Identification of Salmonella taxon-specific peptide markers to the serovar level by mass spectrometry
We present an LC-MS/MS pipeline to identify taxon-specific tryptic peptide markers for identification of Salmonella at the genus, species, subspecies, and serovar levels of specificity. Salmonella enterica subsp. enterica serovars Typhimurium and its four closest relatives, Saintpaul, Heidelberg, Paratyphi B, and Muenchen, were evaluated. A decision tree approach was used to identify peptides common to the five Salmonella proteomes for evaluation as genus-, species-, and subspecies-specific markers. Peptides identified to two or fewer Salmonella strains were evaluated as potential serovar markers. Currently there are approximately 140,000 assembled bacterial genomes publicly available, more than 8,500 of which are for Salmonella. Consequently, the specificity of each candidate peptide marker was confirmed across all publicly available protein sequences in the NCBI non-redundant (nr) database. Performance of a subset of candidate taxon-specific peptide markers was evaluated in a targeted mass spectrometry method. The presented workflow offers a marked improvement in specificity over existing MALDI-TOF-based bacterial identification platforms for identification of closely related Salmonella serovars.