SureQuant Transition Settings

SureQuant Transition Settings romeally  2022-03-11

Has anyone used the SureQuant transition settings to export method settings in a custom assay? I'm curious how this works since I have always used the export spreadsheets provided by Thermo for this. I assume for import this allows the template not to have to use DIA settings as Thermo had recommended, but does it work for exporting with thresholds and calculate the isolation offsets? Just curious how this works in the transition settings.
Thanks! Bob

Nick Shulman responded:  2022-03-12

When you export a method, you always provide a template file. The template file contains all of the settings which Skyline does not know anything about, and then Skyline fills in the other parts of that with the peptide-specific information from your document.
I believe there is no way to tell Skyline about the thresholds which trigger the mass spectrometer to start collecting MS2 spectra, so I am thinking that those already need to be specified in your template file.
Please let us know if anything goes wrong when you try to export a SureQuant acquisition method. You can send us your Skyline document and file and we can make sure it gets fixed or ask our contacts at Thermo how this is supposed to work.
-- Nick