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
• Search LMSD for curated and/or computationally-generated lipids
  Input: mass (m/z) value
  Ouput: LMSD annotations, plus structure and isotopic distribution profile.
• 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
• Use LipidFinder
  Input: High resolution LC/MS datasets that have been pre-aligned using XCMS.
  Output: Datasets which have been optimized to detect lipid-like features by performing contaminant removal, adduct and stack removal, solvent removal, mass reassignment and outlier correction. The workflow includes integrated MS search and statistical analysis tools which may be performed on the filtered datasets.

• Search a computationally-generated database of glycerophospholipid "bulk" masses
  "Bulk" masses where individual chains are undefined (e.g. PC(34:2))
  Input: list of precursor ions and intensities
  Output: possible glycerophospholipid bulk masses and formulae, with isotopic distribution profiles
• Search a computationally-generated database of oxidized glycerophospholipid chain-composition masses
  Input: list of precursor ions with options to filter by intensity threshold, mass tolerance, headgroup, adduct, etc.
  Output: possible oxidized glycerophospholipid chain-composition masses, with various annotations, including predicted product ions.
• Predict MS/MS spectrum and generate a list of commonly occurring product ions for glycerophospholipids (negative ion mode)
  Input: selected ion and headgroups
  Output: commonly occurring product ions, with m/z, description, and structure
• Search database of glycerophospholipid precursor/product ions (negative ion mode)
  Input: tandem MS (MS/MS) peaklist (precursor ion and list of product ions)
  Output: possible glycerophospholipid structures
• Search a computationally-generated database of cardiolipins
  Input: list of precursor ions, with options to filter by mass tolerance, ion type, radyl group
  Output: possible cardiolipin structures

• Search a computationally-generated database of glycerolipid "bulk" masses
  "Bulk" masses where individual chains are undefined (e.g. DG(36:1),TG(54:2))
  Input: list of precursor ions and intensities
  Output: possible glycerolipid bulk structures
• Predict MS/MS spectrum and generate a list of commonly occurring product ions for a glycerolipid (positive ion mode)
  Input: selected ion and headgroups
  Output: commonly occuring product ions
• Search database of glycerolipid precursor/product ions (+ ion mode)
  Input: tandem MS (MS/MS) peaklist (precursor ion and list of product ions)
  Output: possible glycerolipid bulk structures

• Search a computationally-generated database of glycosphingolipids
  Input: list of precursor ions and intensities
• Search (with tandem MS data) a computationally-generated database of glycosylceramides
  Input: tandem MS (MS/MS) peaklist (precursor ion and list of product ions)
• Create in-silico Glycosphingolipid MS/MS peaklist with permethylation options
  Input: glycan sequence, N-acyl chain, sphingoid base, ion type, fragment ions to show
  Output: selected fragment ions
• Compare/contrast 2 different in-silico Glycosphingolipid MS/MS peaklists
  Input: 2 different glycan sequences, N-acyl chain, sphingoid base, ion type, fragment ions to show
  Output: selected fragment ions

• Search for fatty acids in LMSD
  Input: list of precursor ions and intensities, with options to filter by intensity threshold, mass tolerance, ion, etc
  Output: possible cardiolipin structures, with matching LMSD records
• Search computationally-generated database of fatty acids
  Input: list of precursor ions and intensities, with options to filter by intensity threshold, mass tolerance, ion, etc
  Output: possible cardiolipin structures, with matching LMSD records (if any)
• Search LMSD MS/MS spectra of Eicosanoids (negative ion mode)
  Input: precursor and/or product ions
  Ouput: list of precursor and product ions in LMSD, with links to fragmentation spectra for precursor ions, and LMSD records for both precursors and products
• Search cholesteryl ester MS precursor ion search (based on fatty acid structures in LMSD)
  Input: list of precursor ions and intensities, with options to filter by intensity threshold, mass tolerance, ion, etc
  Output: possible cholesteryl esters, with isotopic distributions, plus matching LMSD records (if any)
• Cholesteryl ester MS precursor ion search (based on computationally-generated structures)
  Input: list of precursor ions and intensities, with options to filter by intensity threshold, mass tolerance, ion, etc
  Output: possible cholesteryl esters, with isotopic distributions, plus matching LMSD records (if any)

• Search computationally-generated database of over 2500 Mycobacterium tuberculosis lipids
  Input: list of precursor ions and intensities, with options to filter by intensity threshold, mass tolerance, lipid class/headgroup, and ion
  Output: possible Mycobacterium tuberculosis (Mtb) lipids

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.

• Download LipidFinder

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

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.
• Electrospray Ion Calculator (EIC) — gives m/z for the ions commonly observed in atmospheric pressure ionization mass spectra.
• Greazy — Open-source software for automated phospholipid tandem mass spectrometry identification
• HydroCarbLi — helps to interpret MALDI mass spectra of hydrocarbon mixtures ionized with lithium; calculates possible composition from an ion exact mass
• LIMSA — Finds and integrates peaks in a mass spectrum, matches the peaks with a user-supplied list of expected lipids, corrects for overlap in their isotopic patterns, and quantifies the identified lipid species according to internal standards.
• 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
• LipidMatch — an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data
• LipidMS — Lipid annotation in untargeted liquid chromatography-data independent acquisition-mass spectrometry lipidomics based on fragmentation and intensity rules.
• LipidQA — submit mass spectrometer analysis files and have them analyzed.
• LPPtiger — tool for prediction and identification of oxidized phospholipids
• LIQUID — an-open source software for identifying lipids in LC-MS/MS-based lipidomics data
• 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.
• TriglyAPCI — tool for interpreting atmospheric pressure chemical ionization (APCI) mass spectra of triacylglycerols (TAGs)