Comet parameter: fragindex_skipreadprecursors

• This parameter controls whether or not Comet reads all precursors from the input files. It uses this information to limit the peptides that are included in the fragment ion index. Otherwise, every peptides within the mass range defined by digest_mass_range will be included in the fragment ion index (even though only those with precursor masses corresponding to experimental spectra would be used in the analysis).
• This parameter is meant to reduce the fragment ion index size, saving both memory use and run time in generating the index.
• Typically it is advantageous to apply this parameter. However, for some large input files with many MS/MS spectra, parsing all precursors can take a lot of time and may not provide a meaningful reduction in the fragment ion index.
• Valid values are 0 or 1.
• 0 = read precursors from the input file (aka do not skip)
• 1 = skip reading precursors from the input file

Example:

fragindex_skipreadprecursors = 0
fragindex_skipreadprecursors = 1