Comet parameter: ms_level

• This parameter specifies which scans are searched.
• An input value of 2 will search MS/MS scans.
• An input value of 3 will search MS3 scans.
• This parameter is only valid for mzXML, mzML, and mz5 input files.
• Allowed values are 2 or 3.
• The default value is “2” if this parameter is missing or any value other than 2 or 3 is entered.

Example:

ms_level = 2
ms_level = 3