Refining comparative proteomics by spectral counting to account for shared peptides and multiple search engines.

ABSTRACT: Spectral counting has become a widely used approach for measuring and comparing protein abundance in label-free shotgun proteomics. However, when analyzing complex samples, the ambiguity of matching between peptides and proteins greatly affects the assessment of peptide and protein inventories, differentiation, and quantification. Meanwhile, the configuration of database searching algorithms that assign peptides to MS/MS spectra may produce different results in comparative proteomic analysis. Here, we present three strategies to improve comparative proteomics through spectral counting. We show that comparing spectral counts for peptide groups rather than for protein groups forestalls problems introduced by shared peptides. We demonstrate the advantage and flexibility of this new method in

SUBMITTER: Chen YY 

PROVIDER: S-EPMC3717168 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature