search

rformassspectrometry / MetaboCoreUtils

Core utilities for metabolomics.
https://rformassspectrometry.github.io/MetaboCoreUtils/index.html
9 stars 6 forks source link

Add [M+H-2(H2O)]+ adduct #34

Closed jorainer closed 3 years ago

jorainer commented 3 years ago

This PR adds the [M+H-2(H2O)]+ adduct that we also see sometimes in our HILIC data. Question is however if it is written/defined in the proper way - @michaelwitting ?

michaelwitting commented 3 years ago

No, there is no proper way at the moment. I prefer to have it [M+H-H4O2]+. Discussing some "more common adduct names" could be something for the hackathon.

jorainer commented 3 years ago

Yes, that makes sense. I will update.

jorainer commented 3 years ago

UPDATE: I also added a [M-CHO2]+ adduct - guess the name should be correct - we also called that [M+H-HCOOH]+ but I guess the [M-CHO2]+ might fit better the sum formulas...

michaelwitting commented 3 years ago

Sorry, I think I should have been more clear on how to use the sum formula. I always include the ion that was used for ionization and then the part that is lost or added as sum formula. So [M+H-HCOOH]+ should be better [M+H-CH2O2]+. I think we should discuss this in more detail maybe during a call?

jorainer commented 3 years ago

Excellent! That is perfectly clear (and makes a lot of sense!). I will update

jorainer commented 3 years ago

I always include the ion that was used for ionization and then the part that is lost or added as sum formula.

maybe that could be something that you could add to the vignette? it would users to understand how the adducts are named in this package

jorainer commented 3 years ago

and I've updated the adduct name

michaelwitting commented 3 years ago

I always include the ion that was used for ionization and then the part that is lost or added as sum formula.

maybe that could be something that you could add to the vignette? it would users to understand how the adducts are named in this package

Yes, I can do that. Maybe we can have the adduct translation also in (#35). All togheter in an "adduct vignette"