Dear Skyline support team,
I am currently experiencing difficulties creating a spectral library. While the MaxQuant output MSMS.txt can be read without error messages from Skyline, no y+ are displayed when I explore the library (all other ions are displayed as identified by MQ, also y++). I experience this problem with multiple versions of Skyline (3.7 & 4.1) and multiple different input files from MQ.
The tutorial spectral libraries could be created with y+ displayed and intact, so I don't think I got some setting wrong.
Please find attached the MSMS.txt I'm using. I've looked and it seems die y+ ions are reported correctly.
Could the import be somehow the problem?
Thanks for any help! Best,
Klemens |
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| Kaipo Tamura responded: |
2018-04-19 12:04 |
Hi Klemens,
It looks like the library is being built without the label modifications. Normally with labels we expect to see the msms.txt containing a column "Labeling State", where its value corresponds to the parameter group in the mqpar.xml file. I suppose if there is only one parameter group and the labeling state column is missing, we can just assume the one? I'll make a fix for this; for now you can manually add the "Labeling State" column and fill it with zeros.
Thanks,
Kaipo |
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| klemens froehlich responded: |
2018-04-20 02:55 |
It works!
Thanks a lot for the quick answer and the workaround solution!
Cheers,
Klemens |
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mqpar.xml
msms.txt