A hybrid mass spectrometer design and architecture, and methods of operating mass spectrometers are disclosed. According to one operating method, an analysis time is determined for each one of a plurality of ion species to be analyzed in an ordered sequence, and an injection time is calculated for at least some of the ion species based on an analysis time of a preceding ion species in the ordered list. The method enables more efficient utilization of analyzer time.

A mass spectrometer comprises: an ion source that generates ions having an initial range of mass-to-charge ratios; an auxiliary ion detector, downstream from the ion source that receives a plurality of first ion samples derived from the ions generated by the ion source and determines a respective ion current measurement for each of the plurality of first ion samples; a mass analyser, downstream from the ion source that receives a second ion sample derived from the ions generated by the ion source and to generate mass spectral data by mass analysis of the second ion sample; and an output stage that establishes an abundance measurement associated with at least some of the ions generated by the ion source based on the ion current measurements determined by the auxiliary ion detector.

The present invention relates to a device comprising a biomolecular processor. Each biomolecular processor has one or more bioreactor chambers defined by a solid substrate; a support structure within each bioreactor; a cleaving enzyme immobilized to the support structure and operatively positioned within the bioreactor chamber to cleave monomer or multimer units of a biopolymer molecule operatively engaged by the cleaving enzyme; and one or more time-of-flight channels formed in the solid substrate and fluidically coupled to said one or more bioreactor chambers. Each of the time-of-flight channels have two or more sensors including at least (i) a first sensor contacting the time-of-flight channel proximate to the input end of the channel and (ii) a second sensor contacting the time-of-flight channel proximate to the output end of channel. The present invention further relates to methods of sequencing and identifying biopolymer molecules using the device.

A time-of-flight mass spectrometer (TOF-MS) utilizes a multi-channel ion detector to detect ions traveling in separate flight paths, spatially dispersed along a drift axis and/or a transverse axis, in a flight tube of a TOF analyzer. The ion beams may be dispersed by drift energy, deflection along the drift and/or transverse axis, ion mass, or a combination of two or more of the foregoing. The dispersion may be carried out before, at, or after an ion accelerator of the TOF analyzer. Ion packets may be accelerated into the flight tube at a multi-pulse firing rate. Tandem MS may be implemented on parallel ion beams simultaneously.

A method of analyzing macromolecular complex ions, such protein complex ions, by mass spectrometry and apparatus for performing the method, wherein the method comprises: introducing macromolecular complex ions into a first fragmentation device and trapping the complex ions therein for a trapping period; fragmenting the trapped complex ions in the first fragmentation device to produce monomer subunit ions; optionally selecting one or more species of subunit ions by m/z; introducing one or more of the species of subunit ions into a second fragmentation device, spatially separated from the first fragmentation device; fragmenting the subunit ions in the second fragmentation device to produce a plurality of first fragment ions of the subunit ions; and mass analyzing the first fragment ions in a mass analyzer, or subjecting the first fragment ions to one or more further steps of fragmentation to form further fragment ions and mass analyzing the further fragment ions.

Methods and apparatus for operating a mass spectrometer are described. In various aspects, ions of a mass range of interest may be mass-selectively ejected from an accumulation ion trap into a multi-ion trap structure. Each ion trap of the multi-ion trap structure may be configured to confine ions within a portion of the mass range of interest. The ions may be simultaneously scanned from the ion traps of the multi-ion trap structure for concurrent detection at a detector component.

A gas sensor includes a first chamber containing a plurality of evenly spaced rods having voltages applied thereto to cause gas ions in the first chamber to move in a direction from a first end of the first chamber to a second end of the first chamber and a second chamber coupled to the second end of the first chamber and having at least one ion detector, where ions pass from the first chamber to the second chamber through a plurality of channels between the first chamber and the second chamber and are detected by the at least one ion detector. The voltages applied to the rods may include a first voltage applied to a first subset of the rods and a second voltage applied to a second subset of the rods, each of first and second voltages containing a DC component and an AC component.

A method and apparatus for tandem mass spectrometry is disclosed. Precursor ions are fragmented and the fragments are accumulated in parallel, by converting an incoming stream of ions from an ion source (10) into a time separated sequence of multiple precursor ions which are then assigned to their own particular channel of a multi compartment collision cell (40). In this manner, precursor ion species, being allocated to their own dedicated fragmentation cell chambers (41, 42 . . . 43) within the fragmentation cell (40), can then be captured and fragmented by that dedicated fragmentation chamber at optimum energy and/or fragmentation conditions.

Methods and apparatus for operating a mass spectrometer are described. In various aspects, ions of a mass range of interest may be mass-selectively ejected from an accumulation ion trap into a multi-ion trap structure. Each ion trap of the multi-ion trap structure may be configured to confine ions within a portion of the mass range of interest. The ions may be simultaneously scanned from the ion traps of the multi-ion trap structure for concurrent detection at a detector component.

A gas sensor includes a first chamber containing a plurality of evenly spaced rods having voltages applied thereto to cause gas ions in the first chamber to move in a direction from a first end of the first chamber to a second end of the first chamber and a second chamber coupled to the second end of the first chamber and having at least one ion detector, where ions pass from the first chamber to the second chamber through a plurality of channels between the first chamber and the second chamber and are detected by the at least one ion detector. The voltages applied to the rods may include a first voltage applied to a first subset of the rods and a second voltage applied to a second subset of the rods, each of first and second voltages containing a DC component and an AC component.