Patents by Inventor Ignat V. Shilov

Ignat V. Shilov has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Patent number: 10497466
    Abstract: Protein confidence values are calculated in proteomic analysis. A protein database is searched for proteins matching peptides found from mass spectrometry of a sample producing a set of proteins and a corresponding set of peptides. Peptide confidence values for the set of peptides are determined. Protein confidence values are calculated for the set of proteins based on the peptide confidence values. A protein is selected from the set of proteins with a largest protein confidence value, the largest protein confidence value is saved for the protein, the protein is removed from the set of proteins, and one or more peptides corresponding to the protein are removed from the set of peptides. Protein confidence values are recalculated for the set of proteins based on the peptide confidence values and an effect of removing the one or more peptides from the set of peptides.
    Type: Grant
    Filed: May 12, 2011
    Date of Patent: December 3, 2019
    Assignee: DH Technologies Development Pte. Ltd.
    Inventor: Ignat V. Shilov
  • Patent number: 8712695
    Abstract: The present teachings provide for identification of peptides using small sequence tags to focus computational resources on searching regions of a protein database that are the most likely to yield correct identifications. They allow for the incorporation of modifications and in doing so focuses the search to peptides with a precursor mass match. Additionally, probability or relevance factors can be used to determine peptide hypotheses. Various embodiments are presented that search for peptides when a single precursor is selected or when multiple precursors are simultaneously fragmented.
    Type: Grant
    Filed: October 6, 2005
    Date of Patent: April 29, 2014
    Assignee: DH Technologies Development Pte. Ltd.
    Inventors: Ignat V. Shilov, Sean L. Seymour, Ron Bonner, Alpesh A. Patel
  • Publication number: 20130211734
    Abstract: Protein confidence values are calculated in proteomic analysis. A protein database is searched for proteins matching peptides found from mass spectrometry of a sample producing a set of proteins and a corresponding set of peptides. Peptide confidence values for the set of peptides are determined. Protein confidence values are calculated for the set of proteins based on the peptide confidence values. A protein is selected from the set of proteins with a largest protein confidence value, the largest protein confidence value is saved for the protein, the protein is removed from the set of proteins, and one or more peptides corresponding to the protein are removed from the set of peptides. Protein confidence values are recalculated for the set of proteins based on the peptide confidence values and an effect of removing the one or more peptides from the set of peptides.
    Type: Application
    Filed: May 12, 2011
    Publication date: August 15, 2013
    Applicant: DH TECHNOLOGIES DEVELOPMENT PTE LTD
    Inventor: Ignat V. Shilov
  • Publication number: 20130204582
    Abstract: Singular spectrum analysis is used to detect a feature from mass spectrometry data. A plurality of scans of a sample is performed producing mass spectrometry data using a spectrometer. A singular spectrum analysis is performed on the mass spectrometry data using a fixed window width in which one or more components other than the highest ranked component are grouped in a set and the one or more components grouped in the set are summed producing reconstructed data using the processor. A feature of the mass spectrometry data is detected by analyzing an aspect of the reconstructed data using the processor. Analyzing an aspect of the reconstructed data includes using pairs of zero crossings in the reconstructed data to detect bounds on a location of the feature in the mass spectrometry data.
    Type: Application
    Filed: May 17, 2011
    Publication date: August 8, 2013
    Applicant: DH Technologies Development PTE. LTD
    Inventors: Ignat V. Shilov, Gordana Ivosev, Alpesh A. Patel
  • Patent number: 7982180
    Abstract: A background component of reporter ion signals is determined by fitting a distribution function. A plurality of samples that include a protein labeled with a plurality of isobaric reporter ions is analyzed at a plurality of different times using a mass spectrometer, producing a plurality of mass spectra for the plurality of isobaric reporter ions. A cumulative distribution is calculated for an inverse coefficient of differential expression of the plurality of mass spectra using a processor. A Pearson Type IV distribution shifted by a constant value is fitted to the cumulative distribution and the constant value is solved for using the processor. A background component for each spectrum of the plurality of mass spectra is calculated from the constant value, a calculated coefficient of differential expression for each spectrum, and an average reporter ion signal value for each spectrum using the processor.
    Type: Grant
    Filed: June 1, 2009
    Date of Patent: July 19, 2011
    Assignee: DH Technologies Development Pte. Ltd.
    Inventors: Ignat V. Shilov, Wilfred H. Tang
  • Patent number: 7919745
    Abstract: A corrected reporter ion intensity is calculated in tandem mass spectrometry based quantitation using isobaric labels. An analyte in each of two or more samples of a mixture of samples is labeled with a different isobaric label. The analyte is eluted from the mixture of samples and intensities of the eluting analyte are measured. An analyte intensity is selected at each of at least two times from the measured intensities. Tandem mass spectrometry is performed on the eluting analyte at each of the at least two times. A plurality of reporter ion intensities is produced. A system of linear equations is created expressing each reporter ion intensity of the plurality of reporter ion intensities as a sum of a background noise intensity and the product of a fragmentation efficiency and an analyte intensity. A corrected reporter ion intensity is calculated from a solution of the system of linear equations.
    Type: Grant
    Filed: September 10, 2008
    Date of Patent: April 5, 2011
    Assignee: DH Technologies Development Pte. Ltd.
    Inventors: Ignat V. Shilov, Wilfred H. Tang
  • Publication number: 20090283673
    Abstract: A background component of reporter ion signals is determined by fitting a distribution function. A plurality of samples that include a protein labeled with a plurality of isobaric reporter ions is analyzed at a plurality of different times using a mass spectrometer, producing a plurality of mass spectra for the plurality of isobaric reporter ions. A cumulative distribution is calculated for an inverse coefficient of differential expression of the plurality of mass spectra using a processor. A Pearson Type IV distribution shifted by a constant value is fitted to the cumulative distribution and the constant value is solved for using the processor. A background component for each spectrum of the plurality of mass spectra is calculated from the constant value, a calculated coefficient of differential expression for each spectrum, and an average reporter ion signal value for each spectrum using the processor.
    Type: Application
    Filed: June 1, 2009
    Publication date: November 19, 2009
    Inventors: Ignat V. Shilov, Wilfred H. Tang
  • Publication number: 20090065686
    Abstract: A corrected reporter ion intensity is calculated in tandem mass spectrometry based quantitation using isobaric labels. An analyte in each of two or more samples of a mixture of samples is labeled with a different isobaric label. The analyte is eluted from the mixture of samples and intensities of the eluting analyte are measured. An analyte intensity is selected at each of at least two times from the measured intensities. Tandem mass spectrometry is performed on the eluting analyte at each of the at least two times. A plurality of reporter ion intensities is produced. A system of linear equations is created expressing each reporter ion intensity of the plurality of reporter ion intensities as a sum of a background noise intensity and the product of a fragmentation efficiency and an analyte intensity. A corrected reporter ion intensity is calculated from a solution of the system of linear equations.
    Type: Application
    Filed: September 10, 2008
    Publication date: March 12, 2009
    Inventors: Ignat V. Shilov, Wilfred H. Tang