Informatics of protein and posttranslational modification detection via shotgun proteomics

Jerry D. Holman, Surendra Dasari, David L. Tabb

Research output: Chapter in Book/Report/Conference proceedingChapter

13 Scopus citations

Abstract

Frequently, proteomic LC-MS/MS data may contain sets of modi fi cations that evade identi fi cation during standard database search. For many laboratories, the standard technique to seek posttranslational modi fi cations (PTMs) adds a short list of speci fi ed mass shifts to database search con fi guration. This technique provides information for only the speci fi ed PTMs, takes substantial time to run, and drives false discoveries upward through an exponential expansion of search space. This protocol describes a more structured approach to blind PTM discovery through reducing protein lists, targeting attention to a datadriven list of mass shifts, and seeking the resulting short list of modi fi cations through targeted search.

Original languageEnglish (US)
Title of host publicationProteomics for Biomarker Discovery
Subtitle of host publicationMethods and Protocols
EditorsMing Zhou, Timothy Veenstra
Pages167-179
Number of pages13
DOIs
StatePublished - Dec 1 2013

Publication series

NameMethods in Molecular Biology
Volume1002
ISSN (Print)1064-3745

Keywords

  • Database search
  • Posttranslational modi fi cation
  • Protein identi fi cation
  • Proteome informatics
  • Sequence tagging
  • Shotgun proteomics
  • Software

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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  • Cite this

    Holman, J. D., Dasari, S., & Tabb, D. L. (2013). Informatics of protein and posttranslational modification detection via shotgun proteomics. In M. Zhou, & T. Veenstra (Eds.), Proteomics for Biomarker Discovery: Methods and Protocols (pp. 167-179). (Methods in Molecular Biology; Vol. 1002). https://doi.org/10.1007/978-1-62703-360-2_14