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Could I please get the exact masses and isotopic abundances that skyline uses?

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Could I please get the exact masses and isotopic abundances that skyline uses? pavel shliaha  2024-09-04 03:22
 

I tried to predict mz for certain compounds using publically available isotope exact masses and my calculations agree with the raw data much worse than skyline calculations (I interpret this as skyline using more accurate exact element massess). Is there a way I could get the element masses out of skyline and also understand where the developers took them from?
 
 
Brian Pratt responded:  2024-09-04 08:27
You can find the monoisotopic mass and isotope distribution values, and where they're taken from, here:
https://github.com/ProteoWizard/pwiz/raw/master/pwiz_tools/Shared/CommonUtil/Chemistry/IsotopeAbundances.cs

You can read, for example, the line
 {"H", new[]{1.00782503223,0.999885,2.01410177812,0.000115,}},

as meaning 99.9885% of naturally occurring H has mass 1.00782503223, and the other 0.0115% has mass 2.01410177812

Thanks for using the Skyline support board!

Brian Pratt