Target-Decoy FDR in Peptide Mass Spectrometry (2D)

Every peptide identification made by a modern mass spectrometer is a statistical bet, not a certainty. This 2D simulator draws a real time-of-flight flight tube in cross-section: 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). A third panel plots the live target vs. decoy score histograms so you can see the overlap the FDR estimate is built from. 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.