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Target-Decoy FDR in Peptide Mass Spectrometry

Interactive time-of-flight mass spectrometer: peptide ions separate by m/z in flight, hit the detector, and get scored against a target-decoy database so you can tune the FDR threshold and watch false discoveries in real time.

Biomarker Discovery Proteomics3DAdvanced60 FPS

Every peptide identification made by a modern mass spectrometer is a statistical bet, not a certainty. This simulator renders a real time-of-flight flight tube: peptide ions launched together separate in space as they drift because lighter m/z ions travel faster (v = sqrt(2zeV/m)), exactly as in a real TOF instrument, then land on a detector spectrum binned by mass. Each ion is secretly a target (real peptide) or a decoy (reversed-sequence null hit) with a database search score drawn from overlapping distributions, and a live target-decoy FDR estimator computes the score cutoff for your chosen false-discovery-rate threshold, coloring each detector bar green (true identification), red (false identification that slipped through) or gray (correctly rejected). Switching between DDA and DIA acquisition modes changes both the ion throughput and how much the target and decoy score distributions overlap, showing directly why DIA's extra coverage comes with a harder identification problem.

⚙ Under the hood

A time-of-flight mass spectrometer where peptide ions separate by m/z in flight and land on a detector spectrum scored against a target-decoy database, letting you tune the false-discovery-rate threshold and watch decoy hits slip through in real time.

proteomicsmass spectrometryFDRtarget-decoypeptide identificationbioinformatics

3D · Three.js / WebGL renderer · 60 FPS target · runs fully client-side, no install