IsoformResolver: A peptide-centric algorithm for protein inference

J Proteome Res. 2011 Jul 1;10(7):3060-75. doi: 10.1021/pr200039p. Epub 2011 Jun 7.

Abstract

When analyzing proteins in complex samples using tandem mass spectrometry of peptides generated by proteolysis, the inference of proteins can be ambiguous, even with well-validated peptides. Unresolved questions include whether to show all possible proteins vs a minimal list, what to do when proteins are inferred ambiguously, and how to quantify peptides that bridge multiple proteins, each with distinguishing evidence. Here we describe IsoformResolver, a peptide-centric protein inference algorithm that clusters proteins in two ways, one based on peptides experimentally identified from MS/MS spectra, and the other based on peptides derived from an in silico digest of the protein database. MS/MS-derived protein groups report minimal list proteins in the context of all possible proteins, without redundantly listing peptides. In silico-derived protein groups pull together functionally related proteins, providing stable identifiers. The peptide-centric grouping strategy used by IsoformResolver allows proteins to be displayed together when they share peptides in common, providing a comprehensive yet concise way to organize protein profiles. It also summarizes information on spectral counts and is especially useful for comparing results from multiple LC-MS/MS experiments. Finally, we examine the relatedness of proteins within IsoformResolver groups and compare its performance to other protein inference software.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Chromatography, Liquid
  • Data Mining / methods*
  • Databases, Protein
  • Humans
  • Peptide Fragments / analysis*
  • Peptide Fragments / chemistry
  • Protein Isoforms* / analysis
  • Protein Isoforms* / chemistry
  • Proteomics / methods*
  • Software
  • Tandem Mass Spectrometry
  • Trypsin / metabolism

Substances

  • Peptide Fragments
  • Protein Isoforms
  • Trypsin