I am not sure I understand your question.

In order to collect MRM data from a triple quad mass spectrometer, you need to tell the mass spectrometer the precursor m/z's of the intact peptides and the product m/z's of the peptide fragments. It is not possible to collect MRM data without knowing the identity of the peptides ahead of time.

We have a lot of great tutorials for using Skyline with triple quad mass spectrometers:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorials

The tutorials in the first section ("Introductory") deal with using Skyline with triple quads.

Hope this helps,
-- Nick

Hello Nick,

Thank you for you response.

For example, I am finding 10 most abundant ions in a biological matrix. I am doing MS/MS to that. In this case I have 10 transitions. My question is can I use the information to possibly identify the proteins?

Are you using your triple quad in the mode where the Q3 scans across a range of m/z's so that you end up collecting MS2 spectra?
I am not very familiar with that sort of data from a triple quad, but if they look like MS2 spectra then you should be able to use a peptide search engine on it.

Skyline has a peptide search engine built in called "MSAmanda". In order to tell Skyline to perform a peptide search on your data using MSAmanda, you would use the menu item:
File > Import > Peptide Search
On the first page of the Import Peptide Search wizard, tell Skyline that you are starting from "DDA raw".

Here is the tutorial for doing that sort of peptide search in Skyline:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_dda_search

-- Nick

It is possible to use the mProphet scoring if you have plenty of transitions, have a spectrum in a library (with iRT values), and collect decoy transitions. It should be possible to use Prosit to make a spectrum library too.

Mike