Those are the collected MIDAS spectra for your precursors. They are extracted from your WIFF files and stored in a .midas file with the same base name as your Skyline document .sky file. No ID matching has been performed on these spectra. They are simply matched to the precursor by virtue of the way they were collected. They are there for your consideration. We may not have created a way for you to turn off these annotations. If you would like one, I am sure we can implement it.

It seems we did not anticipate that you would run a search pipeline (Mascot) on the spectra post-acquisition.

Thanks for reporting this. It would be helpful to have a screenshot of what you are seeing in the chromatogram graphs.

--Brendan

Hi Brendan,

thanks for the quick response. Having a way of disabling those MIDAS annotations would be nice, but I guess I could also achieve this by simply deselecting the .midas library. The IDs from the Mascot generated spectral library are in a separate library anyway.

I'll upload the screenshot(s) in due time.

Best

Robert

Here are the screenshots...

Robert

Yeah. I guess we should put something like Triggered Spectra in the Peptide ID Times dropdown menu, even though they are not really peptide IDs. But, obviously, we need a way to turn them off.

--Brendan