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README.md


github lipidex

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

LipiDex

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

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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

Prerequisites

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

Java: https://java.com/en/download/
Proteowizard MS/MS file converter: http://proteowizard.sourceforge.net/
Compound Discoverer: https://www.thermofisher.com/order/catalog/product/OPTON-30783
mzMine2: http://mzmine.github.io/

Installing

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.

Citation

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

Hutchins et al., LipiDex: An Integrated Software Package for High-Confidence Lipid Identification, Cell Systems
(2018), https://doi.org/10.1016/j.cels.2018.03.011

Hutchins et al., Mapping Lipid Fragmentation for Tailored Mass Spectral Libraries, Journal of The American Society for Mass Spectrometry
(2019), https://doi.org/10.1007/s13361-018-02125-y

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Lipid identification software for discovery LC-MS/MS

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