LipidXplorer 1.2.9

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.

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.

Detailed Changelog

Bug Fixes:

1. The order how m/z candidates in both MS¹ and MS² (MS/MS) has been changed from being sorted by error value (errppm) ascending to being sorted by absolute value. Before, "remove permutations" was activated in the UI, due to the way the software handles permutation comparison (m/z candidates that are mass spectrometric evidence of isomeric structure with the same chemical composition), and the candidate with the lowest errppm was taken after the removal. Now, when looping through candidates, they are sorted correctly, reporting the candidate with the lowest relative errppm. Further technical information on how this bug happened and how it was fixed can be found in the source code (lx/mfql/runtimeExecution.py, lines 3451 ff., within the ‘removePermutations’ function).

2. All links in the help menu (MFQL Tutorial, About, Documentation, etc) have been updated.

3. GUI, ‘Import Settings‘ panel: Abbreviation for Full Width Half Maximum (FWHM) is now displayed correctly.

Concessions:

1. While assignment of chemical sum compositions to m/z was corrected for the regular usage of MFQLs in the ‘Run‘ panel there remains an inconsistence with results of the ‘MS Tools‘ panel function ‘Mass-to-sum-composition‘. For sum composition constraints that are not strict on heteroatom numbers ‘Mass-to-sum-composition‘ might not provide the correct best match with lowest error.

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.