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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
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 | ||||||
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| 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: |
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| Date of first compliant deposit: | 27 December 2015 | ||||||
| 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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