IsoDec

IsoDec assigns charge states and deconvolves isotopically resolved mass spectrometry data. Its native core uses IsoGen for peptide and RNA isotope distributions.

Installation

Install a published wheel:

python -m pip install isodec

IsoDec supports Python 3.9 and newer on 64-bit Windows, Linux, and macOS, including Apple silicon. Native builds are also tested on ARM64 Windows and Linux. Compatible wheels include the native IsoDec and IsoGen libraries. A source build requires CMake 3.22.1 or newer, a C/C++ compiler, FFTW, and an initialized IsoGen submodule:

git clone --recurse-submodules https://github.com/michaelmarty/IsoDec.git
python -m pip install ./IsoDec

Python usage

import numpy as np
from isodec import IsoDecRuntime

spectrum = np.loadtxt("spectrum.txt")
engine = IsoDecRuntime()
peaks = engine.batch_process_spectrum(spectrum, centroided=True)

for peak in peaks:
    print(peak.mz, peak.z, peak.monoiso, peak.matchedintensity)

TXT, DAT, CSV, and NPZ single-scan spectra are supported without UniDec. Raw vendor files, mzML/mzXML, and I2MS import use UniDec's extensive importer stack:

python -m pip install "isodec[unidec]"

Command line

isodec spectrum.txt --centroided -o assigned_peaks.tsv
python -m isodec --help

Development

git submodule update --init --recursive
python -m pip install -e ".[test]"
python -m pytest

Documentation sources live in docs/ and are built with MkDocs. Release and wheel-building details are in PUBLISHING.md.

License and citation

IsoDec is released under the BSD 3-Clause License. See THIRD_PARTY_NOTICES.md for IsoGen, FFTW, and Intel runtime notices. When using IsoDec, please cite Pavek et al., “A Fast Neural Network for Isotopic Charge State Assignment,” J. Am. Chem. Soc. 2025, 147, 21610–21620. Machine-readable metadata is provided in CITATION.cff.

Changelog

2.0.1 (2026-08-18)

  • Improved native processing performance with optimized AVX matrix operations, linear-time peak detection, faster isotope matching, and reusable work buffers.
  • Moved installed native libraries and executables into isodec/bin; Windows binaries are included with the package.
  • Added processing-time and matched-peak reporting for native spectrum runs.
  • Added automated MSVC-versus-IntelLLVM performance benchmarking.

2.0.0 (2026-08-17)

  • Split IsoDec from UniDec into the standalone isodec package, with IsoGen as a submodule and an independent version and release cycle.
  • Added experimental charge-state assignment directly from profile-mode data.
  • Added cross-platform tests—including native ARM64 Windows and Linux coverage—documentation, and automated wheel and source distribution publishing.

1.0.0

  • Initial IsoDec release with IsoGen integration for isotopic charge-state assignment and deconvolution of mass spectrometry data, distributed as part of UniDec.

Project links

Data verified by PyPI on Aug 18, 2026
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1 maintainer

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Avatar for michaelmarty from gravatar.com michaelmarty

Credits

Author: Michael T. Marty

GitHub Statistics

Data verified by PyPI on Aug 18, 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 expression

BSD-3-Clause
View SPDX License List

Requires

Python >=3.9

Provides Extra

test docs training unidec release

Tags

mass spectrometry charge state deconvolution isotope distribution

Classifiers

Report project as malware

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