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LipidXplorer Wiki

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Quick Start

Click on the link above for a quick overview and start to LipidXplorer

News

2019-10-14 New release: LipidXplorer Version 1.2.8

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 available in the official release notes.

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.

2019-02-12 LipidXplorer available as LIFS Web Application

A web-based version of LipidXplorer is available via the LIFS web application portal. Please note that the application is not yet publicly available. If you want to test it, please request access.

2018-03-01 LipidXplorer Wiki now hosted by LIFS

LIFS Portal

As of March 1st, 2018, the LipidXplorer Wiki has been relocated to the LIFS infrastructure.

2016-05-09 New release: LipidXplorer Version 1.2.7

The new version Single file installerLipidXplorer v1.2.7 source code can now be downloaded. It includes some minor bug fixes and some speed improvements for MFQL lipid identification.


LipidXplorer Documentation

MFQL library

Troubleshooting

LXMerge: A tool for merging multiple results

Get LipidXplorer

If you are on Windows you can try the Single file executable for Windows If you are on Linux you can try the Single file executable for Linux

LipidXplorer is published under GPL and available here: [LipidXplorer GitLab@ISAS]. Check out the LipidXplorer installation instructions for help.

Citing LipidXplorer

If you use LipidXplorer, please cite the original LipidXplorer 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

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.

Feature suggestions

LipidXplorer will be further developed all the time. If you have suggestions for useful features, please write to the LipidXplorer mailing list and we will post them here. We also will post a status report on the suggested features: the LipidXplorer wishlist.


Contact

For any questions and suggestions please put them on the [LipidXplorer Google Group]

If you do not want to join google, please write us (mirandaa@mpi-cbg.de or herzog@mpi-cbg.de) an email and I'll add you to the group.

If you want to contribute to the Wiki please write to mirandaa@mpi-cbg.de or herzog@mpi-cbg.de or also to the google group.

Known bugs

Please check out the [LipidXplorer Google Group] to be up-to-date on found bugs.

Bug reports

Please send Bug reports directly to mirandaa@mpi-cbg.de

Example spectra

Example spectra for the LipidXplorer tutorial
All spectra used in the LipidXplorer article
  • Spectra of E.coli and bovine heart acquired on LTQ Orbitrap XL, LTQ Orbitrap Velos and ABI QStar pulsar (in DDA and MPIS mode):File:Spectra article.zip