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Error importing MaxQuant msms.txt file

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Error importing MaxQuant msms.txt file SChen  2024-09-11 08:42
 

Dear Skyline team,

I encountered an error while trying to import peptide search result (MaxQuant msms.txt file) into Skyline (see attached error message). I have tested this in Skyline Daily 23.1.1.520 & 24.1.1.254 as well as Skyline 24.1.0.199 and got the same errors from all.

I uploaded both mqpar.xml and msms.txt file to https://skyline.ms/files.url. Because the msms.txt file is quite large (50 GB), I uploaded a smaller version (only the top 10000 line in the original msms.txt). Since I encounter the same issue with the smaller version, hopefully you will also be able to reproduce the error on your end. I also had to change the mqpar.xml file name because there is already a file named after that in https://skyline.ms/files.url.

Please let me know if I can provide more information about the issue.

Thank you in advance!
Shimin
 
 
Nick Shulman responded:  2024-09-11 09:58
Thank you for uploading that msms.txt file.
BiblioSpec is trying to output a message saying that it was not able to find a spectrum file for a bunch of files.
Unfortunately, the way that we wrote this code, it crashes if that message is more than 4096 characters long.
There are 200 files in that msms.txt file.

One thing that you could do is put your mass spec data files into the same folder as the msms.txt file and then BiblioSpec will not try to output a message saying it cannot find the files.
One of the files that BiblioSpec is looking for would have the name "200117_postDREurine_R001_S018_1" and it could have any of the following extensions:
.mz5, .mzML, .raw, .wiff, .d, .lcd, .mzXML, .cms2, .ms2, .mgf

If you have a bunch of files like that, you would probably be able to successfully build your library without error.

It is better if BiblioSpec is able to find mass spec data files to go with the msms.txt.
If BiblioSpec cannot find the original mass spec data file then BiblioSpec has to use the spectra from the msms.txt file which have been charge state deconvoluted, so they do not give any information about what charges were seen for the fragment ions.

I will try to find someone to fix this bug.
-- Nick
 
SChen responded:  2024-09-11 10:51
Hi Nick,

Thank you so much for your quick response. I put the msms.txt, mqpar.xml, and the Skyline file in the same folder as the raw file and it is no longer giving me the same error.

Thank you for your help!

Shimin