Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings.

ABSTRACT: In shotgun proteomics analysis, user-specified parameters are critical to database search performance and therefore to the yield of confident peptide-spectrum matches (PSMs). Two of the most important parameters are related to the accuracy of the mass spectrometer. Precursor mass tolerance defines the peptide candidates considered for each spectrum. Fragment mass tolerance or bin size determines how close observed and theoretical fragments must be to be considered a match. For either of these two parameters, too wide a setting yields randomly high-scoring false PSMs, whereas too narrow a setting erroneously excludes true PSMs, in both cases, lowering the yield of peptides detected at a given false discovery rate. We describe a strategy for inferring optimal search parameters by assembling

SUBMITTER: May DH 

PROVIDER: S-EPMC5738039 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature