Matching cross-linked peptide spectra: only as good as the worse identification.

ABSTRACT: Chemical cross-linking mass spectrometry identifies interacting surfaces within a protein assembly through labeling with bifunctional reagents and identifying the covalently modified peptides. These yield distance constraints that provide a powerful means to model the three-dimensional structure of the assembly. Bioinformatic analysis of cross-linked data resulting from large protein assemblies is challenging because each cross-linked product contains two covalently linked peptides, each of which must be correctly identified from a complex matrix of potential confounders. Protein Prospector addresses these issues through a complementary mass modification strategy in which each peptide is searched and identified separately. We demonstrate this strategy with an analysis of RNA polymerase II.

SUBMITTER: Trnka MJ 

PROVIDER: S-EPMC3916644 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature