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] (see also below). 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 below.

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

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

imp_read-2026.8.21.tar.gz (22.7 kB view details)

Uploaded Aug 20, 2026 Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files.

imp_read-2026.8.21-py3-none-any.whl (31.0 kB view details)

Uploaded Aug 20, 2026 Python 3

File details

Details for the file imp_read-2026.8.21.tar.gz.

File metadata

Download URL: imp_read-2026.8.21.tar.gz
Upload date: Aug 20, 2026
Size: 22.7 kB
Tags: Source
Uploaded using Trusted Publishing? Yes
Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for imp_read-2026.8.21.tar.gz
Algorithm	Hash digest
SHA256	`4d6f3ed8447a49b0c756a5013d30699401c91f946833835f3641ae24626c81cb`
MD5	`228e41e44fbb6c718e81f6013ab31458`
BLAKE2b-256	`d09857db4e33855b2c107e3735f41c63374fcb8237b9e5fcf3f4e58d7e6ee6ad`

See more details on using hashes here.

Provenance

The following attestation bundles were made for imp_read-2026.8.21.tar.gz:

Publisher: publish.yml on hgb-bin-proteomics/READ

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Statement:
- Statement type: https://in-toto.io/Statement/v1
- Predicate type: https://docs.pypi.org/attestations/publish/v1
- Subject name: imp_read-2026.8.21.tar.gz
- Subject digest: 4d6f3ed8447a49b0c756a5013d30699401c91f946833835f3641ae24626c81cb
- Sigstore transparency entry: 2539462646
- Sigstore integration time: Aug 20, 2026
Source repository:
- Permalink: hgb-bin-proteomics/READ@443df46ea9845ff2f51f877764a8a0fa3d2c811f
- Branch / Tag: refs/heads/master
- Owner: https://github.com/hgb-bin-proteomics
- Access: public
Publication detail:
- Token Issuer: https://token.actions.githubusercontent.com
- Runner Environment: github-hosted
- Publication workflow: publish.yml@443df46ea9845ff2f51f877764a8a0fa3d2c811f
- Trigger Event: workflow_dispatch