Abundance-based classifier for the prediction of mass spectrometric peptide detectability upon enrichment (PPA).

ABSTRACT: The function of a large percentage of proteins is modulated by post-translational modifications (PTMs). Currently, mass spectrometry (MS) is the only proteome-wide technology that can identify PTMs. Unfortunately, the inability to detect a PTM by MS is not proof that the modification is not present. The detectability of peptides varies significantly making MS potentially blind to a large fraction of peptides. Learning from published algorithms that generally focus on predicting the most detectable peptides we developed a tool that incorporates protein abundance into the peptide prediction algorithm with the aim to determine the detectability of every peptide within a protein. We tested our tool, "Peptide Prediction with Abundance" (PPA), on in-house acquired as well as published data sets

SUBMITTER: Muntel J 

PROVIDER: S-EPMC4350037 | biostudies-literature | 2015 Feb

REPOSITORIES: biostudies-literature