MS Analysis Tools

LIPID MAPS Online 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 (LMSD). 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.

Multiple Lipid Classes




Fatty Acids

Species-specific lipidomes


LipidFinder is an open-source Python workflow for discovery of lipids. LipidFinder quickly distinguishes and quantifies lipid-like features from contaminants, adducts and noise in high resolution liquid chromatography/mass spectrometry (LC/MS) datasets that have been pre-aligned using SIEVE (ThermoFisher) or XCMS. An algorithm is included that optimizes analysis based on users' own data, and outputs are screened against online databases and categorized into LIPID MAPS classes. LipidFinder software and userguides are available on GitHub (

Reference: LipidFinder: A computational workflow for discovery of lipids identifies eicosanoid-phosphoinositides in platelets JCI Insight 2017;2(7):e91634. doi: 10.1172/jci.insight.91634

External Lipidomics tools and online resources

  • LipidBlast: in silico tandem mass spectrometry database for lipid identification
  • Lipid Data Analyzer: software for identifying novel lipid molecular species from mass spectrometry data
  • LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data
  • LipidHunter: tool for de novo identification of native phospholipids
  • LPPtiger: tool for prediction and identification of oxidized phospholipids
  • LipidCircos: tool for visualization of identified phospholipids via Circos plot

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 Javascript / Ketcher and may be saved in a number of formats.

Generate structures for:

LIPID MAPS Stand-alone Tools

LIPID MAPS Mass Spectrometry Combinatorial Expansion Package

The LIPID MAPS Mass Spectrometry Combinatorial Expansion Package includes 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 Tools Package

The LIPID MAPS Tools Package uses 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. | | | | |

Reference: 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 Ontology Tools Package

The LIPID MAPS Ontology Tools Package is a 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.

logo LIPID MAPS is funded by a Wellcome Trust.