This is a demonstration of how we use Prosit to predict peptide CID spectra of non-human origins. The original CSV files cannot be found (APEX2-NES, 8/17/22 and avidin, 8/19/22).
Two CSV files were created separately for FLAG-APEX2-NES and chicken avidin, based on the instruction below:
Tryptic peptides of interest were pasted to CSV files. For methionine-containing peptides, both intact and oxidized (ox) versions were included. Collision energy was set to 35. Charge states of interest were 2 and 3. Fragmentation method was set to CID for LTQ Orbitrap Velos Pro.
The intensity prediction model and iRT predict