MRMaid 2.0: mining PRIDE for evidence-based SRM transitions.

ABSTRACT: Selected reaction monitoring (SRM) is becoming the tool of choice for targeted quantitative proteomics. The fundamental principle of proteomic SRM is that, for a given protein of interest, there is a set of peptides that are unique to that protein. The characteristic retention time (RT), and intact peptide m/z of these so-called proteotypic peptides are then programmed into the mass spectrometer, along with the m/z of high-intensity product ions for targeted quantitation. The particular combination of RT, peptide m/z, and product m/z for a given peptide is referred to as a transition. Selection of the most appropriate set of transitions for a given set of proteins is crucial to any SRM experiment. We previously developed the web-based MRMaid tool, which suggested the optimal transitions fo

SUBMITTER: Fan J 

PROVIDER: S-EPMC3437039 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature