How to develop MRM method for Metabolites

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How to develop MRM method for Metabolites Drymoglossum  2024-10-02 05:35
 

I have untargeted DDA data for metabolite samples and have used public .msp libraries from RIKEN for MS-DIAL data analysis.
I have access to .raw files of the samples & .msp libraries.
I identified over 100 differentially abundant metabolites that I want to further investigate.
How can I develop an MRM method for these metabolites?
Does anyone have a latest tutorial or guidance on how to approach this? I’ve heard that Skyline might be useful, but I'm unsure where to start. Any advice would be appreciated!

 
 
Brian Pratt responded:  2024-10-02 11:31

Have a look at these tutorials available on the Skyline website, or within Skyline itself:
Small Molecule Method Development and CE Optimization
Hi-Res Metabolomics

One difference from the workflow in these tutorials is that they start with a transition list, it sounds like you will want to start with the ,msp spectral library. For that you'd use the Skyline menu item "View | Library Explorer", then add the .msp library, then use the "Add All" button to add the precursors and fragments to your Skyline document's Targets tree. After that it's the same - extract chromatograms) for the targets ("File | Import | Results", see which targets give strong signa's, refine, export method, iterate on that.

Thanks for using the Skyline support board,
Brian Pratt