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Python library for connecting to the METASPACE platform

Project description

METASPACE Python client

Python module that provides programmatic access to the METASPACE platform.


  • Running batch jobs
  • Exploratory analysis of submitted data
  • Quick access to things hidden from web interface (such as location of files on S3 and other metadata)


You need to have Python 3.6 or higher to use this library.

pip install metaspace2020

Jupyter Notebooks

There are several playbooks available to retrieve dataset information as well as to upload it on Metaspace.

Notebook Description
access_change_PI_names Reads and updates PI names in dataset metadata
api_examples Illustrates how to access all the information about a dataset that is visible on the METASPACE platform
compare-reference-engine-results Compares engine results against the pySM reference implementation
iso_img_retrieval Retrieves isotopic images for the provided dataset
simple_database_queries A few queries to get annotations for a dataset, show stats on the annotations, and compare annotations between two datasets
top_hits Retrieves ions with the highest average MSM score across all datasets
update_DBs_dataset_api Reprocesses a dataset with a different set of databases
upload_dataset_api Uploads a new dataset with the provided metadata


This project is funded from the European Horizon2020 project METASPACE (no. 634402), NIH NIDDK project KPMP and internal funds of the European Molecular Biology Laboratory.


Unless specified otherwise in file headers, all files are licensed under the Apache 2.0 license.

Project details

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