{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,5]],"date-time":"2024-08-05T12:35:33Z","timestamp":1722861333678},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2014,4,20]],"date-time":"2014-04-20T00:00:00Z","timestamp":1397952000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,1]]},"abstract":"Motivation: The determination of absolute quantities of proteins in biological samples is necessary for multiple types of scientific inquiry. While relative quantification has been commonly used in proteomics, few proteomic datasets measuring absolute protein quantities have been reported to date. Various technologies have been applied using different types of input data, e.g. ion intensities or spectral counts, as well as different absolute normalization strategies. To date, a user-friendly and transparent software supporting large-scale absolute protein quantification has been lacking.<\/jats:p>\n Results: We present a bioinformatics tool, termed aLFQ, which supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS\/MS proteomics data, together with validation algorithms enabling automated data analysis and error estimation.<\/jats:p>\n Availability and implementation: \u00a0aLFQ is written in R and freely available under the GPLv3 from CRAN (http:\/\/www.cran.r-project.org). Instructions and example data are provided in the R-package. The raw data can be obtained from the PeptideAtlas raw data repository (PASS00321).<\/jats:p>\n Contact: \u00a0lars.malmstroem@imsb.biol.ethz.ch<\/jats:p>\n Supplementary information: \u00a0Supplementary Data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu200","type":"journal-article","created":{"date-parts":[[2014,4,22]],"date-time":"2014-04-22T00:28:11Z","timestamp":1398126491000},"page":"2511-2513","source":"Crossref","is-referenced-by-count":61,"title":["aLFQ: an R-package for estimating absolute protein quantities from label-free LC-MS\/MS proteomics data"],"prefix":"10.1093","volume":"30","author":[{"given":"George","family":"Rosenberger","sequence":"first","affiliation":[{"name":"1 \u00a01Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, 2PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and 3Faculty of Science, University of Zurich, Zurich, Switzerland"}]},{"given":"Christina","family":"Ludwig","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, 2PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and 3Faculty of Science, University of Zurich, Zurich, Switzerland"}]},{"given":"Hannes L.","family":"R\u00f6st","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, 2PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and 3Faculty of Science, University of Zurich, Zurich, Switzerland"}]},{"given":"Ruedi","family":"Aebersold","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, 2PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and 3Faculty of Science, University of Zurich, Zurich, Switzerland"}]},{"given":"Lars","family":"Malmstr\u00f6m","sequence":"additional","affiliation":[{"name":"1 \u00a01Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, 2PhD Program in Systems Biology, University of Zurich and ETH Zurich, Zurich, Switzerland and 3Faculty of Science, University of Zurich, Zurich, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2014,4,20]]},"reference":[{"key":"2023012711525213500_btu200-B1","doi-asserted-by":"crossref","first-page":"2567","DOI":"10.1002\/pmic.201300135","article-title":"Critical assessment of proteome-wide label-free absolute abundance estimation strategies","volume":"13","author":"Ahrn\u00e9","year":"2013","journal-title":"Proteomics"},{"key":"2023012711525213500_btu200-B2","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1016\/j.jprot.2009.03.007","article-title":"Isotope dilution strategies for absolute quantitative proteomics","volume":"72","author":"Brun","year":"2009","journal-title":"J. Proteomics"},{"key":"2023012711525213500_btu200-B3","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1074\/mcp.M112.025445","article-title":"Statistical approach to protein quantification","volume":"13","author":"Gerster","year":"2014","journal-title":"Mol. Cell. Proteomics"},{"key":"2023012711525213500_btu200-B4","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nbt1270","article-title":"Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation","volume":"25","author":"Lu","year":"2007","journal-title":"Nat. Biotechnol."},{"key":"2023012711525213500_btu200-B5","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.M111.013987","article-title":"Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry","volume":"11","author":"Ludwig","year":"2012","journal-title":"Mol. Cell. Proteomics"},{"key":"2023012711525213500_btu200-B6","doi-asserted-by":"crossref","first-page":"762","DOI":"10.1038\/nature08184","article-title":"Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans","volume":"460","author":"Malmstr\u00f6m","year":"2009","journal-title":"Nature"},{"key":"2023012711525213500_btu200-B7","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature10098","article-title":"Global quantification of mammalian gene expression control","volume":"473","author":"Schwanhausser","year":"2011","journal-title":"Nature"},{"key":"2023012711525213500_btu200-B8","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":"2023012711525213500_btu200-B9","doi-asserted-by":"crossref","first-page":"2339","DOI":"10.1021\/pr060161n","article-title":"Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae","volume":"5","author":"Zybailov","year":"2006","journal-title":"J. Proteome Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/17\/2511\/48927082\/bioinformatics_30_17_2511.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/30\/17\/2511\/48927082\/bioinformatics_30_17_2511.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T12:15:32Z","timestamp":1674821732000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/30\/17\/2511\/2748144"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,4,20]]},"references-count":9,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2014,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu200","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,4,20]]}}}