A mass spectrometer includes a controller operable to: transfer first ions of a first charge into an ion trap; apply an RF pseudopotential that radially confines the first ions in an elongate ion channel of the trap; generate a first potential well that confines the first ions within a first volume; after a specified pre-cooling time, transfer second ions of a second, opposite charge into the trap; apply one or more additional DC potentials that generate a second potential well that confines the second ions within a second volume, the first potential well being within the second potential well; cause, after cooling the second ions, the first ions and the second ions to interact and generate product ions; and generate at least one third potential well that confines the product ions, that is adjacent to the second potential well and that has a same polarity as the first potential well.

A system for trapping ions for measurement thereof may include an electrostatic linear ion trap (ELIT), a source of ions to supply ions to the ELIT, a processor operatively coupled to ELIT, and a memory having instructions stored therein executable by the processor to produce at least one control signal to open the ELIT to allow ions supplied by the source of ions to enter the ELIT, determine an ion inlet frequency corresponding to a frequency of ions flowing from the source of ions into the open ELIT, generate or receive a target ion charge value, determine an optimum threshold value as a function of the target ion charge value and the determined ion inlet frequency, and produce at least one control signal to close the ELIT when a charge of an ion within the ELIT exceeds the optimum threshold value to thereby trap the ion in the ELIT.

Disclosed herein are various methods and apparatus for performing charge detection mass spectrometry (CDMS). In particular, techniques are disclosed for monitoring a detector signal from a CDMS device to determine how many ions are present in the ion trap (10) of the CDMS device. For example, if no ions are present the measurement can then be terminated early. Similarly, if more than one ion is present, the measurement can be terminated early, or ions can be removed from the trap (10) until only a single ion remains. Techniques are also provided for increasing the probability of there being a single ion in the trap (10). A technique for attenuating an ion beam is also provided.

A method of mass spectrometry is provided. The method comprises eluting a sample from a chromatography system, and calculating a desired maximum scan duration for the sample eluting from the chromatographic system based on a duration of a chromatographic peak of the sample as it elutes from the chromatography system, and a minimum number of scans per chromatographic peak to be performed. A maximum accumulation duration is calculated based on the desired maximum scan duration. The sample is ionised to produce sample ions using an ion source. The sample ions are directed along an ion path from the ion source to a mass analyser. A first set of mass analysis scans are performed. Each of the first set of mass analysis scans comprises: accumulating a portion of sample ions at a point along the ion path, wherein the portion of sample ions are accumulated for a duration not exceeding the maximum accumulation duration, and mass analysing the portion of sample ions using the mass analyser. The mass analyser is a Fourier Transform mass analyser or a Time of Flight mass analyser.

A method for controlling the filling of an ion trap with a predetermined quantity of ions. The method comprises generating an ion current by transmitting ions along an ion path to an ion trap, such that ions are accumulated in the ion trap over a transmission time period, wherein the magnitude of the ion current varies in time. The method further comprises detecting at an ion detector at least some ions from the source of ions during a plurality of distinct sampling time intervals interspersed within the transmission time period, and setting the duration of the transmission time period based on the detection of ions at the ion detector. The time difference between the start of a sampling time interval and the start of an immediately subsequent sampling time interval is less than a timescale for variation of the magnitude of the ion current. A controller for controlling the filling of an ion trap with a predetermined quantity of ions and a mass spectrometer comprising the controller is also described.

An electrostatic linear ion trap has first and second axially aligned ion minors separated by a charge detection cylinder axially aligned with each ion minor. Electric fields are selectively established within the first and second ion minors in a manner which causes an ion in the trap to oscillate back and forth through the charge detection cylinder between the first and second ion minors with a duty cycle, corresponding to a ratio of time spent by the ion passing through the charge detection cylinder and total time spent traversing a combination of the first and second ion mirrors and the charge detection cylinder during one complete oscillation cycle, of approximately 50%.

A method of mass spectrometry is disclosed comprising obtaining first data at a first time and/or location and second data at a second subsequent time and/or location. A future trend or rate of change in the data is predicted from the first and second data. An attenuation factor of an attenuation device is adjusted in response to the predicted future trend or rate of change in the data so as to maintain operation of a detector or detector system within the dynamic range of the detector or detector system and/or to prevent saturation of the detector or detector system.

A method of injecting analyte ions into a mass analyser comprises: injecting analyte ions of a first charge and counter ions of a second charge into an ion trap; cooling the analyte ions and the counter ions simultaneously in the ion trap such that a spatial distribution of the analyte ions therein is reduced; and injecting the analyte ions as an ion packet from the ion trap into the mass analyser. A mass spectrometer controller is configured to: cause an ion source to inject an amount of analyte ions of a first charge and an amount of counter ions of a second charge into an ion trap; cause the ion trap to simultaneously cool the analyte ions and the counter ions in the ion trap, thereby reducing a spatial distribution of the analyte ions therein; and cause the ion trap to inject the analyte ions into a mass analyser.

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.

A system for analyzing a sample includes a source configured to generate ions from constituent components of the sample; a mobility separator configured to separate ions received from the source based on the mobility in a gas; a plurality of ion channels arranged adjacent to the plurality of exit apertures of the mobility separator such that ions from the mobility separator are directed to different channels according to their respective mobility; a mass analyzer configured to determine the mass-to-charge ratio of the ions; and a controller. The controller is configured to identify retention time windows with minimum overlap of ions with similar mobility and sets of ions within the retention time windows; adjust mobility separation parameters for specific sets of ions to optimize separation of compounds; and quantify a plurality of target analytes.