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, Spectronaut, and DIA-NN.

READ supports Thermo RAW files via ThermoRawFileParser or 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 (recommended), or the TMT Resolution GUI Tool [publication] (see also Usage). 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 and run via the command line. We also provide executables with a graphical user interface for Microsoft Windows which can be downloaded here. In-depth information on how to install and run READ can be found in the Installation section.

Quick Start

Quick start with uvx:

uvx --python 3.13 --from imp-read tmt_chimerys --help

• Use tmt_chimerys for Chimerys DIA result files.
• Use tmt_chimerys_dda for Chimerys DDA result files.
• Use tmt_spectronaut for Spectronaut result files.
• Use tmt_diann for DIA-NN result files.

Acknowledgements

We thank Dasha Pototska for designing the READ logo!

License

• The READ software and code are MIT licensed.
• The READ logo © 2026 by Dasha Pototska and Micha Birklbauer is licensed under CC BY-NC-ND 4.0.

Citing

If you are using READ please cite the following publication:

• Manuscript in preparation

  (wip)