Introduction

We present a pipeline to identify taxon-specific tryptic peptide markers for Salmonella identification downto the serovar level, with the end goal of use in complex matrices. Currently there more than 2,500 knownSalmonella serotypes and over 220,000 publicly available sequenced bacterial genomes, nearly 15,000 ofwhich are for Salmonella. Consequently, the specificity of a peptide marker needs to be confirmed with allpublicly available genomic data for use in analysis of unknown samples. The pipeline presented herecombines LC-MS/MS analysis of a subset of closely related Salmonella serovars with a bioinformaticspipeline to determine combinations of viable peptide markers based on results of BLAST searches againstpublicly available protein sequences.