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On the proper use of mass accuracy in proteomics
Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Ion Physics. (BMMS)
2007 (English)In: Molecular & Cellular Proteomics, ISSN 1535-9476, E-ISSN 1535-9484, Vol. 6, no 3, 377-381 p.Article, review/survey (Refereed) Published
Abstract [en]

Mass measurement is the main outcome of mass spectrometry-based proteomics yet the potential of recent advances in accurate mass measurements remains largely unexploited. There is not even a clear definition of mass accuracy in the proteomics literature, and we identify at least three uses of this term: anecdotal mass accuracy, statistical mass accuracy, and the maximum mass deviation (MMD) allowed in a database search. We suggest using the second of these terms as the generic one. To make the best use of the mass precision offered by modern instruments we propose a series of simple steps involving recalibration of the data on "internal standards" contained in every proteomics data set. Each data set should be accompanied by a plot of mass errors from which the appropriate MMD can be chosen. More advanced uses of high mass accuracy include an MMD that depends on the signal abundance of each peptide. Adapting search engines to high mass accuracy in the MS/MS data is also a high priority. Proper use of high mass accuracy data can make MS-based proteomics one of the most "digital" and accurate post-genomics disciplines.

Place, publisher, year, edition, pages
2007. Vol. 6, no 3, 377-381 p.
National Category
Engineering and Technology
Identifiers
URN: urn:nbn:se:uu:diva-24999DOI: 10.1074/mcp.M600380-MCP200ISI: 000245214900001OAI: oai:DiVA.org:uu-24999DiVA: diva2:52773
Available from: 2007-02-08 Created: 2007-02-08 Last updated: 2017-12-07Bibliographically approved

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Zubarev, Roman

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