spxtacular 0.3.0

Mass spectrometry spectrum processing library.

spxtacular

spxtacular is a Python library for mass spectrometry spectrum processing. It provides a chainable Spectrum API covering the full centroid-to-neutral-mass pipeline: denoising, isotope deconvolution, neutral mass conversion, fragment matching, and PSM scoring — with interactive Plotly visualizations throughout.

Part of the tacular-omics ecosystem alongside peptacular, paftacular, and mzmlpy.

Install

pip install spxtacular

# Optional: Numba JIT acceleration (~3–4× faster deconvolution)
pip install spxtacular[numba]

Quick start

import spxtacular as spx

spec = spx.Spectrum(mz=mz_array, intensity=intensity_array)

# Full pipeline: denoise → deconvolute → filter → neutral mass
neutral = (
    spec
    .denoise(method="mad", snr=3.0)
    .deconvolute(charge_range=(1, 5), tolerance=10, tolerance_type="ppm", min_score=0.4)
    .decharge()
)

neutral.plot(title="Neutral masses").show()

Features

Feature	Description
Isotope deconvolution	Bhattacharyya-scored greedy algorithm; optional Numba JIT acceleration
Quality filtering	min_score, m/z, intensity, charge, and ion mobility filters
Neutral mass conversion	decharge() converts charged clusters to neutral masses
Fragment matching	match_fragments() with ppm/Da tolerance
PSM scoring	Hyperscore, spectral angle, matched fraction, and more
Interactive visualization	Stick plots, mirror plots, annotated fragment spectra (Plotly)
File reading	Bruker timsTOF .d files (DReader) and mzML (MzmlReader)

Deconvolution pipeline

# 1. Find isotope clusters → assign monoisotopic m/z + charge + Bhattacharyya score
decon = spec.deconvolute(charge_range=(1, 5), tolerance=10, tolerance_type="ppm")

# charge > 0  → assigned cluster
# charge = -1 → singleton / unassigned
# score 0–1   → isotope profile quality (0.0 for singletons)

# 2. Keep only high-confidence clusters
filtered = decon.filter(min_score=0.5)

# 3. Convert to neutral masses (drops singletons)
neutral = filtered.decharge()

Documentation

Full documentation with API reference, guides, and interactive plots is available at tacular-omics.github.io/spxtacular.

• Spectrum API
• Deconvolution
• Readers
• Visualization
• API Reference

License

MIT