alphabase.pg_reader.maxquant_pg_reader

MaxQuant Protein Group Reader.

Classes:

MaxQuantPGReader(*[, column_mapping, ...])

Reader for protein group matrices from the MaxQuant search engine.

class alphabase.pg_reader.maxquant_pg_reader.MaxQuantPGReader(*, column_mapping: dict[str, str] | None = None, measurement_regex: str | Literal['raw', 'lfq', 'ibaq'] | None = 'raw')

Bases: PGReaderBase

Reader for protein group matrices from the MaxQuant search engine.

By default, the reader will read raw protein intensities from the protein group matrix. By passing a suitable regular expression, it is also possible to extract LFQ

Examples

Get example data

import os
import tempfile
from alphabase.tools.data_downloader import DataShareDownloader
from alphabase.pg_reader import MaxQuantPGReader

# Download to temporary directory
URL = "https://datashare.biochem.mpg.de/s/KvToteOu0zzH17C"
download_dir = tempfile.mkdtemp()

download_path = DataShareDownloader(url=URL, output_dir=download_dir).download()

Per default, the reader will return the raw intensities. Additional protein features are stored in the dataframe index, samples are stored as columns.

# Get raw intensities
reader = MaxQuantPGReader()
results = reader.import_file(download_path)
results.index.names
> FrozenList(['proteins', 'uniprot_ids', 'genes', 'is_decoy'])
results.columns
> Index([...], dtype='object', length=312)

You can get other intensity types by passing a specific pattern to the measurment_regex parameter during class initialization. To checkout all preconfigured regular expressions that enable you to retrieve different intensity modalities, use the get_preconfigured_regex method:

MaxQuantPGReader.get_preconfigured_regex()
> {
    'raw': '^Intensity(?!\\s[LHM]\\s).+$',
    'lfq': '^LFQ intensity(?!\\s[LHM]\\s).+$',
    'ibaq': '^iBAQ(?!\\s[LHM]\\s).+$'
}

You can also pass a custom regular expression, e.g. to retrieve specific channels in TMT experiments

# Match "Intensity H+ <sample>"
reader = MaxQuantPGReader(measurement_regex="^Intensity H .+")

References

• MaxQuant Documentation (Cox Lab, 2024-06-27): https://cox-labs.github.io/coxdocs/output_tables.html#protein-groups,

(last viewed 2025-08)

Methods:

__init__(*[, column_mapping, measurement_regex])

Initialize MaxQuant protein group matrix reader.

__init__(*, column_mapping: dict[str, str] | None = None, measurement_regex: str | Literal['raw', 'lfq', 'ibaq'] | None = 'raw')

Initialize MaxQuant protein group matrix reader.

Parameters:

• column_mapping – Dictionary mapping alphabase column names (keys) to MaxQuant column names (values). If None, uses default mapping from configuration file.

• measurement_regex –

  Pattern to select quantity columns

  • ”raw” (default): Raw intensities

  • ”lfq”: LFQ-corrected intensities

  • ”ibaq”: Intensity-Based Absolute Quantification-corrected intensities

  • custom: Any valid regular expression

  See class documentation for usage examples and get_preconfigured_regex() for available patterns.