A mass spectrometer includes a collision cell and a system controller. The collision cell includes a plurality of rod pairs configured to generate pseudopotential well through the application of radio frequency potentials to the rod pairs. The collision cell configured to generate a target fragment from a parent ion by colliding the parent ion with one or more gas molecules. The system controller is configured to set a radio frequency amplitude of the radio frequency potentials to a default amplitude; monitor the production of a target fragment ion while adjusting the collision energy; set the collision energy to optimize the production of the target fragment ion; apply a linear full range ramp to the radio frequency amplitude to determine an optimal radio frequency amplitude; and set the radio frequency amplitude to the optimal radio frequency amplitude for the parent ion, target fragment ion pair.

A method of mass spectrometry is disclosed comprising selecting a modification of interest that may modify the mass to charge ratios of precursor ions of interest when said precursor ions are subjected to a fragmentation or reaction condition for producing product ions. The method then filters the product ions (or product ion data) such that only a subset of the product ions are transmitted and detected (or a subset of the data remains) and so as to exclude product ions (or product ion data) that could not have possibly resulted from the modification of interest. This significantly simplifies the product ion data, enabling the product ions to be identified or compared to precursor ion spectra more efficiently.

A mass spectrometer or ion mobility spectrometer is disclosed comprising: a first device for separating ions or molecules according to a physicochemical property (3); an ion mobility separation device (4) for receiving and separating at least some of said ions or ions derived from said molecules according to their ion mobility; a gas supply (6-10) connected to said ion mobility separation device (4) for supplying gas into said ion mobility separation device (4); and a control system (11) configured to adjust said gas supply (6-10) so as to change the composition of gas within the ion mobility separation device (4) as a function of time.

A method of operating a quadrupole device is disclosed that comprises operating the quadrupole device in a first mode of operation, passing ions into the quadrupole device while the quadrupole device is operated in the first mode of operation, and then operating the quadrupole device in a second mode of operation. Operating the quadrupole device in the second mode of operation comprises applying one or more drive voltages to the quadrupole device, and operating the quadrupole device in the first mode of operation comprises applying one or more reduced drive voltages or not applying one or more drive voltages to the quadrupole device.

A traveling wave multipole comprising two or more pairs of segmented electrodes arranged around a central axis; and a voltage supply. The voltage supply configured to supply the segments of each pair of electrodes with a different RF and DC potential; and match RF and DC potentials with a location of an ion of target m/z moving through the traveling wave multipole such that as the ion travels along the multipole the ion experiences the same RF and DC potentials while another ion of a second target m/z concurrently experiences a different RF and DC potentials at another location within the traveling wave multipole.

An ion filter for a mass spectrometer, the apparatus compr sing an ion inodifier; an ion selector configured to select a subset of a sample of ions based on their mobility in a gas; and a controller configured to operate the ion modifier in a first mode to modify the ions selected by the ion selector to provide daughter ions, and configured to operate the ion modifier in a second mode to Coutput the ions selected by the ion selector;wherein the ion filter is adapted for providing output ions from the ion modifier to an in-take of a mass spectrometer.

A method for parallel accumulation and serial fragmentation of ions, wherein ions are injected into a device capable of serial ejection using a pseudopotential barrier created by an RF voltage. In all instances, the ions may be filtered prior to accumulation in the device capable of serial ejection. In some cases this filtering may take the form of discrete isolation windows using isolation waveforms with multiple notches. In some cases these waveforms may be applied to a quadrupole mass filter. Following accumulation of the precursor ions, the initial population may be serially ejected using a pseudopotential barrier created by an RF voltage. Following serial ejection, the individual precursor ion populations are analyzed. In some cases, this analysis might involve additional rounds of ion isolation and manipulation (e.g., MSn, CID, ETD, etc.).

A connection determiner determines which one of a wired communicator and a wireless communicator an information processing apparatus is connected to. Mass spectrometry of a sample is performed by an analyzer based on an operating instruction given by the connected information processing apparatus. Mass profile data of the sample is acquired by a data acquirer based on a result of analysis by the analyzer. When the connection determiner determines that the information processing apparatus is connected to the wireless communicator, a data amount of the mass profile data acquired by the data acquirer is reduced by a data amount reducer. The mass profile data, the data amount of which has been reduced by the data amount reducer, is transmitted to the information processing apparatus through the wireless communicator by a transmitter.

A method of operating a mass spectrometer that allows for high-speed operation is disclosed. The method consists in separating the various steps needed to produce a mass spectrum into three or more conceptual stages in a pipeline, such that the instrument is performing steps to process more than two precursor-ion species simultaneously. In general, the number of stages in the pipeline should at least one more and, preferably, at least two more than the number of buffering storage devices in the instrument. The presently-taught methods and apparatus allow for nearly 100% duty cycle of ion accumulation for precursors of interest.

A mass spectrometry method comprising steps of generating an ion beam from an ion source; directing the ion beam into a collision cell; introducing into the collision cell through a gas inlet on the collision cell a charge-neutral analyte gas or reaction gas; ionizing the analyte gas or reaction gas in the collision cell by means of collisions between the analyte gas or reaction gas and the ion beam; transmitting ions from the ionized analyte gas or reaction gas from the collision cell into a mass analyzer; and mass analyzing the transmitted ions of the ionized analyte or reaction gas. The methods can be applied in isotope ratio mass spectrometry to determine the isotope abundance or isotope ratio of a reaction gas used in mass shift reactions between the gas and sample ions, to determine a corrected isotope abundance or ratio of the sample ions.