An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics

J Proteome Res. 2009 Jul;8(7):3239-51. doi: 10.1021/pr800835x.

Abstract

Currently, the precursor ion selection strategies in LC-MS mainly choose the most prominent peptide signals for MS/MS analysis. Consequently, high-abundance proteins are identified by MS/MS of many peptides, whereas proteins of lower abundance might elude identification. We present a novel, iterative and result-driven approach for precursor ion selection that significantly increases the efficiency of an MS/MS analysis by decreasing data redundancy and analysis time. By simulating different strategies for precursor ion selection on an existing data set, we compare our method to existing result-driven strategies and evaluate its performance with regard to mass accuracy, database size, and sample complexity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Cell Line
  • Chromatography, Liquid / methods*
  • Computer Simulation
  • Databases, Protein
  • Escherichia coli / metabolism
  • Humans
  • Ions
  • Mass Spectrometry / methods*
  • Models, Statistical
  • Peptides / analysis
  • Proteins / chemistry
  • Proteomics / methods*
  • Reproducibility of Results
  • Software

Substances

  • Ions
  • Peptides
  • Proteins