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Peptide-Centric Proteome Analysis: An Alternative Strategy for the Analysis of Tandem Mass Spectrometry Data
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2015 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 14, no 9, 2301-2307 p.Article, review/survey (Refereed) Published
Abstract [en]

In mass spectrometry-based bottom-up proteomics, data-independent acquisition is an emerging technique because of its comprehensive and unbiased sampling of precursor ions. However, current data-independent acquisition methods use wide precursor isolation windows, resulting in cofragmentation and complex mixture spectra. Thus, conventional database searching tools that identify peptides by interpreting individual tandem MS spectra are inherently limited in analyzing data-independent acquisition data. Here we discuss an alternative approach, peptide-centric analysis, which tests directly for the presence and absence of query peptides. We discuss how peptide-centric analysis resolves some limitations of traditional spectrum-centric analysis, and we outline the unique characteristics of peptide-centric analysis in general.

Place, publisher, year, edition, pages
[Ting, Ying S.; Egertson, Jarrett D.; MacLean, Brendan; Noble, William Stafford; MacCoss, Michael J.] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA. [Payne, Samuel H.; Kim, Sangtae; Smith, Richard D.] Pacific NW Natl Lab, Div Biol Sci, Richland, WA 99352 USA. [Kall, Lukas] Royal Inst Technol KTH, Sci Life Lab, Stockholm, Sweden. [Aebersold, Ruedi] ETH, Inst Mol Syst Biol, Dept Biol, Swiss Fed Inst Technol, Zurich, Switzerland. [Noble, William Stafford] Univ Washington, Dept Comp Sci & Engn, Seattle, WA 98195 USA. [Aebersold, Ruedi] Univ Zurich, Fac Sci, Zurich, Switzerland., 2015. Vol. 14, no 9, 2301-2307 p.
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Biochemistry and Molecular Biology
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URN: urn:nbn:se:kth:diva-174234DOI: 10.1074/mcp.O114.047035ISI: 000360823000001PubMedID: 26217018Scopus ID: 2-s2.0-84940553225OAI: oai:DiVA.org:kth-174234DiVA: diva2:861436
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QC 20151016

Available from: 2015-10-16 Created: 2015-10-02 Last updated: 2017-12-01Bibliographically approved

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Käll, Lukas

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