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SALSA: An Algorithm for Mining Specific Features of Tandem MS Data

  • Daniel C. Liebler
Chapter

Abstract

When using Sequest and similar tools described in previous chapters, we typically have peptide MS-MS data and we ask, “What proteins do these peptides come from?” Sequest and similar programs are well-suited to the task of protein identification from peptide MS-MS data. However, the proposition becomes a bit different if we want to do something other than simply identify what proteins are present in a sample. Consider the following scenarios:
  • We know that our sample contains many proteins, but we only wish to identify those that bear some specific modification. This could be a posttranslational modification, such as phosphorylation, or a modification by a drug or other chemical.

  • We want to identify peptides in a mixture that all share some sequence identity, but may differ in other ways. This could be due to the presence of wild-type and mutant forms of a protein.

  • We know or suspect that our sample contains a particular protein, but we also suspect that it may be present in multiple modified forms and we wish to detect all of them.

Keywords

Neutral Loss Neutral Fragment Residue Mass Stable Amino Acid Virtual Ruler 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Suggested Reading

  1. Hansen, B. T., Jones, J. A., Mason, D. E., and Liebler, D. C. (2001) SALSA: a pattern recognition algorithm to detect electrophile-adducted peptides by automated evaluation of CID spectra in LC-MS-MS analyses. Anal. Chem. 73, 1676–1683.PubMedCrossRefGoogle Scholar
  2. Liebler, D. C., Hansen, B. T., Davey, S. W., Tiscareno, L., and Mason, D. E. (2001) Peptide sequence motif analysis of tandem ms data with the SALSA algorithm. Anal. Chem., in press.Google Scholar

Copyright information

© Springer Science+Business Media New York 2002

Authors and Affiliations

  • Daniel C. Liebler
    • 1
  1. 1.College of PharmacyThe University of ArizonaTucsonUSA

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