Abstract: An apparatus and method for generating analyte ions from a sample. An ion generating device is provided having a chamber with an outlet and a surface having a material and means for applying a high velocity gas flow through the chamber toward the outlet such that charged particles are produced by physical interaction between the high velocity gas and the material. The charged particles then induce the generation of primary ions by interaction with molecules of the high velocity gas. The primary ions are emitted from the outlet of the ion generating device toward a sample-bearing surface and analyte ions are generated by impact of the primary ions on the analyte sample on the surface.

Abstract: A method of performing tandem mass spectrometry (MS/MS) for identifying contents of a sample includes performing a mass spectrometry (MS) scan of the sample to obtain an MS/MS mass spectrum; identifying a first precursor ion species in the MS mass spectrum; performing an initial MS/MS scan of the first precursor ion species to obtain an initial MS/MS mass spectrum; and determining whether the initial MS/MS mass spectrum has a quality acceptable for peptide sequencing. When the first MS/MS mass spectrum has an unacceptable quality, the method further includes performing a subsequent MS/MS scan of the first precursor ion species to obtain a corresponding subsequent MS/MS mass spectrum of the first precursor ion species, and determining whether the subsequent MS/MS mass spectrum has a quality acceptable for peptide sequencing.

Abstract: An apparatus and method for generating analyte ions from a sample. An ion generating device is provided having a chamber with an outlet and a surface having a material and means for applying a high velocity gas flow through the chamber toward the outlet such that charged particles are produced by physical interaction between the high velocity gas and the material. The charged particles then induce the generation of primary ions by interaction with molecules of the high velocity gas. The primary ions are emitted from the outlet of the ion generating device toward a sample-bearing surface and analyte ions are generated by impact of the primary ions on the analyte sample on the surface.

Abstract: An apparatus and method for generating analyte ions from a sample. An ion generating device is provided having a chamber with an outlet and a surface having a material and means for applying a high velocity gas flow through the chamber toward the outlet such that charged particles are produced by physical interaction between the high velocity gas and the material. The charged particles then induce the generation of primary ions by interaction with molecules of the high velocity gas. The primary ions are emitted from the outlet of the ion generating device toward a sample-bearing surface and analyte ions are generated by impact of the primary ions on the analyte sample on the surface.

Abstract: Systems and methods for optimizing the analysis of co-eluting compounds during a cycle of a tandem mass spectrometer system are provided. The tandem mass spectrometer system switches fast from analyzing one compound ion to analyzing another compound ion and from one collision cell energy to another. The fast switching allows complex sampling patterns that improve coverage of the ionic signal of the co-eluting compounds while allowing different collision cell energies to be analyzed.

Abstract: A MALDI ion source includes a sample plate for receiving a sample, a laser for producing laser radiation to ionize the sample, a first optical element arranged so as to direct the laser radiation along a first optical path toward the target area, and a second optical element arranged along the first optical path to focus the laser radiation onto the target area. The first and second optical elements are arranged that light that is reflected from the target area travels along the first optical path through the first and second optical elements, the first optical element reflecting the laser radiation along a first direction and transmitting the light reflected from the target area that has traversed the first optical path in a second direction. An imaging device for viewing the plate surface may be arranged to receive the light that has been reflected from the target area and has traversed the first optical path through the first and second optical elements.

Abstract: The invention provides a method of producing an in-focus image of an area on a sample plate for an ion source, e.g., a matrix-based ion source or any other type of ion source that employs a sample plate onto which samples are deposited. The method generally includes: a) positioning an area of the sample plate in the field of view of an imaging device; b) producing a plurality of images of the area having different in-focus regions; and c) generating an in-focus image of the area using the plurality of images. The in-focus image may be two-dimensional or three-dimensional. Systems and programming for performing the methods are also provided.

Abstract: Systems and methods for optimizing the analysis of co-eluting compounds during a cycle of a tandem mass spectrometer system are provided. The tandem mass spectrometer system switches fast from analyzing one compound ion to analyzing another compound ion and from one collision cell energy to another. The fast switching allows complex sampling patterns that improve coverage of the ionic signal of the co-eluting compounds while allowing different collision cell energies to be analyzed.

Abstract: An apparatus and method for generating analyte ions from a sample. An ion generating device is provided having a chamber with an outlet and a surface having a material and means for applying a high velocity gas flow through the chamber toward the outlet such that charged particles are produced by physical interaction between the high velocity gas and the material. The charged particles then induce the generation of primary ions by interaction with molecules of the high velocity gas. The primary ions are emitted from the outlet of the ion generating device toward a sample-bearing surface and analyte ions are generated by impact of the primary ions on the analyte sample on the surface.

Abstract: A mass spectrometer system comprises an internal surface exposed to contamination and an optical sensor assembly positioned so as to monitor a reflection of optical radiation from said internal surface. A method of determining a level of contamination of an internal surface within a mass spectrometer comprises illuminating the internal surface with optical radiation, detecting optical radiation reflected from the internal surface upon illumination, determining a reflectivity value of the internal surface based on the detected optical radiation, and determining the level of contamination based on the reflectivity value.

