Tools

Online Tools

• MS Analysis Tools

  Perform searches with precursor ion or product ion peaklists on a variety of lipid classes, where structures are generated by computational methods or are present in the LIPID MAPS structure database. Display various structural properties (exact mass, formula, abbreviation, etc.) for matched ions with links to molecular structures and isotopic distribution profiles where appropriate. Generate in-silico product ion peaklists for glycosphingolipids.
  • General MS precursor ion search on multiple lipid classes
  • Calculate the exact mass (m/z) for a lipid. Display structure and isotopic distribution profile
  • Search the LMSD for lipids with a given mass (m/z) value. Display structure and isotopic distribution profile
  • Referenced Kendrick mass defect analysis for high-resolution MS data
  • Glycerophospholipid MS precursor ion search
  • Predict MS/MS spectrum for a glycerophospholipid (- ion mode)
  • Perform MS/MS data search against a database of glycerophospholipid precursor/product ions (- ion mode)
  • Glycerolipid (Mono/Di/Triacylglycerols) MS precursor ion search
  • Predict MS/MS spectrum for a glycerolipid (+ ion mode)
  • Perform MS/MS data search against a database of glycerolipid precursor/product ions (+ ion mode)
  • Sphingolipid MS precursor ion search
  • Glycosphingolipid MS precursor ion analysis (Search computationally generated glycosphingolipid structures)
  • Glycosphingolipid MS/MS product ion search tool (Match your tandem MS data with computationally generated glycosphingolipid structures)
  • Create in-silico Glycosphingolipid MS/MS peaklist with permethylation options
  • Compare/contrast 2 different in-silico Glycosphingolipid MS/MS peaklists
  • Cardiolipin MS precursor ion search
  • Fatty acid MS precursor ion search (based on structures in the LIPID MAPS database)
  • Fatty acid MS precursor ion search (based on computationally generated structures)
  • Search a database of MS/MS spectra of Eicosanoids for precursor and product ions (neg. ion mode)
  • Cholesteryl ester MS precursor ion search (based on fatty acid structures in the LIPID MAPS database)
  • Cholesteryl ester MS precursor ion search (based on computationally generated structures)
  • Species-specific lipidomes
    • Mycobacterium tuberculosis lipid MS analysis (based on a database of computationally generated ions)



• Structure Drawing Tools

  Draw and save complex lipid structures using either a simple menu-based interface or by entering an abbreviation (where appropriate). Structures are rendered with the Java-based MarvinView applet (ChemAxon) and may be saved in a number of formats.
  • Generate Fatty Acyl Structures
  • Generate Glycerolipid Structures
  • Generate Glycerophospholipid Structures
  • Generate Cardiolipin Structures
  • Generate Sphingolipid Structures
  • Generate Sterol (cholestane, ergostane, campestane and stigmastane) Structures
  • Generate Glycan strucures (attached to either an R group or ceramide)
  • Species-specific lipidomes
    • Generate Mycobacterium tuberculosis strucures

Stand-alone 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 (488) or lipidmapstools.zip (712)
  • View online documentation

  References

  Sud M, Fahy E, Subramaniam S. Template-based combinatorial enumeration of virtual compound libraries for lipids. Journal of Cheminformatics 2012, 4:23. PMID:23006594 doi: [10.1186/1758-2946-4-23]

• LIPID MAPS Mass Spectrometry Combinatorial Expansion Package
  A set of command line PHP scripts to generate tabular datasets contining species name, m/z and molecular formula for some of the main lipid categories. User-defined options include a range of chain-lengths and a choice of poitive and negative ion-types. The generated MS datasets may then be used as databases or references to aid in identification and assignment of ions in mass spectrometry experiments of lipids. The current version supports Glycerolipids (GL), Glycerophospholipids (GP), Cardiolipins (CL) and Sphingolipids (SP).
  
  • Download Mass Spectrometry Combinatorial Expansion package and documentation: Details
• LIPID MAPS Ontology Tools Package
  Command line Perl script to generate ontology data using structure data in SD file(s). The LIPID MAPS ontology script uses Perl modules from MayaChemTools package, an external open source Perl package, to generate ontology data and requires its local installation.
  
  • Download LIPID MAPS Ontology Tools package: lmontologytools.tar.gz (13kb) or lmontologytools.zip (13kb)