I am trying to understand the nature of a H2O2 neutral loss in HCD fragmentation data of cysteic acid containing peptides. The y-series showing the neutral loss is complete so we believe it must be true. Can anyone make sense out of it? Thanks!
Your question is ambiguous, are you trying to make sense for the loss of 34a.m.u. in cysteine containing peptides or are you trying to make sense for the loss of 34 a.m.u. in oxidised cysteine containing peptides?
The loss of 34 a.m.u. can be attributed to loss of H2S (-34 a.m.u.) or to the loss of H2O2 (-34 a.m.u.). Withou more details it is difficult to help you.