Whether you are new to lipids or a seasoned researcher, this collection of websites, databases, and software contains an abundance of resources to help you navigate lipid nomenclature and biology, develop laboratory protocols, and report data analyses.

Websites

Cayman Chemical's Lipid Resource Center

This hub is a collection of Cayman's lipid products, services, literature, tools, and other relevant information. The main page provides an overview of lipid standards and links to products of various lipid classes, while separate pages focus on the roles of lipids in biology as well as health and disease. Additional resources (news articles, protocols, wall posters, and publications) can be found on the resources & literature page.

The Murphy Lipid Calculator

This mass spectrometry tool calculates exact mass and abundance by enabling a search via lipid class, types of acyl groups, ESP ion polarity, and m/z. It is maintained by the Department of Pharmacology at the University of Colorado School of Medicine.

Atlas of Inflammation Resolution

This research tool for bioinformatics analyses related to inflammation and inflammation resolutions covers damage- and pathogen-associated molecular patterns (DAMPs and PAMPs), relevant signaling events, protein-protein interactions, and gene regulatory mechanisms underlying acute inflammatory clinical phenotypes. It includes an interactive, searchable representation of events underlying acute inflammation and its resolution that allows for the identification of regulatory motifs, including feedback and feed-forward loops, and serves as a portal to databases such as DrugBank, ChEMBL, UniProt, GenBank, and PubMed. Using a molecular interaction network visualization platform, users are able to map experimental data onto the molecular interaction map and to develop mathematical models for further analysis.

LIPID MAPS^® Lipidomics Gateway

This gateway provides access to lipid nomenclature, relational databases, tools for lipid drawing and calculation of lipid parameters, analysis protocols, standards, tutorials, publications, and other resources, including Bill Christie’s encyclopedia, the LipidWeb. LIPID MAPS^® preserves the largest internationally recognized classification system and public lipid-only structure database in the world.

LION/web | Lipid Ontology

This lipid ontology (LION) enrichment analysis web application is a bioinformatics tool for lipidomics that enables users to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPID MAPS^®, biophysical data, lipid functions, and organelle associations.

Lipid Mining and Ontology (Lipid Mini-On)

This open-source tool performs lipid enrichment analyses and visualizations of lipidomics data through a text-mining process to cluster individual lipid names into multiple lipid ontology groups based on the classification (e.g., LIPID MAPS^®) and other characteristics, such as chain length. Lipid Mini-On provides users with the capability to conduct enrichment analysis of the lipid ontology terms using a Shiny app with options of five statistical approaches.

Lipidomics Standards Initiative

This website offers guidelines for the major lipidomic workflows including sample collection and storage as well as data deconvolution and reporting. This represents a community-wide effort, covering methodological progress based on the input of researchers in the field.

International Lipidomics Society (ILS)

This non-profit organization promotes lipidomics by fostering the development of new technologies, techniques, resources, skills, and training. It serves as a point of contact for lipidomics research, development, and commercialization activities worldwide by gathering leading international laboratories from a wide range of disciplines to help organize meetings, workshops, funding, and training courses and to support large-scale inter-lab lipidomics projects.

SphinGOMAP^©

This is an evolving pathway map for sphingolipid biosynthesis that includes many of the known sphingolipids and glycosphingolipids arranged according to their biosynthetic origin(s). Representing ~450 compounds, SphinGOMAP^© was created with support from the LIPID MAPS^® Consortium, the Smithgall Institute Chair in Molecular Cell Biology and the Petit Institute for Bioengineering & Bioscience at Georgia Tech, and the NCRR Integrated Technology Resource for Biomedical Glycomics at the University of Georgia. This site also provides a general introduction to the sphingolipid structure, function, metabolism and tools to study sphingolipids.

Serhan Lab Protocols

The Serhan lab website offers detailed protocols for the detection of specialized pro-resolving mediators and their biosynthesis pathway markers as well as an annotated guide to bioactive lipid metabolome. Protocols for sample collection and preparation, lipid mediator metabolomics, lipoxin and aspirin-triggered 15-epi lipoxin-related methods, inflammation resolution proteomics, and targeted LC-MS/MS analyses are provided.

