For research use only. Not for use in diagnostic procedures.
Answer
There are 3 filters that can be applied in the Feature tab for ProteinPilot™ software:
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All modifications must be a biological modification to be considered.
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The minimum protein confidence filter default must be set to an Unused score of 0.47.
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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.
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