Tools

• Calculate exact mass (m/z) for various lipid classes (and adducts)
  Input: lipid class, functional groups and ion adduct;
  Output: structure, formula, isotopic distribution profile, exact mass (m/z)
• Search a computationally-generated database of lipid classes or the LIPID MAPS® structure database (LMSD)
  Input: list of precursor ions, with options to filter by mass tolerance, ion type, lipid class or category, etc
  Output: list of matching masses
• Calculate referenced Kendrick mass defect analysis for high-resolution MS data.
  Input: ion type, class/headgroup/base; OR molecular formula
  Output: precursor ion peaklist that can be used to screen the selected lipid class

BioPAN

BioPAN perform a pathway analysis from lipidomics dataset. In this analysis, it is possible to explore systematic changes in lipid pathways at different levels: lipid subclass and lipid molecular species. Those pathways will be highlighted and changes in gene activity will also be predicted.

• Use BioPAN online
• View the documentation
• Watch the tutorial video

Reference: Using lipidomics analysis to determine signalling and metabolic changes in cells Current Opinion in Biotechnology 2017
DOI: 10.1016/j.copbio.2016.10.003

LipidFinder

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.

• Use LipidFinder online
• Download LipidFinder

References:

• LipidFinder on LIPID MAPS: peak filtering, MS searching and statistical analysis for lipidomics. Bioinformatics 2019.
  DOI: 10.1093/bioinformatics/bty679
• LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications. Bioinformatics 2020.
  DOI: 10.1093/bioinformatics/btaa856



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.

FAStrGen.pl | GLStrGen.pl | GPStrGen.pl | CLStrGen.pl | SPStrGen.pl | STStrGen.pl
• Download Tools package and documentation: lipidmapstools.tar.gz (496) or lipidmapstools.zip (704)
• View online documentation

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).

• Download LIPID MAPS® Ontology Tools package: lmontologytools.tar.gz (13kb) or lmontologytools.zip (13kb)



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

• ALEX¹²³ lipid calculator — An online lipid calculator with m/z values of intact lipid molecules (MS1) and their fragment ions at the MS2 and MS3 level.
• Greazy — Open-source software for automated phospholipid tandem mass spectrometry identification
• LION/web — bioinformatics tool for lipidomics that enables users to search for enriched LION-terms in lipidomic subsets. LION-terms contain detailed lipid classification by LIPIDMAPS, biophysical data, lipid functions and organelle associations.
• LIPEA — works with compound IDs for lipids found in the Kyoto Encyclopedia of Genes and Genomes (KEGG) Database and finds significantly perturbed pathways, applying statistical tests
• LipidBlast — in silico tandem mass spectrometry database for lipid identification
• LipidCircos — tool for visualization of identified phospholipids via Circos plot
• Lipidcreator — A new Skyline plugin for targeted LC-MS/MS-based lipidomics
• LipiDex — unifies all stages of LC-MS/MS lipid identification, empowering intelligent data filtering to greatly reduce manual result curation and increase identification confidence
• LipidIMMS Analyzer — integrates multi-dimensional information including m/z, retention time (RT), collision cross-section (CCS) and MS/MS spectra for lipid identification from ion mobility mass spectrometry
• LipidXplorer — for Data Dependent Acquisition (DDA) using the Molecular Fragmentation Query Language (MFQL) in shotgun lipidomics
• Lipid Calculator — draw and search lipid structures
• Lipid Data Analyzer (LDA) — software for identifying novel lipid molecular species from mass spectrometry data
• LipidHunter — tool for de novo identification of native phospholipids
• LipidMS — Lipid annotation in untargeted liquid chromatography-data independent acquisition-mass spectrometry lipidomics based on fragmentation and intensity rules.
• LPPtiger — tool for prediction and identification of oxidized phospholipids
• LIQUID — an-open source software for identifying lipids in LC-MS/MS-based lipidomics data
• MS-DIAL — software package for data-independent acquisition (DIA)-based identification and quantification of small molecules by mass spectral deconvolution for untargeted LC-MS/MS and GC-MS data, with graphical user interface. Reference: Tsugawa H et al. Nat Methods 2015; Tsugawa et al. Nat Methods 2019. DOI: 10.1038/nmeth.3393
• massPix — an R package for processesing high resolution mass spectrometry imaging data; performs multivariate statistics (PCA, clustering) and lipid identification
• Mass Spectrometry based Lipid(ome) Analyzer and Molecular Platform (MS-LAMP)MS-LAMP — standalone software capable of aiding in interpreting electrospray ionization (ESI) and/or matrix assisted laser desorption and ionization (MALDI) mass spectrometric data of lipids.
• Skyline — open source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM - Targeted MS/MS), Data Independent Acquisition (DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data.