Informatics Methods to Enhance Bacterial Peptide Detection

Detecting low-abundance bacterial peptides in samples dominated by human proteins using liquid chromatography tandem mass spectrometry (LC MS/MS) is challenging. Bacterial peptides are typically far less abundant than host-derived peptides, and sequence similarity between bacterial and human peptides can complicate confident attribution to a bacterial origin. To address this problem, we developed and benchmarked an in silico spectral library protein identification workflow for detecting Staphylococcus aureus USA300 peptides against a background of A375 cells. Peptide and protein identifications obtained at a 1% peptide-level false discovery rate were compared between the in silico spectral library search and a conventional sequence database search across a defined bacterial dilution series containing 0, 1%, 2%, 10%, 25%, 50%, and 100% bacterial protein. A human sequence similarity filter was applied to identifications from both search strategies to reduce the likelihood of retaining human derived or human like peptide sequences. Both search strategies showed concentration dependent bacterial detection and shared a practical detection limit of approximately 1 to 2% bacterial protein but exhibited distinct performance profiles. The in silico spectral library search produced fewer bacterial-like background identifications in the human-only control, whereas MS2Rescore substantially increased spectral library identifications at higher bacterial concentrations, exceeding database search at 100% bacterial protein. The partially overlapping peptide sets identified by the two strategies indicate that they provide complementary coverage of the bacterial proteome.