modifications.xml ziyang zhang  2020-12-22

Hi again skyline gods,

I recently had an issue when importing a DDA search (done by MaxQuant). The peptides carry a custom modification "ARS", which is defined in the modifications.xml file. When importing, Skyline prompts that there is no matching modification for "ARS".

I did the following:

  1. adding modifications.xml file to the data folder containing msms.txt
  2. adding modifications.xml file to the spectral library folder under the user home folder
  3. adding modifications.xml file to replace the skyline installation folder (with new App installation tool, this is now at C:\Users[user]\AppData\Local\Apps\2.0\\\skyl..tion_xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
  4. adding a modification in peptide settings named "ARS" with the same formula as in modifications.xml

But still cannot import the search result - the error persists. Could I please get some help...

Many thanks,

Nick Shulman responded:  2020-12-22

I believe we also need a file of yours called "mqpar.xml" in order to reproduce this issue. Can you give us that file?

-- Nick
ziyang zhang responded:  2020-12-22
Hi Nick, yes, attached.
Nick Shulman responded:  2020-12-22

It appears that the problem is that BiblioSpec does not support Chlorine in MaxQuant results.

If I run BlibBuild.exe with the additional "-v warn" command-line argument, I get a helpful warning message:

> BlibBuild.exe -v warn msms.txt mylibrary.blib
Reading results from msms.txt.
WARNING: Unknown element for 'C(21) H(17) Cl F(2) N(4) O(2)': 'Cl'
ERROR: No matching mod for ARS in sequence VVGAC(ARS)GVGK (line 8). Make sure you have provided the correct modifications[.local].xml file.

For some reason, the only elements that BiblioSpec supports for MaxQuant are H, O, C, N, P, S, and Na.
BiblioSpec also supports the heavy elements "Hx", "Ox", "Cx", and "Nx", along with the synonyms "2H" and "13C".

I will ask around and see whether we can fix this.
-- Nick

ziyang zhang responded:  2020-12-22

Ohh wow how weird... any chance I can get around this with mass modifications?

Thanks for the rapid response and spending the extra time fixing this!


Matt Chambers responded:  2021-12-03

All MaxQuant elements will be supported in the next Skyline release and next Skyline-daily. Thanks for your patience!