LIPID MAPSIf you haven't already listened to our latest #podcast with Corinne Spickett discussing Redox Biology and includes an overview of the #EpiLipidNET games then CLICK THE LINK NOW to listen!! www.lipidmaps.org/resources/ed...
sneumannZhixu Ni presenting LipidCXSMILES developed together with @egonw and #epilipidnet and #lipidmaps here at #MetSoc2025 bridging real lipid chemical structures, and the uncertainty because MS gives only so much structural hints.
Egon WillighagenThe second topic brought to our attention is the mzQC, with this preprint: https://biologists.social/@biorxivpreprint/112408135435078047 #epilipidnet
bioRxiv (@[email protected])
Communicating mass spectrometry quality information in mzQC with Python, R, and Java https://www.biorxiv.org/content/10.1101/2024.05.06.592686v1?med=mas
Only the highest level indicates enough evidence on the double bond location and the stereochemistry. That this is a thing is shown by the article which I posted about earlier today: https://social.edu.nl/@egonw/112444260752022998 #epilipidnet
Egon Willighagen (@[email protected])
this article (https://onlinelibrary.wiley.com/doi/10.1002/anie.202318582) corrects the chemical structure of DAT₂ (HT Matt from LIPID MAPS) It cites five articles that had the wrong structure: "This means that a number of studies provides an incorrect structure of mycolipanolic acid and DAT₂. [9, 20, 21, 39]" I annotated these citations with CiTO intentions and created a nanopublication: https://w3id.org/np/RApE4XpLLnxs3HtbYDNt5PvfLr0gaOeWSsc-4wt_iRnwE #epilipidnet
NH reminds us why we do FAIR, for the I and the R. Why? Ideally reusability, but we can settle for now interpretability.
He then talks us through various approaches on how to annotated experimentally measured lipids with identifiers and their certainty.
E.g. the scoring levels reflecting how much evidence have for the structural detail #epilipidnet
jumping to the last #epilipidnet session, another few interesting talks, like the previous session, very practical. There is a lot of great lipids use cases in the clinic heading our way.
I cannot, however, not post about @TheLipidHoff's talk, the last one of the day and whole meeting: "Proposition of a scoring system for data quality assessment in MS-based #lipidomics"
this article (https://onlinelibrary.wiley.com/doi/10.1002/anie.202318582) corrects the chemical structure of DAT₂ (HT Matt from LIPID MAPS)
It cites five articles that had the wrong structure: "This means that a number of studies provides an incorrect structure of mycolipanolic acid and DAT₂. [9, 20, 21, 39]"
I annotated these citations with CiTO intentions and created a nanopublication: https://w3id.org/np/RApE4XpLLnxs3HtbYDNt5PvfLr0gaOeWSsc-4wt_iRnwE #epilipidnet
one main point they bring up is that using [M+Ag]+ a lot of MS properties improve, making metabolites a lot easier to detect, see e.g. https://scholia.toolforge.org/work/Q125934790 #epilipidnet
the third #epilipidnet meeting day has started,with a keynote by Prof. Ingela Lanekoff (#UppsalaUniversitet) focussing on new technologies to measure metabolites. Her @wdscholia page: https://scholia.toolforge.org/author/Q57079194
after the coffee break we continue with the #epilipidnet session on #lipidomics in health and disease (well, we say a lot of that already, but then again, human health does involve a lot of research funding). Here ceramides, like Cer(16:0) though not the class but a specific instance was shown on the slide (basically, wrong identifier; but this only stresses that we rather have some redundant/overlapping info than too little, leaving us to guessing).