LIPID MAPS® Highlights
Selected content from the LIPID MAPS® Consortium, including new and updated tools, data interfaces, tutorials, meeting notices, and more.
LIPID MAPS & WikiPathways Pathway Curation project
25th September 2024
An ELIXIR-funded project to curate lipid pathways, concluded in June 2024 after two and a half years.
The primary objective, of the collaboration between the WikiPathways open science platform and the LIPID MAPS community, was to curate high-quality biochemical knowledge on lipid metabolism by engaging lipid experts worldwide. The project was further enhanced by the EpiLipidNET COST network to curate lipid signalling pathways.
This initiative significantly boosted community interest and ensured the sustained co-curation of high-quality biochemical knowledge on lipid metabolism. A total of 24 pathways were curated/ updated through the project and are now available on both, LIPID MAPS and WikiPathways platforms.
LIPID MAPS® Highlights Archive
ALERT: Downtime of LIPID MAPS Webpage
17th September 2024
There will be essential work taking place on our servers on Tuesday 24th of September. The work will cause intermittent connectivity issues that could last for several hours. During this time LIPID MAPS will temporarily go offline.
We apologise for any inconvenience this causes.
New Isotopic Distribution Tool
5th September 2024
For a long time, you’ve been able to view the isotopic distribution for a molecule in LMSD by clicking on its formula on the relevant page of our main database, LMSD.
We’ve now added an interface where you can input the formula of a molecule of interest and directly see the isotopic distribution, reflecting the probability of the occurrence of different isotopes being incorporated within your molecule.
Find the tool here
Tools Guide Update – General call
22nd July 2024
It have been almost 2 years since the first version of the Lipidomics Tools Guide was published and made available via LIPID MAPS website.
With the constant development of computational solutions for lipidomics data processing, we are planning to update the Guide with new open-access tools and software, which serve the lipidomics community. If you are interested in sharing your tools and software, please fill the form below before September 1st and we will contact you directly.
Remember; Lipidomics Tools Guide aims to support researchers with varying degree of bioinformatics expertise, thus, to be included in the Guide the tool needs to have graphical user interface and have open access for academic users.
Complete the form
LIPID MAPS Network Updates 20th and 21st July
14th July 2024
There will be essential work taking place to the network on Saturday 20th July. The work will begin at 10am BST and will cause intermittent connectivity issues that could last for several hours. During this time LIPID MAPS will temporarily go offline. Please note services should also be considered at risk on Sunday 21st July in case of any issues.
We apologise for any inconvenience this causes, but this work is essential and unavoidable to ensure network performance, security and stability.
Professor Bengt Samuelsson (1934 - 2024)
9th July 2024
We are deeply saddened to learn of the passing of Professor Bengt Samuelsson, Nobel laureate and former president of Karolinska Institute. Professor Samuelsson was co-discoverer of prostaglandins, with Sune Bergström, and a founder of the field of lipid mediators. These hormone-like substances regulate several important processes in the body relevant to health and disease, including development, inflammation, allergies, glaucoma and cardiovascular disease and are the targets of numerous drug therapies.
We send our sincere condolences to his family and all his friends.
Tribute Page
LIPID MAPS Network Updates 20th and 21st July
1st July 2024
There will be essential work taking place to the network on Saturday 20th July. The work will begin at 10am BST and will cause intermittent connectivity issues that could last for several hours. During this time LIPID MAPS will temporarily go offline. Please note services should also be considered at risk on Sunday 21st July in case of any issues.
We apologise for any inconvenience this causes, but this work is essential and unavoidable to ensure network performance, security and stability.
Chirality change for lipids in LMSD
5th June 2024
A recent paper in Angewandte Chemie by the Minnaard group highlighted that the long-established chirality of Mycolipanolic acid was incorrect. Stereoselective chemical synthesis of this mycobacterial cell-wall constituent proved the chirality of the alpha-methyl and beta-hydroxy groups needed to be inverted.
