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ahmohamed / lipidr

Data Mining and Analysis of Lipidomics datasets in R
https://www.lipidr.org/
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lipid name parsing for class(O+P-chain) #35

Closed Summer1019 closed 2 years ago

Summer1019 commented 2 years ago

Hi Ahmed,

It seems that lipidr can parse molecules named with class(P-chain) or class(O-chain), which is quite good, but not with class(O+P-chain). sorry if it is a silly question, I'm new to lipidomics.

thanks for your time, Yao

ahmohamed commented 2 years ago

Thanks Yao, and sorry for the late response. I'm not quite familiar with O+P chains or their naming conventions. Can you send an example from lipidmaps https://www.lipidmaps.org/ ?

Cheers, Ahmed.

Summer1019 commented 2 years ago

Hi Ahmed,

Sorry for the late response. I found that it's because the normal phase column can not chromatographically separate the nature of the ether species (alkyl/alkenyl) and have this O+P. The reversed-phase column can separate them and have the “P-” prefix for an alkenyl ether substituent, and the "O-" prefix for alkyl. And our mass spectrum center used both normal phase and reversed phase which generated both “P-”, “O-”, and “O+P-”.

Thanks for your time. Yao