A method for operating a mass spectrometer (1, 307, 407, 507) so as to detect a presence of or a quantity of one or more analytes of a sample, comprising: for each of the one or more analytes, identifying one or more selected-reaction-monitoring transitions to be used for detecting the presence or quantity of the respective analyte; ionizing the sample in an ionization source of the mass spectrometer (1, 307, 407, 507) so as to produce one or more populations of first-generation ions; and for each of the one or more identified SRM transitions, performing the steps of: isolating a sub-population of the one or more populations of first-generation ions corresponding to a precursor-ion mass-to-charge (m/z) ratio associated with the respective SRM transition; fragmenting the respective isolated sub-population of ions in a one of two portions of a partitioned fragmentation cell of the mass spectrometer (1, 307, 407, 507) so as to produce a respective population of fragment ions; and analyzing, with a mass analyzer of the mass spectrometer (1, 307, 407, 507), for the presence or quantity, among the respective fragment ions, of ions corresponding to a product-ion m/z ratio associated with the respective SRM transition, the method characterized by: determining, for each of the one or more identified SRM transitions, a time duration required for a subsequent fragmentation step corresponding to the identified SRM transition to proceed to a certain threshold percentage of completion; and in that for each identified SRM transition, the portion of the partitioned fragmentation cell that is used for fragmenting the isolated sub-population of ions corresponding to the respective precursor-ion m/z ratio is determined from the time duration determined for the respective identified SRM transition. for each of the one or more analytes, identifying one or more selected-reaction-monitoring transitions to be used for detecting the presence or quantity of the respective analyte; ionizing the sample in an ionization source of the mass spectrometer (1, 307, 407, 507) so as to produce one or more populations of first-generation ions; and for each of the one or more identified SRM transitions, performing the steps of: isolating a sub-population of the one or more populations of first-generation ions corresponding to a precursor-ion mass-to-charge (m/z) ratio associated with the respective SRM transition; fragmenting the respective isolated sub-population of ions in a one of two portions of a partitioned fragmentation cell of the mass spectrometer (1, 307, 407, 507) so as to produce a respective population of fragment ions; and analyzing, with a mass analyzer of the mass spectrometer (1, 307, 407, 507), for the presence or quantity, among the respective fragment ions, of ions corresponding to a product-ion m/z ratio associated with the respective SRM transition, isolating a sub-population of the one or more populations of first-generation ions corresponding to a precursor-ion mass-to-charge (m/z) ratio associated with the respective SRM transition; fragmenting the respective isolated sub-population of ions in a one of two portions of a partitioned fragmentation cell of the mass spectrometer (1, 307, 407, 507) so as to produce a respective population of fragment ions; and analyzing, with a mass analyzer of the mass spectrometer (1, 307, 407, 507), for the presence or quantity, among the respective fragment ions, of ions corresponding to a product-ion m/z ratio associated with the respective SRM transition, determining, for each of the one or more identified SRM transitions, a time duration required for a subsequent fragmentation step corresponding to the identified SRM transition to proceed to a certain threshold percentage of completion; and in that for each identified SRM transition, the portion of the partitioned fragmentation cell that is used for fragmenting the isolated sub-population of ions corresponding to the respective precursor-ion m/z ratio is determined from the time duration determined for the respective identified SRM transition.