A Python package for working with mass spectrometry data in the quantms.io format.
- Convert data from various mass spectrometry formats to quantms.io format
- Analyze and process quantms.io data
- Visualize results
- Manage project metadata
- Transform data between different formats
# To install the stable release from PyPI:
pip install quantmsio# Fork the repository on GitHub
# Clone the repository
git clone https://github.com/your-username/quantms.io.git
cd quantms.io
# Install the package locally
pip install .For development with all dependencies:
# Using Poetry (recommended)
poetry install
# Or using pip
pip install -r requirements.txt
pip install -e .The package provides a command-line interface (CLI) with several command groups:
Usage: cli [OPTIONS] COMMAND [ARGS]...
quantmsio - A tool for converting and analyzing mass spectrometry proteomics
data
Options:
--version Show the version and exit.
-h, --help Show this message and exit.
Commands:
convert Convert external formats to quantms.io format.
project Project management commands.
stats Statistical analysis of quantms.io data.
transform Transform quantms.io data into different representations.
visualize Visualize quantms.io data.Convert data from various external formats to quantms.io:
Usage: convert [OPTIONS] COMMAND [ARGS]...
Convert external formats to quantms.io format.
Options:
--help Show this message and exit.
Commands:
diann Convert DIA-NN report to quantms.io format
diann-pg Convert DIA-NN report to protein group format
fragpipe Convert FragPipe PSMs from psm.tsv to parquet file in
quantms.io
idxml Convert IdXML to PSM parquet file in quantms io
idxml-batch Convert multiple IdXML files to a single merged PSM parquet
file
maxquant-feature Convert feature data from MaxQuant evidence.txt to parquet
format
maxquant-pg Convert MaxQuant proteinGroups.txt to quantms.io protein
group format
maxquant-psm Convert PSM data from MaxQuant msms.txt to parquet format
quantms-feature Convert feature data from mzTab to quantms.io format.
quantms-pg Convert protein groups from mzTab quantms TMT and LFQ...
quantms-psm Convert PSM data from mzTab to quantms.io format.Transform data within the quantms.io ecosystem:
Usage: transform [OPTIONS] COMMAND [ARGS]...
Transform quantms.io data into different representations.
Options:
--help Show this message and exit.
Commands:
ae Convert IBAQ absolute file into quantms.io format
anndata Merge multiple AE files into a file in AnnData format.
differential Convert a MSstats differential file into a quantms.io file
format
gene Map gene information from FASTA to parquet format
ibaq Convert feature data to IBAQ format
spectra Map spectrum information from mzML to parquet format
uniprot Map feature data to latest UniProt versionVisualize quantms.io data:
Usage: visualize [OPTIONS] COMMAND [ARGS]...
Visualize quantms.io data.
Options:
--help Show this message and exit.
Commands:
plot Visualization commands for quantms.io dataAnalyze quantms.io data:
Usage: stats [OPTIONS] COMMAND [ARGS]...
Statistical analysis of quantms.io data.
Options:
--help Show this message and exit.
Commands:
analyze Statistical analysis commands for quantms.io dataManage project metadata:
Usage: project [OPTIONS] COMMAND [ARGS]...
Project management commands.
Options:
--help Show this message and exit.
Commands:
attach Register the file to project.json.
create Generate a project file from original PRIDE accessionMost commands support a --verbose flag that enables more detailed logging to stdout. The CLI uses standard logging configuration and does not require environment variables.
quantmsio/
├── __init__.py
├── quantmsioc.py # CLI entry point (poetry script: quantmsioc)
├── commands/ # CLI command groups
│ ├── convert/ # Converters: quantms, maxquant, diann, idxml, fragpipe
│ ├── transform/ # Transforms: ibaq, ae, gene, spectra, anndata, differential, uniprot
│ └── utils/ # Utility CLIs: project(create/attach), stats(analyze), plot
├── core/ # Core logic & formats
│ ├── quantms/ # quantms feature/psm/pg, mztab helpers
│ ├── diann/, maxquant/, fragpipe/, idxml_utils/ ...
│ └── project.py, duckdb.py, format.py, common.py
├── operate/ # High-level operations (stats, plotting, tools)
│ ├── plots.py, query.py, statistics.py, tools.py
│ └── ...
└── utils/ # Utilities
├── logger.py # Basic logger getter
├── file_utils.py # File helpers (e.g., AE file discovery)
├── pride_utils.py # PRIDE archive helpers
├── mztab_utils.py # mzTab helpers
├── system.py # System utilities
└── constants.py # Constants and configurations
- Fork the repository
- Create a feature branch
- Make your changes
- Run tests
- Submit a pull request
This project is licensed under the Apache-2.0 License - see the LICENSE file for details.
The project is run by different groups:
- Yasset Perez-Riverol (PRIDE Team, European Bioinformatics Institute - EMBL-EBI, U.K.)
- Ping Zheng (Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China)
IMPORTANT: If you contribute with the following specification, please make sure to add your name to the list of contributors.
As part of our efforts toward delivering open and inclusive science, we follow the Contributor Covenant Code of Conduct for Open Source Projects.
This information is free; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This information is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this work; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.