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

ABSTRACT: Genomic studies of bacteria have long pointed toward widespread prevalence of small open reading frames (sORFs) encoding for short proteins, <100 amino acids in length. Despite the mounting genomic evidence of their robust expression, relatively little progress has been made in their mass spectrometry-based detection and various blanket statements have been used to explain this observed discrepancy. In this study, we provide a large-scale riboproteogenomics investigation of the challenging nature of proteomic detection of such small proteins as informed by conditional translation data. A panel of physiochemical properties alongside recently developed mass spectrometry detectability metrics was interrogated to provide a comprehensive evidence-based assessment of sORF-encoded polypeptide (SEP) detectability. Moreover, a large-scale proteomics and translatomics compendium of proteins produced by Salmonella Typhimurium (S. Typhimurium), a model human pathogen, across a panel of growth conditions is presented and used in support of our in silico SEP detectability analysis. This integrative 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 pinpoints current limitations in proteomics-based detection of novel small proteins currently missing from bacterial genome annotations.

SUBMITTER: Fijalkowski I

PROVIDER: S-EPMC10117744 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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

Fijalkowski Igor I Willems Patrick P Jonckheere Veronique V Simoens Laure L Van Damme Petra P

microLife 20220514

Genomic studies of bacteria have long pointed toward widespread prevalence of small open reading frames (sORFs) encoding for short proteins, <100 amino acids in length. Despite the mounting genomic evidence of their robust expression, relatively little progress has been made in their mass spectrometry-based detection and various blanket statements have been used to explain this observed discrepancy. In this study, we provide a large-scale riboproteogenomics investigation of the challenging natur ...[more]

PMID: 37223358

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

Publications

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

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