An instrument for separating ions may include an ion source configured to generate ions from a sample, at least one ion separation instrument configured to separate the generated ions as a function of at least one molecular characteristic and an electrostatic linear ion trap (ELIT) positioned to receive ions exiting the at least one ion separation instrument. The ELIT has first and second ion mirrors separated by a charge detection cylinder, and is configured such that an ion trapped therein oscillates back and forth through the charge detection cylinder between the first and second ion mirrors with a duty cycle, corresponding to a ratio of time spent by the trapped ion traversing the charge detection cylinder and total time spent by the trapped ion traversing a combination of the first and second ion mirrors and the charge detection cylinder during one complete oscillation cycle, of approximately 50%.

Methods and apparatuses for ion manipulations, including ion trapping, transfer, and mobility separations, using traveling waves (TW) formed by continuous alternating current (AC) are disclosed. An apparatus for ion manipulation includes a surface to which are coupled a first plurality of continuous electrodes and a second plurality of segmented electrodes. The second plurality of segmented electrodes is arranged in longitudinal sets between or adjacent to the first plurality of electrodes. An RF voltage applied to adjacent electrodes of the first plurality of electrodes is phase shifted by approximately 180° to confine ions within the apparatus. An AC voltage waveform applied to adjacent electrodes within a longitudinal set of the second plurality of segmented electrodes is phase shifted on the adjacent electrodes by 1°-359° to move ions longitudinally through the apparatus for separation.

An apparatus for analysing ions, including a first mass analyser configured to eject groups of ions in a predetermined sequence during different time windows; an ion transport device having a plurality of electrodes arranged around a transport channel; control means configured to control voltages applied to the electrodes to generate a transport potential in a transport channel, the transport potential having a plurality of potential wells configured to move along the transport channel such that each group of ions received by the ion transport device is respectively transported along the transport channel by one or more selected potential; fragmentation means configured to fragment precursor ions in each group of ions so as to produce product ions; and a second mass analyser configured to produce a respective mass spectrum using each group of ions after the group of ions has been fragmented and transported.

An improved multi-pass time-of-flight or electrostatic trap mass spectrometer (70) with an orthogonal accelerator, applicable to mirror based multi-reflecting (MR) or multi-turn (MT) analyzers. The orthogonal accelerator (64) is tilted and after first ion reflection or turn the ion packets are back deflected with a compensated deflector (40) by the same angle α to compensate for the time-front steering and for the chromatic angular spreads. The focal distance of deflector (40) is control by Matsuda plates or other means for producing quadrupolar field in the deflector. Interference with the detector rim is improved with dual deflector (68). The proposed improvements allow substantial extension of flight path and number of ion turns or reflections. The problems of analyzer angular misalignments by tilting of ion mirror (71) is compensated by electrical adjustments of ion beam (63) energy and deflection angles in deflectors (40) and (68).

To acquire a mass spectrum for a wide mass range, a normal analysis execution controlling unit controls components to repeatedly perform measurement while changing setting m/z by a predetermined m/z at a time, and a mass spectrum summarizing processing unit summarizes data pieces each obtained by each time of measurement to generate the mass spectrum. Radio-frequency voltage applied to an ion guide and the like is changed based on the setting m/z. The radio-frequency voltage for the setting m/z is determined using a table in which a relationship between a position on an axis between upper and lower limits of the mass range and the radio-frequency voltage is substantially the same regardless of the mass range.

A space-time buffer includes a plurality of discrete trapping regions and a controller. The plurality of discrete trapping regions is configured to trap ions as individual trapping regions or as combinations of trapping regions. The controller is configured to combine at least a portion of the plurality of trapping regions into a larger trap region; fill the larger trap region with a plurality of ions; split the larger trap region into individual trapping regions each containing a portion of the plurality of ions; and eject ions from the trapping regions.

An apparatus for ion manipulation having improved duty cycle includes first and second separation regions separated by a switch that alternates between guiding ions to each of the separation regions. The separation regions separate the ions based on mobility over respective time periods that at least partially overlap. The apparatus can additionally or alternatively include a pre-separation region that filters ions prior to accumulating ions, thus allowing an accumulation region to accumulate for a longer time period. The apparatus can additionally or alternatively include a plurality of gates along the separation region(s) to simultaneously filter a plurality of ion packets sequentially released into the separation region(s). Methods for ion manipulation having improved duty cycle involve separating ions on two separation regions over first and second time periods that at least partially overlap, pre-filtering ions prior to accumulation and separation, and/or simultaneously filtering a plurality of ions packets are also provided.

A method of determining one or more interference parameters for a particular peak of an isotopic distribution corresponding to a precursor molecule in MS scan data is provided. The MS scan data comprises a plurality of peaks. Each peak has a mass-to-charge ratio and a relative abundance. The isotopic distribution comprises a subset of the plurality of peaks. The one or more interference parameters comprises a peak purity, p.sub.i, for the particular peak. The method comprises determining that there are no interfering peaks relevant to the isotopic distribution and determining that the peak purity, p.sub.i, for the particular peak should be a maximum purity value. Alternatively, the method comprises identifying one or more interfering peaks from the MS scan data, wherein the one or more interfering peaks do not belong to the subset of peaks of the isotopic distribution, and determining the peak purity, p.sub.i, for the particular peak based on: the relative abundance, I.sub.i, of the particular peak, and the relative abundance of the one or more interfering peaks.

A high throughput mass spectrometry system that includes one or more sample preparation devices located at one or more of first locations configured to prepare samples for mass spectrometry analysis; one or more ionization sources configured to produce ions from the prepared samples at the one or more of the first locations; one or more mass spectrometers located at one or more of second locations configured to analyze the produced ions from the prepared samples based on mass to charge ratio of the produced ions; and one or more ion transfer devices configured to transfer the produced ions from the one or more of the first locations to the one or more of the second locations.

A mass spectrometry imaging system includes an ionization source located at a first location configured to produce ions from a surface of a sample at the first location; a mass spectrometer located at a second location configured to perform mass spectrometry analysis by analyzing the produced ions based on mass to charge ratio of the ions; and an ion transfer device configured to transfer the ions from the first location to the second location such that the ion transfer device includes a plurality of electrodes, the plurality of electrodes configured to be flexible or flexibly connected to each other, and the ion transfer device is configured to be flexible or re-configurable while transferring the ions.