Error with the mqpar.xml file litielecruz  2023-04-20 09:31

Hello Skyline team,

I am stuck with an error message after trying to build my peptide library : I am trying to load the file msms.txt , then I receive this message.
Error parsing mqpar file / / mqpar.xml (line 408) parameter group index was 0 was outside the range of parameter group (0).
I did my search on Maxquant Version and I'm trying to use the msms.txt to build a library on Skyline-daily version I need to use the daily version because of some modifications to add.

I don't know if the problem is in the versions that I use.

Hope you can help me.

Thank you!


Nick Shulman responded:  2023-04-20 10:40
I do not know what that error means but if you send us your files, we can probably figure it out.
If your files are less than 50MB you can attach them to this support request.
If they are larger you can package them in a zip file and upload them here:

We will probably need the "msms.txt", "modifications.xml" and "mqpar.xml" files, but feel free to send us more files if you think we might need them.
-- Nick
litielecruz responded:  2023-04-20 10:54
Hi Nick,
I saw here someone reporting the same error.
I just attach the files with the name: Litiele files.

Thank you!

Nick Shulman responded:  2023-04-20 13:04
Can you send me your "modifications.xml" file (or it might be called "modifications.local.xml")?
BiblioSpec is complaining to me that it doesn't know what the "Br" modification is.
-- Nick
litielecruz responded:  2023-04-20 14:13
Where is this modifications.xml? The only modification file that I got is modificationSpecificPeptides.
This modification "Br" is a bromination modification that I add to tyrosines. I already use it in Skyline daily before, I don't know what is happening now, because appears this error.

Nick Shulman responded:  2023-04-20 17:32
I have never used MaxQuant before, but I think the modifications.xml file might be found somewhere in the folder where MaxQuant was installed.
C:\Program Files\MaxQuant\bin\conf\modifications.xml

-- Nick
litielecruz responded:  2023-04-21 03:30
Hi Nick,
Got it. It is in the software files, I was looking in the generated files post-search. Here is.
One thing that happened also, depending on the Skyline version I had different Errors. This one that I have sent was in one of the versions and in another version, it was the Bromination modification, the software was not recognizing too, that maybe is the same as you see.

Nick Shulman responded:  2023-04-21 08:52
I cannot get the error that you described to happen.
I suspect that the mqpar.xml file that you sent me is different from the one that is causing you the error.

Also, the "modifications.local.xml" file that you sent me is a little different from what would work with the msms.txt file that you sent me. Your "modifications.local.xml" file has modifications named "BromoTyr" and "2BromoTyr" but the modifications in msms.txt are named "Br" and "2Br". I was able to work around this by editing the "modifications.local.xml" file.

I have attached the library that I ended up building from your search results.
-- Nick
litielecruz responded:  2023-04-24 12:49
Hi Nick,
Thank you for your help.
I have found what I was doing wrong.
Thank you!