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Topic: RIKEN lipids identified (Read 213 times) previous topic - next topic

RIKEN lipids identified

Hi All,

I am attempting to analyze a lipidomics DDA dataset that was acquired on an orbitrap QE plus instrument. I converted the *.raw file to *.ABF files. I've noticed that in the final alignment some of the compounds were annotated as such: "RIKEN P-VS1 ID-7082 from Mouse_Macrophage_WT_N_F1AA", but in the identification step (i'm working in lipidomics mode) these kind of lipid are not presents. Is there a database somewhere where I can search for the molecules associated with this type of annotation? How do we can use this information of ID's?

Thanks,
Sara

Re: RIKEN lipids identified

Reply #1
the RIKEN ** ID is something like BinBase Unknown ID (https://www.nature.com/articles/nmeth.4512).
The spectra have been acquired many times in our RIKEN laboratory although it is still unknown. Therefore, now, you cannot directly access the compound structure for that.
Actually, there are a lot of redundant IDs including cluster ions and different adduct forms of known metabolites.
The ID title means the origin (at least the peak was highly detected at that place) , so in your example, the peak was obtained in macrophage from mouse's PEC in the arachidonic acid-rich diet. And in fact, the statistics of such unknown profile can be browsed in BinVestigate (BinV.) button (on the right panel of MS-DIAL gui).

Hiroshi

Re: RIKEN lipids identified

Reply #2
Thank you for your reply. Now, I've understood.
About the BinVestigate button in MSDIAL I can't use it because it works only for GC-MS projects.

Best regards



Re: RIKEN lipids identified

Reply #3
In the case this kind of lipids are regulated in our results how can we assign them an ID?
Or do you suggest we can delete the "RIKEN ID" from our final results?

Thanks in advance

 

Re: RIKEN lipids identified

Reply #4
Basically, you should delete these. It can be considered unknowns at this moment.