Journal of Lipid Research Methods Papers

Browse the methods papers published by the Journal of Lipid Research to embark on or improve a specific protocol in your lab.

ASBMB Lipid Corner

This website represents the Lipid Research Division of the American Society for Biochemistry and Molecular Biology. Its purpose is to increase national and international visibility for lipid research and increase funding for lipid research. This website supports the lipid community by highlighting research, offering a forum for ongoing discussions, spotlighting members, and maintaining a job board.

The Lipid Web

This website introduces the chemistry and biochemistry of individual lipid classes, along with a compendium of information on mass spectrometry of fatty acids. It also includes a survey of peer-reviewed literature that is updated monthly and a personal blog called Lipid Matters that aims to explain the importance of naturally occurring lipids to a broad scientific readership, especially young scientists.

Cyberlipid Center

This site from a non-profit scientific organization features an encyclopedia and annotated bibliography devoted to the study of all aspects of lipidology. The site seeks to establish contacts between students, teachers, scientists, and technicians, and to represent various models in the field of lipids, including forgotten studies of the past, work in progress, and hot research topics.

The Probes & Drugs Portal

This portal is a public resource joining together focused libraries of bioactive compounds (e.g., probes, drugs, specific inhibitor sets, etc.) with commercially available screening libraries. The purpose of the portal is to reflect the current state of bioactive compound space and to enable its exploration from different points of view.

Databases

mzCloud

This extensively curated mass spectral database of high-resolution tandem mass spectra is arranged into spectral trees. Besides the experimental and processed data, each database record contains the compound name with synonyms, the chemical structure, computationally and manually annotated fragments (peaks), identified adducts and multiply charged ions, molecular formulas, predicted precursor structures, detailed experimental information, peak accuracies, mass resolution, InChI, InChIKey, and other identifiers. It is a fully searchable library that allows spectra searches, tree searches, structure and substructure searches, monoisotopic mass searches, peak (m/z) searches, precursor searches, and name searches.

METLIN

This MS/MS database has multiple searching capabilities including single, batch, precursor ion, neutral loss, accurate mass, and fragment searches. It was generated at multiple collision energies and in positive and negative ionization modes using multiple instrument types including SCIEX, Agilent, Bruker, and Waters QTOF mass spectrometers. The database includes over a million molecules ranging from lipids, steroids, plant and bacteria metabolites, small peptides, carbohydrates, exogenous drugs/metabolites, central carbon metabolites, and toxicants. The metabolites and other small molecules have been individually analyzed to provide both empirical and in silico MS/MS data.

Software

LipidHunter

This software for de novo identification of native phospholipids can perform bottom-up identification of native phospholipids from LC-MS/MS and shotgun lipidomics data by resembling a workflow of manual spectra annotation. The software generates output in an interactive HTML format with a unique six-panel-image feature, which provides an easy way to review, store, and share the identification results.

LipidSearch™

This software from Thermo Scientific™ processes LC-MS data, including the high-resolution accurate-mass data generated by Thermo Scientific™ Orbitrap™-based mass spectrometers, to provide accurate lipid identification. It automatically integrates complex data into reports and reduces data analysis time.

Lipostar

This software from Molecular Discovery was developed to assist LC/MS-based lipidomics from direct import of raw data files to lipid identification, statistical analysis, and report generation. It can be applied either in untargeted, semi-targeted, or targeted lipidomics, and dedicated workflows have also been developed to assist flux analysis when stable isotope labeling experiments are performed. During a Lipostar session, the user can also combine different modes of lipidomics analysis to increase the knowledge and obtain a more comprehensive analysis of lipid profiles. Key features include automatic lipid identification (with or without the use of a lipid fragment database) and an ultimate module for statistical analysis, designed to be user-friendly for beginners as well as exhaustive for advanced users.

