2.1 Employed approach
This study was based on a proteogenomic investigation that reevaluated previously used raw bottom-up MS/MS proteomics data for a honey bee pathogen, P. larvae . We used raw MS/MS data obtained on a state-of-the-art nano-LC‒MS/MS instrument from Thermo (Waltham, MA, USA) that consisted of an nano-LC Ultimate 3000 and a tribrid (q-OT-IT) MS Orbitrap Fusion instrument. The raw data were published in two previous studies [11, 12] examining the virulence of P. larvae and are publicly available in datasets that can be accessed in MassIVE (MassIVE MSV000089235 and MSV000083636) or ProteomeXchange (PXD033155 and PXD013272).