The invention generally relates to systems and methods for conducting neutral loss scans in a single ion trap. In certain aspects, the invention provides systems that include 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 a scan function that excites a precursor ion, rejects the precursor ion after its excitation, and ejects a product ion in the single ion trap.

A gas analyzing apparatus includes: an ionization device that generates an ion flow of a sample gas; an analyzer that analyzes the ion flow supplied from the ionization device; a first ion path that non-linearly guides the ion flow from the ionization device to an inlet of the analyzer; and a blocking device for intermittently blocking and releasing, using an electric field or a magnetic field, the ion flow on at least part of a path of the ion flow through the first ion path to a mass filter of the analyzer. It is possible to perform measurement in a state where the ion flow is blocked and measurement in a state where the ion flow is not blocked.

A method of quantitative mass analysis of precursor ion species of different mass-to-charge (m/z) ratios from the same or common ion injection event is disclosed. A plurality of precursor ion species with different respective m/z ratios are introduced into an ion trap mass analyzer at the same time. The precursor ion species are isolated. A first subset of the isolated precursor ions, which are multiply charged and have a first m/z ratio range, is fragmented and scanned by dividing the scan into at least two separate scan windows. A first mass spectrum is generated for the fragment ions of the first subset of precursor ions. A second subset of the isolated precursor ions having a second m/z ratio is fragmented and scanned, and a second mass spectrum is generated for the fragment ions of the second subset of precursor ions.

The invention generally relates to mass spectrometry via frequency tagging.

A method of mass spectrometry is disclosed involving scanning a parameter of a first device through which a mixture of components is passed. Different components are transmitted through or produced in the first device at different values of the parameter and hence scanning the device parameter introduces a temporal modulation or profile to the components. This temporal variation is then removed prior to mass analyzing the components through a process of homogenization.

A mass spectrometry apparatus includes an ion source configured to generate ions; an ion guide configured to guide ions from the ion source towards a detector; the ion detector configured to detect ions; and a mass spectrometry controller. The mass spectrometry controller is configured to generate a tune curve for the ion guide; determine an observed low mass cutoff for the ion guide from the tune curve; calculate an effective r0 for the ion guide based on the observed low mass cutoff; determine an RF voltage based on the effective r0 and the RF frequency; apply the RF voltage to the ion guide; and perform a mass analysis of ions in a sample.

The invention relates to the operation of ion mobility spectrometers based on gases pushing the ions over electrical field barriers, preferably in combination with mass spectrometers, and relates to trapped ion mobility spectrometers (TIMS). The invention proposes to accumulate and to scan the ions of a selected range of mobilities by using a long and flat electric field ramp created by additional voltages. By a voltage supplied at the beginning of the flat ramp, the lowest mobility of the mobility range of ions to be collected can be selected. By the difference of the voltages at the beginning and the end, the width of the mobility range is determined. The spatial zoom advantageously can collect considerable more ions of interest than a temporal zoom without severe losses by space charge effects, and more ions can be detected in the mass-mobility map.

The invention generally relates to ion traps that operate by applying an inverse Mathieu q scan. In certain embodiments, the invention provides systems that include a mass spectrometer having an ion trap and a central processing unit (CPU). The CPU includes storage coupled to the CPU for storing instructions that when executed by the CPU cause the system to apply an inverse Mathieu q scan to the ion trap.

The invention generally relates to systems and methods for separating ions at about or above atmospheric pressure. In certain embodiments, the invention provides systems that include an ionization source that generates ions and an ion trap. The ion trap is maintained at about or above atmospheric pressure and includes a plurality of electrodes and at least one inlet configured to receive a gas flow and at least one outlet. The system is configured such that a combination of a gas flow and one or more electric fields produced by the electrodes separates the ions based on mass-to-charge ratio and sends the separated ions through the at least one outlet of the ion trap.

A tuning system may acquire, from a mass spectrometer during a batch of one or more analytical runs performed with the mass spectrometer, tune data associated with an operating characteristic of the mass spectrometer. The tuning system may determine, based on the tune data, a value of an operating parameter configured to adjust the operating characteristic of the mass spectrometer and set the operating parameter to the determined value.