November 1, 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:
1) This release addresses a critical issue where the software incorrectly prioritizes m/z candidates with the smallest absolute error value over those with the smallest relative error value, when MFQLs are used negative mode in MS1 only. This was not intended and could led to incorrect results when the error range would consist of several m/z candidates.
2) Inconsistency in the result of the “Batch mode”- across operating system were corrected.
Download:
v1.5.1 for Windows v1.5.1 for Linux v1.5.1 for Mac (ARM) v1.5 benchmark data
Installation instructions and Tutorials for LipidXplorer are available here.
Benchmark Data
Detailed Changelog
Bug fixes
- For MS1-only MFQL queries, the reported precursor is now the one with the lowest relative errppm. Previously it was the one with the lowest signed “errppm” value.
- Results are now consistent across operating systems using the “Batch mode”.
- A new warning message is shown when saving the Dump file from RUN panel if this file is open at the same time.
- The MFQL editor now shows syntax warnings and highlights important terms.
- A query whose precursor is matched by a constraint without a sum composition (no `errppm`) no longer crashes when its results are sorted. Such candidates are now sorted last.
Changed behaviour
- Batch mode: `batch_results_<polarity>.csv` now uses the same layout as normal mode -- one header line, then one `###` block per lipid class -- instead of a flat table.
- Batch mode: The log, the per-sample results folder and the result file are named after the ion mode read from the MFQL files, e.g. `batch_log_negative.txt`, `per_sample_results_negative/`, `batch_results_negative.csv` . A per-sample results folder left by an earlier run with the same ion mode is deleted at the start of a run.
- Batch mode: all MFQL queries of a sample now run together, as in normal mode. An error in any one MFQL now fails the whole sample; previously only that query was skipped.
- mzXML import has been removed. Convert mzXML files to mzML (e.g. with ProteoWizard `msconvert`); selecting mzXML now stops with an error saying so.
New features
- When using Windows, *.mfql files are now associated with LipidXplorer. Double-clicking one, or using "Open with", opens it in the LipidXplorer MFQL editor.
Acknowledgements:
The current maintainers, developers and contributors for LX would like to thank Ronny Herzog – initial author of the software for his continued support.
References:
1. Schuhmann, K., et al., Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics. Anal Chem, 2017. 89(13): p. 7046-7052.
2. Eggers, L.F. and D. Schwudke, Shotgun Lipidomics Approach for Clinical Samples. Methods Mol Biol, 2018. 1730: p. 163-174.
3. Herzog, R., et al., LipidXplorer: a software for consensual cross-platform lipidomics. PLoS One, 2012. 7(1): p. e29851.
4. Herzog, R., et al., A novel informatics concept for high-throughput shotgun lipidomics based on the molecular fragmentation query language. Genome Biol, 2011. 12(1): p. R8.
5. Herzog, R., D. Schwudke, and A. Shevchenko, LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms. Curr Protoc Bioinformatics, 2013. 43: p. 14 12 1-30.
6. Chambers, M.C., et al., A cross-platform toolkit for mass spectrometry and proteomics. Nat Biotechnol, 2012. 30(10): p. 918-20.
