grassp.pp.drop_excess_MQ_metadata

grassp.pp.drop_excess_MQ_metadata#

drop_excess_MQ_metadata(data, colname_regex='Peptide|peptide|MS/MS|Evidence IDs|Taxonomy|Oxidation|Intensity|Total Spectral Count|Unique Spectral Count|Spectral Count|Identification type|Sequence coverage|MS/MS count', inplace=True)[source]#

Drop excess metadata columns from MaxQuant output.

Parameters:
data AnnData

The annotated data matrix with proteins as observations (rows).

colname_regex str (default: 'Peptide|peptide|MS/MS|Evidence IDs|Taxonomy|Oxidation|Intensity|Total Spectral Count|Unique Spectral Count|Spectral Count|Identification type|Sequence coverage|MS/MS count')

Regular expression pattern to match column names that should be dropped. Default pattern matches common MaxQuant metadata columns.

inplace bool (default: True)

Whether to modify data in place or return filtered metadata.

Return type:

None | DataFrame

Returns:

  • If inplace=True, modifies the input AnnData object and returns None.

  • If inplace=False, returns a DataFrame with filtered metadata.

Notes

This function removes metadata columns that match the provided regular expression pattern. The default pattern removes common MaxQuant metadata columns that are typically not needed for downstream analysis.

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