Patents Assigned to Protein Metrics Inc.
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Patent number: 11346844Abstract: Methods and apparatuses for the identification and/or characterization of properties of a macromolecule based on mass spectrometry data. Specifically, described herein are methods and apparatuses for converting peptide-level data into a pseudo-intact mass spectra. Also described herein are methods and apparatuses for converting peptide-level data into a pseudo-electropherogram. The methods may be well suited for analyzing proteins and protein complexes, including estimating properties of post-translational modifications of the proteins and protein complexes. Methods may include generating a theoretical graph or spectrum based on peptide-level mass spectrometry data. In some embodiments, the theoretical graph may be a theoretical intact mass spectrum or a theoretical charge distribution spectrum.Type: GrantFiled: April 27, 2020Date of Patent: May 31, 2022Assignee: Protein Metrics Inc.Inventors: Andrew Nichols, Marshall Bern, Yong Joo Kil, Eric Carlson
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Patent number: 11289317Abstract: This invention relates to graphical user-interactive analysis of data, including in particular, mass spectrographic data analysis, as well as methods and software for generating and using such. One aspect provides user-customizable reports, including methods and apparatuses for generating customizable pivot tables and graphs specific to mass spectrographic data.Type: GrantFiled: December 28, 2020Date of Patent: March 29, 2022Assignee: Protein Metrics Inc.Inventors: Yong Joo Kil, Eric Carlson
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Patent number: 11276204Abstract: Described herein are computer-implemented methods for compressing sparse multidimensional ordered series data. In particular, these methods and apparatuses for performing them (including software) may be particularly well suited to efficiently compressing spectrographic data.Type: GrantFiled: August 31, 2021Date of Patent: March 15, 2022Assignee: Protein Metrics Inc.Inventor: Doron Kletter
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Patent number: 11127575Abstract: Methods and apparatuses for the identification and/or characterization of properties of a sample using mass spectrometry. The method involves using a measured spectrum of data from a sample taken with a mass spectrometer, deconvoluting the measured spectrum of data by applying parsimony weighting to minimize the number of charge states based on one or more of: the number of intense peaks in the mass spectrum; the number of harmonic relationships (e.g., masses in small integer ratios); and the number of off-by-one relationships (e.g., m/z bins with high probability for two adjacent charges). Thus, the underlying m/z spectrum may be inferred from the family of plausible deconvoluted spectra determined by applying parsimony and the inferred m/z spectrum may be used to identify and/or characterize the sample.Type: GrantFiled: May 26, 2020Date of Patent: September 21, 2021Assignee: Protein Metrics Inc.Inventor: Marshall Bern
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Patent number: 10991558Abstract: This invention relates to graphical user-interactive displays for use in MS-based analysis of protein impurities, as well as methods and software for generating and using such. One aspect provides a user-interactive display comprising interactive and dynamic selection of one or more masses and concurrent display of peaks (points) corresponding to that predicted mass value across other displays (MS1, deconvolved mass spectrum, etc.).Type: GrantFiled: January 27, 2020Date of Patent: April 27, 2021Assignee: Protein Metrics Inc.Inventors: Marshall Bern, Yong Joo Kil
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Patent number: 10879057Abstract: This invention relates to graphical user-interactive analysis of data, including in particular, mass spectrographic data analysis, as well as methods and software for generating and using such. One aspect provides user-customizable reports, including methods and apparatuses for generating customizable pivot tables and graphs specific to mass spectrographic data.Type: GrantFiled: December 13, 2019Date of Patent: December 29, 2020Assignee: Protein Metrics Inc.Inventors: Yong Joo Kil, Eric Carlson
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Patent number: 10665439Abstract: Methods and apparatuses for the identification and/or characterization of properties of a sample using mass spectrometry. The method involves using a measured spectrum of data from a sample taken with a mass spectrometer, deconvoluting the measured spectrum of data by applying parsimony weighting to minimize the number of charge states based on one or more of: the number of intense peaks in the mass spectrum; the number of harmonic relationships (e.g., masses in small integer ratios); and the number of off-by-one relationships (e.g., m/z bins with high probability for two adjacent charges). Thus, the underlying m/z spectrum may be inferred from the family of plausible deconvoluted spectra determined by applying parsimony and the inferred m/z spectrum may be used to identify and/or characterize the sample.Type: GrantFiled: June 11, 2019Date of Patent: May 26, 2020Assignee: Protein Metrics Inc.Inventor: Marshall Bern
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Patent number: 10546736Abstract: This invention relates to graphical user-interactive displays for use in MS-based analysis of protein impurities, as well as methods and software for generating and using such. One aspect provides a user-interactive display comprising interactive and dynamic selection of one or more masses and concurrent display of peaks (points) corresponding to that predicted mass value across other displays (MS1, deconvolved mass spectrum, etc.).Type: GrantFiled: August 1, 2018Date of Patent: January 28, 2020Assignee: Protein Metrics Inc.Inventors: Marshall Bern, Yong Joo Kil
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Patent number: 10510521Abstract: This invention relates to graphical user-interactive analysis of data, including in particular, mass spectrographic data analysis, as well as methods and software for generating and using such. One aspect provides user-customizable reports, including methods and apparatuses for generating customizable pivot tables and graphs specific to mass spectrographic data.Type: GrantFiled: October 1, 2018Date of Patent: December 17, 2019Assignee: Protein Metrics Inc.Inventors: Yong Joo Kil, Eric Carlson
