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Identification of related peptides through the analysis of fragment ion mass shifts

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Wilhelm, Thomas and Jones, Alexandra M. (2014) Identification of related peptides through the analysis of fragment ion mass shifts. Journal of Proteome Research, Volume 13 (Number 9). pp. 4002-4011. doi:10.1021/pr500347e

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Official URL: http://dx.doi.org/10.1021/pr500347e

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Abstract

Mass spectrometry (MS) has become the method of choice to identify and quantify proteins, typically by fragmenting peptides and inferring protein identification by reference to sequence databases. Well-established programs have largely solved the problem of identifying peptides in complex mixtures. However, to prevent the search space from becoming prohibitively large most search engines need a list of expected modifications. Therefore, unexpected modifications limit both the identification of proteins and peptide-based quantification. We developed Mass Spectrometry-Peak Shift Analysis (MS-PSA) to rapidly identify related spectra in large datasets without reference to databases or specified modifications. Peptide identifications from established tools, such as MASCOT or SEQUEST, may be propagated onto MS-PSA results. Modification of a peptide alters the mass of the precursor ion and some of the fragmentation ions. MS-PSA identifies characteristic fragmentation masses from MS/MS spectra. Related spectra are identified by pattern matching of unchanged and mass-shifted fragment ions. We illustrate the use of MS-PSA with simple and complex mixtures with both high and low mass accuracy datasets. MS-PSA is not limited to the analysis of peptides but can be used for the identification of related groups of spectra in any set of fragmentation patterns.

Item Type: Journal Article
Subjects: Q Science > QD Chemistry
Divisions: Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Mass spectrometry -- Research, Proteomics -- Research, Protein modification
Journal or Publication Title: Journal of Proteome Research
Publisher: American Chemical Society
ISSN: 1535-3893
Official Date: 24 July 2014
Dates:
DateEvent
24 July 2014Published
24 July 2014Accepted
Volume: Volume 13
Number: Number 9
Page Range: pp. 4002-4011
DOI: 10.1021/pr500347e
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
Funder: Gatsby Charitable Foundation (GCF), Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC)
Grant number: BB/J004529/he

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