Accordingly, we have revised the structure in LMSD and that of all those molecules containing mycolipanolic acid, around 750 lipids in total.
Check these lipids out on LMSD
Shorthand nomenclature updates
6th May 2024
Recent research strongly suggests that there may be many more bile acid amidates (bile acids conjugated with amino acids) in nature than previously thought. We have updated the shorthand nomenclature to include these as a suffix of; Xxx, where Xxx is the three letter amino acid code. For instance Phenylalanocholic Acid (LMST05050056) is now ST 24:1;O4;Phe.
For consistency, glycine conjugate shorthand now ends; Gly rather than ;G. Similarly, taurine conjugates change from ;T to ;Tau to remove any potential ambiguity.
We have also updated the shorthand for bile acid conjugates, which previously included the leaving oxygen that is displaced to form the amide bond. This has been removed such that only the oxygens present in the bile acid residue are enumerated. For example the shorthand for glycocholic acid (LMST05030001) changes from ST 24:1;O5;G to ST 24:1;O4;Gly.
Steroid structure drawing tool expanded
1st April 2024
We have recently made extensive updates to our structure drawing tool for sterols.
It now enables drawing of over 20 different sterol cores including the steroid hormones, bile acids and plant sterols such as withanolides. You can use this tool to draw sterol structures defining the stereochemistry of substituents and positions of double bonds.
The tool produces an image downloadable as PNG, along with the formula and systematic name.
View this expansion on the Sterol Structure Drawing Page
EpiLipidNET joins the Community forum
4th March 2024
We are thrilled to announce that the EpiLipidNET community are joining the LIPID MAPS forum.
The community forum, will be an informal platform to source and provide information about various aspects of epilipid analysis – from analytical methods to biochemical pathways integration. If you have new suggestions and ideas for new initiatives; you can post these directly on this forum. You can also use the community forum to start informal conversations on any (epi)lipids of your interest, their biological significance, applied methodologies and data analysis strategies, connecting with others in the field.
Join us now on the community forum
View 3D models in LMSD
5th February 2024
You are now able to visualise 3D models of the lipids in LMSD. Once on a specific lipid page, click the ‘view 3D’ button on the bottom left of the lipid structure image. A rotating 3D representation of the molecule will appear. You can fully control the rotation and scaling of the model with your mouse to alter the view point. Remember that these models are a calculated ‘snapshot’ and only one of many possible conformations available to molecules with many rotatable bonds.
View an example here by clicking 'view 3D'
Similarity 'Tanimoto' Search in LMSD
2nd January 2024
We’ve just improved our structure search of LMSD, our main database of lipid structures. Previously, you were able to sketch your molecule in the search (structure) interface and find exact matches, or hits in LMSD where your query is a part of that molecule. Now, you can find hits which are 'similar to' your query using the Tanimoto similarity search, by defining the threshold for that similarity in the 'search-type' drop-down menu and entering Tanimoto/Similarity.
Sketch a molecule here and find other molecules which have similarity to your query
Happy holiday season!
24th December 2023
Everyone here at LIPID MAPS would like to wish you all a
Merry Christmas / Feliz Navidad / Buon Natale / Frohe Weihnachten / / メリー クリスマス / Joyeux Noel / Feliz Natal / Nadolig Llawen / عيد ميلاد مجيد / Wesołych świąt Bożego Narodzenia / 聖誕快樂 / Happy Holidays
and a joyful and healthy New Year!!!
We would also like to thank you for your ongoing support.
LIPID MAPS becomes an ELIXIR Core Resource and Deposition Database
18th December 2023
LIPID MAPS are thrilled to announce that we have been successful in obtaining accreditations from ELIXIR!!
LIPID MAPS has been added to ELIXIR Core Data Resources (CDRs) and has also been awarded the status of an ELIXIR Deposition Database (EDDs). ELIXIR CDRs are European life science data resources that are important to biological and biomedical research and long-term preservation of biological data and ELIXIR EDDs are key European databases recommended for the deposition of experimental data.