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Patent number: 10354421Abstract: Methods and apparatuses for the analysis of mass spectroscopic (MS) data as well as ultraviolet (UV) absorption data. In particular, described herein are tools and methods to assist in generating annotated peptide maps from a raw MS data.Type: GrantFiled: March 10, 2016Date of Patent: July 16, 2019Assignee: Protein Metrics Inc.Inventors: Christopher Becker, Marshall Bern, Nicholas Bern, Yong Joo Kil, Richard Seipert, Michael Taejong Kim
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Patent number: 10319573Abstract: Methods and apparatuses for the identification and/or characterization of properties of a sample using mass spectrometry. The method involves using a measured spectrum of data from a sample taken with a mass spectrometer, deconvoluting the measured spectrum of data by applying parsimony weighting to minimize the number of charge states based on one or more of: the number of intense peaks in the mass spectrum; the number of harmonic relationships (e.g., masses in small integer ratios); and the number of off-by-one relationships (e.g., m/z bins with high probability for two adjacent charges). Thus, the underlying m/z spectrum may be inferred from the family of plausible deconvoluted spectra determined by applying parsimony and the inferred m/z spectrum may be used to identify and/or characterize the sample.Type: GrantFiled: January 26, 2018Date of Patent: June 11, 2019Assignee: Protein Metrics Inc.Inventor: Marshall Bern
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Patent number: 10199206Abstract: This invention relates to graphical user-interactive displays for use in MS-based analysis of protein impurities, as well as methods and software for generating and using such. One aspect provides a user-interactive display comprising an extracted mass chromatogram (XIC), an MS1 spectrum and an MS2 spectrum, all simultaneously representing a user-selected peptide. Another aspect provides a user interactive display simultaneously presenting paired spectra (XIC, MS1 and/or MS2) for a variant peptide and its corresponding wildtype counterpart.Type: GrantFiled: May 1, 2017Date of Patent: February 5, 2019Assignee: Protein Metrics Inc.Inventors: Christopher Becker, Marshall Bern, Yong Joo Kil, Michael Taejong Kim, Boyan Zhang
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Patent number: 9859917Abstract: Disclosed are methods and systems for significantly compressing sparse multidimensional ordered series data comprised of indexed data sets, wherein each data set comprises an index, a first variable and a second variable. The methods and systems are particularly suited for compression of data recorded in double precision floating point format.Type: GrantFiled: February 13, 2017Date of Patent: January 2, 2018Assignee: Protein Metrics Inc.Inventor: Doron Kletter
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Publication number: 20170269099Abstract: Embodiments of a computer system, a method, and a computer-program product (e.g., software) for analyzing tandem-mass-spectrometry data are described. Using this analysis technique, unanticipated chemical modifications to peptides associated with proteins can be identified. In particular, a modification called a wild-card modification is used to identify the most likely chemical modifications in the peptides. A wild-card modification allows the addition of any mass, typically any integer atomic mass within a range, to any one amino acid residue within a candidate peptide.Type: ApplicationFiled: May 31, 2017Publication date: September 21, 2017Applicant: Protein Metrics Inc.Inventor: Marshall W. Bern
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Patent number: 9671408Abstract: Embodiments of a computer system, a method, and a computer-program product (e.g., software) for analyzing tandem-mass-spectrometry data are described. Using this analysis technique, unanticipated chemical modifications to peptides associated with proteins can be identified. In particular, a modification called a wild-card modification is used to identify the most likely chemical modifications in the peptides. A wild-card modification allows the addition of any mass, typically any integer atomic mass within a range, to any one amino acid residue within a candidate peptide.Type: GrantFiled: November 18, 2008Date of Patent: June 6, 2017Assignee: PROTEIN METRICS INC.Inventor: Marshall W. Bern
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Patent number: 9640376Abstract: This invention relates to graphical user-interactive displays for use in MS-based analysis of protein impurities, as well as methods and software for generating and using such. One aspect provides a user-interactive display comprising an extracted mass chromatogram (XIC), an MS1 spectrum and an MS2 spectrum, all simultaneously representing a user-selected peptide. Another aspect provides a user interactive display simultaneously presenting paired spectra (XIC, MS1 and/or MS2) for a variant peptide and its corresponding wildtype counterpart.Type: GrantFiled: June 16, 2014Date of Patent: May 2, 2017Assignee: Protein Metrics Inc.Inventors: Christopher Becker, Marshall Bern, Yong Joo Kil, Michael Taejong Kim, Boyan Zhang
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Patent number: 9571122Abstract: Disclosed are methods and systems for significantly compressing sparse multidimensional ordered series data comprised of indexed data sets, wherein each data set comprises an index, a first variable and a second variable. The methods and systems are particularly suited for compression of data recorded in double precision floating point format.Type: GrantFiled: July 1, 2016Date of Patent: February 14, 2017Assignee: Protein Metrics Inc.Inventor: Doron Kletter
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Patent number: 9385751Abstract: Disclosed are methods and systems for significantly compressing sparse multidimensional ordered series data comprised of indexed data sets, wherein each data set comprises an index, a first variable and a second variable. The methods and systems are particularly suited for compression of data recorded in double precision floating point format.Type: GrantFiled: October 7, 2015Date of Patent: July 5, 2016Assignee: Protein Metrics Inc.Inventor: Doron Kletter