A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.

ABSTRACT: Large databases (>10(6) sequences) used in metaproteomic and proteogenomic studies present challenges in matching peptide sequences to MS/MS data using database-search programs. Most notably, strict filtering to avoid false-positive matches leads to more false negatives, thus constraining the number of peptide matches. To address this challenge, we developed a two-step method wherein matches derived from a primary search against a large database were used to create a smaller subset database. The second search was performed against a target-decoy version of this subset database merged with a host database. High confidence peptide sequence matches were then used to infer protein identities. Applying our two-step method for both metaproteomic and proteogenomic analysis resulted in twice the n

SUBMITTER: Jagtap P 

PROVIDER: S-EPMC3633484 | biostudies-literature | 2013 Apr

REPOSITORIES: biostudies-literature