Abstract: A method for calibrating a time-of-flight (ToF) mass analyser comprises an ion injection device and an ion mirror comprising a plurality of electrodes, comprising: applying a plurality of acceleration voltages to cause ions to exit the ion injection device; at each ion energy, measuring the resolving power of the mass analyser with a plurality of sets of electrode voltages applied to the electrodes by varying a first tuning parameter to a respective plurality of values, wherein the first tuning parameter parameterises the electrode voltages applied to the plurality of electrodes; determining maximising values of the first tuning parameter; identifying a point of inflection in the dependence of the maximising values of the first tuning parameter; determining a set of calibrated operating parameters for the massanalyser based on the point of inflection; and causing the mass analyser to operate with the calibrated operating parameters.

Abstract: A method of determining a calibration model for an analytical instrument comprises receiving mass spectral data, wherein the mass spectral data is generated by analysing one or more calibration samples using an analytical instrument; processing the mass spectral data to produce processed data indicative of one or more properties of the analytical instrument; and determining a calibration model for the analytical instrument by performing Gaussian Process Regression (GPR) on the processed data.

Abstract: Methods of calibrating a Time of Flight (TOF) mass analyser comprise performing a plurality of calibration analyses of calibrant ions using the TOF mass analyser, each calibration analysis measuring flight times of the calibrant ions. The TOF mass analyser has an associated instrument parameter which effects the flight times of the calibrant ions. Each calibration analysis also comprises determining a reference calibration curve based on known mass to charge ratios of the calibrant ions and the respective flight times, wherein the reference calibration curve is associated with the instrument parameter for the respective calibration analysis. For each calibration analysis, a value of the instrument parameter of the TOF mass analyser is different. A calibration curve for use in a TOF mass analysis performed by the TOF mass analyser can be determined based on the plurality of reference calibration curves and the instrument parameter.

Abstract: An analytical instrument comprises a first mass filter and a mass filter arranged downstream of the first mass filter. A method of operating the instrument comprises operating the first mass filter in a first mode of operation in which the first mass filter transmits ions having mass-to-charge ratios within a first mass-to-charge ratio (m/z) window, wherein the first m/z window is centred at a first m/z; switching, at a first time, the first mass filter to a second mode of operation in which the first mass filter transmits ions having mass-to-charge ratios within a second different m/z window, wherein the second m/z window is centred at a second different m/z; and beginning accumulating ions in an ion store and/or beginning acquiring mass spectral data of ions at a second time, wherein the second time follows the first time after a delay time.

Abstract: A method of gain calibration for an ion detector operating at a detector voltage is described. The method includes steps of: generating single ions; determining a parameter of a first relationship between a detector output of an ion detector and a number of ions for a first detector voltage; detecting an ion peak at the ion detector using the first detector voltage; adjusting the detector voltage; and determining a parameter of a second relationship between the detector output and the number of ions for the second detector voltage. A system including a mass spectrometer arrangement and a controller configured to operate the mass spectrometer arrangement in accordance with this method is also described.

Abstract: A method of analysing a signal generated by a mass analyser comprises receiving a signal generated by the mass analyser, determining the area of a first ion peak of one or more ion peaks in the signal, and estimating the number of ions that contributed to the first ion peak. The number of ions that contributed to the first ion peak is estimated by determining a correction to be applied to the area of the first ion peak from a correction function, and applying the correction to the area of the first ion peak. The correction function describes a relationship between average single ion area and ion mass, mass-to-charge ratio and/or charge for the mass analyser.

Abstract: Embodiments provide methods of disambiguating the spectra produced by cyclic ion analysers. Systems, methods, and computer readable media described herein can compare two sets of ion data that have been obtained using different analyser settings such that the number of passes N through the cyclic segment of the ion path taken by ions contributing to an ion peak can be determined. As a result of the determination of the number of passes N taken by ions, the physicochemical property of those ions can be unambiguously assigned to the ion peak.

Abstract: A method of analysing data generated by an ion analyser comprises (i) receiving a segment of data generated by an ion analyser, wherein the segment of data comprises data associated with a first arrival time range, and (ii) applying a filter to the segment of data so as to produce a filtered version of the segment of data. A width associated with the filter is configured to depend upon a width of an expected ion arrival time distribution for the ion analyser for arrival times within the first arrival time range. The method further comprises (iii) identifying one or more ion peaks in the filtered version of the segment of data, and then (iv) determining one or more characteristics of each ion peak of the one or more identified ion peaks.

Abstract: Systems, methods, and computer-readable media described provide multi-reflection time-of-flight analyser (e.g. of a type in which the ion beam is allowed to spread out relatively broadly) and methods for use in a zoom mode, in which time-of-flight perturbations induced by reflections at the deflector are cancelled out or removed, such that they do not give rise to a significant increase in the arrival time spread of ions at the detector. This accordingly facilitates high resolution operation of the analyser in the zoom mode. Furthermore, this is done in a way which allows the analyser to remain drift focussed, which in turn means that the analyser can be straightforwardly and seamlessly switched between its normal mode of operation and the zoom mode of operation.

Abstract: Method and system for characterising an isolation profile of a mass spectrometer, the method comprising obtaining data of an, or at least one ion species transmitted by a mass spectrometer forming an isolation profile of the mass spectrometer. Normalizing the obtained data. Providing the normalized data to a deep neural network trained using a plurality of previous isolation profiles. Generating from the deep neural network a set of fit parameters of a curve representing a fit to the normalized data. Providing as an output, data representing the curve. The method may also be used as part of a calibration procedure for the mass spectrometer.

Abstract: A method for correcting mass spectral data obtained for a sample is described, where the mass spectral data is a time-of-flight mass spectral data. The method includes receiving mass spectral data obtained from a sample, the mass spectral data being indicative of an ion abundance. The method further includes applying a correction function to the mass spectral data based on the ion abundance indicated by the mass spectral data and on one or more trapping parameters associated with the mass spectral data. The correction function defines correction values for the mass spectral data for a range of ion abundances and for a range of trapping parameters.

Abstract: A method of gain calibration for an ion detector operating at a detector voltage is described. The method includes steps of: generating single ions; determining a parameter of a first relationship between a detector output of an ion detector and a number of ions for a first detector voltage; detecting an ion peak at the ion detector using the first detector voltage; adjusting the detector voltage; and determining a parameter of a second relationship between the detector output and the number of ions for the second detector voltage. A system including a mass spectrometer arrangement and a controller configured to operate the mass spectrometer arrangement in accordance with this method is also described.