Patents Assigned to Ciphergen Biosystems, Inc.
  • Patent number: 6586728
    Abstract: A method and system of detecting mass to charge ratio of ions. The method includes producing charged ions in a vacuum, accelerating the charged ions in an electric field into a free flight tube and detecting the charged ions at a detector associated with the free flight tube. A control system selects a bandwidth for filtering a signal produced by the detector and the signal produced by the detector is then filtered with a variable width digital filter based upon the selected bandwidth. The bandwidth for filtering the signal may be selected from a look-up table within the control system based upon the mass to charge ratio of an ion of interest. Alternatively, a peak bandwidth within the signal produced by the detector may be determined and the signal produced by the detector may then be filtered with the variable width digital filter based upon the determined peak bandwidth.
    Type: Grant
    Filed: May 11, 2000
    Date of Patent: July 1, 2003
    Assignee: Ciphergen Biosystems, Inc.
    Inventors: Edward J. Gavin, Leonid Braginsky
  • Patent number: 6580071
    Abstract: A method for calibrating a time-of-flight mass spectrometer is disclosed. The method includes determining the time-of-flight values, or values derived from the time-of-flight values for a calibration substance at each of a plurality of different addressable locations on a sample substrate. Then, one of the addressable locations on the substrate is identified as a reference addressable location. A plurality correction factors are then calculated for the respective addressable locations on the substrate using the time-of-flight value, or a value derived from the time-of-flight value.
    Type: Grant
    Filed: July 11, 2002
    Date of Patent: June 17, 2003
    Assignee: Ciphergen Biosystems, Inc.
    Inventors: Scot R. Weinberger, Edward J. Gavin, Michael G. Youngquist
  • Patent number: 6579719
    Abstract: This invention provides methods of retentate chromatography for resolving analytes in a sample. The methods involve adsorbing the analytes to a substrate under a plurality of different selectivity conditions, and detecting the analytes retained on the substrate by desorption spectrometry. The methods are useful in biology and medicine, including clinical diagnostics and drug discovery.
    Type: Grant
    Filed: June 19, 1998
    Date of Patent: June 17, 2003
    Assignee: Ciphergen Biosystems, Inc.
    Inventors: T. William Hutchens, Tai-Tung Yip
  • Publication number: 20030106997
    Abstract: This invention provides a mass spectrometry probe including a substrate having a surface and a film that coats the surface. The film includes openings that define features for the presentation of an analyte. The film also has a lower surface tension that the surface tension of the substrate surface, and has a water contact angle between 120° and 180°.
    Type: Application
    Filed: November 21, 2002
    Publication date: June 12, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Jody Beecher, Frank Scheufele, Kamen Voivodov, Scot Weinberger, William Landgraf
  • Publication number: 20030098413
    Abstract: Laser desorption/ionization tandem mass spectrometer instruments that include immediate post source collisional cooling are presented, as are analytical methods that employ such instruments to achieve increased sensitivity and ion yield. Also presented are laser desorption/ionization mass spectrometry methods that improve sensitivity and relative ion yield by combining affinity capture probes with matrices having low melting point energy absorbing molecules combined with alkali metal scavengers.
    Type: Application
    Filed: June 26, 2002
    Publication date: May 29, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Scot R. Weinberger, Pete Tornatore
  • Publication number: 20030091976
    Abstract: The invention provides methods of monitoring the production of a target polypeptide by generating surface enhanced laser desorption/ionization mass spectral profiles of samples taken from multiple cell culture batches or of samples taken at different times from a given batch. The invention additionally provides methods for monitoring the purification of a target polypeptide from a mixture by generating surface enhanced laser desorption/ionization mass spectral profiles of samples taken at various times during a purification process. In addition, the invention relates to methods of identifying conditions that can be used in increasing the scale of a given purification process.
