Riana — Relative Isotope Abundance Analyzer

Riana takes standard mass-spectrometry spectra (mzML) and peptide-spectrum-match files (Percolator output today; mzTab via quantms in 1.0) and returns mass isotopomer distributions, e.g. for protein turnover analysis. It also fits kinetic models (one-exponential, Guan, Fornasiero) to time-series isotopomer data.

Full documentation: https://ed-lau.github.io/riana/

Install

Riana requires Python 3.10 or newer. We recommend a virtual environment.

pip install riana

For a development install from a clone:

git clone https://github.com/ed-lau/riana
cd riana
pip install -e ".[dev]"

Quickstart

Integrate

Extract isotopomer intensities from one fraction's mzML using a Percolator PSM table:

riana integrate <mzml_dir> <percolator_psms.txt> \
    --sample time1 \
    --iso 0 1 2 3 4 5 6 \
    --q_value 0.01 \
    --r_time 0.5 \
    --mass_tol 25 \
    --out ./out

Fit

Fit a kinetic model across timepoints:

riana fit ./out/time0_riana.txt ./out/time1_riana.txt ./out/time3_riana.txt \
    --model simple \
    --label 1 \
    --ria 0.06 \
    --depth 3 \
    --out ./out

See riana integrate --help and riana fit --help for the full argument set, or the online docs for tutorials.

File formats

• mzML (gzipped or plain) — MS1 spectra, parsed with pymzml
• Percolator target.psms.txt — Crux Percolator or standalone Percolator output (auto-detected by header)
• Output — tab-delimited <sample>_riana.txt with one row per PSM and one column per integrated isotopomer

mzTab (quantms) intake is planned for the 1.0 release; see PROJECT_REVIEW.md.

Snakemake workflow

A reference Snakemake pipeline (Comet → Percolator → Riana integrate → Riana fit) is bundled at workflow/Snakefile. Edit config_template.yaml to point at your tooling and data, then:

snakemake -c -s workflow/Snakefile -d out/snakemake_test --configfile config_template.yaml

Citation

If you use Riana in published work, please cite:

Lau, E. Riana — Relative Isotope Abundance Analyzer. Zenodo. https://doi.org/10.5281/zenodo.17613314

Contributing

Bug reports and pull requests welcome at https://github.com/ed-lau/riana/issues. See PROJECT_REVIEW.md for the current development roadmap.

License

MIT — see LICENSE.md.