Build spectral library with propionamide modification

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Build spectral library with propionamide modification benoit fatou  2020-02-19
 

Dear Skyline Team,

I have an issue with building a spectral library from Maxquant search using propionamide modification on the cysteine residues.
It seems Skyline does not recognize it. I attached the screen shots from Maxquant and Skyline and I don't really see the problem.

Thanks for your help,
Benoit

 
 
Brendan MacLean responded:  2020-02-19

Hi Benoit,
Nor do I see the problem. Could you possibly provide a screenshot of the error you are seeing? It may actually be a failure in the library builder program BlibBuild, which Skyline calls to build libraries. Or it may just be a failure of that program to find the necessary modification specification in your MaxQuant parameters.

Please provide a screenshot of the error, and I will try to have the developer responsible for BlibBuild look into your issue.

--Brendan

 
benoit fatou responded:  2020-02-19

Hi Brendan,

Thanks for your quick reply.
Please find attached a screen shot of the error message provided by Skyline.
Thanks,
Benoit

 
Brendan MacLean responded:  2020-02-19

Hi Benoit,
This is definitely an error from BlibBuild. It is instructing you to provide the modifications.xml file used with your MaxQuant search, which must be the source of the modification you are showing in your MaxQuant screenshot. It seems that our default modifications.xml must not have this modification. I just checked the modifications.xml that our build process puts in the same directory as Skyline.exe and indeed it does not contain this modification.

It is date stamped 8/14/2018. Maybe it is time for us to update our default modifications.xml. Can you locate yours and let us know how recent it is?

The quickest solution for you, however, is to follow the instructions of the error report and place your modifications.xml in the same folder as your msms.txt file.

Hope this helps. Thanks for the quick response.

--Brendan

 
benoit fatou responded:  2020-02-19

Hi Brendan,
The default modifications.xml is from December 2018.

Thanks for your helps, it seems to be working.

Benoit

 
matt.chambers42 responded:  2020-02-19

Hi Benoit,

Propionamide is not in the modifications.xml file I got when downloading MaxQuant a few minutes ago. Did you add it yourself? Or get the file from someone else?

I'm glad you got it working in the mean time.
-Matt

 
benoit fatou responded:  2020-02-19

Hi Matt,

We manually added this modification into MaxQuant.
Thanks for checking,

Benoit