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LIFS Tools
From raw files to biological insight: the LIFS tools in four steps. 1 Raw data from the mass spectrometer. 2 Identify and quantify: for shotgun lipidomics, LipidXplorer identifies lipids in mzML files and lxPostman filters and quantifies them; for targeted lipidomics, LipidCreator designs the assay and Skyline processes the vendor files. 3 Explore and enrich: LipidSpace and Lipidome Projector compare and explore the lipid results; MAPtoGO runs GO-term enrichment on lipid features with their abundances, together with features and counts from other omics. 4 Report and share: the Lipidomics Checklist reports the methods used in step 2 and provides the mzTab-M metadata that goes with the results into LipidCompass. Goslin keeps lipid names consistent across all steps; mzTab-M and mzQC are the standard formats, checked by the mzTab Validator. Each LIFS service shows its de.NBI lifecycle phase: lxPostman and LipidCompass are emerging, all others mature.
How the LIFS tools work together, from your mass spectrometer to publication. Every tool also works on its own: start wherever your data is. Select the figure to open it in full size, or download it as PNG or SVG.

Lipidomics Minimal Reporting Checklist

  • tagline: Reports the analytical, identification and quantification methods of a lipidomics study — the basis for mzTab-M metadata, and a PDF for your publication.
  • kind: web
  • platforms: Browser
  • primary_url: https://lipidomicstandards.org/reporting_checklist/
  • primary_label: Start the checklist
  • imports: csv (samples, lipids)
  • doi: https://doi.org/10.1038/s42255-022-00628-3
  • citation: McDonald, J.G., Ejsing, C.S., Kopczynski, D. et al. Introducing the lipidomics minimal reporting checklist. Nature Metabolism 4(9), 1086–1088 (2022).
  • workflow_step: data
  • flow_before: LipidXplorer, lxPostman, LipidCreator, Skyline (methods)
  • flow_after: LipidCompass (mzTab-M metadata)

This virtual reporting checklist summarises key details of all steps of lipidomic workflows, such as how to collect and store samples, extract lipids, perform mass spectrometric analysis, perform data processing, and how to report results (see related commentary). This questionnaire will create a PDF document that may be linked to any study containing lipidomic data. The aim is to give editors and reviewers an easy overview regarding the quality and completeness of lipidomic data, to further harmonise the field, and to improve the quality of lipidomic analyses. When using the reporting checklist, please cite the checklist.

Go to 'Reporting Checklist' server

 

Citing the checklist
Please reference the minimal reporting checklist by citing the following publication:
McDonald, J.G., Ejsing, C.S.,  Kopczynski, D. et al. Introducing the lipidomics minimal reporting checklist Nature Metabolism 4(9), 1086-1088 (2022). https://doi.org/10.1038/s42255-022-00628-3
Kopczynski, D., Ejsing, C.S., McDonald, J.G.et al. The lipidomics reporting checklist a framework for transparency of lipidomic experiments and repurposing resource data Journal of lipid research 65(9), (2024). https://doi.org/10.1016/j.jlr.2024.100621

MAPtoGO - Multiomics Analysis Platform towards Gene Ontology

  • tagline: GO-term enrichment for lipid, metabolite, protein and transcript features, from their abundances or counts.
  • kind: web
  • version: 1.2.5
  • released: 2026-05-20
  • platforms: Browser
  • license: MIT
  • primary_url: https://maptogo.lifs-tools.org
  • primary_label: Open web app
  • repo_url: https://github.com/lifs-tools/maptogo
  • imports: feature lists with abundances or counts (not mzTab-M or lipid tables)
  • workflow_step: cmp
  • flow_before: lxPostman, Skyline (lipid features + abundances), other omics (features + abundances or counts)

MAPtoGO is the first tool designed for GO term enrichment analysis across the three major MS-based omics fields: proteomics, lipidomics, metabolomics, and transcriptomics. It begins with a background list of identified biomolecules and a separate list of (differentially) regulated biomolecules, mapping each entry through proteins involved in metabolic reactions. GO term analysis is conducted using a statistical test that is based on this mapping. Depending on the chosen domain—biological process, molecular function, cellular compartment, physical or chemical properties, or metabolic and signaling pathways—the analysis generates a ranked list of GO terms, each accompanied by a p-value.

Go to 'MAPtoGO' server

LipidXte

The LipidXte web application provides automatic correction for lipid HCD MS/MS spectra from Orbitrap instruments and is dedicated to supporting accurate quantification of molecular lipid species. The application is specifically designed to support easy access to established correction functions with minimum interference requirements.

Kai Schuhmann, HongKee Moon, Henrik Thomas, Jacobo Miranda Ackerman, Michael Groessl, Nicolai Wagner, Markus Kellmann, Ian Henry, André Nadler, and Andrej Shevchenko.
Quantitative Fragmentation Model for Bottom-Up Shotgun Lipidomics.
Analytical Chemistry 2019 91 (18), 12085-12093
DOI: 10.1021/acs.analchem.9b03270

mzTab-M Validator Webapplication

Reference validator for mzTab 2.0-M

mzTab-m 2.0 structure

mzTab 2.0 for metabolomics is a data exchange format for mass-spectrometry-based experimental data from the "omics" and neighboring sciences, focusing on small molecules like metabolites and lipids.

  • It is hierarchically organized, from metadata to summary information to ms features and evidence,
  • captures quantitative and qualitative information about reported molecules for individual ms runs and aggregated across study variables,
  • follows minimum recommended reporting guidelines for omics experiments, and
  • provides structural, logical and semantic (controlled vocabulary terms) validation.

This application provides a web-based validator for mzTab 2.0-M and the prior mzTab version 1.0 (mainly for proteomics) below, and a REST API for programmatic validation against mzTab 2.0-M.

It is based on the jmzTab-M reference implementation.

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Subcategories

LipidXplorer

Goslin

LipidSpace

LipidCompass

lxPostman

Lipidome Projector

LipidCreator

LUX Score

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