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	LIPID Metabolites And Pathways Strategy

About Data Pathways Tools Protocols Home

Site Map

• About

  • Core Laboratories and Bridges
  • Focus Areas
  • Lipid Species Analyzed
  • Research Plan
  • Key Personnel
  • Organization Chart

• Data

  Lipid Classification Scheme

  The LIPID MAPS Lipid Classification Scheme
  is comprised of eight categories containing distinct classes and subclasses of molecules, chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid.
  
  The LIPID MAPS Lipid Classification Scheme with Wikipedia links

  Component ("Parts List") Databases

  • 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 scheme.
  • Proteome Database (LMPD)
    Lipid-associated protein sequences with annotations from UniProt, EntrezGene, ENZYME, GO, KEGG and other public resources. Browse or search by species, lipid class association, and/or keywords.

  Standards

  • Lipid Standards
    These analytical standards include
    • MS/MS value (nominal mass of precursor ion in negative-ion mode), with links to fragmentation spectrum, including structures of principal product ions.
    • Links to Cayman catalog product descriptions for Eicosanoids
    • Literature reference(s) pertaining to identification of fragment structures.

  Experimental Results

  Lipidomics Studies on Macrophages

  • RAW 264.7 cells
    • Kdo2-lipid A Timecourse Experiments
    • Compactin/Kdo2-lipid A Timecourse Experiments
  • Primary Macrophages
    • Thioglycolate-elicited peritoneal Macrophages
      • Foam cell study with wild-type and LDLR(-/-) mice
      • Thioglycolate-elicited Macrophage Timecourse Experiments
      • Compare TGEM and BMDM cell Timecourse Experiments (0,6,24 hrs)
      • Compare TGEM, BMDM and RAW cell Timecourse Experiments for sterols(full timecourse)
    • Bone marrow-derived Macrophages
      • Bone marrow-derived Macrophage Timecourse Experiments

  Gene array data on Macrophages

  • RAW 264.7 cells
    • Kdo2-lipid A Timecourse Experiments
    • Compactin/Kdo2-lipid A Timecourse Experiments
  • Primary Macrophages
    • Thioglycolate-elicited Macrophages
      • Foam cell study with LDLR(-/-) and wild-type mice
      • Thioglycolate-elicited Macrophage Timecourse Experiments
    • Bone marrow-derived Macrophages
      • Bone marrow-derived Macrophage Timecourse Experiments

• Pathways

  Integrated Pathways with heatmap data

  • Kdo2-lipid A Timecourse Experiments
    • Eicosanoids
      • Tabular display Eicosanoids [media]
      • Pathway display Eicosanoids [media]
    • Fatty Acids
      • Tabular display Fatty acids [cells]
      • Pathway displays
        • Omega-3 and omega-6 fatty acids [cells]
        • Omega-9 and other fatty acids [cells]
        • Omega-3 and omega-6 fatty acids [media]
        • Omega-9 and other fatty acids [media]
    • Glycerolipids/Glycerophospholipids
      • Tabular display
      • Pathway display(acyl chains): 32:0 32:1 34:0 34:1 36:0 36:1 38:0 38:1 38:4
    • Sphingolipids
      • Tabular display
      • Pathway display(N-acyl chain): C16 C18 C20 C22 C24 C24:1 C26 C26:1
        All chain lengths
    • Sterol lipids
      • Tabular display
      • Pathway display
  Pathway maps were created using the VANTED application (http://vanted.ipk-gatersleben.de/). For more information on VANTED, please refer to: Björn H. Junker, Christian Klukas and Falk Schreiber (2006): VANTED: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7:109 (http://www.biomedcentral.com/1471-2105/7/109)

• Tools

  Online Tools

  • Mass Spectrometry: Find mass, number of carbons, number of double bonds, abbreviation, MS/MS product ions (neutral loss), formula, and ion based on input criteria, with links to structure and isotopic distribution.
    • Cardiolipins
    • Glycerophospholipids
    • Mono/Di/Triacylglycerols
    • Glycerophospholipid analysis in batch mode
    • Glycerolipid analysis in batch mode
    • Sphingolipid analysis in batch mode
    • Fatty acid analysis in batch mode (based on structures in the LIPID MAPS database)
    • Fatty acid analysis in batch mode (based on computationally generated structures)
    • Cholesteryl ester analysis in batch mode (based on fatty acid structures in the LIPID MAPS database)
    • Cholesteryl ester analysis in batch mode (based on computationally generated structures)
  • Structure Drawing
    • Draw Fatty Acyl Structures
    • Draw Glycerolipid Structures
    • Draw Glycerophospholipid Structures
    • Draw Cardiolipin Structures
    • Draw Sphingolipid Structures
    • Draw Sterol (cholestane) Structures

  Standalone Tools

  • LIPID MAPS Tools Package
    Command line Perl scripts to generate SD files containing structure and ontological data for various lipid categories. The current version supports structure generation for Fatty acyls (FA), Glycerolipids (GL), Glycerophospholipids (GP), Cardiolipins (CL), Sphingolipids (SP) and Sterols (ST). Please see our documentation for specific main and subclasses. FAStrGen.pl | GLStrGen.pl | GPStrGen.pl | CLStrGen.pl | SPStrGen.pl | STStrGen.pl
    
    
    • Download Tools package and documentation: lipidmapstools.tar.gz (361 KB) or lipidmapstools.zip (552 KB)
    • View online documentation
  • LIPID MAPS MS Prediction Tool
    A standalone Windows application for predicting possible molecular species for a given MS ion. This application enables a user to enter the m/z value of an unknown lipid ion and predict the most likely molecular species, based on internally generated lists of side-chains and headgroups typically found in mammalian versions of glycerolipids, glycerophospholipids (including cardiolipins) and sphingolipids. There are separate user intefaces for:glycerolipids, glycerophospholipids, cardiolipins, sphingolipids, fatty acids and cholesteryl esters. There is also a user interface to calculate the exact mass of glycerophospholipid and glycerolipid ions with defined side-chains and headgroups, along with a display of the isotopic distribution profile.
    
    • Download Installer (Lipid_MS_Predict_App_v1.1.msi)
    • Installation requirements: Windows 2000/XP/Vista containing the Microsoft .NET Framework