Tools

Mass Spectrometry Analysis Tools

  • Perform searches with precursor ion or product ion peaklists on a variety of lipid classes, where masses are generated by computational methods or are present in the LIPID MAPS® Structure Database (LMSD)
  • Search for discrete structures or search for "bulk" structures, with links to examples of discrete structures. Calculate exact mass of lipid ions or predict MS/MS spectra
  • 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 several lipid classes.

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 as molfiles.

Generate structures for:

Statistical Analysis Tools for User-Uploaded Data

Load your own table of processed data grouped by experimental conditions and perform online statistical analyses.
Analysis options include:
  • Normalization and scaling
  • Bargraphs and Boxplots
  • Univariate Analysis (Volcano plots and ANOVA analysis)
  • Class enrichment analysis via RefMet and Volcano plots
  • Clustering and Correlation
  • Multivariate Analysis (PCA, LDA analysis)
  • Classification/Feature Analysis (Random-Forest, OPLS-DA/VIP analysis)

Perform data analysis on user-uploaded data.

Nomenclature Tools

Facilitate sharing of lipidomics data and comparison of data across studies:
  • Convert lipid names to standardized nomenclature.
  • Displays levels of lipid structural resolution (useful for finding common denominators across studies in which levels of lipid resolution vary).

Convert lipid names to LIPID MAPS® standardized nomenclature

Input: list of lipid names
Output: input name; standardized name; formula; exact mass.

Standardizing to LIPID MAPS® nomenclature is recommended for both discrete lipid structures and lipid species identified by mass spectroscopic techniques — an essential prerequisite for the ability to compare and contrast data across different experiments and studies.

Example
Input Output
4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoic acid->DHA
Cervonic acid->DHA
Docosahexaenoic acid->DHA
C22:6n-3,6,9,12,15,18->DHA
DHA->DHA

This tool uses RefMet (Fahy & Subramaniam Nat. Methods 2020)

Convert lipid names to species level only

LipidLynxX provides the possibility to convert, cross-match, and link various lipid annotations to the tools supporting lipid ontology, pathway, and network analysis aiming systems-wide integration and functional annotation of lipidome dynamics in health and disease.

Useful links:

Lipidomics Analysis Software

Download software developed by the LIPID MAPS® Consortium or link to resources offered on external websites.

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.

References:

  • BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS F1000Research 2021
    DOI: 10.12688/f1000research.28022.1
  • 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.

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 Calculator

Lipid Calculator is an iPhone app can calculate the accurate mono-isotopic molecular weight of tens of thousands lipid molecular species as well as positive and negative molecular ions and several molecular ion adducts.


Lipid Calculator

Lipid Calculator is an iPhone app can calculate the accurate mono-isotopic molecular weight of tens of thousands lipid molecular species as well as positive and negative molecular ions and several molecular ion adducts.


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

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).


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.