Proteome-wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes

Christofer Karlsson, Lars Malmström, Ruedi Aebersold and Johan Malmström ()
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Christofer Karlsson: Lund University
Lars Malmström: Institute of Molecular Systems Biology, ETH Zurich
Ruedi Aebersold: Institute of Molecular Systems Biology, ETH Zurich
Johan Malmström: Lund University

Nature Communications, 2012, vol. 3, issue 1, 1-9

Abstract: 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.

Date: 2012
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DOI: 10.1038/ncomms2297

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