Abstract: A method of analysing ions, comprising performing an initial multidimensional survey scan comprising separating parent ions according to a first physico-chemical property and separating said parent ions according to a second physico-chemical property, producing a two-dimensional data set comprising data corresponding to said first physico-chemical property and data corresponding to said second physico-chemical property, identifying one or more target ion species of interest and determining a mode of operation of a mass spectrometer for said target ion species of interest using data relating to said target ion species of interest in said two-dimensional data set, wherein said mode of operation comprises the location of fragmentation of said target ions of interest.

Abstract: A method of analysing ions is disclosed comprising: (i) separating ions according to a physico-chemical property in a separator; (ii) transmitting ions which emerge from the separator through a transfer device with a first transit time t1, energising a pusher electrode or orthogonal acceleration electrode and obtaining first data; (iii) transmitting ions which subsequently emerge from the separator through the transfer device with a second greater transit time t2, energising the pusher electrode or orthogonal acceleration electrode and obtaining second data; and (iv) repeating steps (ii) and (iii) one or more times. The pusher electrode or orthogonal acceleration electrode is energised with a period t3, wherein t2?t1 is arranged to equal t3/2. The first and second data are combined to form a composite data set.

Abstract: A method of identifying ions or confirming the identity of ions is disclosed comprising determining a physico-chemical or other property of first ions under first conditions, determining the physico-chemical or other property of the first ions or second ions derived from the first ions under second different conditions, and identifying or confirming the identity of the first ions or determining a class of the first or the second ions on the basis of the physico-chemical or other property of the first ions as determined under the first conditions and on the basis of the physico-chemical or other property of the first ions or second ions derived from the first ions as determined under the second conditions.

Abstract: A mass spectrometer is disclosed comprising an ion mobility separation device for separating ions according to their ion mobility, a first quadrupole mass filter downstream of the ion mobility separation device, a control system arranged and adapted to scan and/or step the set mass of the first quadrupole mass filter a plurality of times over a first mass to charge ratio range of <±2 amu during the elution time of an ion mobility peak from the ion mobility separation device, and an analyser or ion detector downstream of the first quadrupole mass filter arranged and adapted to analyse or detect ions so as to acquire multi-dimensional ion mobility-mass to charge ratio data.

Abstract: A method of calibrating a mass spectrometer is disclosed comprising mass analysing first ions derived from an analyte molecule, wherein the first ions have a first charge state; determining a first mass or mass to charge ratio of the first ions; mass analysing second ions derived from the analyte molecule, wherein the second ions have a second different charge state and wherein the second ions comprise protonated or adduct variants of the first ions; determining a second mass or mass to charge ratio of the second ions; a determining a calibration correction based upon the first mass or mass to charge ratio and the second mass or mass to charge ratio.

Abstract: A method of mass spectrometry is disclosed comprising digitising at least one individual signal or transient, determining in relation to the digitised signal or transient an indication of overlap and/or coalescence of ion arrivals in the digitised signal or transient, or one or more ion arrival envelopes in the digitised signal or transient, and marking or flagging the digitised signal or transient as suffering from overlap or coalescence of ion arrivals based on the indication.

Abstract: A method of mass spectrometry is disclosed that comprises predicting 1 one or more first reaction products which may result from subjecting an analyte to one or more reactions of interest, calculating 2 one or more first masses or mass to charge ratios and one or more first ion mobility values, collision cross sections or interaction cross sections of at least some first reaction product ions which may be generated from the one or more first reaction products under first conditions, and calculating one or more second masses or mass to charge ratios and one or more second ion mobility values, collision cross sections or interaction cross sections of at least some second reaction product ions which may be generated from the one or more first reaction products under second different conditions.

Abstract: A method of mass spectrometry for analysing lipids and similar biological molecules is disclosed. The lipid molecules may be ionised to form a plurality of lipid parent ions and subjected to photon-induced fragmentation to form a plurality of fragment or product ions. The position of one or more unsaturated bonds in the lipid molecules may be determined by mass analysing the fragment and product ions and analysing their intensity profile.

Abstract: A control system and method of determining a signal to noise (S/N) ratio of an ion detector system, including an ion detector, electron multiplier or photomultiplier, operates by determining an area of a noise peak, determining an area of a signal peak and determining a ratio of the area of the signal peak to the area of the noise peak. Based thereon, the signal to noise ratio can be optimized. The system has particular applicability for use in mass spectrometry.

Abstract: A mass spectrometer is disclosed comprising a liquid chromatography device for separating ions. A gas phase ion-neutral reaction device is arranged downstream to perform a gas phase ion-neutral reaction such as Hydrogen-Deuterium exchange. A control system is arranged to automatically and repeatedly switch the reaction device back and forth between a first mode of operation and a second mode of operation, wherein in the first mode of operation at least some parent or precursor ions are caused to react within the reaction device and wherein in the second mode of operation substantially fewer or no parent or precursor ions are caused to react.

