Top-Down Mass Spectrometry for Trace Level Quantification of Staphylococcal Enterotoxin A Variants

We addressed here the need for improved sensitivity of top-down mass spectrometry for identification, differentiation, and absolute quantification of sequence variants of SEA, a bacterial toxin produced by Staphylococcus aureus and regularly involved in food poisoning outbreaks (FPO). We combined immunoaffinity enrichment, a protein internal standard, and optimized acquisition conditions, either by full-scan high-resolution mass spectrometry (HRMS) or multiplex parallel reaction monitoring (PRM) mode. Deconvolution of full-scan HRMS signal and PRM detection of variant-specific fragment ions allowed confident identification of each SEA variant. Summing the PRM signal of variant-common fragment ions was most efficient for absolute quantification, illustrated by a sensitivity down to 2.5 ng/mL and an assay variability below 15%. Additionally, we showed that relative PRM fragment ion abundances constituted a supplementary specificity criterion in top-down quantification. The top-down method was successfully evaluated on a panel of enterotoxin-producing strains isolated during FPO, in parallel to the conventional whole genome sequencing, ELISA, and bottom-up mass spectrometry methods. Top-down provided at the same time correct identification of the SEA variants produced and precise determination of the toxin level. The raw files generated in this study can be found on PASSEL (Peptide Atlas) under data set identifier PASS01710.

Automated summary

This study highlights the importance of improving the sensitivity of top-down mass spectrometry for the identification, differentiation, and absolute quantification of SEA sequence variants. By utilizing immunoaffinity enrichment, a protein internal standard, and optimized acquisition conditions, the top-down method demonstrated efficient identification and precise quantification of SEA variants, as well as providing a supplementary specificity criterion for quantification. The successful evaluation on enterotoxin-producing strains isolated during food poisoning outbreaks showcases the potential of top-down mass spectrometry in complementing traditional methods for toxin analysis.