Probem in creating library from Maxquant results

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Probem in creating library from Maxquant results nicolas pierre  2020-06-10
 

Hello,

I want to create a library from Maxquant results but I did not find the modifications.xml file.
So, I have an error message. Where to find the modifications.xml file ?
Thank you for your help,

Nicolas Pierre

 
 
matt.chambers42 responded:  2020-06-10

Hi Nicolas,

A default modifications.xml is installed with MaxQuant. If it has been customized, recent versions of MaxQuant create a modifications.local.xml file as well. You need to copy modifications.xml (and the .local.xml file as well if it exists) next to your msms.txt or mqpar.xml file for Skyline to be able to import the msms.txt.

 
nicolas pierre responded:  2020-06-11

Ok thank you very much, it works.
However, the retention time does not appear. I cannot clic "retention time" in the view bar. How to fix the problem ?

Nicolas

 
Brendan MacLean responded:  2020-06-11

Hi Nicolas,
Can you post screenshots of what you are describing? It is not immediately clear to me. Have you looked at View > Spectral Libraries to see if your spectral library ended up with retention times in it? Here is a link to a page with some information on troubleshooting missing retention time information:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=mascot_missing_rt

It should be informative, even if you are using MaxQuant instead of Mascot, but I have not heard of a library build of MaxQuant results that lacks retention time information.

If it doesn't help you solve your problem, please post screenshots and explain in more detail.

--Brendan

 
nicolas pierre responded:  2020-06-16

Hello,

Actually it works. It was just because i saw "chromatogram information unavailable" in the replicate but with the addition of the other replicates it is ok (see the capture).
Thank you very much,

Nicolas

 
Brendan MacLean responded:  2020-06-16

You may need to use Edit > Manage Results > Reimport to get chromatograms extracted for your first replicate. The most likely explanation is that you added the target you are viewing after your import. Otherwise, this indicates that the target was not measured in the replicate datafile, e.g. if it was PRM, by not including it's precursor in your MS/MS inclusion list.

Glad to hear that it is now otherwise working as you had hoped.

 
nicolas pierre responded:  2020-06-17

Your right, thank you very much.
A saw the results in the 3 replicates now.
I am beginner in SRM but fortunately the software is not very complicate to use. It is a very good job, thank you.

Nicolas