Library Build from MaxQuant Results Error Message

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Library Build from MaxQuant Results Error Message brian mcdonagh  2022-04-13
 

Dear Skyline,
Having trouble building a spectral library from MaxQuant results and don't know the best way to solve it. Error message is attached but is an unexpected closing parenthesis found in sequence.......NETVVK(NEM)EK (line 84).
ERROR reading file msms.txt.

Any advice or help would be greatly appreciated.
Thanks,
Brian

 
 
Kaipo responded:  2022-04-13

Hi Brian,
Would you mind zipping up the msms.txt and mqpar.xml (and modifications.xml if applicable) files and uploading them to https://skyline.ms/files.url so we can take a look?

Thanks,
Kaipo

 
brian mcdonagh responded:  2022-04-14

Thanks Kaipo,

That would be great if you could have a look, have uploaded the msms.txt, mqpar and modifications files using the link you provided.

Any help would be appreciated.
Thanks,
Brian

 
Kaipo responded:  2022-04-14

Hi Brian,
Just to confirm, is the modifications.local.xml file in the same directory as the msms.txt file when you try to build the library, and which version of Skyline are you using (Help > About)?
To debug further, would you mind also uploading the "120mins_OTIT_FusionMS_Ctrl_4" raw file to the same link?

Thanks,
Kaipo

 
brian mcdonagh responded:  2022-04-15

Thanks Kaipo,

Just checked the Skyline version and was using 19.1.0.193, installed the updated version and it has built the library, sorry should have tried this first.

Thanks again for your help, much appreciated.

Best wishes,
Brian