For research use only. Not for use in diagnostic procedures.
There are 3 filters that can be applied in the Feature tab for ProteinPilot™ software:
All modifications must be a biological modification to be considered.
The minimum protein confidence filter default must be set to an Unused score of 0.47.
The minimum peptide confidence filter default must be set to 0.66 (66% confidence).
Points 2 and 3 can be adjusted and tuned using the config file from ProteinPilot software.