rt-anchor

Standard-panel retention-index (iRT) calibration for LC-MS lipidomics.

Purpose

Convert the retention time of every feature in an LC-MS table into a dimensionless, portable retention index (RI/iRT) anchored on a spiked standard panel — so retention is comparable across injections, batches, and instruments. A monotone warp is fitted from the standards and applied to all features; nothing in the original table is dropped, calibration only appends columns.

Download

pip install rt-anchor
pip install "rt-anchor[report,structures]"   # + HTML/PDF report and structure hover

Input

Required:

Optional: per-injection files (per-sample tier + repeatability QC), a custom standard manifest / reference baseline, and the matching parameters (mz_tol_ppm, rt_window_min, min_anchors, extrapolate).

from rt_anchor import calibrate, write_results
res = calibrate("samples.txt", polarity="positive", standards_table="standards.txt")
write_results(res, "out/run1")

rt-anchor calibrate --samples samples.txt --standards standards.txt --polarity positive --out out/run1

Output

• *_calibrated.csv — the original table + appended columns: RI (iRT-style index), RI_uncertainty, RI_reliability (high/medium/low/none), RI_spread, n_contributing, is_extrapolated, calibration_scope, warp_source.
• *_model.json — the fitted warp, anchors, and QC metrics.
• *_anchors.csv, *_log.txt — anchors used and a run log.
• *_report.html + *_report.pdf — an interactive + static report (detection, calibration warp, repeatability). On by default; --no-report to skip.

License

MIT