READ

Usage ​

  • On Microsoft Windows READ can be run as a standalone executable or via python.
  • Other operating systems are limited to python, please see below.
  • Quick start with uvx:
    bash
    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.
  • Runtime per RAW file is usually between 15-30 minutes.

Usage with OpenMS ​

To use OpenMS quantification you will need a dedicated configuration file that can be generated via:

bash
IsobaricAnalyzer -write_ini tmt18plex_default.ini

Alternatively, you can use the tmt18plex_default.ini file in the config/ directory ➡️ see here.

WARNING

On Microsoft Windows you might have to unblock the downloaded tmt18plex_default.ini file for usage with READ either via its Properties (right-click) or using PowerShell.

IMPORTANT

You might want to adapt the tmt18plex_default.ini file to your TMT lot. Please refer to the OpenMS documentation!

Usage with the TMT Resolution GUI Tool ​

TMT Resolution GUI Tool screenshot

You might also want to use the output of the Resolution GUI tool developed by Dina L. Bai, Tian Zhang et al.[1] as additional input for better quality control. Please refer to this repository for instructions: https://github.com/hgb-bin-proteomics/TMT_Resolution_GUI.

Using the GUI ​

GUI screenshot

We provide compiled standalone binaries for Microsoft Windows that offer a graphical user interface (GUI). Please download the executables from releases.

The source code for the built executables is available at this repository.

IMPORTANT

Please note that using the GUI still requires installation of OpenMS if quantification via OpenMS is enabled! Python is bundled with the application and is not required to be installed!

Using the CLI ​

You can run READ from the command line using the python or uv command line interface (CLI) as detailed below.

IMPORTANT

Please note that RAW file input is only supported on Microsoft Windows-based systems! If you use another OS please convert your RAW files to .mzML beforehand!

TIP

If you are using uv/uvx you can clear the uv cache after running READ with uv cache clear!

Using the CLI: Chimerys DIA ​

  • Export Chimerys PSMs from Proteome Discoverer in tab-separated .txt format.
  • [Optionally] Export Chimerys Proteins from Proteome Discoverer in tab-seperated .txt format.
  • Set you desired parameters in config.toml.
  • READ supports both .raw files and .mzML files as input, .raw files will be automatically converted to .mzML when READ is run.
  • The following steps are optional if you want to convert your .raw files manually:
    • Download ThermoRawFileParser from here.
    • Convert your RAW file with:
      bash
      ThermoRawFileParser.exe -i RAW_FILE_NAME.raw
  • Install OpenMS.
    • We recommend and tested using OpenMS version 3.4.0!
  • Option A (recommended): Running via uv.
    • Install uv if it's not already installed on your system, e.g.:
      bash
      pip install uv
    • Run READ with:
      bash
      uvx --python 3.13 --from imp-read tmt_chimerys -s SPECTRA.mzML -i PROTEOME_DISCOVERER_PSMs.txt -c config.toml -t tmt18plex_default.ini
    • or if you also have proteins with:
      bash
      uvx --python 3.13 --from imp-read tmt_chimerys -s SPECTRA.mzML -i PROTEOME_DISCOVERER_PSMs.txt -c config.toml -t tmt18plex_default.ini -p PROTEOME_DISCOVERER_Proteins.txt
    • To display all possible parameters run:
      bash
      uvx --python 3.13 --from imp-read tmt_chimerys --help
  • Option B: Running via native python.
    • Install python 3.12 or 3.13 from here.
    • Install READ with:
      bash
      pip install imp-read
    • Run READ with:
      bash
      tmt_chimerys -s SPECTRA.mzML -i PROTEOME_DISCOVERER_PSMs.txt -c config.toml -t tmt18plex_default.ini
    • or if you also have proteins with:
      bash
      tmt_chimerys -s SPECTRA.mzML -i PROTEOME_DISCOVERER_PSMs.txt -c config.toml -t tmt18plex_default.ini -p PROTEOME_DISCOVERER_Proteins.txt
    • To display all possible parameters run:
      bash
      tmt_chimerys --help
  • The result will be new files with name extension _purity_tmt_quant that are written out, containing purity and quantification values.
  • Please refer to Output for a description of the new columns in the output file(s).

