MRM triggered MSMS

MRM triggered MSMS heyang  2020-02-04

Dear Skyline team,

I want to compare MRM triggered MS2 with library spectra. Could I do this in skyline? if yes, how?



Nick Shulman responded:  2020-02-04
I am not sure I understand your question.

What brand of mass spectrometer do you have?

If you are reading chromatograms from SCIEX wiff files where there were triggered MS2 scans (MIDAS), Skyline will collect those spectra and put them in a .midas file which you can look at in a similar way to a spectral library in Skyline.

If you want a computer program to compare spectra, Skyline is probably not the correct tool. Skyline's quantitative features all revolve around extracting chromatograms and calculating chromatogram peak areas. Skyline can let you look at spectra in a library, but does not provide any real functionality for comparing them other than what you can do with your own eyes by looking at them.

Let us know what sort of data files you have and we might be able to point you in the right direction.
-- Nick
heyang responded:  2020-02-05
Thank you Nick for help.
The MS we used is 6500 QTRAP from Sciex. I can't find .midas file. Could you tell me where I can find these file. Also I want to compare them with std spectra which are from synthesized Peptides. How can I do it?


Nick Shulman responded:  2020-02-05

.midas is a file format that only Skyline understands. When you use Skyline to extract chromatograms from a .wiff file, Skyline will create a .midas file if Skyline finds any MIDAS spectra in the .wiff file.

It might be easier for us to help you if we could see the files that you already have.

In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms, spectral libraries, and that .midas file if it got created.

It would also be helpful if you sent us at least one of your .wiff files and the .wiff.scan file that goes along with it.

You can upload all of those files here:

-- Nick
heyang responded:  2020-10-26
Hi Nick,

It is long time for this topic. Actually I want to compare MS2 spectra in midas file with MS2 in the library. It is very important to for us to get rid of false MRM signal. could we do this?