Processing Workflow (to search every spectrum - standard proteomics):
Spectrum Files - No parameters just to get files
Spectrum Selector (set to just take every scan)
Precursor Selection - Use MS1 Precursor
Provide Profile Spec - Automatic
RT, Scan, Charge State - all 0
Min Precursor Mass - 600 Da
Max Precursor Mass - 5000 Da
Database - FASTA of your species (must be parsed in PD before can choose - restart PD after parsing and before search set up)
Precursor Tolerance - 10 ppm
Fragment Tolerance - 0.02 Da
Neutral loss a,b,y and flanking ions - true
Max equal modifications = 3
Dynamic modification oxidation M
Static modification carbamidomethyl C
4. Target Decoy PSM Validator
Target/Decoy - concatenated