READ

[R]eporter Ion [E]xtractor and [A]nnotation [D]irector

READ is a python-based tool to orchestrate mass spectrometry-based TMTpro-18plex protein 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]. 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.