Instrument, including an elecrostatic linear ion trap with charge detector reset or calibration, for separating ions

An instrument for separating ions, comprising:

• an ion source configured to generate ions from a sample,
• a first mass spectrometer configured to separate the generated ions as a function of mass-to-charge ratio,
• an ion dissociation stage positioned to receive ions exiting the first mass spectrometer and configured to dissociate ions exiting the first mass spectrometer,
• a second mass spectrometer configured to separate dissociated ions exiting the ion dissociation stage as a function of mass-to-charge ratio, and
• a charge detection mass spectrometer (CDMS) coupled in parallel with and to the ion dissociation stage such that the CDMS can receive ions exiting either of the first mass spectrometer and the ion dissociation stage, the CDMS comprising (i) at least one ion separation instrument configured to separate ions as a function of at least one molecular characteristic, (ii) an electrostatic linear ion trap (ELIT) having a charge detection cylinder disposed between first and second ion mirrors, wherein ions exiting the at least one ion separation instrument are supplied to the ELIT, (iii) a charge generator for generating free charges, (iv) a field free region between the charge generator and the charge detection cylinder, and (v) a processor configured to control the charge generator to generate a target number of free charges and cause the target number of free charges to travel across the field-free region and into contact with the charge detection cylinder to deposit the target number of free charges thereon and thereby calibrate or reset the charge detection cylinder to a corresponding target charge level,
• wherein masses of precursor ions exiting the first mass spectrometer are measured using the CDMS, mass-to-charge ratios of dissociated ions of precursor ions having mass values below a threshold mass are measured using the second mass spectrometer, and mass-to-charge ratios and charge values of dissociated ions of precursor ions having mass values at or above the threshold mass are measured using the CDMS.