Check out ELIXIR Europe’s news release
Accreditation success for LIPID MAPS
11th December 2023
LIPID
MAPS are thrilled to announce that we have been successful in obtaining an accreditation
from Global Biodata Coalition (GBC).
LIPID
MAPS is one of the additional 15 Global Core Biodata Resources (GCBRs) that
join the existing 37, forming an important focus of the GBC’s work with global
life science funders to better understand the challenges and needs for biodata
resource long-term sustainability.
Check out the official Global Biodata announcement
New publication from LIPID MAPS
6th November 2023
Our recent paper in Nucleic Acids Research database issue describes the updates to LIPID MAPS databases, tools and engagement that have taken place over the last few years. It describes the expansion of LMSD with richer metadata including display of reactions, programmatic access and improved FAIR compliance. It also describes other LIPID MAPS databases, tools and the training and engagement we’re doing.
Read the full journal article here
Lipid nomenclature update
2nd October 2023
A word on the use of the "C" prefix in lipid shorthand nomenclature (e.g "C16:0"). Some institutions and companies use it to describe acyl carnitines whereas others use it for fatty acids. This ambiguous nomenclature should be avoided by choosing "CAR" (e.g "CAR 16:0") for acyl carnitines and "FA" (e.g "FA 16:0") for fatty acids. More details on recommendations by the Lipidomics Standards Initiative and International Lipid Classification and Nomenclature Committee are found in the LIPID MAPS nomenclature section.
Read a recent JLR publication on this recommendation
More crosslinks from LMSD pages
4th September 2023
Lipids are substrates, products and inhibitors of enzymes, some are needed to stabilise membrane proteins. They're often found in complex with the 3D structures of proteins in the Protein Data Bank and we've added links from LMSD to our ELIXIR partners, the Protein Data Bank in Europe, where we have a molecule in common across our respective databases.
See an example of one of our crosslinks with PBDe here
LMSD reaches a new milestone
24th July 2023
The LIPID MAPS Structure Database is our flagship database containing fully characterised structures of biologically relevant lipids. Recently, that database reached the milestone of exceeding 48000 unique lipid structures. A paper from the Blanksby Group describing lots of previously unknown fatty acids got us over the line. It's a really exciting time in lipid mass spectrometry with new techniques enabling better characterisation of lipids being developed. These will no doubt keep us busy adding new lipids to LMSD for the foreseeable future.
LMSD overview page
New reactions in BioPAN
3rd July 2023
We have added new reactions to BioPAN to accommodate the cholesterol biosynthesis pathway.
We have also added the ability to analyse datasets containing lipids with molecular species annotation (for example PC 16:0_12:0). for cases where the acyl chain identities are known.
See more details on the BioPAN documentation page
New headgroup in our Structure Drawing tool
8th June 2023
We've recently added the facility to draw Phosphatidyl-L-threonine (PT)
in a standardised form to our structure drawing tool.
PT is closely related structurally and metabolically to phosphatidylserine and is
a minor component of eukaryotic membranes and present in bacterial membranes
too. It is known to be important in the
membranes of the parasite Toxoplasma gondii, which causes toxoplasmosis.
Use the new head group for PT here!
Upcoming events
2nd May 2023
EpiLipidNET - The 4th annual meeting will take place from 10th to 12th of July in Toulouse, France.
Find
more information and register here
EAS - Our very own Dr M. Conroy & Prof. W Griffiths will present at this years Lipotoxicity Course in Prague on the 8th and 9th of June.
Find more information and register here
A new structure drawing tool
5th March 2023
A new glycan drawing & mass calculation tool for glycosylceramides has been created. By inputting an LM_ID of a generic glycosylceramide, a SpingoMap ID present in LMSD or a full glycan name this tool takes a glycosylceramide glycan sequence and generates all possible intermediates, starting from glucosyl-ceramide and also gives the mass of the glycan group present.
