LIPID MAPS Main Class for Deoxyceramide/Cer m/Cer XX:X;O is unexpectedly in Other Sphingolipids [SP00] instead of Ceramides [SP02]

[JauntyJJS]

Not sure if your team is already aware of this.

When I run the master version of rgoslin for a deoxyceramide like Cer m18:0/18:0
The system tells me that is it located in the Ceramide Class

suppressPackageStartupMessages(library("rgoslin"))

m18_1_results <- rgoslin::parseLipidName("Cer m18:1/18:0")
m18_1_results[["Lipid.Maps.Main.Class"]]
#> [1] "Cer"

^{Created on 2021-12-03 by the reprex package (v2.0.1)}

It seems to agree with the web application as well

However, when I try to search for this in Lipid Maps, I had troubles finding it... until I click on Other Sphingolipids [SP00]

I found most of the deoxyceramide hidden in this group

I am not sure what is the best way to approach this...
Maybe for the web application of Goslin, perhaps it is best to update this link so that others will not spend too much looking for it in LIPID MAPS.

[dominik-kopczynski]

Hi Jaunty, thank you again very much for spotting this issue. In fact, we have here a problem that we only store one description for one class. Since Ceramides apparently occur in two classification groups, it breaks a little bit our model. The only quick solution would be to report the highest common description, i.e. [SP]. However, I wonder why LipidMaps calls these lipids Cer(mxx:x) ceramides. Ceramides have a hydroxy headgroup, Cer(mxx:x) have a CH3 end. Actually they should get an own class specification. Nevermind. Do you have any other suggestion how to treat them?

Cheers, Dominik

[JauntyJJS]

I have sent a note to LIPIDMAPS to see if there are able to move the deoxyceramide to another class, ideally in the Ceramide[SP02] so that not much will be done from your side.

It seems that RefMet also classify the deoxyceramide as ceramide as well.

As for those Cer(mxx:x) has a CH3 end, looking at this paper, I believe they are more specifically 1-deoxyceramide. It seems that there are other deoxyceramide (like 3-deoxyceramide) that still retains its hydroxy headgroup.

[JauntyJJS]

Hi,
Not sure if this is good news.

I have managed to "convince" the LIPIDMAPS team to move the deoxyceramide from Other Sphingolipids [SP00].
The committee has decided to move them to Ceramide [SP02].

https://lipidmaps.org/lmsd_search/40206

I guess, nothing is required to change from your end. Attached are my chain of emails with the LIPIDMAPS team.

User feedback received.pdf

[dominik-kopczynski]

Hi,

Cool, thank you for the effort. I guess this makes classifications easier, at least for ceramides. However, the cleanest would be if deoxy-ceramides would get their own class name identifier, e.g., "DCer". But I don't know if LIPID MAPS just can or wants to introduce new identifiers.

Cheers,
Dominik

[JauntyJJS]

They mentioned that they can't add new identifiers yet because of the need to be FAIR compliant