Patents by Inventor James L. Stephenson, Jr.
James L. Stephenson, Jr. 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).
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Methods for mass spectrometry of mixtures of proteins or polypeptides using proton transfer reaction
Patent number: 10497549Abstract: A method comprises: (1) making an extract of a biological sample; (2) repeatedly: (a) choosing a respective one of a plurality of pre-determined protein or polypeptide analyte compounds; (b) introducing a portion of the extract into an electrospray ionization source, thereby generating positive ions comprising a plurality of ion species; (c) isolating a plurality of subsets of the ion species comprising respective mass-to-charge (m/z) ratio ranges, each range including an m/z ratio corresponding to a respective protonation state of the chosen compound; (d) reacting the isolated plurality of subsets of first-generation ion species with proton transfer reaction reagent anions for a pre-determined time duration; (e) generating a mass spectrum of the product ion species; and (g) identifying either the presence or absence of the compound based on the mass spectrum; and (3) identifying the presence or absence of the microorganism within the sample based on analytes present.Type: GrantFiled: December 4, 2017Date of Patent: December 3, 2019Assignee: THERMO FINNIGAN LLCInventors: James L. Stephenson, Jr., John E. P. Syka, August A. Specht -
Patent number: 10460919Abstract: The present disclosure establishes new dissociation parameters that may be used to determine the collision energy (CE) needed to achieve a desired extent of dissociation for a given analyte precursor ion using collision cell type collision-induced dissociation. This selection is based solely on the analyte precursor ion's molecular weight, MW, and charge state, z. Metrics are proposed that may be used as a parameter for the “extent of dissociation”, and then predictive models are developed of the CEs required to achieve a range of values for each metric. Each model is a simple smooth function of only MW and z of the precursor ion. Coupled with a real-time spectral deconvolution (m/z to mass) algorithm, methods in accordance with the invention enable control over the extent of dissociation through automated, real-time selection of collision energy in a precursor-dependent manner.Type: GrantFiled: May 9, 2018Date of Patent: October 29, 2019Assignee: THERMO FINNIGAN LLCInventors: Ping F. Yip, Helene L. Cardasis, James L. Stephenson, Jr.
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Patent number: 10369521Abstract: An embodiment of a method for real time material identification is described that comprises determining an approximate mass value for an unknown material from spectral information derived from mass spectral analysis of the unknown material; retrieving profile models that correspond to a known material from a data structure using the approximate mass value; fitting a sample profile for the unknown material from the spectral information to the profile models to generate a fit score for each fit, wherein the lowest fit score corresponds to the best fit; calculating a mass value from the best fitting profile model and the sample profile.Type: GrantFiled: October 5, 2017Date of Patent: August 6, 2019Assignee: THERMO FINNIGAN LLCInventors: Scott R. Kronewitter, James L. Stephenson, Jr., Ping F. Yip
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Publication number: 20190164735Abstract: A method for mass spectral analysis of a sample containing a plurality of intact protein molecule species comprises: (a) mass analyzing a plurality of ion species generated from a sample portion; (b) automatically recognizing, for each of at least one intact protein molecule species, a respective subset of m/z ratios corresponding to ion species generated from the each intact protein molecule species; and (c) storing or reporting to a user information relating to each subset of the m/z ratios, wherein step (b) comprises: automatically assigning a tentative charge state to each above-threshold m/z ratio; automatically adjusting the tentative charge to achieve a set of self-consistent assigned charge states; and decomposing the assigned charge states into analyte-specific clusters, each analyte-specific cluster being a one of the subsets of the m/z ratios.Type: ApplicationFiled: January 30, 2019Publication date: May 30, 2019Inventors: Ping F. YIP, James L. STEPHENSON, JR., Oksana GVOZDYAK
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Publication number: 20190072566Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) and real-time data analysis methods are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.Type: ApplicationFiled: November 7, 2018Publication date: March 7, 2019Inventors: Ping F. YIP, James L. STEPHENSON, JR., John E. P. SYKA
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Patent number: 10217619Abstract: A method for mass spectral analysis of a sample containing a plurality of biomolecule species comprises: (a) mass analyzing a plurality of first-generation ion species generated from a sample portion; (b) automatically recognizing, for each of at least one biomolecule species, a respective subset of m/z ratios corresponding to respective first-generation ion species generated from the each biomolecule species; (c) selecting, from each recognized subset, a single representative m/z ratio; (d) isolating a sub-population of ions having each representative m/z ratio from ions having other m/z ratios; and (e) fragmenting each isolated sub-population of ions so as to generate second-generation ion species.Type: GrantFiled: March 11, 2016Date of Patent: February 26, 2019Assignee: THERMO FINNIGAN LLCInventors: Ping F. Yip, James L. Stephenson, Jr., Oksana Gvozdyak
