The invention generally relates to systems and methods for performing multiple precursor, neutral loss and product ion scans in a single ion trap. In certain aspects, the invention provides systems including a mass spectrometer having a single ion trap, and a central processing unit (CPU), and storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to apply at least one of the following ion scans to a single ion population in the single ion trap: multiple precursor ion scans, a plurality of segmented neutral loss scans, or multiple simultaneous neutral loss scans.

The present invention comprises a method for automated, high throughput molecular identification of macromolecular organic compounds. The method may provide an approximate solution to a momentum transfer cross section of an analyte in a buffer gas as measured by an ion mobility spectrometer that has low computational demand, has a high level of accuracy, and is adaptable for a variety of drift gases.

A system and method are provided for controlling the temperature gradient along a differential mobility spectrometer having a differential mobility spectrometer having an inlet and an outlet, wherein the inlet is configured to receive ions transported from an ion source by a transport gas. The differential mobility spectrometer has an internal operating pressure, electrodes, and at least one voltage source for providing DC and RF voltages to the electrodes for separating ions that are transported from the inlet to the outlet. A gas port is provided near the outlet for introducing a throttle gas to control the flow rate of the transport gas through the differential mobility spectrometer and thereby adjust the ion residence time. A heater is provided for controlling the temperature of the throttle gas to minimize the temperature gradient between the inlet and outlet of the differential mobility spectrometer. A method of calibrating a DMS is also disclosed.

A method is disclosed comprising: trapping ions in an ion trap (40); applying a first force on the ions within the ion trap in a first direction, said force having a magnitude that is dependent upon the value of a physicochemical property of the ions; applying a second force on these ions in the opposite direction so that the ions separate according to the physicochemical property value as a result of the first and second forces; and then pulsing or driving ions out of one or more regions of the ion trap.

One mode of a chromatograph mass spectrometer according to the present invention includes: a measurement unit (1) that includes a chromatograph unit (1A) and a mass spectrometry unit (1B) capable of performing MS/MS analysis, and collects chromatograph mass spectrometry data having three dimensions of time, m/z, and a signal intensity by repeatedly performing the MS/MS analysis by data independent analysis in the mass spectrometry unit on a sample containing a compound separated by the chromatograph unit; a component detection unit (42) that detects a compound and a component corresponding to a partial structure of the compound by obtaining MS/MS spectra of a bar graph presentation based on chromatograph mass spectrometry data over a predetermined m/z range for a target sample, estimating precursor ion peaks in each of the MS/MS spectra, and selecting peaks based on a predetermined standard regarding an m/z direction in each of the MS/MS spectra and a predetermined standard regarding a time direction for peaks that can be considered to be identical or an identical group on the MS/MS spectra; a narrowing unit (43, 44) that narrows down components to be analyzed by performing screening using prior information on the detected component; and a composition estimation unit (45) that, by using m/z information corresponding to a narrowed down component, estimate a composition or a chemical formula of the component.

A sample analysis system having a continuous beam ion mobility filter incorporates an ion removal mechanism for removing residual ions from the ion mobility filter to reduce cross-talk. A sample to be analyzed by the sample analysis system can be entered into the continuous beam ion mobility filter, which filters the ions of the sample and passes the filtered group of ions to a detector or a mass analyzer (e.g., via an ion optics assembly disposed between the mass analyzer and the ion mobility filter), where some or all of the ions in the group are detected. The ion removal mechanism then removes all or a substantial portion of the residual ions from the ion mobility filter that are left over from the first filtered group before a second filtered group is passed through. In some aspects, the ion removal mechanism can be operated concurrent with an ion removal mechanism for removing residual ions from an ion optics assembly.

The present teachings are directed to methods and systems for the selection of ions for subsequent ion fragmentation in the analysis of a sample. Rather than select the most intense subset of precursor ions for further analysis in an attempt to maximize the number of high quality, identifiable MS/MS spectra, in some settings, systems and methods for analyzing and 5 identifying precursor ions for further processing can benefit from a discovery approach in which precursor ions are selected randomly/stochastically.

A method comprises: obtaining, from a series of mass spectra including a most recent mass spectrum and a plurality of previously-acquired mass spectra, an elution profile comprising a plurality of detection points each representing intensity of ions accumulated over an accumulation time and detected by a detector as a function of time; classifying, based on a subset of detection points included in the plurality of detection points, a current signal state of the elution profile; and setting, for a next acquisition of a mass spectrum, the accumulation time based on the classified current signal state of the elution profile.

A mass spectrometer device comprising an ion mobility separation device and a mass spectrometer that are coupled together. In order to achieve high efficiency, high throughput, and high sensitivity, the mass spectrometer is provided with: a first flow passageway 24 through which ions from an ion source 1 are introduced into the mass spectrometer 11 by passing through an ion mobility separation unit 2; a second flow passageway 21 through which the ions from the ion source are introduced into the mass spectrometer without passing through the ion mobility separation unit; and a switch means, such as shield units 4, 5, for switching between the first flow passageway 24 and the second flow passageway 21.

A chromatograph mass spectrometer including: an MS.sup.n−1 analysis setter for setting an analysis execution period for performing an MS.sup.n−1 analysis, an execution time for the analysis and a loop time; an analysis period divider for dividing the analysis period into segments according to a change in number or analysis condition of MS.sup.n−1 analyses to be performed within the same time window; an MS.sup.n analysis setter for performing MS.sup.n−1 analysis to obtain mass spectrum data and for scheduling MS.sup.n analysis, an ion corresponding to a peak satisfying a set condition being designated as a precursor ion; an MS.sup.n analysis execution time allotter for allotting, in each segment, a time period for execution of the MS.sup.n analysis, the time period being calculated by subtracting an event execution time from the loop time; and an analysis executer for repeatedly performing MS.sup.n−1 analysis and MS.sup.n analysis in each segment.