LPPtiger

This software for prediction and identification of oxidized phospholipids is pioneering the field of high-throughput identification with its unique ability to perform in silico oxidation and theoretical CID fragmentation. The software can predict oxidized lipids from a given lipidome and identify corresponding predicted structures. A five-criteria score system evaluates the identification quality to provide confident identification results.

LipidCircos

This software for visualization of identified phospholipids can generate Circos plots based on identified unmodified and corresponding oxidized phospholipids. The Circos plot can visualize the relationships between unmodified phospholipids and their oxidation products, making it an informative resource to investigate phospholipid remodeling under experimental conditions.

Progenesis QI

This software enables accurate quantification and identification of compounds in samples that are significantly changing. With support for all common vendor data formats and an intuitive menu-guided workflow, the software helps to overcome data analysis challenges, enabling rapid, objective, and reliable discovery of compounds of interest. One of the key features is its highly graphical data displays, which allow you to fully visualize and understand your data.

Seminal References

Suggested reading from the thought leaders of the lipid research community:

Buczynski, M.W., Dumlao, D.S., and Dennis, E.A. An integrated omics analysis of eicosanoid biology. J. Lipid Res.50(6), 1015-1038 (2009). [PMID: 19244215]

FitzGerald, G.A., Pedersen, A.K., and Patrono, C. Analysis of prostacyclin and thromboxane biosynthesis in cardiovascular disease. Circulation 67(6), 1174-1177 (1983). [PMID: 6342834]

Hammarström, S., Murphy, R.C., and Samuelsson, B., et al. Structure of leukotriene C identification of the amino acid part. Biochem. Biophys. Res. Commun. 91(4), 1266-1272 (1979). [PMID: 43155]

Hla, T. and Neilson, K. Human cyclooxygenase-2 cDNA. Proc. Natl. Acad. Sci. USA. 89(16), 7384-7388 (1992). [PMID: 1380156]

Kurumbail, R.G., Stevens, A.M., Gierse, J.K., et al. Structural basis for selective inhibition of cyclooxygenase-2 by anti-inflammatory agents. Nature 384(6610), 644-648 (1996). [PMID: 8967954]

Morrow, J.D. and Roberts, L.J.,II. Mass spectrometric quantification of F₂-isoprostanes in biological fluids and tissues as measure of oxidant stress. Methods Enzymol. 300, 3-12 (1999). [PMID: 9919502]

Murphy, R.C. and FitzGerald, G.A. Current approaches to estimation of eicosanoid formation in vivo. Adv. Prostaglandin Thromboxane Leukot. Res. 22, 341-348 (1994). [PMID: 7771348]

Murphy, R.C., Hammarström, S., and Samuelsson, B. Leukotriene C: A slow-reacting substance from murine mastocytoma cells. Proc. Natl. Acad. Sci. USA. 76(9), 4275-4279 (1979). [PMID: 41240]

Oates, J.A., FitzGerald, G.A., Branch, R.A., et al. Clinical implications of prostaglandin and thromboxane A₂ formation. N. Engl. J. Med. 319(11), 689-698 (1988). [PMID: 3045550]

Patrono, C., Ciabattoni, G., Pugliese, F., et al. Estimated rate of thromboxane secretion into the circulation of normal humans. J. Clin. Invest. 77(2), 590-594 (1986). [PMID: 3944270]

Picot, D., Loll, P.J., and Garavito, R.M. The X-ray crystal structure of the membrane protein prostaglandin H₂ synthase-1. Nature 367, 243-249 (1994). [PMID: 8121489]

Song, W-L., Stubbe, J., Ricciotti, E., et al. Niacin and biosynthesis of PGD₂ by platelet COX-1 in mice and humans. J. Clin. Invest. 122(4), 1459-1468 (2012). [PMID: 22406532]

Welsh, T.N., Hubbard, S., Mitchell, C.M., et al. Optimization of a solid phase extraction procedure for prostaglandin E₂, F_2α and their tissue metabolites. Prostaglandins Other Lipid Mediat. 83(4), 304-310 (2007). [PMID: 17499750 ]

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