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The  command, implemented as part of the Crux software toolkit, implements four previously reported spectral counting methods, the spectral index (SI<jats:sub>\n                <jats:italic>N<\/jats:italic>\n              <\/jats:sub>), the exponentially modified protein abundance index (emPAI), the normalized spectral abundance factor (NSAF), and the distributed normalized spectral abundance factor (dNSAF).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We compared the reproducibility and the linearity relative to each protein\u2019s abundance of the four spectral counting metrics. Our analysis suggests that NSAF yields the most reproducible counts across technical and biological replicates, and both SI<jats:sub>\n                <jats:italic>N<\/jats:italic>\n              <\/jats:sub>and NSAF achieve the best linearity.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>With the  command, Crux provides open-source modular methods to analyze mass spectrometry data for identifying and now quantifying peptides and proteins. The C++ source code, compiled binaries, spectra and sequence databases are available at<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/noble.gs.washington.edu\/proj\/crux-spectral-counts\" ext-link-type=\"uri\">http:\/\/noble.gs.washington.edu\/proj\/crux-spectral-counts<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-308","type":"journal-article","created":{"date-parts":[[2012,11,19]],"date-time":"2012-11-19T13:14:50Z","timestamp":1353330890000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":92,"title":["Estimating relative abundances of proteins from shotgun proteomics data"],"prefix":"10.1186","volume":"13","author":[{"given":"Sean","family":"McIlwain","sequence":"first","affiliation":[]},{"given":"Michael","family":"Mathews","sequence":"additional","affiliation":[]},{"given":"Michael S","family":"Bereman","sequence":"additional","affiliation":[]},{"given":"Edwin W","family":"Rubel","sequence":"additional","affiliation":[]},{"given":"Michael J","family":"MacCoss","sequence":"additional","affiliation":[]},{"given":"William Stafford","family":"Noble","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,11,19]]},"reference":[{"issue":"5","key":"5738_CR1","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1093\/bfgp\/eln031","volume":"7","author":"M Wang","year":"2008","unstructured":"Wang M, You J, Bemis KG, Tegeler TJ, Brown DP: Label-free mass spectrometry-based protein quantification technologies in proteomic analysis. 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