FineFDR: Fine-grained Taxonomy-specific False Discovery Rates Control in Metaproteomics.

ABSTRACT: Microbial community proteomics, also termed metaproteomics, investigates all proteins expressed by a microbiota. Tandem mass spectrometry (MS/MS) is the typical method for identifying proteins in metaproteomics, which involves searching the mass spectra against a protein sequence database. A major post-analysis step is controlling the false discovery rate (FDR), i.e., the ratio of false positives to the total number of annotations. The current popular target-decoy FDR estimation method treats all the peptides and proteins equally and overlooks that they could have varied probabilities of being identified. In this study, we report FineFDR, a framework for FDR assessment at fine-grained levels with taxonomy information considered. FineFDR groups the identified peptide-spectrum matches, pepti

SUBMITTER: Wang S 

PROVIDER: S-EPMC9998077 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature