Patents by Inventor Steven J. Ciavarini
Steven J. Ciavarini 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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Patent number: 11887700Abstract: Techniques and apparatus for generating encoded representations of compounds are described. In one embodiment, for example, an apparatus may include at least one memory, and logic coupled to the at least one memory. The logic may be configured receive analytical information associated with at least one compound, generate at least one encoded representation of the at least one compound, the encoded representation comprising at least one segment representing at least one property of the at least one compound using a plurality of symbols. Other embodiments are described.Type: GrantFiled: May 4, 2020Date of Patent: January 30, 2024Assignee: WATERS TECHNOLOGIES IRELAND LIMITEDInventors: Steven J. Ciavarini, Curt Devlin, Patrick Brophy, Scott J. Geromanos
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Patent number: 11404258Abstract: A method of mass spectrometry is disclosed comprising mass analysing an eluent from a chromatography device and obtaining parent ion data sets and corresponding product ion data sets, and determining whether, in a first product ion data set, one or more product ions are present that are related to one or more parent ions in a corresponding first parent ion data set, based on the mass or mass to charge ratio and/or intensity of the one or more product ions and the one or more parent ions. If it is determined that the one or more product ions are present, the method further comprises removing the one or more product ions from one or more second product ion data sets to produce one or more second modified product ion data sets and/or removing ions other than the one or more product ions from the first product ion data set to produce a first modified product ion data set.Type: GrantFiled: June 5, 2015Date of Patent: August 2, 2022Assignee: Water Technologies CorporationInventors: Daniel Golick, Scott Geromanos, Marc V Gorenstein, Steven J Ciavarini, Keith Fadgen
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Publication number: 20210333251Abstract: Exemplary embodiments provide methods, mediums, and systems for analyzing spectrometry and/or chromatography data, and in particular to techniques to improve the reproducibility of results of spectrographic and/or chromatographic experiments. For example, some embodiments provide techniques for normalizing mass spectrometry (MS) and/or liquid chromatography (LC) data across different experimental devices, allowing data from different cohorts to be directly compared. To this end, exemplary embodiments provide a reliable, reproducible target library usable across different platforms, laboratories, and users. One embodiment leverages statistical techniques to select experimental parameters configured to reduce or minimize the chance of misidentifying a target molecule. Another embodiment leverages the law of large numbers to produce a composite product ion spectrum usable across different experiments.Type: ApplicationFiled: April 23, 2021Publication date: October 28, 2021Inventors: Scott J. Geromanos, Steven J. Ciavarini, Marisa Gioioso, Ovidiu Pop
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Patent number: 11137380Abstract: A method of analyzing a complex sample includes performing a sequential chromatographic-IMS-MS analysis of a sample to obtain a plurality of experimental mass spectra having isotopic clusters, wherein each spectrum of the plurality of spectra is associated with a chromatographic retention time and an ion-mobility drift time. The method also includes calculating a model isotopic cluster of a precursor or product ion associated with a candidate compound in the sample, in correspondence to the natural isotopic-abundance ratios of elements composing the compound. The method further includes comparing peaks of the model isotopic cluster to corresponding peaks of an isotopic cluster of one of the experimental mass spectra to extract one or more saturated or interfered peaks of the experimental isotopic cluster, wherein at least one of the peaks of the experimental isotopic cluster is un-saturated and un-interfered.Type: GrantFiled: May 19, 2020Date of Patent: October 5, 2021Assignee: Waters Technologies CorporationInventors: Scott J. Geromanos, Marc V. Gorenstein, Daniel Golick, Steven J. Ciavarini
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Patent number: 11011359Abstract: Techniques for performing data acquisition and analysis are described. A multi-mode acquisition strategy may be performed which iteratively selects mass isolation windows of different sizes in different scan cycles to acquire experimental data. The mass isolation windows selected may provide for acquiring elevated energy scan data for a defined set of m/z values. Single scan data analysis may be performed. Data analysis may include forming precursor charge clusters, chaining precursor charge clusters having the same mass to charge ratio to form peaks profiles, and using criteria to align precursor and product ions of the experimental data. Unsupervised and supervised clustering may be performed using a database and composite ion spectra formed from experimental data. Also described are a small molecule acquisition enhancement and additional techniques applicable for biopharmaceutical and other applications.Type: GrantFiled: January 17, 2020Date of Patent: May 18, 2021Assignee: Waters Technologies CorporationInventors: Scott J. Geromanos, Steven J. Ciavarini, Curt Devlin
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Publication number: 20210123891Abstract: A solvent delivery subsystem for a chromatography device performs relatively low pressure, high flow mixing of solvents to form a gradient and subsequent high pressure, low flow delivery of the gradient to the separation column. The mixing of the gradient is independent and does not interfere with the gradient delivery. To form the gradient, the outputs of an aqueous pump and an organic pump are mixed to fill a storage capillary while a downstream point from the storage capillary is vented to atmosphere. After gradient formation, the vent to atmosphere is closed, the solvent delivery system rises to high pressure, and only the aqueous pump runs for gradient delivery. To maintain integrity of the fluid stream, the solvent delivery system uses feed forward compensation and controls at least one parameter selected from the group consisting of pressure and flow in the conduit means to follow a gradual ramp.Type: ApplicationFiled: January 7, 2021Publication date: April 29, 2021Applicant: Waters Technologies CorporationInventors: Steven J. Ciavarini, Stanley P. Pensak, JR., Jeffrey W. Finch, Keith Fadgen, Hongji Liu
