021\/pr1012784","article-title":"General statistical modeling of data from protein relative expression isobaric tags","volume":"10","author":"Breitwieser","year":"2011","journal-title":"J. Proteome Res."},{"key":"2023020111560595900_btv675-B5","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1002\/pmic.201000711","article-title":"iTRAQ protein quantification: a quality-controlled workflow","volume":"11","author":"Burkhart","year":"2011","journal-title":"Proteomics"},{"key":"2023020111560595900_btv675-B6","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1093\/bioinformatics\/btp610","article-title":"Methods for combining peptide intensities to estimate relative protein abundance","volume":"26","author":"Carrillo","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020111560595900_btv675-B7","doi-asserted-by":"crossref","first-page":"2437","DOI":"10.1002\/elps.200410336","article-title":"A comparison of the consistency of proteome quantitation using two-dimensional electrophoresis and shotgun isobaric tagging in Escherichia coli cells","volume":"26","author":"Choe","year":"2005","journal-title":"Electrophoresis"},{"key":"2023020111560595900_btv675-B8","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1126\/science.1124619","article-title":"Mass spectrometry and protein analysis","volume":"312","author":"Domon","year":"2006","journal-title":"Science"},{"key":"2023020111560595900_btv675-B9","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1038\/nbt.1524","article-title":"Prediction of high-responding peptides for targeted protein assays by mass spectrometry","volume":"27","author":"Fusaro","year":"2009","journal-title":"Nat. Biotechnol."},{"key":"2023020111560595900_btv675-B10","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1021\/pr060474i","article-title":"Technical, experimental, and biological variations in isobaric tags for relative and absolute quantitation (iTRAQ)","volume":"6","author":"Gan","year":"2007","journal-title":"J. Proteome Res."},{"key":"2023020111560595900_btv675-B11","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1093\/bioinformatics\/btr645","article-title":"MSnbase \u2013 an R\/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation","volume":"28","author":"Gatto","year":"2012","journal-title":"Bioinformatics"},{"key":"2023020111560595900_btv675-B12","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1038\/13690","article-title":"Quantitative analysis of complex protein mixtures using isotope-coded affinity tags","volume":"17","author":"Gygi","year":"1999","journal-title":"Nat. Biotechnol."},{"key":"2023020111560595900_btv675-B13","doi-asserted-by":"crossref","first-page":"4321","DOI":"10.1002\/pmic.200600026","article-title":"Optimized proteomic analysis of a mouse model of cerebellar dysfunction using amine-specific isobaric tags","volume":"6","author":"Hu","year":"2006","journal-title":"Proteomics"},{"key":"2023020111560595900_btv675-B14","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1093\/bioinformatics\/18.suppl_1.S96","article-title":"Variance stabilization applied to microarray data calibration and to the quantification of differential expression","volume":"18","author":"Huber","year":"2002","journal-title":"Bioinformatics"},{"key":"2023020111560595900_btv675-B15","doi-asserted-by":"crossref","first-page":"2021","DOI":"10.1074\/mcp.M112.021592","article-title":"Defining, comparing and improving iTRAQ quantification in mass spectrometry proteomics data","volume":"12","author":"Hultin-Rosenberg","year":"2013","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020111560595900_btv675-B16","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1093\/bioinformatics\/btn551","article-title":"MS-specific noise model reveals the potential of iTRAQ in quantitative proteomics","volume":"25","author":"Hundertmark","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020111560595900_btv675-B17","doi-asserted-by":"crossref","first-page":"1885","DOI":"10.1074\/mcp.M900628-MCP200","article-title":"Addressing accuracy and precision issues in iTRAQ quantitation","volume":"9","author":"Karp","year":"2010","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020111560595900_btv675-B18","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1038\/nmeth1113","article-title":"Semi-supervised learning for peptide identification from shotgun proteomics datasets","volume":"4","author":"K\u00e4ll","year":"2007","journal-title":"Nat. Methods"},{"key":"2023020111560595900_btv675-B19","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":"2023020111560595900_btv675-B20","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1093\/bioinformatics\/btp607","article-title":"Computational protein profile similarity screening for quantitative mass spectrometry experiments","volume":"26","author":"Kirchner","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020111560595900_btv675-B21","doi-asserted-by":"crossref","first-page":"6648","DOI":"10.1021\/ac034633i","article-title":"Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry","volume":"75","author":"Li","year":"2003","journal-title":"Anal. Chem."