Extended Data Fig. 6: Entrapment analyses on DIA data.
From: Unifying the analysis of bottom-up proteomics data with CHIMERYS
Scatter plots of run-specific precursor-level self-reported (x axis) and entrapment FDR (y axis) from three different entrapment approaches (Supplementary Methods). Data is shown for CHIMERYS (A), DIA-NN (B), Spectronaut with default settings (C) and Spectronaut with more stringent settings41 (D) on triplicate 2-h DIA single-shot measurements from two different conditions (n = 6). Data was acquired on an Orbitrap QE HF-X with 8 Th isolation windows and taken from the LFQbench-type dataset37. (E) same as in (B), but for the corresponding TimsTOF Pro data. (F) same as in (C), but for the corresponding TimsTOF Pro data.
