About LipidHunter 2
LipidHunter 2 has significant improvements from the original LipidHunter. Major improvements are listed below:
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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
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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
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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)
How to install LipidHunter 2 from source code
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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
gitto 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.zipfile 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 condaenv{OS}.yml for
condausers and requirements.txt forpipusers.- conda: run
conda env create -f conda_env.ymlyou will get an environment namedenvlipidhunter - pip: activate your virtual environment, then
pip install -r requirements.txt
- conda: run
- 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.testto test on Windows, Linux, and macOS. - Use command
pytestin LipidHunter folder to run all tests. - Optionally, you can test individual unit test in the
testfolder
- LipidHunter 2 is configured to use travis-ci with
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
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For academic and non-commercial use:
GPLv2 License: -
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
- 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).
Further questions?
- Report any issues here: https://github.com/SysMedOs/lipidhunter/issues
Funding
We acknowledge all projects that supports the development of LipidHunter:
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BMBF - Federal Ministry of Education and Research Germany:
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e:Med Systems Medicine Network:
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SysMedOS Project :