Tools

Online Tools

• Mass Spectrometry: 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.
  • 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
  • Glycerophospholipid MS analysis
  • Glycerolipid (Mono/Di/Triacylglycerols) MS analysis
  • Sphingolipid MS analysis
  • 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 analysis
  • Fatty acid MS analysis (based on structures in the LIPID MAPS database)
  • Fatty acid MS analysis (based on computationally generated structures)
  • Cholesteryl ester MS analysis (based on fatty acid structures in the LIPID MAPS database)
  • Cholesteryl ester MS analysis (based on computationally generated structures)
  • Search a database of MS/MS spectra of Eicosanoids for precursor and product ions (neg. ion mode)
  • Species-specific lipidomes
    • Mycobacterium tuberculosis lipid MS analysis (based on a database of computationally generated ions)
• Structure Drawing: 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 (456k) or lipidmapstools.zip (672k)
  • 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 MS Prediction Tool (Lipid_MS_Predict.zip) View Changelog
  • Installation requirements: Windows 2000/XP/Vista containing the Microsoft .NET Framework (available free at http://www.microsoft.com/net/).
  • Viewing help files: In order to view the help files, you may need to unblock the Compiled HTML Help file, LIPID_HELP.chm. To enable viewing, move LIPID_HELP.chm to your desktop, right click, select properties, press the 'Unblock' button, then 'Apply'.
  • Uninstalling: Since no registry entry is created, the program will not be included in the Windows add/remove program list. Simply delete the 3 files found in Lipid_MS_Predict.zip to remove.
• 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 (16kb) or lmontologytools.zip (16kb)