Each sample of a series of samples is ejected at an ejection time and according to a sample order. Each ejected sample of the series is ionized, producing ion beam. A list of different sets of MRM transitions is received. Each set of the list corresponds to a different sample. A group of one or more different sets is selected from the list. Initially, each set selected for the group corresponds to a different sample of one or more first samples of the series. A mass spectrometer is instructed to execute each transition of each set of the group on the ion beam until a transition of a set of the group is detected, upon which, one or more next sets are selected from the list to be monitored using the set of the detected transition and the sample order.

The invention generally relates to logical operations in mass spectrometry. The system comprising a mass spectrometer comprising one or more ion traps; 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 one or more scan functions to the one or more ion traps, the scan functions being combine together.

An ion-mobility spectrometer system includes a housing with an upstream end, a downstream end, and a drift region defined along a longitudinal axis through the housing between the upstream and downstream ends. A first ionizer is operatively connected the housing to supply ions at the upstream end. A second ionizer is operatively connected to the housing to supply ions at the upstream end, wherein the first and second ionizers are both situated upstream of the drift zone relative to an ion flow path through the drift zone. An electric field generator is operatively connected to the housing to drive ions through the drift zone in a direction from the upstream end toward the downstream end. The second ionizer is a radioactive ionizer mounted to the housing at the upstream end positioned to direct irradiated ions into the housing.

First, an MS scan of a mass range of a control sample that does not include a metabolite is performed (601) producing background peak m/z and intensity values for background precursor ions (602). Background peaks are selected for an exclusion list and in the exclusion list an m/z value and an intensity value are included for each background peak (604). Next, an MS scan of the mass range of an experimental sample that does include a metabolite is performed (610) producing peak m/z and intensity values for precursor ions (612). Peaks are selected for a peak list and in the peak list an m/z value and an intensity value are included for each peak (614). Finally, each peak of the peak list that has both an m/z value and an intensity value that correspond to an m/z value and an intensity value of a background peak of the exclusion list is excluded from the peak list (616).

A time-of-flight, TOF, mass spectrometer, MS, comprising: an ion source for supplying a group of ions, including a first ion having a first mass-to-charge ratio m.sub.1/z.sub.1, a second ion having a second mass-to-charge ratio m.sub.2/z.sub.2 and a third ion having a third mass-to-charge ratio m.sub.3/z.sub.3 wherein m.sub.3/z.sub.3>m.sub.2/z.sub.2>at a time t.sub.0; a first set of electrodes, including a first electrode, and a second set of electrodes, including a first electrode and an Nth electrode, wherein the first set of electrodes and the second set of electrodes are mutually spaced apart by a gap therebetween; an ion detector for detecting the ions; a set of power supplies, including a first power supply, electrically coupled to the first set of electrodes and to the second set of electrodes; and a controller configured to control the set of power supplies to apply respective potentials to the first set of electrodes and the second set of electrodes; wherein the controller is configured to control the set of power supplies to: provide a first substantially field-free region between the ion source and the first set of electrodes to allow the group of ions to expand theretowards and/or therein, at the time t0; apply an extraction potential V.sub.extraction to the first set of electrodes at a time t.sub.extraction>t.sub.0, to extract the expanded group of ions, while maintaining a second substantially field-free region beyond the first set of electrodes, in the gap between the first set of electrodes and the second set of electrodes; and optionally, change an acceleration potential V.sub.acceleration applied to the second set of electrodes during a time period Δt=t.sub.off−t.sub.on, wherein ton>t.sub.extraction, to vary acceleration of the extracted group of ions based, at least in part, on respective mass-to-charge ratios.

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 invention relates to a tandem mass spectrometer comprising an ionization source that can produce ions; a mass analyzer comprising an ion trap arranged in such a way as to receive ions from the ion source and a detector that can detect ions leaving the ion trap according to the mass to charge (m/z) ratio thereof; ion activation means for activating ions that can fragment at least some of the ions trapped in the ion trap; and coupling means arranged between the ion trap and said ion activation means. According to the invention, the ion activation means consists of a glow discharge lamp that can generate a light beam oriented towards the ion trap, said light beam being electromagnetic radiation in the vacuum ultraviolet wavelength range with photon energies of between 8 eV and 41 eV in such a way as to fragment at least some of the ions trapped in the ion trap.

A method of performing tandem mass spectrometry includes supplying a sample to a chromatography column, directing components included in the sample and eluting from the chromatography column to a mass spectrometer, acquiring a series of mass spectra including intensity values of ions produced from the components as a function of m/z of the ions, extracting, from the series of mass spectra, a plurality of detection points representing intensity as a function of time for a selected m/z, estimating, based on the plurality of detection points extracted from the series of mass spectra, a relative position of a selected detection point included in the plurality of detection points, and performing, at the mass spectrometer and based on the estimated relative position, a dependent acquisition for the selected m/z. The relative position of the selected detection point represents a position of the selected detection point relative to an expected reference point.

The invention generally relates to logical operations in mass spectrometry. The system comprising a mass spectrometer comprising one or more ion traps; 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 one or more scan functions to the one or more ion traps, the scan functions being combine together.

A method of performing tandem mass spectrometry includes supplying a sample to a chromatography column, directing components included in the sample and eluting from the chromatography column to a mass spectrometer, acquiring a series of mass spectra including intensity values of ions produced from the components as a function of m/z of the ions, extracting, from the series of mass spectra, a plurality of detection points representing intensity as a function of time for a selected m/z, estimating, based on the plurality of detection points extracted from the series of mass spectra, a relative position of a selected detection point included in the plurality of detection points, and performing, at the mass spectrometer and based on the estimated relative position, a dependent acquisition for the selected m/z. The relative position of the selected detection point represents a position of the selected detection point relative to an expected reference point.