},{"key":"2023020111560595900_btv675-B22","doi-asserted-by":"crossref","first-page":"2328","DOI":"10.1021\/pr060132c","article-title":"Multi-Q: a fully automated tool for multiplexed protein quantitation","volume":"5","author":"Lin","year":"2006","journal-title":"J. Proteome Res."},{"key":"2023020111560595900_btv675-B23","doi-asserted-by":"crossref","first-page":"4325","DOI":"10.1021\/pr2001308","article-title":"Relative quantification: characterization of bias, variability and fold changes in mass spectrometry data from iTRAQ-labeled peptides","volume":"10","author":"Mahoney","year":"2011","journal-title":"J. Proteome Res."},{"key":"2023020111560595900_btv675-B24","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1074\/mcp.M200025-MCP200","article-title":"Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics","volume":"1","author":"Ong","year":"2002","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020111560595900_btv675-B25","doi-asserted-by":"crossref","first-page":"3533","DOI":"10.1002\/pmic.201000189","article-title":"LTQ-iQuant: a freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments","volume":"10","author":"Onsongo","year":"2010","journal-title":"Proteomics"},{"key":"2023020111560595900_btv675-B26","doi-asserted-by":"crossref","first-page":"5347","DOI":"10.1021\/pr900634c","article-title":"iTRAQ underestimation in simple and complex mixtures: \u2018\u2018the good, the bad and the ugly\u2019\u2019","volume":"8","author":"Ow","year":"2009","journal-title":"J. Proteome Res."},{"key":"2023020111560595900_btv675-B27","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1074\/mcp.M400129-MCP200","article-title":"Multiplexed protein quantitation in Saccharomyces cerevisiaeusing amine-reactive isobaric tagging reagents","volume":"3","author":"Ross","year":"2004","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020111560595900_btv675-B28","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.jprot.2013.10.035","article-title":"Quantitative accuracy in mass spectrometry based proteomics of complex samples: the impact of labeling and precursor interference","volume":"96","author":"Sandberg","year":"2014","journal-title":"Proteomics"},{"key":"2023020111560595900_btv675-B29","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":"2023020111560595900_btv675-B30","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1186\/1471-2164-6-145","article-title":"i-Tracker: for quantitative proteomics using iTRAQ (TM)","volume":"6","author":"Shadforth","year":"2005","journal-title":"BMC Genomics"},{"key":"2023020111560595900_btv675-B31","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1074\/mcp.M500230-MCP200","article-title":"Absolute quantification of proteins by LCMSE. A virtue of parallel ms acquisition","volume":"5","author":"Silva","year":"2006","journal-title":"Mol. Cell. Proteomics"},{"key":"2023020111560595900_btv675-B32","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1021\/ac100775s","article-title":"Impact of peptide modifications on iTRAQ quantitation accuracy","volume":"83","author":"Tenga","year":"2011","journal-title":"Anal. Chem."},{"key":"2023020111560595900_btv675-B33","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1038\/nmeth.1714","article-title":"MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics","volume":"8","author":"Ting","year":"2011","journal-title":"Nat. Methods"},{"key":"2023020111560595900_btv675-B34","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1021\/ac0262560","article-title":"Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS\/MS","volume":"75","author":"Thompson","year":"2003","journal-title":"Anal. Chem."},{"key":"2023020111560595900_btv675-B35","doi-asserted-by":"crossref","DOI":"10.1137\/1.9781611971002","volume-title":"The Total Least Squares Problem: Computational Aspects and Analysis","author":"Van Huffel","year":"1991"},{"key":"2023020111560595900_btv675-B36","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1002\/pmic.200900481","article-title":"Peptide and protein quantification: a map of the minefield","volume":"10","author":"Vaudel","year":"2010","journal-title":"Proteomics"},{"key":"2023020111560595900_btv675-B37","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1093\/bioinformatics\/btt722","article-title":"A hierarchical statistical modeling approach to analyze proteomic isobaric tag for relative and absolute quantitation data","volume":"30","author":"Zhou","year":"2014","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/7\/1040\/49018403\/bioinformatics_32_7_1040.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/32\/7\/1040\/49018403\/bioinformatics_32_7_1040.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T22:19:17Z","timestamp":1675289957000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/32\/7\/1040\/1743612"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,11,20]]},"references-count":37,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2016,4,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btv675","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2016,4,1]]},"published":{"date-parts":[[2015,11,20]]}}}