    Type: Application
    Filed: April 16, 2002
    Publication date: May 15, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Egisto Boschetti, Lisa Bradbury, Huw Davies, Lee O. Lomas, Thang T. Pham, Vanitha Thulasiraman, Tai-Tung Yip
  • Patent number: 6555813
    Abstract: This invention provides a mass spectrometry probe including a substrate having a surface and a film that coats the surface. The film includes openings that define features for the presentation of an analyte. The film also has a lower surface tension that the surface tension of the substrate surface, and has a water contact angle between 120° and 180°.
    Type: Grant
    Filed: April 27, 2000
    Date of Patent: April 29, 2003
    Assignee: Ciphergen Biosystems, Inc.
    Inventors: Jody Beecher, Frank Scheufele, Kamen Voivodov, Scot Weinberger, William Landgraf
  • Publication number: 20030077616
    Abstract: This invention relates to methods for comparing the relative amounts of biomolecules and identifying biomolecules in samples using affinity tags and mass spectrometry.
    Type: Application
    Filed: April 18, 2002
    Publication date: April 24, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventor: Lee O. Lomas
  • Publication number: 20030062473
    Abstract: A method for calibrating a time-of-flight mass spectrometer is disclosed. The method includes determining the time-of-flight values, or values derived from the time-of-flight values for a calibration substance at each of a plurality of different addressable locations on a sample substrate. Then, one of the addressable locations on the substrate is identified as a reference addressable location. A plurality correction factors are then calculated for the respective addressable locations on the substrate using the time-of-flight value, or a value derived from the time-of-flight value.
    Type: Application
    Filed: July 11, 2002
    Publication date: April 3, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Scot R. Weinberger, Edward J. Gavin, Michael G. Youngquist
  • Publication number: 20030054367
    Abstract: The present invention relates to methods for correlating gene and protein expression in a cell.
    Type: Application
    Filed: February 15, 2002
    Publication date: March 20, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: William E. Rich, T. William Hutchens
  • Publication number: 20030032043
    Abstract: The present invention provides an adsorbent chip, which includes three components, a substrate, an intermediate layer of linker arms and an adsorbent film, which is attached to the linker arms. The adsorbent film is made up of a plurality of adsorbent particles, each of which includes a binding functionality. The invention also provides a method of making the chips of the invention in which the substrate-intermediate film cassette is formed and the adsorbent film is subsequently immobilized thereon. When the adsorbent film is from the same preparation across a particular batch of chips, the chips provide for the acquisition of data that are highly reproducible from one chip to the next throughout the particular batch of chips. Additionally, the invention provides methods for using the chips to perform assays.
    Type: Application
    Filed: July 16, 2002
    Publication date: February 13, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Christopher A. Pohl, Steven C. Papanu
  • Publication number: 20030017464
    Abstract: The present invention provides an adsorbent chip, which includes three components, a substrate, an intermediate layer of linker arms and an adsorbent film, which is attached to the linker arms. The adsorbent film is made up of a plurality of adsorbent particles, each of which includes a binding functionality. The invention also provides a method of making the chips of the invention in which the substrate-intermediate film cassette is formed and the adsorbent film is subsequently immobilized thereon. When the adsorbent film is from the same preparation across a particular batch of chips, the chips provide for the acquisition of data that are highly reproducible from one chip to the next throughout the particular batch of chips. Additionally, the invention provides methods for using the chips to perform assays.
    Type: Application
    Filed: July 17, 2001
    Publication date: January 23, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventor: Christopher A. Pohl
  • Publication number: 20020182649
    Abstract: Presented are novel apparatus and methods for protein characterization, identification, and sequencing using affinity capture laser desorption/ionization tandem mass spectrometry.
    Type: Application
    Filed: January 31, 2002
    Publication date: December 5, 2002
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Scot R. Weinberger, Huw A. Davies, Ning Tang
  • Patent number: 6464942
    Abstract: Device and method for processing biological, biochemical or chemical samples are provided wherein a first multiwell plate is stacked atop a second multiwell plate. The first multiwell plate has x wells arranged in a regular array, each capable of receiving a separate sample. Each well of the x wells has an outlet at a lower surface of the first plate. The second multiwell plate has y wells arranged in a regular array, each well of the y wells being capable of receiving a separate sample, and wherein y>x. The outlets at the lower surface of the first multiwell plate are arrayed to register with corresponding inlets of a subset of the y wells of the second multiwell plate when the first plate is stacked atop the second plate. A mechanism for aligning the first plate to the second plate is provided, as well as transfer indicia for tracking transfer of sample from the first plate to the second plate.
