.williams_2018

proteopy.download.williams_2018(intensities_path='williams-2018_ms-proteomics_mouse-tissue_intensities.tsv', var_annotation_path='williams-2018_ms-proteomics_mouse-tissue_peptide-annotation.tsv', sample_annotation_path='williams-2018_ms-proteomics_mouse-tissue_sample-annotation.tsv', *, sep=None, fill_na=None, force=False)[source]

Save Williams 2018 SWATH-MS mouse tissue dataset to disk.

Download and process the peptide-level SWATH-MS dataset from Williams et al. (2018) [1] and save it as three tabular files: intensities in long format, peptide annotations, and sample annotations.

The dataset consists of the protein expression of eight genetically diverse BXD mouse strains across five tissues. Only the whole cell fraction is included; peptide intensities from different charge states are summed per peptide sequence.

Data are sourced from the Elsevier supplementary archive (DOI: 10.1074/mcp.RA118.000554).

Parameters:

  • intensities_path (str | Path, optional) – Destination path for the intensities file. Columns: sample_id, peptide_id, intensity.

  • var_annotation_path (str | Path, optional) – Destination path for the peptide annotation file. Columns: peptide_id, protein_id, gene_id.

  • sample_annotation_path (str | Path, optional) – Destination path for the sample annotation file. Columns: sample_id, tissue, mouse_id.

  • sep (str | None, optional) – Column separator for all output files. When None, the separator is inferred from each file extension via detect_separator_from_extension() (.tsv → tab, .csv → comma).

  • fill_na (float | int | None, optional) – If not None, replace NaN values in the long-format intensities DataFrame with this value before saving.

  • force (bool, optional) – If True, overwrite existing files at the output paths. Otherwise, raise FileExistsError when a destination file already exists.

Returns:

Writes files to disk; does not return a value.

Return type:

None

Examples

>>> import proteopy as pr
>>> pr.download.williams_2018(
...     intensities_path="intensities.tsv",
...     var_annotation_path="peptide_annotations.tsv",
...     sample_annotation_path="sample_annotations.tsv",
... )

References