Draw and save glycan structures
Query retention time data on Metabolomics Workbench
6th February 2023
A
new tool on Metabolomics Workbench enables searching chromatography metadata to
view retention time information, chromatography conditions, and
instrumentation. It is possible view data for one particular metabolite or compare
data for a pair of metabolites. This information might help confirm the
identity of a compound with reference to other observations of it's
chromatographic behaviour.
Search Retention Time Data
New paper on choosing informatics software and tools for lipidomics
5th January 2023
The many different choices of software and tools for analysing lipidomics data can be confusing or even daunting for a researcher. A recent paper in Nature Methods "Guiding the choice of informatics software and tools for lipidomics research applications" from the LIPID MAPS team and many others provides a guide to navigating through this complex area, and includes our interactive online portal listing open-access tools with a graphical user interface.
Community Forum
11th October 2022
We are delighted to announce the LIPID MAPS community forum.
The community forum is an informal way to provide feedback on the LIPID MAPS databases and resources. Have you suggestions for new initiatives; would you like to ask for advice on how to use the resources; or send through information on items that need updating or correcting?
You can also use the community forum to start informal conversations on lipidomics in general and link up with others to create discussion amongst the community.
You can view online discussions, and/or create your own profile so you can freely post questions or comments.
We look forward to you joining us on the forum and contributing to our lipid conversations!
Community Forum
Look-up tables for shorthand notation
9th August 2022
We have produced easy look-up tables for shorthand notation for lipid mass-spectrometric (MS) data. These will allow you to quickly find the correct shorthand notation for lipid data fitting validated MS-output, depending on the resolution of your experimental data.
The tables are based on
Liebisch et al. J. Lipid Res. 61, 1–17 (2020).
This “fast-track” version presents succinct application rules and
provides examples for hierarchical shorthand notation.
https://www.lipidmaps.org/shorthand_nomenclature
LIPID MAPS SPARQL Endpoint
17th June 2022
The LIPID MAPS SPARQL Endpoint is now available!
You will be able to programmatically query LIPID MAPS and our partners. More information and examples can be found here: https://lipidmaps.org/resources/sparql
We gratefully acknowledge members of the ELIXIR 2021 Hackathon “FAIR lipids” for collaborative working on this project, with specific mention of Maksim Kolchin, Jerven Bolleman (SIB), Denise Slenter (WikiPathways) and Egon Willighagen (WikiPathways).
SPARQL Endpoint
Search Functionality
27th April 2022
We have recently updated the search facility of the LIPID MAPS homepage. We have added auto-complete functionality, so as you type, the search will indicate which areas of the LIPID MAPS databases contain the term you’ve typed, enabling you to get to the result you’re looking for more efficiently.
We’ve also incorporated RefMet into the search, which will standardise many non-standard lipid names prior to the search (eg DAG C36:3 will become DG 36:3), enabling lipids described this way to be found more easily.
New lipid classes added to COMP_DB
15th March 2022
COMP_DB, the LIPID MAPS computationally-generated database of "bulk" lipid species has just been extended to include new classes of betaine lipids which occur in organisms such as algae, bryophytes and fungi.
Whilst LMSD contains fully characterised lipids, COMP_DB species indicate only the number of carbons and double bond equivalents, but not chain positions or double bond regiochemistry and geometry.
In many lipidomics studies, this is the level of characterisation achieved, so expanding COMP_DB to include DGCC, DGTA and DGTS lipid classes will help those working on these to identify potential lipids in their data.
COMP_DB link
NEW: Reactions explorer
9th February 2022
We are developing a reactions explorer to visualise and obtain information on biochemical reactions and metabolic pathways involving lipids.
In the explorer, you can navigate through the complex network of lipid reactions and use the filtering tools to quickly find relevant reactions for your lipid class of interest.
Our
lipid reactions database is linked to the LMSD database so you can now find on
specific lipid pages reactions in which they might take part.
https://lipidmaps.org/resources/tools/reactions
Link to Reactions
Lots more carotenoids in LMSD
20th January 2022
We've added a splash of colour by including a lot more carotenoids in LMSD over the past few months.
