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).