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

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      Journal of proteome research

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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 data sets 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 data sets. 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.

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          Author and article information

          Journal
          J. Proteome Res.
          Journal of proteome research
          1535-3907
          1535-3893
          Sep 5 2014
          : 13
          : 9
          Affiliations
          [1 ] Institute of Food Research , Norwich Research Park, Norwich NR4 7UA, United Kingdom.
          Article
          10.1021/pr500347e
          25058668

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