Installation
Python package
MS²Rescore is installable as a Python package on Windows, macOS and Linux.
In a fresh virtual environment, run:
pip install ms2rescore
Or, in a fresh conda environment, run:
conda install -c bioconda ms2rescore
Bioconda packages are only available for Linux and macOS.
Windows installer
Download the .exe
file from the
latest release
and go through the installation steps. If Microsoft Defender SmartScreen displays a warning, click
“More info” and then click “Run anyway”.
Docker container
First check the latest version tag on biocontainers/ms2rescore/tags. Then pull and run the container with:
docker container run -v <working-directory>:/data -w /data quay.io/biocontainers/ms2rescore:<tag> ms2rescore <ms2rescore-arguments>
where <working-directory>
is the absolute path to the directory with your MS²Rescore input
files, <tag>
is the container version tag, and <ms2rescore-arguments>
are the ms2rescore
command line options (see Command line interface).
Installing Percolator
To use Percolator as rescoring engine, it must be installed separately. Percolator is
available for most platforms and can be downloaded from the
GitHub releases page. Ensure that
the percolator
executable is in your PATH
. On Windows, this can be done by checking the
Add percolator to the system PATH for current user
option during installation:

Note
Alternatively, Mokapot can be used as rescoring engine, which does not require a separate installation.
For development
Clone this repository and use pip to install an editable version:
pip install --editable .