Mass spectrometry confirms small proteins from sRNA ORFs

Many sRNA short ORFs could be occasionally translated without accumulation of a protein product to appreciable levels if the protein were quickly degraded. Conversely, detection of sRNA ORF protein products in cells by methods with limited sensitivity would be strong evidence against this possibility. Therefore, we used mass spectrometry specifically designed to find small proteins to search for sRNA ORF products in Helicobacter pylori. For the purposes of this search, we included the widest set of sRNA ORF predictions possible, filtering neither for predicted coding score nor potential overlaps with annotated full-length ORFs. This search resulted in 25 peptide hits from 17 sRNA ORFs at an FDR less than 0.05, with 6 hits having an FDR less than 0.01. Despite the statistical significance of these matches, most novel proteins were identified by only a single peptide, making their identification unreliable. The ultimate confirmation of protein identification must be made by matching the observed spectrum to that of a synthetic peptide with the expected sequence. Therefore, we synthesized each of our putative matching peptides. 17 of the synthetic peptides resulted in useable mass spectra, of which 6 tested peptides were validated with a spectrum match. One of the hits, shpy580.1.10, was likely due to an alternative start site of a previously-annotated ORF, i.e. a misannotated or alternative start codon (Supplemental table 1). Another peptide hit in shpy1027.1.1 is for a short sequence shared by an annotated ORF, so may not be considered strong evidence for a novel protein-coding sRNA. However, another peptide comes from an sRNA labeled here as shpy839.1, which is a tmRNA with a known (but unannotated) coding peptide that helps to recycle stalled ribsomes (Figure \ref{fig:mass_spec}, Supplemental table 1). One other, shpy997.1.2 appears to be a bona fide novel coding peptide arising from an sRNA antisense to an annotated ORF (Figure \ref{fig:mass_spec}).