Nearly 700 of the molecules curated in http://carotenoiddb.jp/ but previously not part of LMSD are now incorporated.
Most are to be found in the tetraterpene class https://www.lipidmaps.org/lmsd_search/60107
LMSD
New classes of betaine lipids
29th November 2021
Research over the last few years has shown the abundance of diacylglycerols with betaine headgroups in organisms such as seaweeds, algae and fungi. Recognising this, we’ve updated LMSD and added classes of betaine mono- and di-radylglycerols in the glycerolipids category. Existing betaine lipids have been moved into these classes.
Due to the experimental difficulty, the position of acyl chains, and double bonds within them, has yet to be determined for many betaine lipids, so there are doubtless many more to add to LMSD in coming years.
Betaine monoradylglycerols Betaine diradylglycerols
**Job Alert**
2nd November 2021
We have an opportunity to join the LIPID MAPS team, as a
Biocurator.
The
role will provide core support for a new curation
project, building lipid biochemical pathways in LIPID MAPS (http://www.lipidmaps.org) and WikiPathways (https://www.wikipathways.org/index.php/WikiPathways).
This post is funded by ELIXIR, based at Cardiff University and
may support remote working.
For further
information and to apply, please visit https://bit.ly/3GIPKWv
Job Description
'Scalable Curation' project
16th September 2021
We are delighted to announce a successful award in
collaboration with WikiPathways and EpiLipidNet from the ELIXIR Data Platform
Implementation Study call for ‘Scalable Curation’.
This award funds a full time curator to support expert community curation of lipids and pathways/networks for lipidomics. This work will add expert-curated and reviewed pathways to the WikiPathways lipid portal (https://www.wikipathways.org/index.php/Portal:Lipids), and link reactions back to the new LIPID MAPS reaction database. New Pathway curation will enable development of tools for lipidomics systems biology.
This award will start in January 2022.
New look to the LMSD lipid pages
26th May 2021
We’ve added a taxonomy section to indicate which species we curated the lipid from, and the paper describing it. Of course many lipids are ubiquitous, but these data should help inform your study. For instance, in a human lipidomics study, one is unlikely to encounter lipids found in starfish (such as 24-northornasterol A). Populating this information for the lipids we already have is an ongoing task, but as we add new lipids, we’ll definitely show where they have come from.
Updating the LMSD pages enables us to add other exciting features we have planned, so watch this space!
Spring School Recordings are now Live!
10th May 2021
Visit our LIPID MAPS YouTube channel to listen to the whole week of recordings. There are over 40 presentations for you to watch, with 33 speakers who are top-level experts in lipid biology and lipidomics. The presentations include a variety of tools, resources and research.
All of the presentations are clearly displayed so you can choose which themes/topics you would like to watch!
Our YouTube channel hosts our live webinar series, and a vast array of tutorials, including BioPAN. Plus you can listen to our recently launched Podcasts with Bill Christie and Matthew Conroy.
Don’t forget if you subscribe to our YouTube channel you will receive alerts when we upload new recordings!
Go to YouTube
Lipid Calculator
9th April 2021
Lipid Calculator is an iPhone app that can calculate the accurate mono-isotopic molecular weight of tens of thousands lipid molecular species as well as positive and negative molecular ions and several molecular ion adducts.
This application provided by LIPIDMAPS can be used to support lipid biochemists in their lipidomic investigations when electrospray ionization mass spectrometry is employed.
LipidCalc can calculate the accurate mono-isotopic molecular weight of tens of thousands lipid molecular species as well as positive and negative molecular ions and several molecular ion adducts.
View in App Store
12th March 2021
We are looking for experts in lipid biochemistry to help create a new knowledge base.
During the next 6 months LIPID MAPS will be working with WikiPathways to support expert community curation of lipids and pathways/networks for lipidomics. We plan to create new pathways and then integrate these with LIPID MAPS Structure Database (LMSD) to enable development of tools for lipidomics systems biology.
