LipidXplorer is a software that supports a variety of untargeted shotgun lipidomics experiments and experiments from LC/MS lipidomics. It is designed to support bottom-up and top-down shotgun lipidomics experiments performed on all types of tandem mass spectrometers. Lipid identification does not rely on a database resource of reference or simulated mass spectra.

Please check the release history below for the latest available version of LipidXplorer.

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The current documentation is available in the LipidXplorer Wiki.

Contact and Help Desk

Please use the support contact form.

August 25, 2026

Citing LipidXplorer
If you use this software release in your own work, please cite it with the following DOI:


Please reference LipidXplorer in general by citing the following publications:
Herzog R, Schuhmann K, Schwudke D, Sampaio JL, Bornstein SR, Schroeder M, et al. (2012) LipidXplorer: A Software for Consensual Cross-Platform Lipidomics. PLoS ONE 7(1): e29851. https://doi.org/10.1371/journal.pone.0029851
Herzog R, Schwudke D, Schuhmann K, Sampaio JL, Bornstein SR, Schroeder M, Shevchenko A (2011) A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol. 2011;12(1):R8. https://doi.org/10.1186/gb-2011-12-1-r8

Additionally, if you are using a particular version of LipidXplorer, from version 1.2.8 onwards, each release has a citable DOI for LipidXplorer@Zenodo.

Aims:

For keeping LipidXplorer maintainable and utilize updated programming features as well as libraries the code base was upgraded from Python 2 to Python 3. Official support for Python 2 is no longer available. This version is also meant as bridging element between our legacy workflow for shotgun lipidomics (LipidXplorer 1.5 –> lxPostman) and LipidXplorerNext. We further included features that are aimed to improve user guidance as well as overall performance of Lipidxplorer.

Download:

v1.5 for Windows  v1.5 for Linux  v1.5 for Mac (ARM) v1.5 benchmark data

Installation instructions and Tutorials for LipidXplorer are available here.

Benchmark Data
The samples originated from mice lung tissue. The data consists of data in *.raw and *.mzML format (5 mins positive, 5 mins negative), a batch script to convert data from raw to mzML format using MSConvert, a settings (*.ini) file for LipidXplorer settings, and a standardized MFQLs for both positive and negative ion mode.

March 21, 2025

Citing LipidXplorer
If you use this software release in your own work, please cite it with the following DOI:


Please reference LipidXplorer in general by citing the following publications:
Herzog R, Schuhmann K, Schwudke D, Sampaio JL, Bornstein SR, Schroeder M, et al. (2012) LipidXplorer: A Software for Consensual Cross-Platform Lipidomics. PLoS ONE 7(1): e29851. https://doi.org/10.1371/journal.pone.0029851
Herzog R, Schwudke D, Schuhmann K, Sampaio JL, Bornstein SR, Schroeder M, Shevchenko A (2011) A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol. 2011;12(1):R8. https://doi.org/10.1186/gb-2011-12-1-r8

Additionally, if you are using a particular version of LipidXplorer, from version 1.2.8 onwards, each release has a citable DOI for LipidXplorer@Zenodo.

Aims:

This release fixes a critical issue where the software output falsely prefers m/z candidates with lowest absolute error value instead of lowest relative value. This was not intended and led to incorrect results when the error range would consist of several m/z candidates.

Download:

v1.2.9 for Windows  v1.2.9 benchmark data

Installation instructions and Tutorials for LipidXplorer are available here.

December 11, 2019

Citing LipidXplorer
If you use this software release in your own work, please cite it with the following DOI:


Please reference LipidXplorer in general by citing the following publications:
Herzog R, Schuhmann K, Schwudke D, Sampaio JL, Bornstein SR, Schroeder M, et al. (2012) LipidXplorer: A Software for Consensual Cross-Platform Lipidomics. PLoS ONE 7(1): e29851. https://doi.org/10.1371/journal.pone.0029851
Herzog R, Schwudke D, Schuhmann K, Sampaio JL, Bornstein SR, Schroeder M, Shevchenko A (2011) A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol. 2011;12(1):R8. https://doi.org/10.1186/gb-2011-12-1-r8

Additionally, if you are using a particular version of LipidXplorer, from version 1.2.8 onwards, each release has a citable DOI for LipidXplorer@Zenodo.

Bugfix Release

Fadi Al Machot, Nils Hoffmann, Jacobo Miranda Ackerman and Dominik Schwudke

Aim:

This release fixes issue #25, which prevented users from adding or deleting custom configurations in the import settings dialog. It also adds logging output to the console window concerning the effective time range used for scan filtering.

Download:

v1.2.8.1 for Windows  v1.2.8.1 benchmark data