Fix or remove the warning from ProteinProphet: WARNING: Found the following zero-mass residues in protein entry ***

[fcyu]

I always feels annoying and redundant that ProteinProphet prints the warning such as WARNING: Found the following zero-mass residues in protein entry sp|Q9Y6Y8|S23IP_HUUAN : UUUUUUUUUUUUUUUUUUU. When I tested using U and O for the labeled amino acids (Nesvilab/FragPipe#1673 (comment)), the warning became more annoying because there are more noncanonical amino acids.

Ideally, ProteinProphet could support all 26 letters like what we do in MSFragger and FragPipe.

Best,

Fengchao