I am trying to quantify peptides using our Sciex QTOF 6600. I have made a document of my targets in Skyline and exported an acquisition method. The acquisition method looks good to me and contains multiple 'Product Ion' experiments, one for each of the precursors. There is no MS1 full scan experiment as this was not included in the template. I think this shouldn't be an issue as I only want to quantify on the MS2 level. When I try to load the data in Skyline, I get the following error. This persists after converting to mzML with MSConvert.
The file xxxxx.wiff does not contain SRM/MRM chromatograms. To extract chromatograms from its spectra, go to Settings > Transition Settings > Full-Scan and choose options appropriate to the acquisition method used.
Does anyone have any clue where the issue could lie? Is there any reason why Skyline shouldn't be able to deal with these data files in principle?
The same seems to work when my acquisition method also includes an MS1 experiment (as I have done previously)