READ logo designed by Dasha Pototska and Micha Birklbauer.
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. 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 at hgb-bin-proteomics.github.io/READ.
You can read the pre-print for READ here: bioRxiv