Hi Siok Ghee,
Thank you for reporting this issue. I have added this case to an issue I recently posted about making Background Proteome peptide matching more flexible:
The original case that caught our interest was C-terminal semi-tryptic peptide cleavage. The existing Background Proteome peptide matching algorithm works for N-terminal semi-tryptic cleavage, but not C-terminal. In a sense, your case is also a C-terminal semi-tryptic cleavage, but it also may be a fairly simple matter to fix the matching algorithm to include N-terminal protein peptides minus an initial Methionine.
Either way, this is a bug in the matching algorithm and will need to be fixed for a future release. For now, you will need to settle for monitoring this peptide without its protein association.
Thanks again for your clear report of this issue. The screenshots helped a lot.