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 [1]. 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 on GitHub.

Documentation

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

Contact

In case of questions please contact:

micha.birklbauer@fh-hagenberg.at

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