RTMet: Real-Time Metabolomics using Mass Spectrometry

🏗 [WORK IN PROGRESS] 🏗

⏱ What is RTMet ?

RTMet is a scientific software which aims to facilitate real-time monitoring of metabolites and reaction rates in a bioreactor.

At its core, it is a data pipeline for targeted metabolomics that automatically processes raw data coming from a mass spectrometer, find metabolites, estimate fluxes, and send a feedback command to the bioreactor.

The main goals are:

• Allowing researchers to monitor in real time what is happening in the bioreactor, at the chemical level.
• Better control over the growth of micro-organisms and the bioprocesses at play, by automatically changing the bioreactor parameters.

⭐️ Planned key features

[🔴Todo] [🟠WIP] [🟢Done]

• 🟢 Automatically fetch .raw files produced by the spectrometer,
• 🟢 Upload results to an InfluxDB instance (optional) to allow real-time plotting and easy query of the data,
• 🟠 Process mass spectrometry data to find present metabolites and quantify them,
• 🔴 Estimate extra-cellular and intra-cellular reaction rates and metabolic fluxes,
• 🔴 Send a feedback command to the bioreactor.

📥 Installation

RTMet runs on Unix-like systems including Linux and MacOS. You can find instructions on how to install it in the docs.

📝 Configuration

User configuration is in the rose-suite.conf file at the root of the workflow directory :

[template variables]
# Fraction of max(TIC). Only scans above it will be kept by binneR.
cfg__tic_threshold=0.50
# Tolerance (ppm) for metabolite identification.
cfg__ppm_tol=10
# ...

The compounds_db.csv file in config/ contains metabolites m/z for ions to be matched against. It should also be edited depending on the metabolome you study.

See Configuring the workflow for more info.

🕹 How to use

RTMet uses Cylc as a workflow manager. So launching a run of the workflow (e.g. for a fed-batch run of your bioreactor) is simply launching a run of the bioreactor-workflow with Cylc.

# Validate, install, and run the workflow
cylc vip bioreactor-workflow

It will copy most of the files contained in ~/cylc-src/bioreactor-workflow/ (source directory) to ~/cylc-run/bioreactor-workflow/run1/ (run directory).

You can monitor the workflow using the Cylc GUI (web interface) or TUI (terminal user interface).

# Launch Jupyter Server and open the GUI in your browser
cylc gui bioreactor-workflow

# Or use the TUI
cylc tui bioreactor-workflow

The workflow is awaiting for .raw files. Right now, it simply looks for them in the raws/ folder of the run directory. The raws files you provide should be numbered that way:

yourexperimentname_1.raw
yourexperimentname_2.raw
...
yourexperimentname_14.raw
...

The workflow will automatically detect the files and process them. Results (metabolites, concentrations, etc) are in share/cycle/N/ of the run directory.

For a more detailed guide, see the Tutorial in the docs.

🪲 Bugs and feature requests

If you have an idea on how we could improve RTMet please submit a new issue to our GitHub issue tracker.

📧 Contact

Elliot Fontaine, [email protected]