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]

# Optional: share spectra as compact URL-safe tokens (spectrl)
pip install spxtacular[spectrl]

# Optional: raw-file readers — Bruker .d (bruker) and/or mzML (mzml)
pip install spxtacular[bruker]      # tdfpy — DReader
pip install spxtacular[mzml]        # mzmlpy — MzmlReader
pip install spxtacular[readers]     # both readers

# Everything (numba + both readers + spectrl)
pip install spxtacular[all]

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")
    .deconvolute(charge_range=(1, 5), tolerance=10, tolerance_type="ppm", min_score=0.4)
    .decharge()
)

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

Features

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()

Sharing spectra

With the optional [spectrl] extra, encode a complete spectrum (peaks, charges, ion mobility, and MSn metadata) into a single compact, URL-safe token — or a ready-to-share link — with no backend required.

token = spec.to_spectrl_token()                       # spectrl1.… token
restored = spx.Spectrum.from_spectrl_token(token)

url = spec.to_spectrl_url("https://example.com/view")  # …#spectrl1.… (shareable)
restored = spx.Spectrum.from_spectrl_url(url)

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