Using the CLI: Chimerys DDA ​

  • Export Chimerys PSMs from Proteome Discoverer in tab-separated .txt format.
  • [Optionally] Export Chimerys Proteins from Proteome Discoverer in tab-seperated .txt format.
  • Set you desired parameters in config.toml.
  • READ supports both .raw files and .mzML files as input, .raw files will be automatically converted to .mzML when READ is run.
  • The following steps are optional if you want to convert your .raw files manually:
    • Download ThermoRawFileParser from here
    • Convert your RAW file with:
      bash
      ThermoRawFileParser.exe -i RAW_FILE_NAME.raw
  • Install OpenMS.
    • We recommend and tested using OpenMS version 3.4.0!
  • Option A (recommended): Running via uv.
    • Install uv if it's not already installed on your system, e.g.:
      bash
      pip install uv
    • Run READ with:
      bash
      uvx --python 3.13 --from imp-read tmt_chimerys_dda -s SPECTRA.mzML -i PROTEOME_DISCOVERER_PSMs.txt -c config.toml -t tmt18plex_default.ini
    • or if you also have proteins with:
      bash
      uvx --python 3.13 --from imp-read tmt_chimerys_dda -s SPECTRA.mzML -i PROTEOME_DISCOVERER_PSMs.txt -c config.toml -t tmt18plex_default.ini -p PROTEOME_DISCOVERER_Proteins.txt
    • To display all possible parameters run:
      bash
      uvx --python 3.13 --from imp-read tmt_chimerys_dda --help
  • Option B: Running via native python.
    • Install python 3.12 or 3.13 from here.
    • Install READ with:
      bash
      pip install imp-read
    • Run READ with:
      bash
      tmt_chimerys_dday -s SPECTRA.mzML -i PROTEOME_DISCOVERER_PSMs.txt -c config.toml -t tmt18plex_default.ini
    • or if you also have proteins with:
      bash
      tmt_chimerys_dda -s SPECTRA.mzML -i PROTEOME_DISCOVERER_PSMs.txt -c config.toml -t tmt18plex_default.ini -p PROTEOME_DISCOVERER_Proteins.txt
    • To display all possible parameters run:
      bash
      tmt_chimerys_dda --help
  • The result will be new files with name extension _purity_tmt_quant that are written out, containing purity and quantification values.
  • Please refer to Output for a description of the new columns in the output file(s).

Using the CLI: Spectronaut ​

  • Export matched precursors/the main report from Spectronaut in semicolon-separated .csv format.
    • If your result file is comma-separated you need to pass -d "," to READ.
  • Set you desired parameters in config.toml.
  • READ supports both .raw files and .mzML files as input, .raw files will be automatically converted to .mzML when READ is run.
  • The following steps are optional if you want to convert your .raw files manually:
    • Download ThermoRawFileParser from here
    • Convert your RAW file with:
      bash
      ThermoRawFileParser.exe -i RAW_FILE_NAME.raw
  • Install OpenMS.
    • We recommend and tested using OpenMS version 3.4.0!
  • Option A (recommended): Running via uv.
    • Install uv if it's not already installed on your system, e.g.:
      bash
      pip install uv
    • Run READ with:
      bash
      uvx --python 3.13 --from imp-read tmt_spectronaut -s SPECTRA.mzML -i report.csv -c config.toml -t tmt18plex_default.ini
    • To display all possible parameters run:
      bash
      uvx --python 3.13 --from imp-read tmt_spectronaut --help
  • Option B: Running via native python.
    • Install python 3.12 or 3.13 from here.
    • Install READ with:
      bash
      pip install imp-read
    • Run READ with:
      bash
      tmt_spectronaut -s SPECTRA.mzML -i report.csv -c config.toml -t tmt18plex_default.ini
    • To display all possible parameters run:
      bash
      tmt_spectronaut --help
  • The result will be new files with name extension _purity_tmt_quant that are written out, containing purity and quantification values.
  • Please refer to Output for a description of the new columns in the output file(s).

Using the CLI: DIA-NN ​

  • Use the report.parquet that you get from DIA-NN.
  • Set you desired parameters in config.toml.
  • READ supports both .raw files and .mzML files as input, .raw files will be automatically converted to .mzML when READ is run.
  • The following steps are optional if you want to convert your .raw files manually:
    • Download ThermoRawFileParser from here
    • Convert your RAW file with:
      bash
      ThermoRawFileParser.exe -i RAW_FILE_NAME.raw
  • Install OpenMS.
    • We recommend and tested using OpenMS version 3.4.0!
  • Option A (recommended): Running via uv.
    • Install uv if it's not already installed on your system, e.g.:
      bash
      pip install uv
    • Run READ with:
      bash
      uvx --python 3.13 --from imp-read tmt_diann -s SPECTRA.mzML -i report.parquet -c config.toml -t tmt18plex_default.ini
    • To display all possible parameters run:
      bash
      uvx --python 3.13 --from imp-read tmt_diann --help
  • Option B: Running via native python.
    • Install python 3.12 or 3.13 from here.
    • Install READ with:
      bash
      pip install imp-read
    • Run READ with:
      bash
      tmt_diann -s SPECTRA.mzML -i report.parquet -c config.toml -t tmt18plex_default.ini
    • To display all possible parameters run:
      bash
      tmt_diann --help
  • The result will be new files with name extension _purity_tmt_quant that are written out, containing purity and quantification values.
  • Please refer to Output for a description of the new columns in the output file(s).

  1. Keele, G.R., Dou, Y., Kodikara, S.P. et al. Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration. Nat Commun 16, 4753 (2025). https://doi.org/10.1038/s41467-025-60022-x ↩︎

Released under the MIT License.

Copyright © 2026 Micha J. Birklbauer