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Scoring
rmmiller22 edited this page Nov 22, 2019
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The MetaMorpheus score can be calculated as follows: Number of fragments matching + fraction of intensity matching.
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.
Fragments masses which correspond to diagnostic ions of are computed and subsequently matched to the spectrum. These matched ions contribute to the score of the modified peptide.