    Type: Grant
    Filed: May 21, 1999
    Date of Patent: October 15, 2002
    Assignee: Ciphergen Biosystems, Inc.
    Inventors: Jonathan L. Coffman, Hong Lu, Ernest J. Woods, III
  • Publication number: 20020137106
    Abstract: The present invention provides materials and methods for simultaneously analyzing multiple components of a biological pathway (e.g., signal transduction, immunological, plasma enzyme mediated, cell cycle or developmental cycle).
    Type: Application
    Filed: March 7, 2002
    Publication date: September 26, 2002
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Sau-Mei Leung, Lee Lomas
  • Publication number: 20020138208
    Abstract: A method that analyzes mass spectra using a digital computer is disclosed. The method includes entering into a digital computer a data set obtained from mass spectra from a plurality of samples. Each sample is, or is to be assigned to a class within a class set having two or more classes and each class is characterized by a different biological status. A classification model is then formed. The classification model discriminates between the classes in the class set.
    Type: Application
    Filed: November 15, 2001
    Publication date: September 26, 2002
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Chris D. Paulse, Edward J. Gavin, Leonid Braginsky, William E. Rich, Eric T. Fung
  • Publication number: 20020060290
    Abstract: This invention provides a method for analyzing analytes in a sample by mass spectrometry. The method involves pre-fractionating the sample by size exclusion and/or ion exchange chromatography, applying the sample to an adsorbent attached to the surface of a mass spectrometry probe, and allowing both specific and non-specific adsorption of analytes the adsorbent (e.g., by allowing the sample to dry without washing to remove unbound sample). Then an energy absorbing material is added to the dried sample, and the sample is analyzed by laser desorption/ionization mass spectrometry.
    Type: Application
    Filed: March 19, 2001
    Publication date: May 23, 2002
    Applicant: Ciphergen Biosystems, Inc.
    Inventor: Thang T. Pham
  • Patent number: 6294790
    Abstract: An ion detector includes a secondary charged particle generator that generates secondary charged particles in response to primary ions that engage the secondary charged particle generator. The secondary charged particle generator has an electrostatic potential that repels the secondary charged particles toward an electro-emissive detector that generates electrons in response to primary ions and secondary charged particles that engage the electro-emissive detector The electro-emissive detector has a field that attracts the secondary charged particles. An anode is provided for detecting electrons generated by the electro-emissive detector and for generating a signal.
    Type: Grant
    Filed: September 22, 1998
    Date of Patent: September 25, 2001
    Assignee: Ciphergen Biosystems, Inc.
    Inventor: Scot R. Weinberger
  • Publication number: 20010014461
    Abstract: This invention provides methods of retentate chromatography for resolving analytes in a sample. The methods involve adsorbing the analytes to a substrate under a plurality of different selectivity conditions, and detecting the analytes retained on the substrate by desorption spectrometry. The methods are useful in biology and medicine, including clinical diagnostics and drug discovery.
    Type: Application
    Filed: December 21, 2000
    Publication date: August 16, 2001
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: T. William Hutchens, Tai-Tung Yip
  • Patent number: 6225047
    Abstract: This is invention is directed to methods of identifying analytes that are differentially present between two samples. The methods involve determining retention data by desorption spectrometry for analytes in different samples using the same selectivity conditions, comparing the data, and identifying analytes that are differentially retained.
    Type: Grant
    Filed: June 19, 1998
    Date of Patent: May 1, 2001
    Assignee: Ciphergen Biosystems, Inc.
    Inventors: T. William Hutchens, Tai-Tung Yip