This would allow transitions from proteoforms identified with ET multimod sets that remove one PTM (e.g. dimethyl as {methyl, methyl} could have a transition -14 Da that removes a methyl).
Right now, we can only remove Unlocalized PTMs with the same mass... Therefore, if have a -14 Da transition from a proteoform with a dimethyl annotation (+28 Da), it does not recognize that it should remove one of the existing methyl groups.
Representing this is tough because you have to represent the relationship to other PTMs in the list and number of those PTMs. I think this could best be done by making a new tag in the PTM lists in mzLib that draws the connection to other PTMs in the list with a count of the number of them.
This would allow transitions from proteoforms identified with ET multimod sets that remove one PTM (e.g. dimethyl as {methyl, methyl} could have a transition -14 Da that removes a methyl).