A question about Lipid LynxX[Feature request]

[xiaowenchenjax]

Hi Zhixu
I’d like to use LipidLynxX to convert lipid names in my dataset.
However, I only get annotation for 30 of 135 lipids.
I am new to lipidomics data. Could you give me some suggestions? How I can get the LipidLynxX indentifier for all the 135 lipids I have?

[ZhixuNi]

Hi,
Thanks for using LipidLynxX!
We are working on for some updates and new features for LipidLynxX.
Please send me your list of lipid names if it is possible

zhixu.ni [at] tu-dresden.de

Many thanks!

Best,

[PerCleCarla]

Hello,

I would like to use the BioPAN, LINEX2 or LIPEA tools with my lipidomics data.

The problem is that I can't get my nomenclature to be valid. I have seen that many lipid tools use LipidLynxX to convert the names.

I have used LipidLynxX through LIPIDMAPS. It recognizes 336 lipids out of 602. Of those 336 the lipids corresponding to the FAHFA or HexCer classes did not convert well. Is it necessary to pre-process the names of all lipids before converting them?

Thank you very much in advance.

[ZhixuNi]

Hi @PerCleCarla !

Thanks for the report.
FAHFA is the lipids generally not well covered and tested in many tools.
Please send me your FAHFA names so I can have a look.
There are Known issues mainly coming from Ceramides, I'm already on it for a while.
Please send me your list to me and if possible LIPIDMAPS ID or other ID you have, so I can have a look.
Many thanks!

Best,
Ni

[PerCleCarla]

Thanks for your fast reply!

Here is my list!

lipids_PerCleCarla.csv

Best,
Carla

[ZhixuNi]

Hi @PerCleCarla

I would like to ask you about your FAHFA abbreviations:
Is "FAHFA 16:0_18:0" refer to:

FAHFA(16:0/5-O-18:0)
https://lipidmaps.org/databases/lmsd/LMFA07090001
or
FAHFA(18:0/9-O-16:0)
https://lipidmaps.org/databases/lmsd/LMFA07090044

or both possibilities?

Best,
Ni

[PerCleCarla]

I'm sorry I haven't replied yet but since the data came from a contributor I'm waiting to hear back from her.

Best,

Carla

[PerCleCarla]

Since I am not receiving a response from the other lab, consider the two species as valid and I can continue to move forward with the study. I will write it down and modify it later if necessary.

Thank you very much for your help.