Abstract: A method of analyzing 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 mass spectrometry is disclosed comprising separating first ions according to a first physico-chemical property in a first separator wherein at least some of the first ions undergo a different number of cycles or passes within the separator and separating the first ions which emerge from the first separator according to a second physico-chemical property wherein the second physico-chemical property is correlated with the first physico-chemical property. The method further comprises determining the second physico-chemical property of the first ions and determining, assigning or de-convolving the first physico-chemical property of the first ions based upon the determined second physico-chemical property of the first ions.

Abstract: A method of mass spectrometry for analyzing lipids and similar biological molecules is disclosed. The lipid molecules may be ionized 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 analyzing the fragment and product ions and analyzing their intensity profile.

Abstract: A method of mass spectrometry is disclosed comprising: a) separating first ions or components of an analyte sample according to a physicochemical property other than ion mobility; b) separating said first ions or second ions formed from said components according to ion mobility; c) detecting the intensities of said first ions, or detecting the intensities of second ions formed from said components, or detecting the intensities of ions derived from said first or second ions; wherein the intensity of the ions detected at any given time is recorded together with an associated value of said physicochemical property and an associated value of said ion mobility so as to obtain spectral data; d) examining the intensities of the spectral data as a function of said ion mobility so as to detect an intensity peak in said spectral data, determining a discrete value of ion mobility for said peak, and defining a window of values of ion mobility that encompasses said discrete value; and e) filtering said spectral data so as

Abstract: A method of mass spectrometry is disclosed comprising experimentally determining or measuring one or more first ion mobility values, collision cross sections or interaction cross sections collision cross sections or first ion mobility parameters and one or more mass or mass to charge ratios of one or more analyte ions, generating a first list of possible candidate compounds which correspond to said one or more analyte ions on the basis of the one or more determined or measured masses or mass to charge ratios, and calculating, estimating or determining one or more second ion mobility values, collision cross sections or interaction cross sections collision cross sections or second ion mobility parameters of at least some of the candidate compounds in the first list.

Abstract: A method is disclosed comprising passing a signal output from a detector through a programmable attenuator or a programmable amplifier prior to digitizing the signal, and switching an attenuation factor or gain factor of the programmable attenuator or the programmable amplifier one or more times during a data acquisition period.

Abstract: A mass spectrometer is disclosed comprising a RF ion guide wherein in a mode of operation a continuous, quasi-continuous or pulsed beam of ions is orthogonally sampled from the ion guide and wherein the continuous, quasi-continuous or pulsed beam of ions is not axially trapped or otherwise axially confined within the RF ion guide. The ion guide is maintained, in use, at a pressure selected from the group consisting of: (i) 0.0001-0.001 mbar; (ii) 0.001-0.01 mbar; (iii) 0.01-0.1 mbar; (iv) 0.1-1 mbar; (v) 1-10 mbar; (vi) 10-100 mbar; and (vii) >100 mbar.

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 is disclosed comprising: trapping ions in an ion trap (40); applying a first force on the ions within the ion trap in a first direction, said force having a magnitude that is dependent upon the value of a physicochemical property of the ions; applying a second force on these ions in the opposite direction so that the ions separate according to the physicochemical property value as a result of the first and second forces; and then pulsing or driving ions out of one or more regions of the ion trap.

Abstract: A method of separating ions according to mass to charge ratio is disclosed. The method comprises: providing a separation device comprising a plurality of electrodes; applying one or more transient DC voltages or potentials to at least some of said electrodes in order to urge ions in a first direction through said separation device; and providing a gas flow in a second direction which is substantially inclined or opposed to said first direction. The opposed gas flow unexpectedly improves the mass to charge ratio separation resolution of the device.

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

Abstract: A mass spectrometer is disclosed comprising a first mass filter comprising a plurality of electrodes and a first device arranged and adapted to generate an axial force which drives at least some ions axially through or along the first mass filter and a quadrupole mass filter or mass analyzer arranged downstream of the mass filter.

Abstract: A method of mass spectrometry is disclosed comprising monitoring for the emergence of one or more species of ions of interest and determining during the course of acquiring experimental data whether one or more ions or interest have emerged and then discontinuing monitoring for the emergence of the one or more species of ions of interest if it determined that the one or more ions or interest have emerged.

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 non-linear ion guide is disclosed comprising a plurality of electrodes. An ion guiding region is arranged between the electrodes, and the ion guiding region curves at least in a first direction. A DC voltage is applied to at least some of the electrodes in order to form a DC potential well which acts to confine ions within the ion guiding region in the first direction.

Abstract: There is provided a method of separating ions comprising operating an ion mobility spectrometer or separator at a reduced pressure and at an operating temperature less than 40° C., and providing a drift gas within said ion mobility spectrometer or separator, wherein said drift gas comprises one or more substances that exist as a liquid at atmospheric pressure (optionally about 1013 mbar) and room temperature (optionally about 20° C.) and wherein said one or more substances have a boiling or sublimation point less than said operating temperature of said ion mobility spectrometer or separator, at said reduced pressure.

Abstract: A method of separating ions comprises causing ions to separate according to their ion mobility or differential ion mobility by virtue of their interactions with a buffer gas within an ion mobility or differential ion mobility separation device. The buffer gas comprises one or more organic, organosilicon or silicon-based compounds.

Abstract: A method of mass or ion mobility spectrometry is disclosed comprising: providing an ion source for generating analyte ions and reference ions; providing a mass analyser or ion mobility separator (IMS); providing an ion trap between the ion source and the mass analyser or IMS; guiding reference ions from the ion source into the ion trap and trapping the reference ions in the ion trap; guiding the analyte ions from the ion source into the mass analyser or IMS, wherein the analyte ions bypass the ion trap; and releasing reference ions from the ion trap into the mass analyser or IMS for analysis.

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 Fourier transform ion mobility spectrometry is disclosed wherein an absorption spectrum of the complex spectral data is used to determine the ion mobilities of ions.