Import ms2 ion transition list

Import ms2 ion transition list davidz  2019-05-28

Hi there,

I know I can import a list of peptides with modifications specified for ms2 ion filtering, and refine which b/y ions to use in peak finding, but is there a way for me import a list of pre generated ions for each peptide with charges?


davidz responded:  2019-05-28

BTW, can I specify which peptide with certain PTM to use, including the modification position in the peptide?

Brendan MacLean responded:  2019-06-06

Sorry, we didn't get back to you on this one. I hope you have found that the answer to these questions is, yes.

I believe all of the places Skyline asks for peptides, it will also accept modified peptide sequences, like pasting directly into Skyline, Edit > Insert > Peptides or Transition List, and Refine > Accept Peptides. Some also accept charge state expressions on the end of the peptide sequence for specifying the exact peptide precursor.

Here also is another support request describing the various formats Skyline accepts:

Hope this is helpful, even if you managed to find a solution that worked for you already.


davidz responded:  2019-06-07

Thanks, Brendan!