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Publication number: 20190006161Abstract: Methods and systems for identification of microorganisms either after isolation from a culture or directly from a sample. The methods and systems are configured to identify microorganisms based on the characterization of proteins of the microorganisms via high-resolution/mass accuracy single-stage (MS) or multi-stage (MSn) mass spectrometry. Included herein are also discussion of targeted detection and evaluation of virulence factors, antibiotic resistance markers, antibiotic susceptibility markers, typing, or other characteristics using a method applicable to substantially all microorganisms and high-resolution/mass accuracy single-stage (MS) or multi-stage (MSn) mass spectrometry.Type: ApplicationFiled: May 22, 2015Publication date: January 3, 2019Inventors: James L. Stephenson, Jr., Oksana Gvozdyak, Roger Grist, Clay Campbell, Iain C. Mylchreest, Ian D. Jardine
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Patent number: 10157734Abstract: Methods and systems for identification of microorganisms either after isolation from a culture or directly from a sample. The methods and systems are configured to identify microorganisms based on the characterization of proteins of the microorganisms via high-resolution/mass accuracy single-stage (MS) or multi-stage (MSn) mass spectrometry. Included herein are also discussion of targeted detection and evaluation of virulence factors, antibiotic resistance markers, antibiotic susceptibility markers, typing, or other characteristics using a method applicable to substantially all microorganisms and high-resolution/mass accuracy single-stage (MS) or multi-stage (MSn) mass spectrometry.Type: GrantFiled: May 22, 2015Date of Patent: December 18, 2018Assignee: OXIOD LIMITEDInventors: James L. Stephenson, Jr., Oksana Gvozdyak, Roger Grist, Clay Campbell, Iain C. Mylchreest, Ian D. Jardine
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Patent number: 10151758Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) and real-time data analysis methods are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.Type: GrantFiled: January 13, 2017Date of Patent: December 11, 2018Assignee: THERMO FINNIGAN LLCInventors: Ping F. Yip, James L. Stephenson, Jr., John E. P. Syka
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Publication number: 20180350578Abstract: The present disclosure establishes new dissociation parameters that may be used to determine the collision energy (CE) needed to achieve a desired extent of dissociation for a given analyte precursor ion using collision cell type collision-induced dissociation. This selection is based solely on the analyte precursor ion's molecular weight, MW, and charge state, z. Metrics are proposed that may be used as a parameter for the “extent of dissociation”, and then predictive models are developed of the CEs required to achieve a range of values for each metric. Each model is a simple smooth function of only MW and z of the precursor ion. Coupled with a real-time spectral deconvolution (m/z to mass) algorithm, methods in accordance with the invention enable control over the extent of dissociation through automated, real-time selection of collision energy in a precursor-dependent manner.Type: ApplicationFiled: May 9, 2018Publication date: December 6, 2018Inventors: Ping F. YIP, Helene L. CARDASIS, James L. STEPHENSON, JR.
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Publication number: 20180233340Abstract: Methods and systems for identification of microorganisms either after isolation from a culture or directly from a sample. The methods and systems are configured to identify microorganisms based on the characterization of proteins of the microorganisms via high-resolution/mass accuracy single-stage (MS) or multi-stage (MSn) mass spectrometry. Included herein are also discussion of targeted detection and evaluation of virulence factors, antibiotic resistance markers, antibiotic susceptibility markers, typing, or other characteristics using a method applicable to substantially all microorganisms and high-resolution/mass accuracy single-stage (MS) or multi-stage (MSn) mass spectrometry.Type: ApplicationFiled: April 5, 2018Publication date: August 16, 2018Inventors: James L. Stephenson, JR., Oksana Gvozdyak, Roger Grist, Clay Campbell, Iain C. Mylchreest, Ian D. Jardine
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Publication number: 20180099249Abstract: An embodiment of a method for real time material identification is described that comprises determining an approximate mass value for an unknown material from spectral information derived from mass spectral analysis of the unknown material; retrieving profile models that correspond to a known material from a data structure using the approximate mass value; fitting a sample profile for the unknown material from the spectral information to the profile models to generate a fit score for each fit, wherein the lowest fit score corresponds to the best fit; calculating a mass value from the best fitting profile model and the sample profile.Type: ApplicationFiled: October 5, 2017Publication date: April 12, 2018Inventors: Scott R. KRONEWITTER, James L. STEPHENSON, JR., Ping F. YIP
