Metadata-Version: 2.4
Name: IMP-READ
Version: 2026.8.21
Summary: TMTpro-18plex quantification for [single cell] DIA and DDA searches.
Keywords: mass spectrometry,proteomics
Author: Micha Johannes Birklbauer
Author-email: Micha Johannes Birklbauer <micha.birklbauer@fh-hagenberg.at>
License-Expression: MIT
License-File: LICENSE
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Development Status :: 5 - Production/Stable
Requires-Dist: numpy>=2.3.4
Requires-Dist: pandas<3
Requires-Dist: pyarrow>=22.0.0
Requires-Dist: pyopenms>=3.4.0,<3.5.0
Requires-Dist: pyteomics[xml]>=4.7.5,<5
Requires-Dist: tqdm>=4.67.1
Maintainer: Micha Johannes Birklbauer
Maintainer-email: Micha Johannes Birklbauer <micha.birklbauer@fh-hagenberg.at>
Requires-Python: >=3.12, <3.14
Project-URL: Homepage, https://github.com/hgb-bin-proteomics/READ
Project-URL: Documentation, https://github.com/hgb-bin-proteomics/READ
Project-URL: Repository, https://github.com/hgb-bin-proteomics/READ.git
Project-URL: Issues, https://github.com/hgb-bin-proteomics/READ/issues
Description-Content-Type: text/markdown

# READ
_\[R\]eporter Ion \[E\]xtractor and \[A\]nnotation \[D\]irector_

**READ** is a python-based tool to orchestrate
TMTpro-18plex quantification for \[single cell\] DIA and DDA searches with
[Chimerys](https://www.msaid.de/chimerys),
[Spectronaut](https://biognosys.com/software/spectronaut/), and
[DIA-NN](https://github.com/vdemichev/DiaNN).

**READ** supports Thermo RAW files via [ThermoRawFileParser](https://github.com/compomics/ThermoRawFileParser) or [mzML](https://www.psidev.info/mzml) files, maps
identified precursors to their corresponding MS1 and MS2 spectra, and then quantifies PSMs and/or proteins. Quantification is done either natively, via [OpenMS](https://openms.de/) (recommended), or
the TMT Resolution GUI Tool [\[1\]](https://doi.org/10.1038/s41467-025-60022-x) (see also below). Quantification is additionally quality controlled by optionally several filters including precursor co-isolation purity, reporter ion resolution,
minimum reporter signal, and minimum reporter signal-to-noise. Filtering behavior is easily controlled via a human-readable `.toml` configuration file.

**READ** can easily be installed via [PyPI](https://pypi.org/p/IMP-READ/) and run via the command line. We also provide executables with a graphical user interface for Microsoft Windows
which can be downloaded [here](https://github.com/hgb-bin-proteomics/READ/releases). In-depth information on how to install and run **READ** can be found below.

## Documentation

Please refer to [https://github.com/hgb-bin-proteomics/READ/](https://github.com/hgb-bin-proteomics/READ/) for more information.

## Contact

In case of questions please contact:
- [micha.birklbauer@fh-hagenberg.at](mailto:micha.birklbauer@fh-hagenberg.at)
