STEPS: a grid search methodology for optimized peptide identification filtering of MS/MS database search results.

ABSTRACT: For bottom-up proteomics, there are wide variety of database-searching algorithms in use for matching peptide sequences to tandem MS spectra. Likewise, there are numerous strategies being employed to produce a confident list of peptide identifications from the different search algorithm outputs. Here we introduce a grid-search approach for determining optimal database filtering criteria in shotgun proteomics data analyses that is easily adaptable to any search. Systematic Trial and Error Parameter Selection--referred to as STEPS--utilizes user-defined parameter ranges to test a wide array of parameter combinations to arrive at an optimal "parameter set" for data filtering, thus maximizing confident identifications. The benefits of this approach in terms of numbers of true-positive identifi

SUBMITTER: Piehowski PD 

PROVIDER: S-EPMC3676282 | biostudies-literature | 2013 Mar

REPOSITORIES: biostudies-literature