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.

An ion optical arrangement (1) for use in a mass spectrometer comprises a collision cell defining an ion optical axis along which ions may pass, electrodes comprising a set of parallel poles (11A, 11B, 11C) arranged in the collision cell, and a voltage source for providing voltages to the electrodes to produce electric fields. The ion optical arrangement is arranged for switching between a first operation mode in which the collision cell is pressurized and a second operation mode in which the collision cell is substantially evacuated. The ion optical arrangement is further arranged for producing a radio frequency electric focusing field in the first operation mode and a static electric focusing field in the second operation mode.

An ion optical arrangement (1) for use in a mass spectrometer comprises electrodes (11) defining an ion optical path, a housing (18) for accommodating the electrodes, a voltage source for providing voltages to the electrodes to produce electric fields, and a valve for allowing gas to enter and/or leave the housing. The valve comprises an electrostatic mechanism and/or a pneumatic mechanism. The electrostatic mechanism may comprise a flexible foil (30, 31) configured for covering at least one opening (16) in the ion optical arrangement when a first voltage is applied and being spaced apart from the at least one opening when a second voltage is applied. The pneumatic mechanism may comprise a Bourdon tube.

An ion analyzer 1 includes: an ionization chamber 10; an ionization unit 3 configured to generate ions from a sample 11 in the ionization chamber 10; an analysis chamber 20 separated from the ionization chamber 10 by a partition wall 21 in which an opening 211 is formed; an ion transport unit 22, 23, and 24 provided in the analysis chamber 20 and configured to transport the ions generated in the ionization unit; an ion trapping unit 25 provided in the analysis chamber 20 and configured to trap the ions transported by the ion transport unit 22, 23, and 24; an ion detection unit 26 provided in the analysis chamber 20 and configured to detect the ions released from the ion trapping unit 25; and a single evacuation mechanism 28 connected only to the analysis chamber 20 and configured to evacuate the analysis chamber 20 to a pressure of 10.sup.3 Pa or less.

A mass spectrometer includes: an ion source; a collision cell into which a predetermined gas is introduced, for allowing an ion generated in the ion source to be in contact with the predetermined gas; and a quadruple mass filter for performing mass spectrometry on the ion ejected from the collision cell. The mass spectrometer further includes: an inlet electrode provided at an ion injection port through which the ion is incident in the collision cell; a voltage generator for applying a direct-current voltage to the inlet electrode; and a voltage controller and a controller for controlling the voltage generator to apply, to the inlet electrode, a direct-current voltage with a polarity same as a polarity of an unnecessary ion generated in the ion source, during at least a part of a standby period of time in which no analysis-target ion is analyzed.

There is provided a method of guiding ions, comprising providing an ion guide comprising a plurality of electrodes, confining ions radially within said ion guide by applying one or more voltages to said plurality of electrodes, applying an orthogonal DC field along at least a portion of said ion guide in order to control the temperature of ions as they travel through said ion guide, and applying an electrostatic driving potential to said plurality of electrodes to urge ions along the axial length of the ion guide, wherein said electrostatic driving potential is applied in the form of a DC travelling wave potential or other transient DC potential.

A mass isolation device selects a precursor ion of a sample that has been digested using a protease. A first fragmentation device fragments the precursor ion using collision-induced dissociation (CID), and the resulting product ions are analyzed using a mass analyzer producing a CID spectrum. A list of theoretical candidate glycopeptide sequences is determined from CID spectrum. The mass isolation device again selects the precursor ion of the sample. A second fragmentation device fragments the precursor ion using electron-based dissociation (ExD), and the resulting product ions are analyzed using the mass analyzer producing a CID spectrum. For each sequence of the list, the sequence is computationally fragmented, producing theoretical fragments, mass-to-charge ratio (m/z) values are calculated for the theoretical fragments, and the sequence is scored using c and z fragment matching rules. The highest scoring sequence is identified as a peptide sequence of a glycopeptide of the sample.

A method of identifying and/or characterizing ions comprises separating analyte ions according to a first physico-chemical property (ion-mobility), selecting first ions of the analyte ions, and activating, fragmenting or reacting the first ions to produce first product ions, separating the first product ions according to the first physico- chemical property, and determining a pattern of the first product ions. The first ions are identified and/or characterized using the pattern of the first product ions.

A method of mass spectrometry is disclosed comprising: performing a plurality of cycles of operation during a single experimental run, wherein each cycle comprises: mass selectively transmitting precursor ions of a single mass, or range of masses, through or out of a mass separator or mass filter at any given time, wherein the mass separator or mass filter is operated such that the single mass or range of masses transmitted therefrom is varied with time; and mass analysing ions.

The invention generally relates to mass spectrometry via frequency tagging.