Hi Mike,
Thanks for pointing this out! After years of waiting for support from MaxQuant we decided this release to pull matched DDA spectra directly from the associated raw data files, rather than the msms.txt files, which many people had pointed out contain MS/MS spectra which have been "charge-state deconvoluted", which means all peaks that match charge 2 and higher fragments are mapped back to charge 1 and summed with the peak at that m/z. Not great for using the peak intensities to rank fragment ions and calculate dotp values between library and measured intensities.
However, as you have pointed out, it looks like there is an off-by-one in the code that determines the raw spectrum to use. Sure wish someone had noticed earlier, since this has been in Skyline-daily (our beta release) for a while. But, glad you noticed so quickly after I released Skyline 19.1. We will get a fix out in a patch soon.
In the meantime, you can simply move your raw data away to where Skyline can't find it. Then Skyline should show a message asking if you want to use embedded spectra (i.e. the spectra in the msms.txt file - as it did in version 4.2 and earlier). Once you accept that option you should be back to the (admittedly deconvoluted) spectra Skyline was using before version 19.1 was released.
Again, thanks for your very thorough inspection of this new feature and for alerting us to this issue.
--Brendan