Comet parameter: precursor_NL_ions

• Controls whether or not precursor neutral loss peaks are considered in the xcorr scoring.
• If left blank, this parameter is ignored.
• To consider precursor neutral loss peaks, add one or more neutral loss mass value separated by a space.
• Each entered mass value will be subtracted from the experimentral precursor mass and resulting neutral loss m/z values for all charge states (from 1 to precursor charge) will be analyzed.
• As these neutral loss peaks are analyzed along side fragment ion peaks, the fragment tolerance settings (fragment_bin_tol, fragment_bin_offset, and theoretical_fragment_ion) apply to the precursor neutral loss peaks.
• The default value is blank/unused if this parameter is missing.
• A value of “0” or “0.0” will caues Comet to consider the intact precursor peaks (m/z’s of the precursor in all fragment charge states) as ions to analyze in the ms/ms scan.
• Negative mass values will be ignored.

Example:

precursor_NL_ions =
precursor_NL_ions = 79.96633 97.97689</tt>