protdata.io.read_spectronaut

protdata.io.read_spectronaut#

protdata.io.read_spectronaut(file, intensity_columns=['PG.Quantity'], index_column='PG.ProteinGroups', sample_column='R.FileName', sep='\\t')#

Load Spectronaut results into an AnnData object.

Parameters:
file str

Path to the Spectronaut results file.

intensity_columns Union[List[str], str, None] (default: ['PG.Quantity'])

Name of the intensity column.

index_column Optional[str] (default: 'PG.ProteinGroups')

Name of the column to use as protein index.

sample_column Optional[str] (default: 'R.FileName')

Name of the column to use as sample index.

sep default: '\\t'

File separator.

Returns:

anndata.AnnData object with:

  • X: intensity matrix (samples x proteins)

  • var: protein metadata (indexed by protein group IDs)

  • obs: sample metadata (indexed by sample names)

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