IDPQuantify: combining precursor intensity with spectral counts for protein and peptide quantification.

ABSTRACT: Differentiating and quantifying protein differences in complex samples produces significant challenges in sensitivity and specificity. Label-free quantification can draw from two different information sources: precursor intensities and spectral counts. Intensities are accurate for calculating protein relative abundance, but values are often missing due to peptides that are identified sporadically. Spectral counting can reliably reproduce difference lists, but differentiating peptides or quantifying all but the most concentrated protein changes is usually beyond its abilities. Here we developed new software, IDPQuantify, to align multiple replicates using principal component analysis, extract accurate precursor intensities from MS data, and combine intensities with spectral counts for signi

SUBMITTER: Chen YY 

PROVIDER: S-EPMC3804902 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature