Comet parameter: fragindex_num_spectrumpeaks

• This parameter defines the number of mass/intensity pairs that would be queried against the fragment ion index.
• Raw peaks are parsed and stored. The mass dimension is binned per the fragment_bin_tol and the most intense binned peaks are used to query the fragment ion index.
• The larger this value is, the slower a search will be as each additional peak, from every query spectra, will need to be searched against the fragment ion index.
• Note that specifying too small a value can be detrimental as, for some spectra, correct peptides may not pass the fragment ion index filter if there are not enough peaks queried.
• Valid values are integers, 1 or larger.

Example:

fragindex_num_spectrumpeaks = 100
fragindex_num_spectrumpeaks = 150
fragindex_num_spectrumpeaks = 200