ProMetaInfer

Note

Pipeline is still in the making.

Official repository for ProMetaInfer: A tool for inferring missing metadata in proteomics data using machine learning and database search.

Requirements:

• Python >= 3

• Install OpenMS

• Install Docker

• Download Swissprot database as fasta and speficy path to it (https://www.uniprot.org/uniprotkb?query=reviewed:true)

• Download Comet and specify comet.exe file (make sure it is executable, https://github.com/UWPR/Comet/releases/tag/v2025.01.0)

• Pull docker container for param-medic predictions with (https://hub.docker.com/r/elisamaske/predict_tolerances_container)

  docker pull elisamaske/predict_tolerances_container
  

Run Pipeline with:

python infer_metadata.py --mzml_dir <path_to_mzml_files> \
                         --output_dir <path_to_output_directory> \
                         --idxml_dir <path_to_idxml_directory> \
                         --database <path_to_protein_database> \
                         --comet_exe <path_to_comet_executable>

Note

Give complete path to comet executable