protdata

Proteomics data loaders for the AnnData format.

This package provides loader functions to import proteomics data (e.g., MaxQuant) into the AnnData structure for downstream analysis and integration with single-cell and multi-omics workflows.

Features

• Multiple formats: Support for MaxQuant, FragPipe, DIA-NN, and mzTab files
• Reads metadata: Automatically extracts and organizes sample and protein metadata

Installation

Protdata has minimal dependencies listed in pyproject.toml

To install the latest release from PyPI, run:

pip install protdata

Or install from source:

git clone https://github.com/czbiohub-sf/protdata.git
cd protdata
pip install -e . # or make setup-develop for developers

Usage Example

MaxQuant Import

You can download an example proteinGroups file here

import protdata

adata = load_maxquant_to_anndata("/path/to/proteinGroups.txt")
print(adata)

DIA-NN Import

You can download an example DIA-NN report file here

from protdata.io import read_diann

adata = read_diann("/path/to/report.pg_matrix.tsv")
print(adata)

FragPipe Import

You can download an example FragPipe output file here

from protdata.io import read_fragpipe

adata = read_fragpipe("/path/to/combined_protein.tsv")
print(adata)

mzTab Import

You can download an example mzTab file here

from protdata.io import read_mztab

adata = read_mztab("/path/to/SILAC_SQ.mzTab")
print(adata)

Authors

protdata is created and maintained by the Computational Biology Platform at the Chan Zuckerberg Biohub San Francisco.

To get in touch please use the GihHub issues page.

Contributing

If you want to contribute to protdata, please read the Contribution Guide

Changelog

See Release Notes