Accept peptide function could not match modified sequences

support
Accept peptide function could not match modified sequences schen19  2019-02-13 11:39
 

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

 
 
Brendan MacLean responded:  2019-02-13 12:39

Hi Shimin,
Please provide the modified peptide text you are using to specify your accepted peptides. Hint, you can set up a report that contains Peptide Modified Sequence, and copy the text from this field. That should work. So, if you can find the peptide in your document, then you should be able to collect modified sequences for all of the ones you want to keep, using the Document Grid. Or once you have convinced yourself this works, you may have new insight into why what you were using wasn't working.

Thanks for posting to the Skyline support board.

--Brendan