Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach.

ABSTRACT: Small proteins play essential roles in bacterial physiology and virulence, however, automated algorithms for genome annotation are often not yet able to accurately predict the corresponding genes. The accuracy and reliability of genome annotations, particularly for small open reading frames (sORFs), can be significantly improved by integrating protein evidence from experimental approaches. Here we present a highly optimized and flexible bioinformatics workflow for bacterial proteogenomics covering all steps from (i) generation of protein databases, (ii) database searches and (iii) peptide-to-genome mapping to (iv) visualization of results. We used the workflow to identify high quality peptide spectrum matches (PSMs) for small proteins (≤ 100 aa, SP100) in Staphylococcus aureus Newman. Prot

SUBMITTER: Fuchs S 

PROVIDER: S-EPMC8195425 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature