SRM method creation for TSQ altis plus kmsd  2023-02-22 08:04
 

Hello,
I have made several lists which contain protein/peptide/ms1/ms2/rentention time using skyline from my discovery untargeted proteomics data. Now I want to transfer them to TSQ altis plus for monitoring them. Can you show me tutorials for this task?

Thanks,
kmsd

 
 
Nick Shulman responded:  2023-02-22 08:11
 
qiangzims responded:  2023-05-11 20:00
Hello, Nick
When import mzML format data, skyline(version=22.2.0.351) failed with this error message, while .raw file format is OK.
Can you help me figure out what's wrong with this?

At 10:27 AM:
Failed importing results file 'X:\DDF-demo\03-AAPro\data-20230509\202305-Cal\data\Std_1.mzML'.
[pwiz::CLI::msdata::ReaderList::read] Invalid cvParam accession "1003292"


Thanks
Qiang
 
Nick Shulman responded:  2023-05-11 21:22
Qiang,

I think this will work if you use Skyline-daily instead of Skyline 22.2.
The cvParam accession "1003292" is the one that means "TSQ Altis Plus" and it looks like we did not add the definition for that until November 2022 so it did not become part of Skyline 22.2.

(I don't actually know much about cvParam accessions, but I imagine that another part of the problem is that ProteoWizard has new releases much more frequently than Skyline does, so the msConvert that you used was probably much newer than Skyline 22.2 and therefore knew about it, but the BiblioSpec which ships with Skyline was much older).
-- Nick