Metabolite settting up

support
Metabolite settting up sgler  2020-02-06
 

I’m self-learning on how to use skyline for metabolite. I was going through the tutorial but question is how did you achieve the dot product?

Did you create library for metabolite study just like PRM study in protemics?

 
 
Nick Shulman responded:  2020-02-06
Which tutorial are you working on? Where are you seeing a dot product? Can you send us a screenshot of it?

Skyline has several different dot products. One of them is the "library dot product" which is often just called the "dot product". That one does require having a spectral library.
Another dot product is the "isotope dot product" which Skyline can calculate for your if you have provided the chemical formula for your molecule, and you have told Skyline to extract chromatograms from MS1 spectra.

It is possible to create spectral libraries for small molecule data. One way is if you have a Skyline document with some chromatograms for your metabolites, you can do:
File > Export > Spectral Library
and Skyline will create a .blib file where the spectra in the file have intensities that come from the chromatogram peak areas in your Skyline document.

I am not sure what any of our small molecule tutorials are doing with dot products or spectral libraries, but if you tell me what you're looking at it might make more sense to me.
-- Nick
 
sgler responded:  2020-02-10
https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/Skyline%20Hi-Res%20Metabolomics.pdf

From this above link.

And how do we create spectral library for my lists of small molecule data?

Please advise.

-siokghee
 
Brian Pratt responded:  2020-02-11
As Nick explained previously, you can create spectral libraries from data you have loaded into Skyline.

You can also import spectral libraries from various external sources. This link:
 https://skyline.ms/wiki/home/software/Skyline/page.view?name=building_spectral_libraries
may be useful.

Best regards,

Brian Pratt