Enhanced LC-MS/MS proteomic difference testing via integration of peptide ion intensities with spectral counts

Abstract

Shotgun liquid chromatography/tandem mass spectrometry (LC-MS/MS) technology provides data sets rich in the type of information required proteomic quantitation; however, these data are not fully exploited by existing tools. We present a statistical model for combining MS precursor intensity data with MS/MS spectral count data and obtaining a single p-value using Fisher’s Method of combining p-values. Our model is demonstrated using a new tool, IDPQuantify, which generates MS/MS spectral count data and MS persistent peptide isotopic distribution (PPID) intensity data for peptide group-level difference testing. Using the iPRG 2009 ABRF E. coli data set with known differences in protein content between cohorts, we compared the performance of existing candidate statistical tests using either spectral counts or PPIDs alone. We then compared the performance of our combined model with our candidate tests. Spectral count-based tests showed lower sensitivity but higher specificity than PPID-based tests. In comparison, our combined model yielded a slight drop in sensitivity coupled with an enormous improvement in specificity compared to the PPID-based test alone. We also observed that shared peptide groups tended to yield erroneous rejections of the null hypothesis more often than unshared peptide groups.