Extended Data Fig. 4: Investigating the dynamic range of the Orbitrap.

a–c, Scan sequence to test the dynamic range of the Orbitrap. a, Ions were injected into the mass spectrometer and a single peptide species was isolated (1). Peptide ions were then sent to the ion-routing-multipole (IRM) for fragmentation by HCD (2). Fragment ions were transferred to the dual ion trap for MS3 isolation (3). b, Mass analysis that included the carrier channel was accomplished by setting ion trap isolation for MS3 from 125.13 mz – 133.13 mz, performing isolation (4), and transferring the resulting ions to the Orbitrap for mass analysis (5). c, Mass analysis that excluded the carrier channel was accomplished by setting ion trap isolation for MS3 from 126.63 mz – 134.63 mz, performing isolation (4), and transferring the resulting ions to the Orbitrap for mass analysis (5). d, Instrument method for dynamic range experiments. (A) MS1 scan properties. (B) MS2 scan properties. (C) Targeted mass filter. (D) Include MS3 scan properties. (E) Exclude MS3 scan properties.