Assigning significance in label-free quantitative proteomics to include single-peptide-hit proteins with low replicates.

ABSTRACT: Selecting differentially regulated proteins with an assignment of statistical significance remains difficult for proteins with a single-peptide hit or a small fold-change when sample replicates are limited. This study presents a label-free quantitative proteomics scheme that was used to select differentially regulated proteins with single-peptide hits and with <2-fold change at a 5% false discovery rate. The scheme incorporated a labeled internal control into two unlabeled samples to facilitate error modeling when there were no replicates for the unlabeled samples. The results showed that, while both a power law global error model with a signal-to-noise ratio statistic (PLGEM-STN) and a constant fold-change threshold could be used, neither of them alone was stringent enough to select diffe

SUBMITTER: Li Q 

PROVIDER: S-EPMC2997754 | biostudies-literature | 2010 Jan

REPOSITORIES: biostudies-literature