To do this, we need our curation team to work with domain experts in specific lipid pathways so we can capture high quality accurate biochemical information, including reactions, genes, organism/tissue localisation of lipids and their reactions.
Are you working on a lipid metabolic pathway, and are interested to be involved?
Curated information will be tagged with publications and contributors will be credited.
Please get in touch with Valerie O’Donnell: o-donnellvb@cardiff.ac.uk
Lipid Trends has arrived!
9th March 2021
This new Lipid Trends page, highlights novel and exciting articles and research trends, that are of interest to the lipid community.
A curated collection of hot picks from the world of lipid research will be available for you!
Suggestions for articles to be presented on Lipid Trends may submitted here. The committee will review articles and curate the upcoming trends.
Standardizing Reference Nomenclature
30th November 2020
RefMet provides a standardized reference nomenclature for metabolite species (including over 100,000 lipid annotations) identified by analytical chemistry techniques.
The recent Nature Methods publication "RefMet: a reference nomenclature for metabolomics" describes this resource which is available as
an online name-conversion tool on this website.
22nd November 2020
LIPID MAPS is delighted to announce the development of new partnerships from our recent sponsors from both Merck and SCIEX.
Merck have become sponsors of the webinar series, whilst SCIEX are our first sponsors of the Spring School.
We would like to thank both companies for their support and look forward to working with them throughout 2021. The sponsorship enables us to forge partnerships and assists with the sustainability of LIPID MAPS, a community driven free resource.
Find out more
Webinars
Spring School
LIPID MAPS® Job Vacancy
16th November 2020
LIPID MAPS® is looking for a biocurator to co-ordinate and either lead or support, based on level of expertise, on a major curation and tool development project, focused on network and pathway analysis of lipidomics data at lipid, protein and gene level that will be hosted on LIPID MAPS. Part of the role will include linking with other external lipid/pathways/small module databases and participate in collaborative work to generate information for new interoperable resources. This will include updating current content in LIPID MAPS gene and proteome database.
Job Advert
New publications from LIPID MAPS
14th October 2020
How to describe a lipid by name?
Our new paper in
J. Lipid Res. on Classification, Nomenclature and Shorthand Notation for MS-derived lipid structures
details how to describe lipids at all levels of structural annotation, with COMP_DB updated to facilitate Bulk searches for MS data.
Updated LipidFinder 2.0,
software for post processing lipidomics MS data is now available on the
LIPIDMAPS website
and described in
Bioinformatics.
New features include artefact filtering, contaminant removal, FDA, bulk-structure identification and API link with XCMS.
Classification Paper
LipidFinder 2.0
New nomenclature tools
10th June 2020
New tools, aimed at facilitating data sharing and cross-study comparison of lipidomics data sets:
- Convert lipid names to standardized nomenclature
- Displays levels of lipid structural resolution
View the tools
(1955-2020)
6th March 2020
We are devastated to learn of the passing of our Co-PI, mentor and friend Professor Michael Wakelam, Director of the Babraham Institute in Cambridge, UK. Professor Wakelam brought a wealth of experience and dedication to LIPID MAPS and will be greatly missed by all of us.
We send our sincere condolences to his family and all who knew him.
Tribute Page
New tool available on LIPID MAPS®: BioPAN
1st March 2020
BioPan allows you to perform a pathway analysis from a lipidomics dataset. In this analysis, systematic changes in lipid pathways can be explored at different levels: lipid class and lipid species. Those pathways will be highlighted and changes in enzyme activity will also be predicted.
View BioPAN
LIPID MAPS® Webinar Series: Progress in Quantitative Lipidomics
1st February 2020
Phospholipids and Glycerides to be presented by Professor Emeritus Robert "Bob" Murphy
More Information
LIPID MAPS® Webinar Series: Progress in Quantitative Lipidomics
1st January 2020
Phospholipids and Glycerides to be presented by Professor Emeritus Robert "Bob" Murphy
More Information