Hi Skyline team,
I had a problem after importing DDA peptide search data into Skyline. I was trying to focus on only a list of peptides using the "Accept peptide" function in the Edit>Refine menu. However, even if I select "match modified sequence", it doesn't seem to keep the modified sequences. Only the unmodified ones would stay.
When I try to accept the peptide that only has modified version (I can clearly see the peptide in the Skyline file), there would be an error message saying the peptide does not exist in the file.
Am I doing anything wrong or is it a bug in the software?
Thanks in advance,
Shimin