Scott,
When I look at that .raw file in ProteoWizard SeeMS.exe, it says that all of those spectra are MS2.
I am skeptical that that is the correct behavior, since it also says that the precursor m/z which was isolated was exactly 1000.
Skyline only wants to extract chromatograms from the MS1 spectra, based on the transitions in the document and your settings at "Settings > Transition Settings > Full Scan".
Maybe someone else on this support board has some ideas about why ProteoWizard thinks all those spectra are MS2.
-- Nick |