Skip to main content
Topic: handling double identification (Read 103 times) previous topic - next topic

handling double identification

Dear community,

In a typical lipidomics experiment there are many double identificatiosn, usually lipid with different retention times but same MS1 and MSMS. How are you handling such double ID lipids? Similarly, I noticed that deuterium labelled lipid standard from Splash are also double identified. Have you also experience this? I am usually filtering double identified lipid out of the data but sometimes the internal standard is also filtered out (it happen quite often for LPCd7 and LPEd7 in positive mode).

Well it would be great to exchange on this.

Best regards, Carlos.

Re: handling double identification

Reply #1
Hi Carlos,

First, I am also using RT filters because the retention time values of MS-DIAL lipidomics library are optimized in our experiment.
https://www.nature.com/articles/s41587-020-0531-2
(see method 1 of supplementary information pdf)
The same LC condition was described in the following article.
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0205-3

However, even if I use the RT filtering, I face on the same issue.
In my case, if the retention time, MS/MS are both good, I will modify the lipid names to e.g. PC 16:0_18:1-A and PC 16:0_18:1-B.
In the SPLASH standards, maybe, is there a possibility that it is due to the sn1/sn2 positional isomers?
I also have the same experience: the LPC of SPLASH is mostly detected as sn1-LPC, but the peak of sn2-LPC is also detected.
And, the normalization of other lipids by the SPLASH-LPC is performed by sn1-LPC. And I do not use sn2-LPC as the standard peak.

Hiroshi