Hidden in plain sight; challenges in proteomics detection of small ORF-encoded polypeptides.

ABSTRACT: Genomic studies of bacteria have long pointed towards widespread prevalence of small open reading frames (sORFs) encoding for short proteins, less than 100 amino acids in length. Despite the mounting genomic evidence of their robust expression, little progress has been made in their mass spectrometry-based validation. Various blanket statements have been used to explain this discrepancy with the potentially low expression levels and protein instability being put forward most often. In this study we provide the first systemic investigation of the challenging nature of proteomic detection of such small proteins. A panel of physiochemical properties alongside recently developed mass spectrometry detectability metrics is interrogated to provide the first evidence-based study of SEP detectability. Moreover, a large scale proteomics and genomics compendium of proteins produced by Salmonella Typhimurium (S. Typhimurium), a model human pathogen, across a panel of growth conditions is presented and used to further support our in silico analysis. This integrative riboproteogenomic approach is used to provide a data-driven census of small proteins expressed by S. Typhimurium across growth phases and infection-relevant conditions. Taken together our study delineates current limitations in proteomics based validation of novel small proteins currently missing from bacterial genome annotations.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. Sl1344

SUBMITTER: Igor Fijalkowski  

LAB HEAD: Petra Van Damme

PROVIDER: PXD029391 | Pride | 2023-07-20

REPOSITORIES: Pride