https://github.com/jhsmit/hdx-ms-datasets
Repository for HDX-MS datasets
https://github.com/jhsmit/hdx-ms-datasets
Last synced: 9 months ago
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Repository for HDX-MS datasets
- Host: GitHub
- URL: https://github.com/jhsmit/hdx-ms-datasets
- Owner: Jhsmit
- Created: 2021-11-19T11:29:43.000Z (about 4 years ago)
- Default Branch: master
- Last Pushed: 2024-03-06T08:16:22.000Z (almost 2 years ago)
- Last Synced: 2025-02-12T20:17:02.503Z (11 months ago)
- Language: Python
- Size: 437 KB
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
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README
# HDX-MS-datasets
Repository for HDX-MS datasets
NOTE: This is not the HDX dataset format proposed at the HDX-MS 2022 conference, which includes isotopic envelopes, but a .yaml based format containing metadata and peptide-average deuterium uptake.
The aim of this repository is to collect curated bottom-up HDX-MS datasets for automated
processing, data mining and interactive visualization.
Datasets should consist of .csv D-uptake/exposure peptide tables. Each dataset is described by
a `metadata.yaml` file and a `hdx_spec.yaml` file.
Repository for downloading and loading datasets in python: [hdxms-datasets](https://github.com/Jhsmit/hdxms-datasets)
metadata.yaml
-------------
- Contains a list of authors (and contact email, ORCID, affiliations, ...)
- List of associated publications with the datasets
- List of repositories where raw data or associated data can be found
hdx_spec.yaml
--------------------
- Describes the protein of interest
- Information on the protein state (mutations, ligands, oligomeric state, buffer conditions)
- HDX specific experimental conditions (deuteration percentage, pH, temperature)
- Specification of .csv file format
- Definition of peptide sets per protein state (FD control / ND control / experiment)