An automated platform for analysis of phosphoproteomic datasets: application to kidney collecting duct phosphoproteins.

ABSTRACT: Large-scale phosphoproteomic analysis employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) often requires a significant amount of manual manipulation of phosphopeptide datasets in the post-acquisition phase. To assist in this process, we have created software, PhosphoPIC (PhosphoPeptide Identification and Compilation), which can perform a variety of useful functions including automated selection and compilation of phosphopeptide identifications from multiple MS levels, estimation of dataset false discovery rate, and application of appropriate cross-correlation (XCorr) filters. In addition, the output files generated by this program are compatible with downstream phosphorylation site assignment using the Ascore algorithm, as well as phosphopeptide quantification via QUOIL. In

SUBMITTER: Hoffert JD 

PROVIDER: S-EPMC2481407 | biostudies-literature | 2007 Sep

REPOSITORIES: biostudies-literature