• Sign In
  1. Requests

problem with quantitation method while creating library from mascot datfile

support

View Request

view list print
problem with quantitation method while creating library from mascot datfile evy timmerman  2023-04-20
 

Hello,
when importing a .dat file to create a library I get the following error:
"Cannot get quantitation method Butyl_double_KN_fix in file F008150.dat"

The datfile was created with the newest mascot server and daemon. I suspect this is why it is not working anymore.
I used the exact same quantitation methods before we upgraded the mascot server and then this was not a problem.

Could you have a look at the dat file for me please? Or give me a hint on which things to check in order to get the import working?

Where can i upload the files (dat file and skyline file)
?
 
 
Nick Shulman responded:  2023-04-20
You can upload files here:
https://skyline.ms/files.url
--Nick
 
evy timmerman responded:  2023-04-21
Hello , the files are uploaded:
-skyline file
-dat file from old mascot server, works
-datfile from new mascot server, fails
 
evy timmerman responded:  2023-05-22
Hello,
while waiting for your answer, I also send an email to Mascot asking about any changes we should consider. This is the answer I got:

'The quantitation_2.xsd schema file was updated in Mascot 2.8. You probably may need to update the schema Skyline is using with the one from the Mascot server (you'll find it at mascot\html\xmlns\schema\quantitation_2). I'm not sure where Skyline keeps the xsd files - you'll need to ask the Skyline team about that.'

Is this helpful information?
Could you help me on this? Where do I find this xsd file within skyline, and can I simple replace it with the 'good' one?

Kind regards,
Evy
 
Nick Shulman responded:  2023-05-22
Thanks for that information. Yes, that is very helpful.

I have put a special version of Skyline-daily that fixes this bug here:
https://proteome.gs.washington.edu/~nicksh/SkylineDailyPreview/
(this special build of Skyline-daily has not been signed so Windows might make you hunt around for the "Run Anyway" when you try to run the "setup.exe" that you download from that page)

I think the file that we needed to update might have actually been "unimod.xml" not (or maybe in addition to) "quantitation_2.xsd".

I will try to get this fix into an official release of Skyline-daily soon.
-- Nick