A method of mass spectrometry is disclosed in which one or more AC excitation voltage waveforms are applied to electrodes of an ion guide to radially excite and thereby attenuate ions having mass to charge ratios within respective mass to charge ratio windows. The AC excitation voltage waveforms are varied with time such that ions having different mass to charge ratios are attenuated with different attenuation time profiles. Plural AC excitation voltage waveforms may be varied with time to provide unique mass to charge ratio encoding.

A method of mass and/or ion mobility spectrometry comprising: providing an ion guide comprising a plurality of electrodes and having a background gas therein; applying an RF voltage to electrodes of the ion guide for radially confining ions therein; transmitting clusters of analyte ions and adduct species into the ion guide; applying, in a first mode, one or more AC voltage to the ion guide so as to oscillate the clusters such that they collide with molecules of the background gas and cause adduct species in the clusters to detach from the analyte ions, wherein the one or more AC voltage has a different amplitude and/or frequency to that of said RF voltage; and (i) varying the speed with which the clusters are urged along the ion guide during the first mode; and/or (ii) varying he amplitude and/or frequency of the one or more AC voltage as the clusters travel along the ion guide.

A method of analyzing a sample, the method includes separating precursor ions from the sample into narrow mass range groups based on mass-to-charge ratio; fragmenting the ions from each group to create groups of fragment ions; and mass analyzing fragment ions from each group of fragment ions using a long transient time mass analyzer, wherein the separation and fragmentation are decoupled from the mass analyzing and the cycle time of the high transient mass analyzer is greater than about five times longer than the cycle time of a narrow mass range scan time, and wherein the separation and fragmentation has a high duty cycle and the mass analyzing has a high duty cycle.

An apparatus includes multiple levels of ion transport channels, with successive levels coupled by elevator channels. Efficient three dimensional packing provides long path lengths in practical volumes for ion mobility separation with high resolving power. Disclosed elevator configurations provide efficient routing of ion transport channels across levels with low ion loss, enabling ion mobility separation over 100 levels or more. Elevator configurations include (i) opposed traveling waves meeting at an elevator entrance, (ii) external elevator with a wrap-around electrode bank, (iii) external elevator with electrode banks on parallel extension plates, or (iv) elevator operating in surfing mode, in various combinations. Manufacture is aided by printed wiring boards, with interchangeable boards. Assembly with motherboard, spacer block(s), and alignment pins provides efficient distribution of electrode excitations and accurate reproducible positioning.

An ion sequestering apparatus and methods or systems using one or more auxiliary electrodes in an ion reaction instrument having RF electrodes adapted to guide positively-charged precursor ions along a first axis, and an electron source for introduction of an electron beam along a second axis transverse to the first axis such that electron activated dissociation of the precursor ions into reaction products can occur, the auxiliary electrode configured to apply a supplemental AC signal to permit selective extraction of reaction products while sequestering precursor ions along the second central axis. For example, the supplemental AC signal can comprises an notched white noise signal with a notch that suppresses frequencies at which the precursor ions (and/or charge reduced species that have the same molecular mass but have a different charge state) would otherwise be excited.

In one aspect, a method of performing mass spectrometry is disclosed, which comprises ionizing a plurality of oligonucleotides to generate a plurality of negatively charged oligonucleotide ions, and interacting a plurality of charged reagent ions with the negatively charged oligonucleotide ions to reduce the negative charge state of the negatively charged oligonucleotide ions.

An ion guide electrode assembly (10) for an ion-mobility spectrometer is described. The electrode assembly (10) comprises a first sheet (100), having first and second surfaces (110, 120) comprising a plurality of corresponding regions (111, 112, 121, 122). The first sheet (100) comprises a set of N electrodes (130, 140), including a first electrode (130) and a second electrode (140), provided as tracks mutually spaced apart on the first surface (110) thereof. The electrode assembly (10) is arrangeable in a planar configuration and preferably in a tubular configuration. In the tubular configuration, a first part (131) of the first electrode (130), provided in a first region 111 of the first surface (110), overlays a second region (122) of the second surface (120). In the tubular configuration, the first part (131) of the first electrode (130) overlaps a second part (132) of the first electrode (130) and/or a second part (142) of the second electrode (140), provided in a second region (112) of the first surface (110).

A mass spectrometer is disclosed comprising a rotatable isolation valve (1) having a curved, spherical, cylindrical or concave portion. At least a portion of an ion guide (2) is positioned so as to extend within a swept volume of the isolation valve (1) enabling the ion guide (2) to be positioned close to a second downstream ion guide (3) and for ions to be transmitted from the first (2) ion guide to the second ion guide (3) with high ion transmission efficiency.

A mass spectrometer is disclosed comprising an ion mobility spectrometer or separator and an ion guide arranged downstream of the ion mobility spectrometer or separator. A plurality of axial potential wells are created in the ion guide so that ions received from the ion mobility spectrometer or separator become confined in separate axial potential wells. The potential wells maintain the fidelity and/or composition of ions received from the ion mobility spectrometer or separator. The potential wells are translated along the length of the ion guide.

An ion optical arrangement (1) for use in a mass spectrometer comprises electrodes (11, 12, 14) comprising a multipole arrangement defining an ion optical axis, and a voltage source for providing voltages to the electrodes to produce electric fields. The ion optical arrangement is configured for producing a radio frequency electric focusing field for focusing ions on the ion optical axis. The radio frequency electric focusing field has a varying frequency so as to reduce any mass dependence of ion trajectories through the ion optical arrangement. The ion optical arrangement may further be configured for producing a static electric field in response to a DC bias voltage applied to the multipole arrangement. A superimposed varying electric field may be produced by superimposing an AC voltage upon the DC bias voltage.