IsoSpec

IsoSpec is a fine-structure isotopic distribution calculator for chemical formulas — given a molecule, it computes the masses and probabilities of its isotopologues. It is fast enough to handle large molecules (proteins, oligonucleotides) where the full distribution has astronomically many configurations, and it returns provably-optimal subsets that cover a chosen fraction of the total probability mass.

IsoSpec is primarily used as a library by mass spectrometry software. It is implemented in C++ (src/IsoSpec++/) and shipped with first-class bindings for Python (IsoSpecPy, on PyPI) and R (IsoSpecR, on CRAN).

Installation

Python

pip install IsoSpecPy

The wheel bundles the C++ library — no separate native install required. Compatible with CPython and PyPy on Linux, macOS, Windows, and Cygwin/MinGW. Python ≥ 3.6.

To build from source: pip install . from a checkout. A C++20 compiler is required.

R

install.packages("IsoSpecR")

From source: cd src && R CMD build IsoSpecR && R CMD INSTALL IsoSpecR_*.tar.gz.

C++ library

cd src/IsoSpec++
make            # produces libIsoSpec++.so

Or via CMake from the repo root:

cmake -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build
sudo cmake --install build

Requires a C++20 compiler. CMake produces both shared and static libraries and installs headers under ${CMAKE_INSTALL_INCLUDEDIR}/IsoSpec++.

Quick start

The most common usage is IsoTotalProb: ask for the smallest set of isotopologues whose summed probability covers a chosen fraction of the spectrum (typically 0.99–0.9999). The result is a materialized envelope — arrays of masses and probabilities you can read directly.

Python

import IsoSpecPy

# Isotopologues covering at least 99.9% of the probability mass of water.
iso = IsoSpecPy.IsoTotalProb(formula="H2O1", prob_to_cover=0.999)

for mass, prob in zip(iso.masses, iso.probs):
    print(mass, prob)

# From an amino-acid FASTA sequence:
iso = IsoSpecPy.IsoTotalProb(fasta="AAAPPGQAAC", prob_to_cover=0.999)
print(list(zip(iso.masses, iso.probs)))

See Examples/Python/ for radiolabelling, custom elements, binned spectra, and FASTA modifications.

C++

#include "IsoSpec++/isoSpec++.h"
#include "IsoSpec++/fixedEnvelopes.h"

using namespace IsoSpec;

int main() {
    FixedEnvelope iso = FixedEnvelope::FromTotalProb("H2O1", 0.999, true, true);

    for (size_t i = 0; i < iso.confs_no(); ++i) {
        std::cout << iso.mass(i) << '\t' << iso.prob(i) << '\n';
    }
}

Quickest way to build:

clang++ -std=c++20 water.cpp src/IsoSpec++/unity-build.cpp -o water

(unity-build.cpp is a single translation unit that #includes every source file — see Examples/C++/COMPILING.)

R

library(IsoSpecR)
water <- c(H = 2, O = 1)
IsoSpecify(molecule = water, stopCondition = 0.999)

See Examples/R/ for radiolabelling and full-spectrum extraction.

Advanced features

• Alternative algorithms — for cases where IsoTotalProb isn't the right shape:
  • IsoThreshold — all isotopologues with probability above a fixed threshold.
  • IsoStochastic — simulate a measured spectrum by sampling integer ion counts.
  • IsoBinned — histogram-style envelope at a chosen bin width.
• FASTA support — build an Iso directly from an amino-acid sequence; optionally include the N/C-terminal water.
• Custom isotopic tables — override natural abundances per element (e.g. for radio- or stable-isotope labelling). See Examples/*/radiolabelling.*.
• Fixed-envelope arithmetic — addition, normalization, convolution, Wasserstein distance.
• Nominal-mass mode — compute distributions over nucleon counts instead of real masses.
• Streaming generators (for performance) — the tabulated functions above materialize the full envelope into arrays. For large molecules where that uses too much memory, or for pipelines that consume one configuration at a time (e.g. binning on the fly), use the generator classes instead: IsoThresholdGenerator, IsoLayeredGenerator, IsoOrderedGenerator, IsoStochasticGenerator. They yield one isotopologue per call to advanceToNextConfiguration() without ever storing the full set. IsoOrderedGenerator additionally streams in strict order of decreasing probability.

Algorithmic details are in the papers cited below; the Supporting Information of each is the better starting point for implementation specifics.

Repository layout

src/IsoSpec++/    C++ core library (the algorithms live here)
src/IsoSpecPy/    Python binding, loaded via cffi
src/IsoSpecR/     R binding, via Rcpp
Examples/         Working examples in each language
tests/            C, C++, and Python test suites
skbuild/          scikit-build-core entry point used when installing the Python wheel

Citation

If IsoSpec is useful in your research, please cite:

• Łącki, M. K.; Valkenborg, D.; Startek, M. P. IsoSpec2: Ultrafast Fine Structure Calculator. Analytical Chemistry 2020, 92 (14), 9472–9475. https://doi.org/10.1021/acs.analchem.0c00959
• Łącki, M. K.; Startek, M.; Valkenborg, D.; Gambin, A. IsoSpec: Hyperfast Fine Structure Calculator. Analytical Chemistry 2017, 89 (6), 3272–3277. https://doi.org/10.1021/acs.analchem.6b01459

The Supporting Information of each paper has the algorithmic detail.

License

2-clause BSD (see LICENCE). If you need different licensing terms, contact the authors. The authors appreciate (but do not require) being told when IsoSpec is used in other software.