mzid to Skyline to openswath

mzid to Skyline to openswath srikanth0403  2018-10-04

Hi Brendon,

I have searched my DDA data using three different search engines and created mzid using peptide-shaker. I am trying to create a spectral library by importing the same into skyline to further use it with openswath. I am stuck at the retention time calibration step. Could you please guide me the correct steps to get a transition list (assay library) which I could convert (traml) and use with openswath? I have the retention time peptides from Biognosys in my experiment.


Brendan MacLean responded:  2018-10-05

Hi Srikanth,
I am afraid we are not very familiar with going this route. If you come up with a Skyline report for doing it, please do post it back here. Maybe the OpenSWATH team has something, we have certainly put a lot of time into accepting OpenSWATH library and result formats, but so far left generating the transition list (a.k.a. "Assay Library") up to them.

Great opportunity for someone to write a Skyline External Tool and put it in the Tool Store:

This is essentially what we did with Agilent and Thermo for MPPReport and TFExport for their Mass Profiler Professional and Trace Finder software respectively.