Examples

Quick start with example data

Try winnow in minutes using the bundled example subset under examples/example_data/: spectra (spectra.ipc) and de novo predictions (predictions.csv) from a real HeLa single-shot run, reduced for repository size.

# Train a calibrator
make train-sample

# Run prediction (uses the model from train-sample)
make predict-sample

Comprehensive Example Notebook

For a comprehensive example demonstrating the full Winnow workflow, see our example notebook:

📓 FDR plots example notebook

This notebook shows you how to:

• Load and prepare PSM data using CalibrationDataset
• Train a confidence calibrator with ProbabilityCalibrator
• Apply FDR control using different methods
• Generate visualisation plots for calibration and FDR analysis