artificial modification

artificial modification petra janning  2024-04-17 07:14

I tried to quantify a peptide containing an artificial, variable modification adding 'C13 H8 O2 Cl2' to lysine. I have DDA data and performed a MaxQuant-search including the artificial modification. When I tried to build the library using the msms.txt file I got the error message "No matching mod for.... Make sure that you provided the correct modification[local].xml file."

I checked the support and found very similar questions two times in 2020 and 2021. Both times the answer was, that 'BiblioSpec is unable to handle ... and Chlorine modifications in MaxQuant search results', but from the next Skyline realease on the problem would be solved. I am working with Skyline (64-bit) (599e74ad2), but obviously I have the same problem. Could you please help me? You will find the mqpar.xml file attached to this mail.

Nick Shulman responded:  2024-04-17 07:21
Can you send us your files?

I think we would need the following files:
modifications.xml (or perhaps slight variations of that name)

Files which are less than 50MB can be attached to this support request. If they are larger than that you can zip them up and upload them here:

After we see your files we will probably be able to figure out what is going on.
-- Nick
petra janning responded:  2024-04-17 07:38
Thank you for the fast response. Yes, of course I can send you the files. The mqpar.xml file is already attached to my initial request. Here you will find the other ones.
Nick Shulman responded:  2024-04-17 07:51
I am able to build a library using those files in Skyline.

I think if you put all three of those files ("msms.txt", "modifications.xml" and "mqpar.xml") into the same folder then you will be able to successfully build a library too.
-- Nick
petra janning responded:  2024-04-17 08:03
Yes, thank you very much. After copying the files into the same folder, I could build the library.