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ahmohamed / lipidr

Data Mining and Analysis of Lipidomics datasets in R
https://www.lipidr.org/
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a question about lipid name #46

Closed xiaowenchenjax closed 1 year ago

xiaowenchenjax commented 1 year ago

Hi Ahmed, Thank you for developing this great tool. I have a question about the lipid name. Based on the tutorial, the lipid name must be CLS xx:y. I am a new for lipidomics data. what do xx and y mean? I saw some lipids' name like this "DG 14:0/18:1/0:0", what do those number mean? If I have a lipid name, such as " (+/-)14,15-EET_1" and "9-HpODE(2)", how I can convert those names to the format lipidr requires? Thank you. Look forward to your reply.

ahmohamed commented 1 year ago

lipidr needs lipids named according to LipidMaps abbreviated nomenclature, as in the example you mentioned "DAG 14:0/18:1". The nomenclature consists of two parts, lipid class (DAG) and lipid chain information (14:0/18:1).

Lipid chain information lists all chains attached to a molecule separated by slash /, so in our case, we have 2 chains 14:0 and 18:1. The two numbers indicate chain length (number of carbons) and unsaturation (number of double bonds). 18:1 means 18 carbons length and a single double bond.

Depending on how you setup and acquire your lipidomics data, certain lipid classes may be present or absent. In your case, the examples you listed are fatty acyls, which can be abbreviated as FA XX:Y. You can refer to the 2 links below from LipidMaps.

https://www.lipidmaps.org/databases/lmsd/LMFA03080005 https://www.lipidmaps.org/data/LMSDRecord.php?LMID=LMFA02000286

Converting lipid names, especially for the not-so-common ones, is a quite a hard task. There are a few tools listed here: https://www.lipidmaps.org/resources/tools/nomenclature, but I didn't have any luck getting them to work. apps.lifs-tools.org/goslin is also another alternative that may work for some of the lipids. Feel free to reach to the authors of these tools if needed (github repos below).

https://github.com/lifs-tools/goslin-webapp https://github.com/SysMedOs/LipidLynxX

The last resort is to use lipidr with invalid lipid names. You'll be able to perform all the steps in the workflow except where lipid class is needed (lipid class enrichment, some of the plots). Let me know if this doesn’t work for you.

xiaowenchenjax commented 1 year ago

Hi Ahmed, Thank you for your quick reply. It is clear and helpful. By the way, if my data is signal intensity, is it good to use lipidr? Thanks.

ahmohamed commented 1 year ago

I assume you mean MS signal intensity, right? If so, lipidr should be ideal for your case.

xiaowenchenjax commented 1 year ago

Yes, thank you!