IODA Mass Spec

This repository offers a collection of notebooks and scripts to run Iterative Optimised Data Acquisition (IODA), including MS2Planner - (See article, Zuo, Cao, Nothias, Mohimani, Bioinformatics, Volume 37, Issue Supplement_1, July 2021, Pages i231–i236) and see GitHub repository.

A. Generation custom exclusion list for IODA on Orbitrap MS

1. Feature detection and alignemnent from mzML/RAW files with pyOpenMS.
2. Create an exclusion list for the Exactive/Fusion serie MS or Exploris/Trihybrid serie MS.
3. Run the IODA experiments on the mass spectrometer.

B. Generate a targeted list for targeted IODA experiments on Orbitrap MS

1. Feature detection and alignemnent from mzML/RAW files with pyOpenMS.
2. Optimise target ion distribution accross multiple iterative experiments.
3. Create an targeted list for the Exactive/Fusion serie MS or Exploris/Tribrid serie MS.
4. Run the IODA experiments on the mass spectrometer.

Running IODA on the cloud with Binder

Note that this a temporary web-instance. Nothing will be saved on the server. Download all required results.

Interactive interface with Binder-GESIS [First choice]

Start the notebook on the cloud with Binder on the GESIS server (more RAM for the Curve mode) ->

Interactive interface with Binder [back up and no curve mode]

Binder standard server [LATEST] ->

View-only interface (non-interactive): IODA_notebooks_welcome.ipynb

Running IODA locally

First, if not already installed, install git and conda.

Clone or download this repository. From a terminal, do:

git clone --recursive https://github.com/lfnothias/IODA_MassSpec.git

Navigate to the IODA_MassSpec folder:

cd IODA_MassSpec

Create the conda environment using the conda env create command with your environment.yml file:

conda env create -f environment_IODA_MassSpec.yml

Activate the IODA_MassSpec conda environment

conda activate IODA_MassSpec

Now run the following to install pyOpenMS 3.0:

For Linux:

pip install pyopenms_wheels/pyopenms-3.0.0.dev20230316-cp310-cp310-manylinux_2_17_manylinux_x86_64.whl

For Mac, see the correct wheel build and instructions at https://pypi.cs.uni-tuebingen.de/. For example for ARM:

pip install pyopenms_wheels/pyopenms-3.0.0.dev20230615-cp310-cp310-macosx_13_0_arm64.whl

For Windows, see the correct wheel build and instructions at https://pypi.cs.uni-tuebingen.de/

Alternatively, go to the OpenMS action webpage like here, download the pyOpenMS 3 wheel file corresponding to your system (note that you need to be logged in GitHub). Save it in the IODA_MassSpec folder, and install it similarly as above.

Start the jupyter lab session and notebook(you can use other ipython interface if needed):

jupyter lab IODA_notebooks_welcome.ipynb

Update the submodule

git submodule update --remote