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Transition List for SRM

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Transition List for SRM rsabnis  2018-05-23 15:30
 
Hello,

I made a spectral library with all heavy phosphorylated peptides using msms file from MaxQuant. When we import results, we see very few transitions, most of which are b ions. We think this improper y ions assignment is because the software is not recognizing the heavy peptides. Any help to get the transition list for SRM method would be appreciated.

Thank you!
Renuka
 
 
Brendan MacLean responded:  2018-05-23 15:49
We will probably need to see at least your mqpar.xml and modifications.xml from the MaxQuant Andromeda search. Having the msms.txt file might also be helpful. If they are small enough (<50 MB) you can attach to this support request. Otherwise, you can post them to:

http://skyline.ms/files.url

And let us know. Hopefully we will be able to solve this quickly.

Thanks for posting to the Skyline support board.

--Brendan
 
rsabnis responded:  2018-05-23 17:14
I have attached all three.
 
Kaipo Tamura responded:  2018-05-24 12:11

Hi Renuka,
This looks like a bug that was fixed recently - the fix hasn't made it to the main release yet, only Skyline-daily. You can download Skyline-daily from the main page (https://skyline.ms/project/home/software/Skyline/begin.view), clicking the green "Skyline-daily (beta)".

Thanks,
Kaipo
 
rsabnis responded:  2018-05-24 14:07

Thank you, Kaipo!