Location: Tools Menu on the Peptide Sequence Fragmentation Modelling window
Use the Ion Match Options window to specify the binning and normalization parameters used when parsing a list of ions loaded for matching to predicted fragmentation masses. Additionally, the arbitrary intensities assigned to a, b, and y ions, b/y ion shoulders, and neutral loss ions can be defined here. See the discussion on Ion Matching and Scoring for descriptions of how the parameters affect matching and scoring.
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