pyOpenMS: Jupyter Notebook implementation of UmetaFlow
This is a workflow for untargeted metabolomics data preprocessing and analysis tailored in Jupyter notebooks by Eftychia Eva Kontou and Axel Walter using pyOpenMS which are python bindings to the cpp OpenMS alogithms. The workflow is compatible for Linux, Windows and MacOS operating systems.
Publication DOI: https://doi.org/10.1186/s13321-023-00724-w
The pipeline consists of seven interconnected steps:
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File conversion (optional): Simply add your Thermo raw files in
data/raw/
and they will be converted to centroid mzML files. If you have Agilent or Bruker files, skip that step - convert them independently using proteowizard (see https://proteowizard.sourceforge.io/) and add them to thedata/mzML/
directory. -
Pre-processing: Converting your raw data to a table of metabolic features with a series of algorithms.
-
Re-quantification: Re-quantify all raw files to avoid missing values resulted by the pre-processing workflow for statistical analysis and data exploration (optional step).
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GNPSexport: generate all the files necessary to create a FBMN or IIMN job at GNPS.
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Structural and formula predictions with SIRIUS and CSI:FingerID.
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Annotations: annotate the feature tables with #1 ranked SIRIUS and CSI:FingerID predictions (MSI level 3), spectral matches from a local MGF file (MSI level 2).
-
Data integration: Integrate the #1 ranked SIRIUS and CSI:FingerID predictions to the graphml file from GNPS FBMN for visualization. Optionally, annotate the feature tables with GNPS MSMS library matching annotations (MSI level 2).
Clone this repository to your local system, into the place where you want to perform the data analysis.
(Make sure to have the right access / SSH Key. If not, follow the steps: Step 1: https://docs.github.com/en/github/authenticating-to-github/connecting-to-github-with-ssh/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent
git clone https://github.com/biosustain/pyOpenMS_UmetaFlow.git
Mono, homebrew and wget dependencies:
Install mono with sudo:
sudo apt install mono-devel
Install homebrew and wget:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Press enter (RETURN) to continue
Follow the Next steps instructions to add Linuxbrew to your PATH and to your bash shell profile script, either ~/.profile on Debian/Ubuntu or ~/.bash_profile on CentOS/Fedora/RedHat (https://github.com/Linuxbrew/brew).
test -d ~/.linuxbrew && eval $(~/.linuxbrew/bin/brew shellenv) test -d /home/linuxbrew/.linuxbrew && eval $(/home/linuxbrew/.linuxbrew/bin/brew shellenv) test -r ~/.bash_profile && echo "eval \$($(brew --prefix)/bin/brew shellenv)" >>~/.bash_profile echo "eval \$($(brew --prefix)/bin/brew shellenv)" >>~/.profile
brew install wget
pyOpenMS and other libraries:
Installing pyOpenMS using conda is advised: First, create a conda environment and install the wheels and other dependencies. Then get the latest wheels and install all dependencies:
conda create --name pyopenms python=3.10 conda activate pyopenms pip install --index-url https://pypi.cs.uni-tuebingen.de/simple/ pyopenms-nightly conda install -n pyopenms ipykernel --update-deps --force-reinstall pip install pyteomics pip install --upgrade nbformat pip install matplotlib
For installation details and further documentation, see pyOpenMS documentation.
ThermoRawFileParser
(cd resources/ThermoRawFileParser && wget https://github.com/compomics/ThermoRawFileParser/releases/download/v1.3.4/ThermoRawFileParser.zip && unzip ThermoRawFileParser.zip)
SIRIUS
Download the latest SIRIUS executable. Choose the headless zipped file compatible with your operating system (linux, macOS or windows) and unzip it under the directory
resources/
. Make sure to register using your university email and password.
Specify the operating system
MY_OS="linux64" # or "osx64" for macOS or "win64" for windows
Get the SIRIUS executable
(cd resources && curl -s https://api.github.com/repos/boecker-lab/sirius/releases/latest | tr -d '"' | grep "browser_download_url.*${MY_OS}.zip$"| cut -d : -f 2,3 | wget -i- && unzip *.zip)
(cd data && wget https://zenodo.org/record/6948449/files/Commercial_std_raw.zip?download=1 && unzip *.zip -d raw)
The data can be used for testing the workflow. Otherwise, the user can simply transfer their own data under the directory
data/raw/
ordata/mzML/
.
All the results are in a .TSV format and can be opened simply with excel or using pandas dataframes.
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Kontou, E.E., Walter, A., Alka, O. et al. UmetaFlow: an untargeted metabolomics workflow for high-throughput data processing and analysis. J Cheminform 15, 52 (2023). https://doi.org/10.1186/s13321-023-00724-w
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Pfeuffer J, Sachsenberg T, Alka O, et al. OpenMS – A platform for reproducible analysis of mass spectrometry data. J Biotechnol. 2017;261:142-148. doi:10.1016/j.jbiotec.2017.05.016
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Dührkop K, Fleischauer M, Ludwig M, et al. SIRIUS 4: a rapid tool for turning tandem mass spectra into metabolite structure information. Nat Methods. 2019;16(4):299-302. doi:10.1038/s41592-019-0344-8
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Dührkop K, Shen H, Meusel M, Rousu J, Böcker S. Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci. 2015;112(41):12580-12585. doi:10.1073/pnas.1509788112
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Nothias LF, Petras D, Schmid R, et al. Feature-based molecular networking in the GNPS analysis environment. Nat Methods. 2020;17(9):905-908. doi:10.1038/s41592-020-0933-6
- The current test data are built from known metabolite producer strains or standard samples that have been analysed with a Thermo IDX mass spectrometer. The presence of the metabolites and their fragmentation patterns has been manually confirmed using TOPPView.