Custom derivatization

Claire Moore

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Dec 17, 2024, 5:38:12 AM12/17/24

to GlycReSoft

Hello GlyReSoft folks,

I am wondering if it is possible to include a custom derivatization tag when generating a glycan hypothesis. I have attempted doing this using the "custom substituent" field and the available mammalian glycan library, and the task runs, but it fails to generate a glycan hypothesis I can actually open. The only derivatization I see available is permethylation, but I am using a different commercial tag. Is there a way around this?

Thank you!

Joshua Klein

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Dec 17, 2024, 10:37:59 AM12/17/24

to Claire Moore, GlycReSoft

Hello,

By "custom derivatization tag", are you referring to a reducing end modification or a modification that is applied to all hydroxyl groups of a glycan?

Thank you for pointing out that the "derivatization" input didn't do what was expected. It appears that the option to pass a formula was never implemented, this only accepts known substituent names like "methyl", "acetyl", or the like, where the complete list is enumerated here: https://github.com/mobiusklein/glypy/blob/master/src/glypy/composition/structure_composition.py#L146-L227.

Thank you,

Joshua Klein

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Joshua Klein

Claire Moore

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Dec 17, 2024, 9:11:11 PM12/17/24

to GlycReSoft

I see. It is a reducing end modification, which does not appear to be among the list in the link posted (thank you for sharing by the way!).

So no chance of customizing reducing end modifications?

Claire

Joshua Klein

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Dec 17, 2024, 9:49:53 PM12/17/24

to Claire Moore, GlycReSoft

Actually, it turns out reducing end modifications can legally be a chemical formula under the current implementation. They take the place of the backbone carbon bond, so "plain" reduction adds H2 to the composition of the reducing end monosaccharide. If you have the formula for your tag, adjust it accordingly please.

It was possible to add new custom substituents, but that feature appears to be disabled now. I'll fix this in the next release. For substituents that aren't derivatization rules, it's easier to use a chemical formula unit in the composition, "#<name>#<formula>" in the combinatorial generator form or in the text file format.

Thank you,

Joshua Klein

To view this discussion visit https://groups.google.com/d/msgid/glycresoft/301faccb-509f-4513-8395-d8fd7f0b22d6n%40googlegroups.com.