Support for RDkit isotope aware

support
Support for RDkit isotope aware landerson  2020-05-26
 

Does Skyline support RDkit isotope aware molecular formulas? RDKit uses nomenclature that a heavy carbon is [C13]. For example, if 2 carbons in glucose were heavy you might use C4[C13]2H12O6.

I know of the apostrophe " ' " method e.g. C’C5H12O6 that is embedded in Skyline. The RDkit nomenclature feature would make the synergy between a postgresql database more streamlined.

 
 
Brian Pratt responded:  2020-05-27

That's not an isotope description format we've seen before, but it should be possible to adapt Skyline to handle it. Can you provide example artifacts (transition lists?) that you'd want Skyline to deal with?

Thanks for using the Skyline support board!

Brian Pratt

 
landerson responded:  2020-06-03

Thanks for considering! The application is small molecules, so transition list column headers would be:
Molecule List Name Precursor Name Precursor Formula Precursor Adduct Precursor Charge Product m/z Product Charge Explicit Retention Time Explicit Collision Energy InChiKey Explicit Declustering potential    Label Type

For example inputs, see this reference https://sciex.com/Documents/tech notes/quant_qual_Metabolomics_AnalysisQTRAP.pdf
Is this helpful, or is there other transition list information that you need?

To clarify, I would like Skyline to be able to handle the bracket molecular formula format to calculate the correct heavy precursor mass.

I would double check the molecular formula format (a software engineer college at my company gave me the info about RDkit's isotope molecular formula format, since I'm not a programmer and not familiar with RDkit).

and a related question/request: can skyline handle positional isomers in molecular formula? for example, 1-13C glucose, where the first carbon is labeled versus 2-13C glucose, where the second carbon is labeled.

 
Brian Pratt responded:  2020-06-04

I would like Skyline to be able to handle the bracket molecular formula format to calculate the correct heavy precursor mass

Understood.

For example inputs, see this reference

Nearly there - that example narrowly misses the mark as it has no chemical formulas. We'd need an example with formulas, and specifically with formulas that employ this novel notation. But everything else in that example is, yes, the kind of data Skyline needs for transition list import.

(Note that Skyline can work with masses alone, so that example is a perfectly good transition list for Skyline import. But formulas are the point of the exercise at hand.)

can skyline handle positional isomers in molecular formula?

Yes, it can. Skyline would consider 1-13C glucose and 2-13C glucose to be have identical chemical formulas for calculating isotope distributions etc, but would still consider them to be distinct molecules because they have different names. We also retain InChi and/or SMILES metadata when available, which further differentiates such molecules within Skyline and can be passed along to structure-aware tools downstream from Skyline.

Best,

Brian Pratt