Abstract: A method of analyzing ions is disclosed comprising: (i) separating ions according to a physico-chemical property in a separator; (ii) transmitting ions which emerge from the separator through a transfer device with a first transit time t1, energizing a pusher electrode or orthogonal acceleration electrode and obtaining first data; (iii) transmitting ions which subsequently emerge from the separator through the transfer device with a second greater transit time t2, energizing the pusher electrode or orthogonal acceleration electrode and obtaining second data; and (iv) repeating steps (ii) and (iii) one or more times. The pusher electrode or orthogonal acceleration electrode is energized with a period t3, wherein t2-t1 is arranged to equal t3/2. The first and second data are combined to form a composite data set.

Abstract: An ion detector system for a mass spectrometer is disclosed comprising a first device arranged and adapted to receive ions and emit or output first electrons and a microwave cavity resonator arranged and adapted to deflect the first electrons onto a first detector.

Abstract: A method of mass spectrometry or ion mobility spectrometry is disclosed. The method comprises: providing a plurality of species of ions; analysing the ions during a plurality of sequential acquisition periods so as to obtain spectral data relating to the ions; varying the value of an operational parameter of the spectrometer such that it has different values during the different acquisition periods, wherein the spectral data obtained for a given ion varies depending on the value of the operational parameter; storing the spectral data obtained during the different acquisition periods separately; selecting a target ion; and then interrogating the spectral data so as to identify a set of first acquisition periods that include data corresponding to said target ion. Selecting spectral data from only a subset of the first acquisition periods allows the selection of the optimal spectral data for the target ion, whilst discarding less optimal data.

Abstract: A method of mass spectrometry or ion mobility spectrometry is disclosed in which analyte ions of a desired charge state are isolated. The method comprises: separating analytes according to their electrophoretic mobility; ionising the analytes; and mass filtering the resulting analyte ions, wherein the mass to charge ratios of the ions transmitted by a mass filter are varied as a function of the electrophoretic mobility and according to a predetermined relationship such that substantially only ions having said desired charge state are transmitted by the mass filter.

Abstract: An ion source for a mass spectrometer is disclosed comprising an ionization device which emits a stream of droplets and one or more ultrasonic transmitters which create one or more acoustic standing waves. The acoustic standing waves may be used to further nebulize the stream of droplets and induce internal mixing of the droplets.

Abstract: A method of mass spectrometry is disclosed comprising directing first photons from a laser onto ions located within a 2D or linear ion guide or ion trap. The frequency of the first photons is scanned and first photons and/or second photons emitted by the ions are detected. The ions are then mass analyzed using a Time of Flight mass analyzer.

Abstract: A control system and method of determining a signal to noise (S/N) ratio of an ion detector system, including an ion detector, electron multiplier or photomultiplier, operates by determining an area of a noise peak, determining an area of a signal peak and determining a ratio of the area of the signal peak to the area of the noise peak. Based thereon, the signal to noise ratio can be optimised. The system has particular applicability for use in mass spectrometry.

Abstract: A mass spectrometer is disclosed comprising a liquid chromatography device for separating ions. A gas phase ion-neutral reaction device is arranged downstream to perform a gas phase ion-neutral reaction such as Hydrogen-Deuterium exchange. A control system is arranged to automatically and repeatedly switch the reaction device back and forth between a first mode of operation and a second mode of operation, wherein in the first mode of operation at least some parent or precursor ions are caused to react within the reaction device and wherein in the second mode of operation substantially fewer or no parent or precursor ions are caused to react.

Abstract: A method of ion imaging is disclosed comprising scanning a sample and acquiring first mass spectral data related to a first pixel location at a first spatial resolution and determining whether or not the first mass spectral data satisfies a condition. If it is determined that the first mass spectral data does satisfy the condition then the first mass spectral data is stored, recorded or prioritized. If it is determined that the first mass spectral data does not satisfy the condition then the first mass spectral data is discarded or downgraded. Scanning of the sample then continues at the first spatial resolution and further mass spectral data related to further pixel locations is acquired.

Abstract: A method of mass spectrometry or ion mobility spectrometry is disclosed comprising: providing ions towards an ion storage region; selecting a target maximum charge desired to be stored within the ion storage region at any given time; and reducing the ion current passing to the ion storage region such that the ions entering the ion storage region do not cause the total charge within the storage region to rise above said target maximum charge. The step of reducing the ion current passing to the ion storage region comprises: temporally separating the ions according to their ion mobility in an ion mobility separator; and mass filtering the ions according to mass to charge ratio with a mass filter. Said steps of separating and mass filtering the ions result in substantially only target ions having selected combinations of ion mobility and mass to charge ratio being transmitted towards the ion storage region.