[Bug] Linker problems with specific lipids

[tdrose]

When using lipids in the linker/converter e.g. PE(22:6_16:1) the tool is able to convert them correctly into a notation which works with Swisslipids: Shorthand Notation: PE 16:1_22:6 ; LipidLynxX Notation: PE(16:1_22:6) .

However, For some lipids this does not work correctly:

Examples:

1. Etherlipids: PE(O-22:6_16:1) should be converted into PE(O-16:1_22:6) (Swisslipids ID: SLM:000069971), but does not work. So no Swisslipid DB entries are found.
2. Sphingolipids: Cer(d14:0/26:0) is wrongly converted into Cer(14:0/26:0) , but the correct Swisslipids entry is Ceramide (d14:0/26:0) (Swisslipids ID: SLM:000391713 )

[ZhixuNi]

@tdrose Thanks for the feedback!

This issue Cer(d14:0/26:0) is solved in the current dev version!
I will commit soon after I fix few other UI updates.
Please check the coming release of version 0.9.24 in the next few days.

The PE(O-22:6_16:1) issue is somehow a bit more complicated.
LipidLynxX currently will not change PE(O-22:6_16:1) to PE(O-16:1_22:6), since O-22:6 is a segment and _ indicate 16:0 is another FA.
Actually this is my first time to see PE(O-22:6_16:1) style, since it is not the standard ShortHand notation style.
You can check this paper (PMID: 23549332):
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3646453/
Please let me know if it possible how/where you get the style PE(O-22:6_16:1) which probably means PE( O- (16:0_22:6) ).

Thanks!

preview of Cer(d14:0/26:0)

[ZhixuNi]

@tdrose Please check our latest release v0.9.24 from pull request #12 to get version for Cer. Thanks!

[ZhixuNi]

Hi @tdrose !

Have you tried our new version v0.9.24?
If the issue is solved and there are no further issues related to this topic this week, I will close this issue by the end of this week.

[ZhixuNi]

Hi @tdrose !

I will close this issue for now. Feel free to add more comment if you want.

Best,

Zhixu Ni