LipidXplorer 1.2.8.1 for Windows  LipidXplorer 1.2.8.x benchmark data

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.

LipidXplorer Release History

Contact and Help Desk

Please use the support contact form.

Documentation

The current documentation is available in the LipidXplorer Wiki.

Release Note: LipidXplorer 1.2.9

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.

Release Note: LipidXplorer 1.2.9, March 21, 2025

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:

LipidXplorer for Windows  LipidXplorer benchmark data

Installation instructions and Tutorials for LipidXplorer are available here.

Release Note: LipidXplorer 1.2.8.1

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.

Release Note: LipidXplorer 1.2.8.1, December 11th^th, 2019

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:

LipidXplorer for Windows  LipidXplorer benchmark data

Installation instructions and Tutorials for LipidXplorer are available here.

Further information can be found in the notes on Release of LipidXplorer 1.2.8.

Release Note: LipidXplorer 1.2.8

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 publication:
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.

Release Note: LipidXplorer 1.2.8, October 14^th, 2019

Improved Import Performance and Implementation of Frequency Filtering

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

Aim:

This release is focused on improving the import module and implementing the recently introduced filtering approach based on counting reoccurrences of peaks in MS-scans and MS/MS-scans conceptually following Schuhmann et al. [1]. All other general functionalities of the former releases should not be affected [2-5]. Further changes were made for better documentation and simpler user guidance. Some experimental and/or unused options were deactivated (grouping samples, heuristic hierarchical alignment, dta/csv import). Details are listed below.

Usage:

The frequency based filtering is active for the *.mzXML and *.mzML import module. For this release we have tested both *.mzXML and *.mzML files after conversion with msConvert of *.raw files of a Q Exactive instrument (Thermo Fisher Scientific, Bremen, Germany)[6]. The LipidXplorer (LX) software and also this improved import module were developed for shotgun lipidomics experiments.

Please see the full release notes document for further details on the evaluation.

Download:

LipidXplorer for Windows  LipidXplorer benchmark data

Installation instructions and Tutorials for LipidXplorer are available here.