isotomics 0.1.3

M+1 data processing and simulation for Orbitrap-IRMS fragmentation experiments

Isotomics

isotomics provides tools for M+1 Orbitrap-IRMS workflows:

• simulate expected precision for proposed experiments
• process experimental .isox data to estimate site-specific isotope values

Install

pip install isotomics

Quickstart

Run the packaged example workflow:

isotomics-quickstart

or

python -m isotomics

The package bundles example inputs under isotomics/input_data/ and quickstart reads them directly. Output files are written to your current working directory.

Input CSV Format

Each row describes one constrained site.

Required columns:

• Site Names
• Element
• Number Atoms

Fragment columns:

• add one or more columns named like Fragment 44, Fragment 133, etc.
• use 1 if the site is present in that fragment and 0 if absent

See the bundled example:

• isotomics/input_data/Example_Molecule_Input.csv

Core Workflows

1. Simulation:

• build a molecule definition from the input CSV
• simulate M+N observations from user-provided delta values
• solve and visualize expected site-specific outputs

2. Experimental processing:

• read processed .isox files grouped by fragment and Smp/Std
• compute isotope ratios and uncertainties
• solve for site-specific values using the M+1 Monte Carlo pipeline

Example Dataset

The alanine example dataset is bundled under:

• isotomics/input_data/Experimental_Data/

This is the dataset used by the quickstart command.

Citation

Csernica, Timothy and Zeichner, Sarah S. (2026).
Csernica/isotomics.

Documentation

Build docs locally:

pip install -e .[docs]
cd docs
make.bat