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Scoring
trishorts edited this page Jul 26, 2017
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In general scoring is done as in Morpheus: Number of fragments matching + fraction of intensity matching.
Scoring peptides with modifications that have one or more possible neutral losses is done as follows: All fragment masses for all possible combinations of neutral losses on modifications are computed, and those fragments are then matched to the spectrum. As an example, mass-spec analyis of peptides glycosylated with HexNAc yield fragments with a loss of 203.0793. MS2 fragments are scored with and without the 203Da mass shift depending on localization.
Reporter ions are not currently used in scoring.