Abstract: A mass spectrometer includes an embedded web server that serves one or more web pages to a client computer in data communication with the mass spectrometer via a network. A user may access the one or more web pages via a web browser, and may thereby read data from, and/or control various functions of, the mass spectrometer.

Abstract: A MALDI ion source includes a sample plate for receiving a sample, a laser for producing laser radiation to ionize the sample, a first optical element arranged so as to direct the laser radiation along a first optical path toward the target area, and a second optical element arranged along the first optical path to focus the laser radiation onto the target area. The first and second optical elements are arranged that light that is reflected from the target area travels along the first optical path through the first and second optical elements, the first optical element reflecting the laser radiation along a first direction and transmitting the light reflected from the target area that has traversed the first optical path in a second direction. An imaging device for viewing the plate surface may be arranged to receive the light that has been reflected from the target area and has traversed the first optical path through the first and second optical elements.

Abstract: The invention provides an apparatus for producing an image of a global surface of an ion source sample plate that is exterior to an ion source. In general terms, the apparatus contains a sample plate for an ion source, an imaging device (e.g., a CCD or CMOS camera) and an illumination device that is configured to produce a light beam that contacts the sample plate surface to define a grazing angle between the light beam and the sample plate surface. The apparatus may be present at a location that is remote to the ion source.

Abstract: A mass spectrometer system comprises a flight tube having an operational length, a measurement device for measuring a variation in the longitudinal length of the flight tube, means for compensating for the measured variation in the longitudinal flight tube length, and a detector positioned near a downstream end of the flight tube. The measurement device comprises an optical interferometer, and may specifically comprise a Michelson interferometer. In a first embodiment, the mass spectrometer system includes an actuator coupled to the measurement device and the detector for moving the detector in a longitudinal direction to compensate for the measured variation in the operational flight tube length. In a second embodiment, the mass spectrometer system includes a processor coupled to the measurement device configured to calculate analyte ion mass to charge ratio. The processor is configured to modify a calculation of analyte ion mass to charge ratio using the measured variation in operational flight tube length.

Abstract: The invention provides a method of producing an in-focus image of an area on a sample plate for an ion source, e.g., a matrix-based ion source or any other type of ion source that employs a sample plate onto which samples are deposited. The method generally includes: a) positioning an area of the sample plate in the field of view of an imaging device; b) producing a plurality of images of the area having different in-focus regions; and c) generating an in-focus image of the area using the plurality of images. The in-focus image may be two-dimensional or three-dimensional. Systems and programming for performing the methods are also provided.

Abstract: A method of MALDI sample plate processing includes capturing an image of a plate positioned outside a mass spectrometer. The image is processed to identify one or more attributes of an individual sample on the plate, where the attributes are selected from a position attribute, a geometry attribute and an internal density distribution attribute. A laser impact position is selected within the mass spectrometer based upon one or more of the attributes.

Abstract: A method of MALDI sample plate processing includes capturing an image of a plate positioned outside a mass spectrometer. The image is processed to identify one or more attributes of an individual sample on the plate, where the attributes are selected from a position attribute, a geometry attribute and an internal density distribution attribute. A laser impact position is selected within the mass spectrometer based upon one or more of the attributes.

Abstract: The invention provides a mass spectrometry system ion source containing a sample plate and an illumination device that is configured to produce a light beam that contacts the sample plate surface to define a grazing angle between the light beam and the sample plate surface. The ion source may also contain an imaging device, e.g., a CCD or CMOS camera or the like, for viewing the area. In one embodiment, the imaging device may be connected to a display, e.g., a video monitor. Methods and mass spectrometry systems empliying the ion source are also provided.

Abstract: A mass spectrometry system is described. The mass spectrometry system comprises: (a) a mass spectrometer; and (b) a controller connected to the mass spectrometer. The controller is configured to: (i) direct the mass spectrometer to acquire a precursor ion spectrum of a sample stream; (ii) analyze, in real-time, the precursor ion spectrum to determine whether a first evaluation criterion is satisfied; (iii) if the first evaluation criterion is satisfied, direct the mass spectrometer to acquire a product ion spectrum of the sample stream; (iv) analyze, in real-time, the product ion spectrum to determine whether a second evaluation criterion is satisfied; and (v) if the second evaluation criterion is satisfied, analyze the product ion spectrum to assign an identification to the product ion spectrum. For certain implementations, the controller allows automated, data-dependent acquisition of mass spectrometry data to improve the efficiency at which peptidic data of interest can be acquired.

Abstract: A mass spectrometer that includes a tray on the outer housing of the mass spectrometer for receiving a portable user interface. Each of the user interface and the tray has a transceiver port for transmitting and receiving electromagnetic wave radiation as infrared radiation. More specifically, the tray also includes a serial port connector and the portable user interface includes a receptor for receiving the serial port connected when the user interface is mounted on the tray.