Lipid identification software for discovery LC-MS/MS
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Example Data Updated Jan 18, 2018
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github lipidex

LipiDex: A tool for high-confidence LC-MS/MS lipid identification


LipiDex unifies all stages of LC-MS/MS lipid identification, empowering intelligent data filtering to greatly reduce manual result curation and increase identification confidence


Key Features

  • Create and manage custom in-silico lipid spectral libraries
  • Model complex lipid MS/MS fragmentation using intuitive fragmentation templates
  • Generate high-confidence MS/MS lipid identifications
  • Annotate chromatographic peak tables with lipid identifications
  • Automatically filter peak tables for adduct peaks, in-source fragments, and dimers

Getting Started


Written in Java, LipiDex accepts either .mgf or .mzXML MS/MS files and chromatographic peak tables from either Compound Discoverer or mzMine 2.

Proteowizard MS/MS file converter:
Compound Discoverer:


To install LipiDex, ensure you have installed the most recent version of 64-bit Java and then download LipiDex here

User Guide

Please read the LipiDex Wiki for detailed instructions on the major functions of LipiDex.


If you encounter any issues with this software tool please contact us at


Please cite the following publication if you use LipiDex to analyze your data:

Hutchins et al., LipiDex: An Integrated Software Package for High-Confidence Lipid Identification, Cell Systems