SITA

Natural-abundance correction for GC-MS mass distribution vectors (MDVs) from 13C stable-isotope tracer experiments. Given a fragment's molecular formula and its labelled-backbone carbon count, SITA returns the natural-abundance correction matrix and the corrected MDV*.

A live version is hosted at sita-app.up.railway.app.

Project structure

This repo is a UV workspace with two packages:

• sita-core — pure algorithm library (numpy only). The LabelledCompound class and isotope data.
• sita-web — Flask web UI, REST API. Depends on sita-core.

Quick start

Requires Python 3.10+ and uv.

git clone https://github.com/CMonnin/SITA.git
cd SITA
uv sync
uv run python -m sita_web.app

Then open http://127.0.0.1:5000.

Usage

The web UI has two sections:

1. Correction matrix — enter a molecular formula and the number of backbone carbons; returns the natural-abundance correction matrix.
2. Corrected MDV (MDV*) — additionally enter a measured MDV; returns the natural-abundance-corrected MDV.

backbone_c

Every compound requires a backbone_c argument: the number of carbons in the fragment that are subject to 13C labelling in the tracer experiment. These positions are excluded from the natural-abundance correction because their labelling is the measurement signal (per Fischer & Zamboni 2004).

Example: alanine M-57 is the fragment C11H26NO2Si2 (Nanchen 2007 Table 1, mass 260). Eleven total carbons — three from the alanine backbone, eight from the two TBDMS groups after loss of the tert-butyl (C4H9). So backbone_c=3. The MDV length defaults to backbone_c + 1 (M+0 ... M+n).

Running tests

uv run pytest

Using the core library programmatically

from sita_core import LabelledCompound

compound = LabelledCompound(
    formula="C11H26NO2Si2",
    labelled_element="C",
    backbone_c=3,
)
matrix = compound.correction_matrix()

Tech stack

• sita-core: Python + numpy for the correction math
• sita-web: Flask serving a vanilla-JS frontend
• Deployed on Railway

Citation

References

The mathematical basis follows:

• Nanchen, A., Fuhrer, T., Sauer, U. (2007). Determination of Metabolic Flux Ratios From 13C-Experiments and Gas Chromatography-Mass Spectrometry Data: Protocol and Principles. In: Metabolomics (Methods in Molecular Biology 358), Humana Press, pp. 177-197. doi:10.1007/978-1-59745-244-1_11
• Fischer, E., Zamboni, N., Sauer, U. (2004). High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Analytical Biochemistry 325(2):308-316. doi:10.1016/j.ab.2003.10.036

Natural isotope abundances are from Coursey, J. S., et al. Atomic weights and isotopic compositions with relative atomic masses. NIST Physical Measurement Laboratory (2015). physics.nist.gov

The correction matrix and worked example in the test suite come from Nanchen 2007, §3.7 (alanine M-57 fragment).

Contributing

This is an open-source project — contributions are welcome. Fork the repo, make changes, and open a pull request. For feature requests or bug reports, open an issue or reach out at cianmonnin at gmail dot com.