Lost and Found: Re-searching and Re-scoring Proteomics Data Aids Genome Annotation and Improves Proteome Coverage.

ABSTRACT: Prokaryotic genome annotation is heavily dependent on automated gene annotation pipelines that are prone to propagate errors and underestimate genome complexity. We describe an optimized proteogenomic workflow that uses ribosome profiling (ribo-seq) and proteomic data for Salmonella enterica serovar Typhimurium to identify unannotated proteins or alternative protein forms. This data analysis encompasses the searching of cofragmenting peptides and postprocessing with extended peptide-to-spectrum quality features, including comparison to predicted fragment ion intensities. When this strategy is applied, an enhanced proteome depth is achieved, as well as greater confidence for unannotated peptide hits. We demonstrate the general applicability of our pipeline by reanalyzing public De

SUBMITTER: Willems P 

PROVIDER: S-EPMC7593589 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature