Patents Assigned to Ciphergen Biosystems, Inc.
  • Publication number: 20040149901
    Abstract: The invention provides apparatus and methods for performing time-of-flight (TOF) mass spectrometry. A TOF mass spectrometer of the present invention comprises one or more ion focusing electric sectors. At least one of the electric sectors is associated with an ion optical element. The ion optical elements comprise at least one adjustable electrode, such that the adjustable electrode is able to modify the potential experienced by an ion entering or exiting the electric sector with which it is associated.
    Type: Application
    Filed: January 14, 2004
    Publication date: August 5, 2004
    Applicant: CIPHERGEN BIOSYSTEMS, INC.
    Inventor: Sidney E. Buttrill
  • Publication number: 20040146937
    Abstract: This invention provides methods and materials for mapping interaction characteristics between components of a multicomponent biological complex. The methods involve capturing a multicomponent complex on a solid support and washing the support with a series of elution washes forming a gradient of solute concentrations, and determining whether a particular elution wash eluted a particular component.
    Type: Application
    Filed: July 23, 2003
    Publication date: July 29, 2004
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: William E. Rich, Egisto Boschetti, Lee O. Lomas, Tai-Tung Yip
  • Publication number: 20040142493
    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: July 23, 2003
    Publication date: July 22, 2004
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: T. William Hutchens, Tai-Tung Yip
  • Patent number: 6765199
    Abstract: A method for processing time-dependent signal data is disclosed. The time-dependent signal data are received in a memory, wherein the time-dependent signal data represent a time-dependent signal, and wherein the time-dependent signal data include representations of time-of-flight values of ions, or values derived from time-of-flight values of ions. The time-dependent signal data are scaled with a time-dependent scaling function.
    Type: Grant
    Filed: July 10, 2002
    Date of Patent: July 20, 2004
    Assignee: Ciphergen Biosystems, Inc.
    Inventors: Michael G. Youngquist, Edward Gavin, William E. Rich
  • Publication number: 20040137427
    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: July 23, 2003
    Publication date: July 15, 2004
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: T. William Hutchens, Tai-Tung Yip
  • Publication number: 20040127648
    Abstract: A polymer that is useful for separating plasmid DNA from cell lysates can be dispersed throughout the pores of a porous matrix, forming a chromatographic sorbent.
    Type: Application
    Filed: December 31, 2002
    Publication date: July 1, 2004
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Luc Guerrier, Egisto Boschetti
  • Publication number: 20040124149
    Abstract: For certain mixed mode resins having anionic character, a ligand is joined to a solid support via a linkage that includes a mercapto-, ether- or amino-containing moiety. A suitable ligand comprises an aromatic group, a heteroaromatic group, or a heterocyclic group, optionally fused, that is sulfate-, sulfonate-, phosphonate- or phosphate-substituted and that is linked to such a moiety. These resins possess an anionic character under conditions prescribed for their use. Separation of a biological substance, such as a peptide or protein, can be accomplished with a resin of this type via a change in the pH of eluants, thereby effecting adsorption and desorption.
    Type: Application
    Filed: September 12, 2003
    Publication date: July 1, 2004
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Egisto Boschetti, Pierre Girot, Pil-Je Um
  • Publication number: 20040096820
    Abstract: The invention identifies polypeptide biomarkers of disease progression or nonprogression by comparative protein profiling of samples from progressors and nonprogressors subpopulations of a population exposed to the pathogen or sharing a risk facto causing the disease. The polypeptides, their ligands, and modulators find use as diagnostic, prognostic, and therapeutic agents.
    Type: Application
    Filed: May 30, 2003
    Publication date: May 20, 2004
    Applicants: Ciphergen Biosystems, Inc., Aaron Diamond AIDS Research Center, The Rockefeller University
    Inventors: William E. Rich, David D. Ho, Linqi Zhang
  • Publication number: 20040091498
    Abstract: The present invention relates to inhibition of viruses, e.g., HIV, using defensins. The invention further relates to methods for identifying and using agents, including small molecule chemical compositions, antibodies, peptides, nucleic acids, antisense nucleic acids, and ribozymes, that increase naturally occurring defensin expression or activity, thereby inhibiting HIV in a cell; as well as to the use of expression profiles and compositions in diagnosis and prophylaxis, and therapy related to HIV infection and related disease states such as AIDS.
    Type: Application
    Filed: May 30, 2003
    Publication date: May 13, 2004
    Applicants: Aaron Diamond AIDS Research Center, The Rockefeller University, Ciphergen Biosystems, Inc.
    Inventors: Linqi Zhang, David D. Ho, Rebecca E. Caffrey, Enrique A. Dalmasso, Jianfeng Mei
  • Publication number: 20040056190
    Abstract: The invention provides apparatus and methods for performing time-of-flight (TOF) mass spectrometry. A TOF mass spectrometer of the present invention comprises one or more ion focusing electric sectors. At least one of the electric sectors is associated with an ion optical element. The ion optical elements comprise at least one adjustable electrode, such that the adjustable electrode is able to modify the potential experienced by an ion entering or exiting the electric sector with which it is associated.
    Type: Application
    Filed: April 24, 2003
    Publication date: March 25, 2004
    Applicant: Ciphergen Biosystems, Inc.
    Inventor: Sidney E. Buttrill
  • Publication number: 20040059530
    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: September 23, 2003
    Publication date: March 25, 2004
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Chris D. Paulse, Edward J. Gavin, Leonid Braginsky, William E. Rich, Eric T. Fung
  • Patent number: 6707031
    Abstract: A laser optical bench for use with a laser desorption/ionization mass spectrometer. The laser optical bench includes a laser for producing light, a focusing structure that receives light from the laser and focuses predominantly in a single plane, an attenuator that receives light from the focusing structure, beam steering structure for directing light from the attenuator from the target; and a final focusing element for focusing light from the beam steering structure on the target. Further focusing elements may be included for further focusing and dispersing the light beam in different planes. Additionally, photodetectors or photodiodes may be included for energy measurement and sensing a lasing event.
    Type: Grant
    Filed: May 11, 2000
    Date of Patent: March 16, 2004
    Assignee: Ciphergen Biosystems, Inc.
    Inventors: Scot R. Weinberger, Raymond G. Bryan
  • Publication number: 20040029191
    Abstract: The present invention provides materials and methods for simultaneously analyzing multiple kinase substrates and products using mass spectrometry.
    Type: Application
    Filed: May 16, 2003
    Publication date: February 12, 2004
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Lee Lomas, Vanitha Thulasiraman, Tai-Tung Yip
  • Patent number: 6675104
    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: Grant
    Filed: November 15, 2001
    Date of Patent: January 6, 2004
    Assignee: Ciphergen Biosystems, Inc.
    Inventors: Chris D. Paulse, Edward J. Gavin, Leonid Braginsky, William E. Rich, Eric T. Fung
  • Publication number: 20030219731
    Abstract: The invention provides an analytical instrument comprising an affinity capture probe interface, a laser desorption ionization source, and a tandem mass spectrometer. Also presented are new methods for protein discovery and identification and for characterization of molecular interactions that utilize the instrument of the present invention.
    Type: Application
    Filed: April 1, 2003
    Publication date: November 27, 2003
    Applicants: CIPHERGEN BIOSYSTEMS, INC., HUMAN GENOME SCIENCES, INC.
    Inventors: Scot R. Weinberger, Tina Morris
  • Publication number: 20030218130
    Abstract: The present invention provides a substrate having a polymerized, polysaccharide-based hydrogel attached to the surface. The hydrogel can be derivatized with binding functionalities that bind analytes from a sample. The invention further provides methods of using the device and gels that are capable of selectively binding one or more analytes from a sample.
    Type: Application
    Filed: April 14, 2003
    Publication date: November 27, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Egisto Boschetti, Jian Ding, Pierre Girot, Luc Gurrier, Christopher A. Pohl, Michael T. Grimes
  • Publication number: 20030207460
    Abstract: The present invention provides polymerizable monomers that incorporate moieties derived from energy absorbing molecules (EAM). The invention also provides polymers that are based on the monomers. The polymers have unique properties that make them ideally suited for use in diverse analyses, including desorption/ionization mass spectrometry of analytes. The invention also provides a device that incorporates the polymeric compositions of the inventions, methods of using the device to detect, quantify and identify analytes, and a method of preparing a device of the invention.
    Type: Application
    Filed: December 20, 2002
    Publication date: November 6, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventor: Naotaka Kitagawa
  • Publication number: 20030207462
    Abstract: The present invention provides polymerizable monomers that incorporate moieties derived from energy absorbing molecules (EAM). The invention also provides polymers that are based on the monomers. The polymers have unique properties that make them ideally suited for use in diverse analyses, including desorption/ionization mass spectrometry of analytes. The invention also provides a device that incorporates the polymeric compositions of the inventions, methods of using the device to detect, quantify and identify analytes, and a method of preparing a device of the invention.
    Type: Application
    Filed: December 19, 2002
    Publication date: November 6, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventor: Naotaka Kitagawa
  • Publication number: 20030180128
    Abstract: The present invention comprises a loading device for automating transfer of a plurality of probes between a cassette within which the plurality of probes are initially constrained and an analytical instrument, e.g., mass spectrometer. The loading device may be configured to accept a single or a plurality of cassettes each removably constraining a plurality of probes to be analyzed. The loading device may permit each of the plurality of cassettes to be independently interchanged with a separate cassette removably constraining a separate plurality of probes during mass spectrometric analysis, or for additional cassettes to be loaded into the device during analysis. In a useful embodiment, the loading device comprises a cassette transport assembly and a probe insertion assembly. The cassette transport assembly linearly translates one or more cassettes to align the cassette(s) with respect to the mass spectrometer so that a probe may be translated therebetween by the probe insertion assembly.
    Type: Application
    Filed: February 25, 2003
    Publication date: September 25, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Scott M. DeWinter, John B. Rusconi, Steven M. Clark, Michael P. Lucas, Michael G. Youngquist
  • Publication number: 20030175170
    Abstract: The present invention comprises a system to facilitate sample preparation, common transport, and storage of a plurality of laser desorption ionization probes to be interrogated in a mass spectrometer. The system includes a plurality of probes, a cassette that accepts the plurality of probes, a well-plate that engages the cassette and permits delivery of samples to the probes without fluid communication between samples, and a clamp to secure the well-plate to the cassette. The cassette is configured to constrain the plurality of probes so that the probes suspend from ribs disposed within the cassette. This permits the top and bottom surfaces of the probes to be substantially exposed and facilitates insertion and removal of the probes from the cassette without user contact of active areas on the probes.
    Type: Application
    Filed: February 25, 2003
    Publication date: September 18, 2003
    Applicant: Ciphergen Biosystems, Inc.
    Inventors: Michael G. Youngquist, John B. Rusconi