Tutorials and instructions

Introduction to lipids

Lipidomics methods

  • Overview of Quantitative Lipid Analysis by Mass Spectrometry (png) (PDF) - Flow chart outlining the procedure for lipid analysis of various lipid classes, from extraction to laboratory analysis to bioinformatics.
  • Chemical Reviews 111 (2011), Special issue: Lipid Biochemistry Metabolism and Signaling Edited by H. Alex Brown and Lawrence J. Marnett
  • BBA - Molecular and Cellular Biology of Lipids 1811 (2011), Special issue: Lipidomics and Imaging Mass Spectrometry Edited by Alfred H. Merrill and Robert C. Murphy
  • Methods in Enzymology, Academic Press 432 (2007), LIPID MAPS chapters - (PDF). For the complete Methods in Enzymology volumes, including LIPID MAPS chapters in Volumes 432, 433, and 434, please see http://www.sciencedirect.com/science/bookseries/00766879. References to individual chapters from these volumes can also be found on our LIPID MAPS Publications: 2007 page.
    • Qualitative Analysis and Quantitative Assessment of Changes in Neutral Glycerol Lipid Molecular Species Within Cells
    • Glycerophospholipid Identification and Qualitation by Electrospray Ionization Mass Spectrometry
    • Detection and Quantitation of Eicosanoids via High Performance Liquid Chromotography-Electrospray Ionization-Mass Spectrometry
    • Structure-Specific, Quantitative Methods for Analysis of Sphingolipids by Liquid Chromotography-Tandem Mass Spectrometry: "Inside-Out" Sphingolipidomics
    • Analysis of Ubiquinones, Dolichols, and Dolichol Diphosphate-Oligosaccharides by Liquid Chromatography-Electrospray Ionization-Mass Spectrometry
    • Extraction and Analysis of Sterols in Biological Matrices by High Performance Liquid Chromatography Electrospray Ionization Mass Spectrometry
    • The Lipid Maps Initiative in Lipidomics
    • Bioinformatics for Lipidomics
    • Quantitation and Standardization of Lipid Internal Standards for Mass Spectrometry
  • Lipidomics workshop at EB2009 - (PDFs) The LIPID MAPS Consortium presented a workshop on lipidomics techniques at EB2009 under the auspices of the ASBMB. The slides from each of these presentations contain references to most of the methodoligies described .

LIPID MAPS® databases

  • LIPID MAPS Structure Database (LMSD)
    The LIPID MAPS Structure Database (LMSD) is comprised of structures and annotations of biologically relevant lipids, and includes representative examples from each category of the LIPID MAPS Lipid Classification system.
  • LIPID MAPS Proteome Database (LMPD)
    The LIPID MAPS Proteome Database (LMPD) is an object-relational database of lipid-associated genes and proteins. It contains data for over 8,500 genes and over 12,000 proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio.
  • Lipidomics Gateway "Quick search"
    The Quick search can be used to search the entire Lipidomics Gateway, including all text and database entries.
    • Quick Search Tutorial - Instructions and examples demonstrating how to search by lipid class, name, synonym, abbreviation or lipid-related gene/protein name; lipid abbreviation; SwissProt ID; gene symbol or annotation; chemical formula; lipid mass; LIPID MAPS ID; or InChIKey.

Bioinformatics tools

  • LIPID MAPS MS Prediction Tool
    The LIPID MAPS MS Prediction Tool is a standalone Windows application for predicting possible molecular species for a given MS ion.
    • MS Prediction Tutorial - examples of how to use the tool to predict possible glycerophospholipid structure. A help interface is also included in the application.
  • LIPID MAPS tools package
    The LIPID MAPS tools package is a set of command line Perl scripts to generate SD files containing structure and ontological data for various lipid categories
  • LIPID MAPS Pathway Editor
    The LIPID MAPS Pathway Editor is a program for managing, visualizing, and editing signaling and metabolic pathways.
    • Pathway Editor tutorial - an overview of Pathway Editor features, including how to start the Pathway Editor, access LIPID MAPS pathways and display LIPID MAPS and user-provided experimental data, create pathways from scratch, and edit and save pathway files and images. Instructions for working with SBML and BioPAX formats are also provided.

Author recommendations and tools

LIPID MAPS® outreach

External collaborations

  • Lipid Structures Application at ScienceDirect - identifies lipids in online articles and provides links to LIPID MAPS annotations.
  • LIPID MAPS lipid pathways at NCBI Biosystems - constructed based on LIPID MAPS experimental data and information extracted from scientific literature.
  • LIPID MAPS lipid structures at PubChem - LIPID MAPS regularly deposits structure in PubChem, where they are assigned a PubChem ID.

LIPID MAPS Presentations

As part of our outreach effort, members of the LIPID MAPS Consortium provide workshops, demonstrations, discussion sessions, and poster presentations at relevant conferences. If you would like to inquire about arranging for LIPID MAPS participation in your upcoming event, please contact us.

logo LIPID MAPS® is funded by a grant from the Wellcome Trust.