Fig. 1: Deconvolution of chimeric DDA spectra.

a, CHIMERYS treats chimeric spectra as linear combinations of pure spectra, and its spectrum-centric deconvolution uses non-negative regularized regression to estimate interference-corrected total ion currents for all candidate peptides. b, Peptide group-level entrapment analysis with the classic entrapment FDR (eFDR) approach (Supplementary Methods) of DDA data from a pancreatic mouse cell digest, acquired using different isolation window widths and processed with CHIMERYS. c, Example of a deconvoluted chimeric spectrum with six PSMs from a 2-h HeLa DDA single-shot measurement, acquired on an Orbitrap QE HF-X with 1.3-Th isolation windows from the LFQbench-type dataset³⁷. The inset visualizes how the experimental intensity of shared fragment ions with low m/z values is distributed to multiple PSMs. d, Peptide group-level log₂-ratio density plots for triplicate 2-h DDA single-shot measurements from two different conditions (n = 6), acquired on an Orbitrap QE HF-X with 1.3-Th isolation windows from the LFQbench-type dataset, analyzed with CHIMERYS (top) or Sequest HT (bottom). FDR was controlled at 1% at the global peptide group level. e, Comparison of peptide group identifications from multiple search engines on the same data as in c. FDR was natively controlled at different levels, depending on the search engine.