Ion population control in a mass spectrometer having mass-selective transfer optics

A mass spectrometer system comprising:

• (i) an ion source for providing ions;
• (ii) an ion accumulator for storing, fragmenting or analyzing ions provided by the ion source, the ion accumulator having an ion detector;
• (iii) an ion transport device disposed between the ion source and the ion accumulator for transporting ions from the ion source to the ion accumulator, the ion transport device having efficiency of ion transmission therethrough that is generally non-constant with respect to ionic mass-to-charge ratio (m/z ratio);
• and
• (iv) an electronic processing and control unit electronically coupled to the ion accumulator and the ion transport device, the electronic processing and control unit configured to:
• (a) cause the ion transport device to transport a first sample of ions having a range of m/z ratios from the ion source into the ion accumulator for a first injection time under first operating conditions of the ion transport device, the first operating conditions chosen so as to at least partially counteract the non-constancy of ion transmission efficiency through ion transport device such that an accumulated population of ions transported into the ion accumulator substantially approximates a population of ions produced by the ion source within the range of m/z ratios;
• (b) cause the ion accumulator and detector to acquire a full-scan mass spectrum of the first sample of ions;
• (c) select, based on the full-scan mass spectrum, an ion species having a species m/z ratio and corresponding to a mass spectrum peak intensity within the full-scan mass spectrum;
• (d) calculate a second injection time, the second injection time for transporting a population of the selected ion species through the ion transport device and into the ion accumulator under second operating conditions of the ion transport device, the second operating conditions different from the first operating conditions and chosen such that transmission efficiency through the ion transport device at the species m/z ratio is greater under the second conditions than under the first operating conditions, wherein the calculating is based on the first injection time, the peak intensity, a target value for a number of ion charges in the ion accumulator and a predetermined correction factor;
• (e) cause the ion transport device to transport a second sample of ions having the selected ion species from the ion source into the ion accumulator for the second injection time under the second operating conditions of the ion transport device;
• and
• (f) cause the ion accumulator and detector to acquire a mass spectrum of ions derived from the selected ion species in the mass spectrometer.