…otation, and probably toward using a more general mod naming convention (currently a hardcoded list in the msp reader code, should probably use the same mechanism as rest of Skyline). Putting this up for Nick to look at.

… unknown peptide modifications.

In the event that a modification can't be understood, a message is written to the immediate window (formerly we failed silently, replacing the mod with an unmatchable string, and moved on)