Extended Data Fig. 5: Instrument generations, gradients and wwDDA/WWA.

(A) PSM, peptide and protein group identifications based on Sequest HT (orange), MSFragger (green) and CHIMERYS (blue) from 1-h HeLa single-shot measurements, acquired using various Orbitrap generations (n = 1). FDR was controlled at 1% at the run-specific PSM-, global peptide group- (only available for Sequest HT and CHIMERYS) and global protein level, respectively. (B) PSM, peptide and protein group identifications based on CHIMERYS from pancreatic mouse cell single-shot measurements, acquired using different gradient lengths and isolation window widths (n = 1). FDR was controlled at 1% at the run-specific PSM-, global peptide group- and global protein level, respectively. (C) PSM, peptide and protein group identifications based on Sequest HT (orange), MSFragger (green) and CHIMERYS (blue) from 15 min pancreatic mouse cell single-shot measurements (n = 1). Data was acquired using HCD fragmentation with Orbitrap readout and different isolation window widths. FDR was controlled at 1% at the run-specific PSM-, global peptide group- (only available for Sequest HT and CHIMERYS) and global protein level, respectively. (D) PSM, peptide and protein group identifications based on Sequest HT (orange), MSFragger (green) and CHIMERYS after removal of low-abundance peaks (light blue) from 1-h HeLa single-shot measurements (n = 1). Data was acquired using CID fragmentation with ion trap readout and different isolation window widths. FDR was controlled at 1% at the run-specific PSM-, global peptide group- (only available for Sequest HT and CHIMERYS) and global protein level, respectively.