Extended Data Fig. 3: CHIMERYS-unique identifications and FDR levels.

(A) MS1 apex intensity distribution of peptide groups filtered at 1% global peptide group-level FDR and identified uniquely by CHIMERYS (green) or also by at least one other search engine tested as part of Fig. 1e (orange). The dataset was a 2-h HeLa DDA single-shot measurement (n = 1) from the LFQbench-type dataset, acquired on an Orbitrap QE HF-X with 1.3 Th isolation windows. (B) Distribution of the number of matched peaks between predicted and experimental spectra for the same data as in (A). (C) Distribution of the normalized spectral contrast angle after deconvolution between predicted and experimental spectra for the same data as in (A). (D) Distribution of the support vector machine score from mokapot for the same data as in (A), including targets with a global peptide group-level FDR exceeding 1% (blue). The support vector machine score distribution for decoys (gray) is overlayed. (E) Scatter-plot of the number of unique peptides per protein group identified by Sequest HT (x axis) or CHIMERYS (y axis) for the same data as in (A). Protein groups are filtered to 1% global protein FDR and peptides are filtered to 1% global peptide group-level FDR. (F) The number of precursors (left) or peptide groups (right) identified by CHIMERYS at 1% run-specific PSM-, run-specific precursor- or global peptide group-level FDR. The dataset is a single 2-h HeLa DDA single-shot measurement (n = 1), acquired on an Orbitrap QE HF-X with 1.3 Th isolation windows and taken from the LFQbench-type dataset. (G) Same as (F), but for 2-h DDA single-shot measurements from two different conditions, acquired in three replicates on an Orbitrap QE HF-X with 1.3 Th isolation windows from the LFQbench-type dataset (n = 6).