Accurately Assigning Peptides to Spectra When Only a Subset of Peptides Are Relevant.

ABSTRACT: The standard proteomics database search strategy involves searching spectra against a peptide database and estimating the false discovery rate (FDR) of the resulting set of peptide-spectrum matches. One assumption of this protocol is that all the peptides in the database are relevant to the hypothesis being investigated. However, in settings where researchers are interested in a subset of peptides, alternative search and FDR control strategies are needed. Recently, two methods were proposed to address this problem: subset-search and all-sub. We show that both methods fail to control the FDR. For subset-search, this failure is due to the presence of "neighbor" peptides, which are defined as irrelevant peptides with a similar precursor mass and fragmentation spectrum as a relevant peptide. N

SUBMITTER: Lin A 

PROVIDER: S-EPMC8489664 | biostudies-literature | 2021 Aug

REPOSITORIES: biostudies-literature