title: Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes.
abstract: Selected reaction monitoring mass spectrometry (SRM-MS) is a targeted proteomics technology used to identify and quantify proteins with high sensitivity, specificity and high reproducibility. Execution of SRM-MS relies on protein-specific SRM assays, a set of experimental parameters that requires considerable effort to develop. Here we present a proteome-wide SRM assay repository for the gram-positive human pathogen group A Streptococcus. Using a multi-layered approach we generated SRM assays for 10,412 distinct group A Streptococcus peptides followed by extensive testing of the selected reaction monitoring assays in >200 different group A Streptococcus protein pools. Based on the number of SRM assay observations we created a rule-based selected reaction monitoring assay-scoring model to select the most suitable assays per protein for a given cellular compartment and bacterial state. The resource described here represents an important tool for deciphering the group A Streptococcus proteome using selected reaction monitoring and we anticipate that concepts described here can be extended to other pathogens.
authors.affiliation: Department of Immunotechnology, Lund University, SE-22184 Lund, Sweden.
authors.forename: Christofer
authors.initials: C
authors.lastname: Karlsson
authors.forename: Lars
authors.initials: L
authors.lastname: Malmström
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.forename: Johan
authors.initials: J
authors.lastname: Malmström
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D006801:Humans; D020543:Proteome / Q000235:genetics; D040901:Proteomics / Q000379:methods*; D012680:Sensitivity and Specificity; D013290:Streptococcal Infections / Q000175:diagnosis* / Q000382:microbiology; D013297:Streptococcus pyogenes / Q000235:genetics*; D053719:Tandem Mass Spectrometry / Q000379:methods*
chemical_list: D001426:Bacterial Proteins; D020543:Proteome