Development MRM method from a high resolution MS data

Development MRM method from a high resolution MS data oyku su yildirim  2024-01-04 03:02

I am a master's student who is a new Skyline user. I am wondering if a MRM method can be developed from a high resolution MS data. If available, which webinar or tutorial can help me?

Nick Shulman responded:  2024-01-04 07:58
What sort of high resolution MS data do you have?
Typically, the steps that you would do in Skyline are:
1. Create a spectral library from your high resolution MS data.
2. Use the spectral library to create a SRM method in Skyline.

The Targeted Method Editing tutorial does a good job of showing you how to do step 2:

The way to do step 1 depends on exactly what type of high resolution MS data you have. It is likely that you have DDA data, where the mass spectrometer was told to select the largest MS1 peaks for fragmentation. If that's the case, then I would recommend the DDA Search for MS1 filtering tutorial:
In this tutorial, you end up searching your data using Skyline's built-in peptide search engine, and then building a spectral library from the peptide search results. The spectral library will be a file whose name ends in ".blib", which you can then use when you design your SRM method in Skyline.
-- Nick