Methionine issue sgler  2014-11-26

When submitted to skyline, it gives a list of peptides which are not matching to any proteins. Tracing back the peptide sequence on MaxQuant folder, it does give a protein hit. Checked the peptide sequence on uniprot on the respective protein and found that there was a M before the peptide sequence. Edited the structual modification to include M as modification. It still gives a mismatch. Please advise.
Brendan MacLean responded:  2014-11-27
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.