Citation: Cleavable Cross-Linkers Redefined by a Novel MS3-Trigger Algorithm; Lars Kolbowski, Lutz Fischer, and Juri Rappsilber, Analytical Chemistry 2023 95 (42), 15461-15464, DOI: https://doi.org/10.1021/acs.analchem.3c01673
xiDOUBLET uses pipenv to manage package dependencies.
From the root directory of the project, run
pipenv install
to install all the required packages into a pipenv.
Commands need to be
prefixed with pipenv run to ensure that they are run inside the
pipenv. Alternatively, you can run pipenv shell, which changes the
environment to ensure all subsequent commands are executed within the
pipenv.
To run xiDOUBLET, you first need to setup a config file in JSON
format. An example is given in example_config.json. Please have a
look at that file to see what options are available (although that
file doesn't necessarily list all available options at the moment).
To run xiDOUBLET, you need to tell it what spectra to process, what config to use and what directory to write the results to:
pipenv run python -m xidoublet \
-i example.mgf \
-o output_directory \
-c example_config.json \
-n result_name_prefix