LIPID MAPS® Highlights
Selected content from the LIPID MAPS® Consortium, including new and updated tools, data interfaces, tutorials, meeting notices, and more.
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.
LIPID MAPS® Highlights Archive
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.
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.
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