A method for determining a compensation factor parameter, c, for controlling an amount of ions ionised that are injected from an ion storage unit into mass analyser, where c is an adjustment factor that is applied to optimized injection times that are based on an optimized visible charge of a reference sample, the method comprising: detecting at least one mass spectrum for at least one amount of injected ions; determining from the at least one detected mass spectrum, a slope, s(sample), of a linear correlation of a relative m/z shift with visible total charge Q.sub.v of detected mass spectra; determining the compensation factor c as c=s(reference)/s(sample) where s(reference) is the slope of a linear correlation between reference-sample relative m/z shift values and reference-sample visible charge values determined from a plurality of mass spectra detected from a plurality of respective pre-selected amounts of a clean reference sample.

A method for controlling the filling of an ion trap with a predetermined quantity of ions. The method comprises generating an ion current by transmitting ions along an ion path to an ion trap, such that ions are accumulated in the ion trap over a transmission time period, wherein the magnitude of the ion current varies in time. The method further comprises detecting at an ion detector at least some ions from the source of ions during a plurality of distinct sampling time intervals interspersed within the transmission time period, and setting the duration of the transmission time period based on the detection of ions at the ion detector. The time difference between the start of a sampling time interval and the start of an immediately subsequent sampling time interval is less than a timescale for variation of the magnitude of the ion current. A controller for controlling the filling of an ion trap with a predetermined quantity of ions and a mass spectrometer comprising the controller is also described.

A method of mass and/or ion mobility spectrometry is disclosed that comprises accumulating ions for a first period of time (T1) one or more times so as to form one or more first groups of ions, accumulating ions for a second period of time (T2) one or more times so as to form one or more second groups of ions, wherein the second period of time (T2) is less that the first period of time (T1), analysing the one or more first groups of ions to generate one or more first data sets, analysing the one or more second groups of ions to generate one or more second data sets, and determining whether the one or more first data sets comprise saturated and/or distorted data. If it is determined that the one or more first data sets comprise saturated and/or distorted data, then the method further comprises replacing the saturated and/or distorted data from the one or more first data sets with corresponding data from the one or more second data sets.

A space-time buffer includes a plurality of discrete trapping regions and a controller. The plurality of discrete trapping regions is configured to trap ions as individual trapping regions or as combinations of trapping regions. The controller is configured to combine at least a portion of the plurality of trapping regions into a larger trap region; fill the larger trap region with a plurality of ions; split the larger trap region into individual trapping regions each containing a portion of the plurality of ions; and eject ions from the trapping regions.

A space-time buffer includes a plurality of discrete trapping regions and a controller. The plurality of discrete trapping regions is configured to trap ions as individual trapping regions or as combinations of trapping regions. The controller is configured to combine at least a portion of the plurality of trapping regions into a larger trap region; fill the larger trap region with a plurality of ions; split the larger trap region into individual trapping regions each containing a portion of the plurality of ions; and eject ions from the trapping regions.

A method of fragmenting ions comprises: injecting first ions of a first charge into an ion trap that includes an elongate multipole electrode assembly defining an elongate ion channel; radially confining the first ions within the ion channel by applying an RF pseudopotential to the electrode assembly and axially confining said ions to a first volume within the ion channel by applying a first potential well to the ion channel; injecting second ions of a second charge opposite to the first charge into the ion trap; axially confining the second ions to a second volume within the ion channel by applying a second potential well to the ion channel, the first potential well being within the second potential well; cooling the first and second ions in the ion trap; and allowing the ions to interact such that the first ions and/or second ions are fragmented to produce product ions.

A Liquid Chromatography Mass Spectrometry system comprises: a chromatograph; a mass spectrometer configured to ionize separated fractions of a sample received from the chromatograph; and a programmable processor operable to repeatedly execute the steps of: (i) causing the mass spectrometer to perform a data-independent analysis of the precursor ion species using a mass analyzer of the mass spectrometer; (ii) calculating one or more degree-of-matching scores that relate to detection of an internal standard; and (iii) if each of the degree-of-matching scores meets a respective degree-of-matching condition, performing a quantitative tandem mass spectrometric analyses of both the internal standard and the analyte; the programmable processor further operable to calculate a quantity of the analyte in the sample by comparison between intensities of one or more mass spectral signals generated by the quantitative tandem mass spectrometric analyses of the analyte and the internal standard.

A method of mass spectrometry is disclosed wherein one or more relatively abundant or intense species of ions in a first population of ions are selectively attenuated so as to form a second population of ions. The total ion current of the second population of ions is then adjusted so that the ion current corresponding to ions which are onwardly transmitted to a mass analyser comprising an ion detector is within the dynamic range of the ion detector.

A method of mass and/or ion mobility spectrometry is disclosed that comprises accumulating ions for a first period of time (T1) one or more times so as to form one or more first groups of ions, accumulating ions for a second period of time (T2) one or more times so as to form one or more second groups of ions, wherein the second period of time (T2) is less that the first period of time (T1), analysing the one or more first groups of ions to generate one or more first data sets, analysing the one or more second groups of ions to generate one or more second data sets, and determining whether the one or more first data sets comprise saturated and/or distorted data. If it is determined that the one or more first data sets comprise saturated and/or distorted data, then the method further comprises replacing the saturated and/or distorted data from the one or more first data sets with corresponding data from the one or more second data sets.

An analytical device, includes: an ionization unit that ionizes carrier gas introduced into the separation column; a mass separation unit that mass-separates ions generated in the ionization unit; a detection unit that detects the ions mass-separated by the mass separation unit in amplification with a predetermined multiplication factor, and outputs a detection signal; an analysis unit that analyzes the detection signal having been output from the detection unit; and an adjustment unit performs an adjustment of the multiplication factor of the detection unit and/or voltage applied to an electrode of an ion transport system of the mass separation unit based on magnitude of the detection signal corresponding to the carrier gas detected by the detection unit.