OpenTimsTDF

CI DOI crates.io PyPI docs.rs License: Apache-2.0 Rust MSRV

Part of the OpenMassSpec stack for mass spectrometry raw-file access.

Rust and Python reader for timsTOF .d/ (TDF) acquisition bundles - the SQLite analysis.tdf metadata file and the analysis.tdf_bin binary frame stream. Runs on Linux, macOS, and Windows.

Documentation: sigilweaver.app/opentimstdf/docs

Install

Prefer openmassspec-io with the bruker feature/extra unless you need this parser standalone (minimal dependencies, or building your own abstraction) - the umbrella gives you format auto-detection, mzML conversion, and Arrow streaming across all wired-in vendors for free:

cargo add openmassspec-io --features bruker

pip install openmassspec[bruker]

Standalone:

Rust:

cargo add opentimstdf

Python:

pip install opentimstdf

Quickstart

Rust:

use opentimstdf::Reader;

let reader = Reader::open("my_bundle.d")?;
let calib = reader.calibration()?;
let frame = reader.frame(1)?;
for peak in reader.decode_peaks(&frame)? {
    let mz = calib.tof_to_mz(peak.tof);
    let im = calib.scan_to_inv_mobility(peak.scan);
    println!("scan={} mz={:.4} 1/K0={:.4} i={}", peak.scan, mz, im, peak.intensity);
}

Python:

import opentimstdf

reader = opentimstdf.Reader("my_bundle.d")
calib = reader.calibration()
frame = reader.frame(1)
for peak in reader.decode_peaks(frame):
    mz = calib.tof_to_mz(peak.tof)
    print(peak.scan, mz, peak.intensity)

See the docs site for the full quickstart, guide, and format specification.

License

Apache-2.0. See LICENSE.

The TDF format and codecs were worked out from public sample data (PRIDE accessions). See ATTRIBUTION.md.

Project links

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Credits

Author: Nathan Riley

GitHub Statistics

Data verified by PyPI on Aug 12, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

Apache Software License (Apache-2.0)

Requires

Python >=3.8

Tags

mass-spectrometry bruker timstof tdf proteomics

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