AbstractPost‐translational modification of the antiphagocytic M1 protein of Streptococcus pyogenes can influence its binding properties for human immunoglobulin G subclasses and its invasive potential. Current methods of monitoring this modification event involve N‐terminal sequencing and are cumbersome, slow and not amenable to routine analysis. In this study we demonstrate that surface enhanced laser desorption/ionization‐time of flight mass spectrometry can be used to monitor modification of the M1 protein by the secreted bacterial cysteine protease, SpeB. This method, when combined with a specific antibody capture step provides a specific, rapid and sensitive assay for key virulence factors of the important human pathogen Streptococcus pyogenes.