Illegal character found in sequence when building spectral library from MaxQuant results

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Illegal character found in sequence when building spectral library from MaxQuant results Gqin  2019-08-02
 

Hello All,

I'm a new user of skyline, and trying to build a spectral library from MaxQuant results. I'm not sure whether this is a skyline problem or MaxQuant problem.

Mass Spectrometer: timsTOF Pro
MaxQuant version: 1.6.7.0
System running MaxQuant and skyline daily: Windows 10 enterprise
Problem: when using msms.txt file to build spectral library using skyline daily, an error message window popped up saying "ERROR: illegal character t found in sequence (Acetyl(protein N-term))AAA.... (line 3) ERROR: reading file msms.txt". I then delete this variable modification from the datafile and try to build the library again, however another similar error occurred "ERROR: illegal character d found in sequence AA...(Oxidation (M)) (line25) ERROR: reading file msms.txt". Error message screenshots are attached. It seems that the errors are due to modifications, unfortunately, I can't just delete them in my data file. Please let me know how to go forward.

Thank you very much.

Guoting

 
 
matt.chambers42 responded:  2019-08-06

Hi Guoting,

It seems MaxQuant changed the way they represent mods in the msms.txt file in the latest version. Which is a good thing because the old way was prone to ambiguity between mod names. I will try to get this fixed this week, which means it'll probably be available in the next Skyline-daily.

In the meantime if you have an older version of MaxQuant (1.6.5 should work) you can use that for now to produce compatible files.

Thanks for the report,
-Matt

 
Gqin responded:  2019-08-06

Hello Matt,

Thank you very much! I look forward to the updated Skyline-daily!

Guoting