Patent ID: 8552365

Claim:
A method for operating a mass spectrometer having an ion source, an ion accumulator and at least one ion transport device therebetween having an ion transmission efficiency that is generally non-constant with respect to ionic mass-to-charge-ratio (m/z ratio) comprising: (a) transporting a first sample of ions having a range of m/z ratios through the ion transport device and 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 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) acquiring a full-scan mass spectrum of the first sample of ions; (c) selecting, 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) calculating a 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 operating 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) transporting a second sample of ions having the selected ion species from the ion source through the ion transport device and into the ion accumulator for the second injection time under the second operating conditions of the ion transport device; and (f) acquiring a mass spectrum of ions derived from the selected ion species in the mass spectrometer.