Tutorials and instructions

Tutorials and lectures on lipids

• Lipid Chemistry and Classification (Powerpoint slides) - An introduction to lipids; the role of lipid chemistry in development of the LIPID MAPS Classification System; introduction to the LIPID MAPS Structure Database (LMSD); introduction to the LIPID MAPS Proteome Database (LMPD); and more.
• Lipid Metabolomics (Powerpoint slides) - Based on lectures presented to medical students in the Cell Biology and Biochemistry course at the School of Medicine, University of California, San Diego.
• Lipid Definition - Definitions of lipids, biological lipids, and an introduction to how lipid chemistry is employed to organize lipids into categories.
• Categories of lipids: Fatty Acyls [FA]  Glycerolipids [GL]  Glycerophospholipids [GP]  Sphingolipids [SP]  Sterol lipids [ST]  Prenol lipids [PR]  Saccharolipids [SL]  Polyketides [PK] - for each of these eight categories of lipids, an introduction and examples of each lipid category, with links to classification, examples of core structures, online drawing tools, and tutorials (MS PowerPoint)
• Biological functions: Membranes  Energy storage  Signaling  Other functions - Introductions to key biological functions of 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.
  •   Command line access of the LIPID MAPS Structure Database (LMSD) - instructions for command line data retrieval as CSV, TSV, and SDF files. Command line parameter options are explained and a number of examples are provided.
  •   How to search LMSD by structure or sub-structure - Instructions and screen shots demonstrating how to use the MarvinSketch Applet to search for lipids by drawing a complete or partial structure, and optionally specifying a partial lipid name.
  •   How to search LMSD by text or ontology. - Instructions and screen shots demonstrating how to use the text/ontology search form to search for lipids by various combinations of lipid annotations, including name, classification, and ontology parameters.
  •   How to search LMSD by text and/or ontology. (2:22) - Screencast demo
• LIPID MAPS Proteome Database (LMPD)
  The LIPID MAPS Proteome Database (LMPD) is an object-relational database of lipid-associated human and mouse protein sequences and annotations.
  •  Introduction to the LIPID MAPS Lipid Proteome Database (LMPD) - Screencast demo (2:58)
• 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 tools package documentation - Both downloadable and online documentation are available along with the LIPID MAPS Tools Package on our Tools page under "Stand-alone tools".
• 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 classification, nomenclature and structure drawing - detailed instructions for describing and drawing your lipid according to LIPID MAPS guidelines
• Web forms for submitting structures to the LIPID MAPS Structure Database (LMSD) - Web based forms allow you to draw a lipid structure; classify, and enter annotations
• How to cite the Lipidomics Gateway - how to cite LIPID MAPS resources, Lipidomics Update articles, and the Lipidomics Gateway as a general resource