About LipidHunter 2

LipidHunter 2 has significant improvements from the original LipidHunter. Major improvements are listed below:

• Special Feature for TG & DG

  • ID based both on FA neutral losses & fragments
  • Accurate ID of isomeric species
  • Correction for all identified FA
  • Correction for the fragment intensity of multiply identified FAs
  • Check for cross-contamination signals e.g. PL fragments

• Other Major Feature Updates

  • Multiprocessing
  • Batch mode
  • 10 times faster processing speed
  • Command line mode
  • KNIME workflow integration
  • Multiple vendor support
  • Improved output style
  • Simplified configuration
  • View run parameters in report

• Currently supported Lipid classes in LipidHunter 2:

Lysophospholipids	Phospholipids	Glycerolipids
Lyso PA (LPA)	Phosphatidic acid (PA)	Triacylglycerol (TG)
[M-H]-	[M-H]-	[M+NH4]+, [M+H]+, [M+Na]+
Lyso PC (LPC)	Phosphatidylcholine (PC)	Diacylglycerol (DG)
[M+HCOO]-, [M+CH3COO]-	[M+HCOO]-, [M+CH3COO]-	[M+NH4]+
Lyso PE (LPE)	Phosphatidylethanolamine (PE)
[M-H]-	[M-H]-
Lyso PG (LPG)	Phosphatidylglycerol (PG)
[M-H]-	[M-H]-
Lyso PI (LPI)	Phosphatidylinositol (PI)
[M-H]-	[M-H]-
Lyso PS (LPS)	Phosphatidylserine (PS)
[M-H]-	[M-H]-

LipidHunter 2 new graphical user interface

This repository contains the source code of LipidHunter.

LipidHunter Windows .exe executable version can be found in release page:

https://github.com/SysMedOs/lipidhunter/releases

Please read the following instructions before you start to run LipidHunter.

Instructions

Windows version

• The binary executable version of LipidHunter 2 is provided for Windows users. (Windows 7, 8, and 10, 64bit system required)

  • .exe and .zip installation file

How to install LipidHunter 2 from source code

• Download the LipidHunter 2 as zip file for your system

  • Please use the source code page in the release page https://github.com/SysMedOs/lipidhunter/releases/
  • Download LipidHunter source Code as .zip. Please notice the date and version of LipidHunter source code.
  • Professional users can use git to clone the whole repository, please make sure that you switched to the correct branch.
  • Only the released version is recommended for real data processing. Other development branches may lead to unknown issues and miss interpretation of the data.

• Rename the downloaded file to LipidHunter.zip

• Unzip LipidHunter.zip file to any folder.

• Downloaded LipidHunter test spectra files: LipidHunter_Test_mzML_File

• Python environment

  • LipidHunter 2 is developed under python 3.7, the current version can still run on python 2.7 (not recommended).
  • The best way is to use virtual environment such as conda
  • The requirements is listed in conda_env_{OS}.yml for conda users and requirements.txt for pip users.
    • conda: run conda env create -f conda_env.yml you will get an environment named envlipidhunter
    • pip: activate your virtual environment, then pip install -r requirements.txt
  • Main dependencies are:
    • Data processing: numpy, pandas, scipy, numba, natsort
    • mzML reader: pymzml
    • Image plot: matplotlib, plotly(required by pymzml)
    • Excel output: openpyxl, xlrd, xlwt
    • Graphic interface: pyside2
  • Test source code installation:
    • LipidHunter 2 is configured to use travis-ci with py.test to test on Windows, Linux, and macOS.
    • Use command pytest in LipidHunter folder to run all tests.
    • Optionally, you can test individual unit test in the test folder

• LipidHunter user guide

mzML File conversion

We recommend to use ProteoWizard version 3.0.19217 64 bit version or above to convert your raw files to mzML. You can find the latest version of ProteoWizard from:

http://proteowizard.sourceforge.net/

If you have difficulties to run your mzML file. Please try to run your analysis again in the LipidHunter_debug.exe and post the error messages to the issue tracker or contact us.

Errors/bugs

In case you experienced any problems with running LipidHunter

please report an issue in the issue tracker or contact us.

License

• LipidHunter is Dual-licensed

  • For academic and non-commercial use: GPLv2 License:

    The GNU General Public License version 2

  • For commercial use: please contact the develop team by email.

• Please cite our publication in an appropriate form.

  • Ni, Zhixu, Georgia Angelidou, Mike Lange, Ralf Hoffmann, and Maria Fedorova. "LipidHunter identifies phospholipids by high-throughput processing of LC-MS and shotgun lipidomics datasets." Analytical Chemistry (2017).
    • DOI: 10.1021/acs.analchem.7b01126

Further questions?

• Report any issues here: https://github.com/SysMedOs/lipidhunter/issues

Funding

We acknowledge all projects that supports the development of LipidHunter:

• BMBF - Federal Ministry of Education and Research Germany:

  https://www.bmbf.de/en/

• e:Med Systems Medicine Network:

  http://www.sys-med.de/en/

• SysMedOS Project :

  https://home.uni-leipzig.de/fedorova/sysmedos/