ms2rescore

MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and RTs.

ms2rescore.parse_configurations(configurations)

Parse and validate MS²Rescore configuration files and CLI arguments.

Default configuration, user configuration files, and CLI/class arguments are parsed in cascading order, with each successive configuration taking priority over the previous.

Parameters:

configurations (Dict, str, Path, Namespace, List[Dict, str, Path, Namespace]) – configuration dictionary, path to configuration files, argparse Namespace, or a list of the above.

Return type:

Dict

ms2rescore.rescore(configuration, psm_list=None)

Run full MS²Rescore workflow with passed configuration.

Parameters:

• configuration (Dict) – Dictionary containing ms2rescore configuration.

• psm_list (PSMList | None) – PSMList object containing PSMs. If None, PSMs will be read from configuration psm_file.

Return type:

None