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Publication number: 20180102243Abstract: A method comprises: (1) making an extract of a biological sample; (2) repeatedly: (a) choosing a respective one of a plurality of pre-determined protein or polypeptide analyte compounds; (b) introducing a portion of the extract into an electrospray ionization source, thereby generating positive ions comprising a plurality of ion species; (c) isolating a plurality of subsets of the ion species comprising respective mass-to-charge (m/z) ratio ranges, each range including an m/z ratio corresponding to a respective protonation state of the chosen compound; (d) reacting the isolated plurality of subsets of first-generation ion species with proton transfer reaction reagent anions for a pre-determined time duration; (e) generating a mass spectrum of the product ion species; and (g) identifying either the presence or absence of the compound based on the mass spectrum; and (3) identifying the presence or absence of the microorganism within the sample based on analytes present.Type: ApplicationFiled: December 4, 2017Publication date: April 12, 2018Inventors: James L. STEPHENSON, JR., John E. P. SYKA, August A. SPECHT
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Patent number: 9837255Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.Type: GrantFiled: July 17, 2015Date of Patent: December 5, 2017Assignee: Thermo Finnigan LLCInventors: James L. Stephenson, Jr., John E. P. Syka, August A. Specht
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Publication number: 20170205425Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) and real-time data analysis methods are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.Type: ApplicationFiled: January 13, 2017Publication date: July 20, 2017Inventors: Ping F. YIP, James L. STEPHENSON, JR., John E. P. SYKA
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Publication number: 20170162372Abstract: Applications of ion-ion reaction chemistry are disclosed in which proton transfer reactions (PTR) are used to (1) simplify complex mixture analysis of samples introduced into a mass spectrometer, and (2) improve resolution and sensitivity for the analysis of large proteins in excess of 50 kDa by removing charge and reducing the collisional cross section.Type: ApplicationFiled: July 17, 2015Publication date: June 8, 2017Applicant: Thermo Finnigan LLCInventors: James L. STEPHENSON, Jr., John E. P. SYKA, August A. SPECHT
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Publication number: 20160268112Abstract: A method for mass spectral analysis of a sample containing a plurality of biomolecule species comprises: (a) mass analyzing a plurality of first-generation ion species generated from a sample portion; (b) automatically recognizing, for each of at least one biomolecule species, a respective subset of m/z ratios corresponding to respective first-generation ion species generated from the each biomolecule species; (c) selecting, from each recognized subset, a single representative m/z ratio; (d) isolating a sub-population of ions having each representative m/z ratio from ions having other m/z ratios; and (e) fragmenting each isolated sub-population of ions so as to generate second-generation ion species.Type: ApplicationFiled: March 11, 2016Publication date: September 15, 2016Inventors: Ping F. YIP, James L. STEPHENSON, JR., Oksana GVOZDYAK
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Publication number: 20150255261Abstract: Methods and systems for identification of microorganisms either after isolation from a culture or directly from a sample. The methods and systems are configured to identify microorganisms based on the characterization of proteins of the microorganisms via high-resolution/mass accuracy single-stage (MS) or multi-stage (MSn) mass spectrometry. Included herein are also discussion of targeted detection and evaluation of virulence factors, antibiotic resistance markers, antibiotic susceptibility markers, typing, or other characteristics using a method applicable to substantially all microorganisms and high-resolution/mass accuracy single-stage (MS) or multi-stage (MSn) mass spectrometry.Type: ApplicationFiled: May 22, 2015Publication date: September 10, 2015Inventors: James L. Stephenson, Jr., Oksana Gvozdyak, Roger Grist, Clay Campbell, Iain C. Mylchreest, Ian D. Jardine
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Patent number: 9074236Abstract: Methods and systems for identification of microorganisms either after isolation from a culture or directly from a sample. The methods and systems are configured to identify microorganisms based on the characterization of proteins of the microorganisms via high-resolution/mass accuracy single-stage (MS) or multi-stage (MSn) mass spectrometry. Included herein are also discussion of targeted detection and evaluation of virulence factors, antibiotic resistance markers, antibiotic susceptibility markers, typing, or other characteristics using a method applicable to substantially all microorganisms and high-resolution/mass accuracy single-stage (MS) or multi-stage (MSn) mass spectrometry.Type: GrantFiled: April 30, 2013Date of Patent: July 7, 2015Assignee: OXOID LIMITEDInventors: James L. Stephenson, Jr., Oksana Gvozdyak, Roger Grist, Clay Campbell, Ian D. Jardine, Iain C. Mylchreest