tdfpy 5.0.0

A Python package for extracting data from Bruker timsTOF data files (.tdf and .tdf_bin). Includes a Numba-accelerated centroiding algorithm for efficient extraction of ion mobility data.

tdfpy reads Bruker timsTOF .d acquisitions straight from analysis.tdf and analysis.tdf_bin — no Bruker native library required. It gives you familiar Python objects for DDA, DIA, and PRM runs, plus a tunable, Numba-accelerated centroiding pipeline for pulling clean, ion-mobility-resolved peaks out of raw PASEF frames.

It's for proteomics and mass spec developers who want to script against timsTOF data without hand-rolling SQLite queries or reverse-engineering the binary frame format.

Why tdfpy?

• Pure Python, no native dependency — analysis.tdf_bin is decoded directly, so it runs on Linux, macOS, and Windows, x86-64 and ARM
• One API for DDA, DIA, and PRM — frames, precursors, isolation windows, targets, and transitions are all typed Python objects
• Composable peak pipeline — chain region exclusion, smoothing, and noise filters before centroiding, or use short-hand defaults
• Two centroiders — a Numba-JIT'd greedy merge in float m/z space, and a watershed region-grower in integer TOF-index space, swappable without touching surrounding code
• Lazy spectral access — frame metadata loads upfront; raw peak data is only decoded when you call .merged_peaks(), .scan_peaks(), .raw_peaks(), or .centroid()
• Query by m/z and RT, not just row index

Installation

pip install tdfpy

Requires Python 3.12+. On Python 3.12/3.13 the zstandard package is installed automatically; Python 3.14+ uses the standard library's zstd module.

Optional extras:

pip install "tdfpy[viz]"  # matplotlib-based plotting helpers
pip install "tdfpy[mcp]"  # MCP server for AI-agent access to acquisitions

Quick Start

from tdfpy import DDA

with DDA("sample.d") as dda:
    # Iterate over MS1 frames
    for frame in dda.ms1:
        print(f"Frame {frame.frame_id} at RT {frame.rt:.1f}s")
        peaks = frame.centroid()  # shape (N, 3): [m/z, intensity, 1/K0]
        print(f"  {len(peaks)} centroided peaks")
        break

    # Iterate over precursors (MS2)
    for precursor in dda.precursors:
        print(f"Precursor {precursor.precursor_id}: {precursor.largest_peak_mz:.4f} m/z")
        peaks = precursor.merged_peaks()  # MS2 centroided by tdfpy (mobility collapse + merge)
        break

DIA and PRM acquisitions work the same way with DIA(...) and PRM(...); see the getting started guide for both.

What else it can do

Full pipeline options (region exclusion, smoothing, the two centroiders, and the noise-filter chain) are covered in the analysis guide and API reference.

Related packages

tdfpy is the timsTOF reader in the tacular-omics family. mzmlpy reads mzML files the same way, and spxtacular builds spectrum-processing pipelines on top of either.

Documentation

Full documentation: tacular-omics.github.io/tdfpy

• Changelog
• Contributing

Citation

If you use tdfpy in published work, please cite it — see CITATION.cff or the DOI record.

License

MIT