Abstract: A method of mass spectrometry is disclosed comprising calculating an ion mobility value, collision cross section or interaction cross section of a plurality of different analyte ions under one or more different analytical conditions, and setting one or more operational parameters of a mass spectrometer in response to the calculated ion mobility values, collision cross sections or the calculated interaction cross sections so as to maximize or enhance a subsequent ion mobility separation of a plurality of different analyte ions.

Abstract: An ion detection system is disclosed that comprises one or more first devices (11) configured to produce secondary electrons in response to incident ions. The one or more first devices (11) comprise a first ion collection region and a second ion collection region and are configured to produce first secondary electrons in response to one or more ions incident at the first ion collection region and to produce second secondary electrons in response to one or more ions incident at the second ion collection region. The ion detection system also comprises a first output device (14) configured to output a first signal in response to first secondary electrons produced by the one or more first devices (11) and a second output device (15) configured to output a second signal in response to second secondary electrons produced by the one or more first devices (11).

Abstract: A method of mass spectrometry is disclosed comprising digitising a signal output from a detector to provide a first digitised signal. A finite impulse response (“FIR”) filter, a digital filter or an echo cancellation filter is applied to the first digitised signal in order to reduce the effect of baseline perturbations, echoes or ringing effects. Alternatively, an analogue signal output from a detector is passed to one or more first power splitters or dividers, wherein one or more first transmission lines are attached to one or more ports of one more said first power splitters or dividers in order to reduce the effect of baseline perturbations, echoes or ringing effects.

Abstract: A method of ionizing a sample is disclosed comprising performing an initial experiment comprising: (i) adding one or more reagents to an analyte sample; (ii) varying the composition and/or concentration of the one or more reagents; (iii) ionizing the analyte sample including the one or more reagents; (iv) determining the composition and/or concentration of the one or more reagents which results in a desired, improved or optimized ionization or other condition or parameter for one or more analytes of interest; and (v) determining one or more first retention times or one or more first retention time windows for the one or more analytes of interest. The method then further comprises separating an analyte sample using a first separation device and during the course of a single experimental run or acquisition varying the composition and/or concentration of one or more reagents which are added to an eluent which emerges from the first separation device.

Abstract: A data acquisition system for a TOF mass spectrometer comprises a processing module and a data collection module. The processing module generates a stream of data comprising, for each respective transient of a first scan, a set of time-intensity related parameter pairs. For each new set of data, the data collection module reads out a previous set of data from a previous memory bank, merges that previous set of data with the new set of data, and writes that latest merged set of data into a memory bank other than the previous memory bank. The data acquisition system provides a convenient way to merge sequential sets of time-intensity related parameter pairs for respective transients as a stream of data for a first scan is generated.

Abstract: A method of encoding a parent or precursor ion beam to aid product ion assignment is disclosed. According to an embodiment the energy of parent ions entering a collision cell is progressively increased. Different species of parent ions fragment at different collision energies. Fragment ion intensity profiles are matched with parent ion intensity profiles to correlate fragment ions with corresponding parent ions.

Abstract: An ion trapping system is disclosed comprising an ion urging system for urging ions to spread out within an ion trapping region. Alternatively, the ion trapping system may deflect ions such that ions enter the ion trapping region at different locations. Alternatively, an ion deflector may be arranged upstream of, or at the entrance to, the ion trapping region, for deflecting ions such that ions enter the ion trapping region with different speeds so that the ions spread out within the ion trapping region.

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 method of mass spectrometry is disclosed comprising separating a first population of ions according to their ion mobility and selectively attenuating ions in the first population of ions in one or more ion mobility and/or drift time ranges so as to form a second population of ions. The step of selectively attenuating ions comprises applying a varying, increasing or decreasing attenuation factor to ions in different ion mobility and/or drift time ranges. The method further comprises separating the second population of ions according to their ion mobility.

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: A method of separating ions is disclosed comprising: providing an ion separation device comprising a plurality of electrodes; providing a gas flow (5) so as to urge ions in a first direction along the device; applying voltages to said electrodes so that a plurality of travelling potentials (4) urge the ions in a second opposite direction; and varying at least one operational parameter of the travelling potentials (4) as a function of position along the device such that ions of different mobility or mass to charge ratio become trapped at different locations along the device.

Abstract: A method of mass spectrometry is disclosed comprising digitizing a signal output from a detector to provide a first digitized signal. A finite impulse response (“FIR”) filter, a digital filter or an echo cancellation filter is applied to the first digitized signal in order to reduce the effect of baseline perturbations, echoes or ringing effects. Alternatively, an analog signal output from a detector is passed to one or more first power splitters or dividers, wherein one or more first transmission lines are attached to one or more ports of one more said first power splitters or dividers in order to reduce the effect of baseline perturbations, echoes or ringing effects.

Abstract: An apparatus is provided to separate ions temporally according to a physico-chemical property comprising an ion guide comprising a plurality of electrodes and a first device arranged and adapted to remove undesired ions remaining within the ion guide after ions of interest have exited the ion guide.

Abstract: A method of mass spectrometry is disclosed comprising digitizing a plurality of individual signals or transients and summing the plurality of digitized signals or transients or data relating to the plurality of digitized signals or transients to generate a composite mass spectral data set. The method further comprises determining in relation to the composite mass spectral data set an indication of the proportion of instances that intensity values relating to the individual digitized signals or transients either: (i) exceeded or approached a threshold value; (ii) suffered from saturation or approached saturation; or (iii) resulted from the dynamic range of an ion detector system being exceeded or approached.

Abstract: A method of ion mobility spectrometry is disclosed comprising: transmitting a plurality of ions to an ion mobility separator 6; modulating the introduction of the ions into the ion mobility separator 6 at a first modulation frequency; separating the ions that enter the ion mobility separator 6 according to ion mobility; detecting ions that have exited the ion mobility separator with a detector of a time of flight mass analyser 8; varying the first modulation frequency with time; recording the intensity of the ion signal output from the detector to produce recorded data; modulating the recorded data as a function of the time that the data was recorded and at a second modulation frequency, wherein the second modulation frequency is varied as a function of the time that the data was recorded; and determining, from the variation in intensity of the ion signal in the modulated data as a function of the second modulation frequency, the ion mobilities of the ions that have been detected.

Abstract: A method of mass spectrometry or ion mobility spectrometry is disclosed. The method comprises: providing a plurality of species of ions; analyzing 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, while discarding less optimal data.

Abstract: A method of mass or ion mobility spectrometry is disclosed. The method comprises providing a spectrometer comprising an orifice between an atmospheric and a sub-atmospheric pressure region of the spectrometer, wherein the latter comprises an ion guide or ion trap; providing a sample probe comprising a needle assembly on which a sample is deposited or that is supplied with a sample; inserting the needle assembly through the orifice into the sub-atmospheric pressure region so that the sample is arranged within or adjacent to the ion guide or trap in the sub-atmospheric pressure region; and then desorbing the sample from the needle assembly within the sub-atmospheric pressure region and/or ionizing the sample within the sub-atmospheric pressure region so as to generate ions that enter the ion guide or ion trap. The proximity of the sample to the ion guide or trap allows analyte ions from the sample to be captured efficiently.

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; ionizing 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: 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 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.