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Publication number: 20200350039Abstract: Techniques and apparatus for generating encoded representations of compounds are described. In one embodiment, for example, an apparatus may include at least one memory, and logic coupled to the at least one memory. The logic may be configured receive analytical information associated with at least one compound, generate at least one encoded representation of the at least one compound, the encoded representation comprising at least one segment representing at least one property of the at least one compound using a plurality of symbols. Other embodiments are described.Type: ApplicationFiled: May 4, 2020Publication date: November 5, 2020Inventors: Steven J. Ciavarini, Curt Devlin, Patrick Brophy, Scott J. Geromanos
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Patent number: 10824174Abstract: Exemplary embodiments of the present disclosure are directed to manipulating pressure-related hysteresis in a pressurized flow system by setting the pressure of the system to a predetermined location in the hysteresis band to advantageously minimize an effect of the pressure related hysteresis on the pressure of the system or to advantageously benefit from the effects of the hysteresis on the pressure of the system.Type: GrantFiled: April 13, 2018Date of Patent: November 3, 2020Assignee: Waters Technologies CorporationInventors: Joshua A. Shreve, Paul Keenan, Steven J. Ciavarini
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Patent number: 10825672Abstract: Techniques and apparatus for analyzing mass spectrometry data are described. In one embodiment, for example, an apparatus may include logic to access a product ion data set generated via mass analyzing a sample comprising a target precursor, access precursor composition information for elements of the target precursor that includes nominal mass and mass defect information, determine nominal mass (NM)-mass defect (MD) relationship information for ion fragments associated with the target precursor based on the precursor composition information, determine one or more fragment upper boundaries and one or more fragment lower boundaries, extract candidate ion fragments from the ion fragments via applying the one or more fragment upper boundaries and the one or more fragment lower boundaries to the NM-MD relationship information, and determine target ion fragments from the plurality of candidate ion fragments based on fragmentation efficiency information associated with the candidate ion fragments.Type: GrantFiled: November 21, 2017Date of Patent: November 3, 2020Assignee: WATERS TECHNOLOGIES CORPORATIONInventors: Scott J. Geromanos, Curt Devlin, Steven J. Ciavarini
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Publication number: 20200279726Abstract: A method of analyzing a complex sample includes performing a sequential chromatographic-IMS-MS analysis of a sample to obtain a plurality of experimental mass spectra having isotopic clusters, wherein each spectrum of the plurality of spectra is associated with a chromatographic retention time and an ion-mobility drift time. The method also includes calculating a model isotopic cluster of a precursor or product ion associated with a candidate compound in the sample, in correspondence to the natural isotopic-abundance ratios of elements composing the compound. The method further includes comparing peaks of the model isotopic cluster to corresponding peaks of an isotopic cluster of one of the experimental mass spectra to extract one or more saturated or interfered peaks of the experimental isotopic cluster, wherein at least one of the peaks of the experimental isotopic cluster is un-saturated and un-interfered.Type: ApplicationFiled: May 19, 2020Publication date: September 3, 2020Inventors: Scott J. Geromanos, Marc V. Gorenstein, Daniel Golick, Steven J. Ciavarini
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Publication number: 20200266042Abstract: Techniques for performing data acquisition and analysis are described. A multi-mode acquisition strategy may be performed which iteratively selects mass isolation windows of different sizes in different scan cycles to acquire experimental data. The mass isolation windows selected may provide for acquiring elevated energy scan data for a defined set of m/z values. Single scan data analysis may be performed. Data analysis may include forming precursor charge clusters, chaining precursor charge clusters having the same mass to charge ratio to form peaks profiles, and using criteria to align precursor and product ions of the experimental data. Unsupervised and supervised clustering may be performed using a database and composite ion spectra formed from experimental data. Also described are a small molecule acquisition enhancement and additional techniques applicable for biopharmaceutical and other applications.Type: ApplicationFiled: January 17, 2020Publication date: August 20, 2020Inventors: Scott J. Geromanos, Steven J. Ciavarini, Curt Devlin
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Patent number: 10692709Abstract: A method of analyzing a complex sample includes performing a sequential chromatographic-IMS-MS analysis of a sample to obtain a plurality of experimental mass spectra having isotopic clusters, wherein each spectrum of the plurality of spectra is associated with a chromatographic retention time and an ion-mobility drift time. The method also includes calculating a model isotopic cluster of a precursor or product ion associated with a candidate compound in the sample, in correspondence to the natural isotopic-abundance ratios of elements composing the compound. The method further includes comparing peaks of the model isotopic cluster to corresponding peaks of an isotopic cluster of one of the experimental mass spectra to extract one or more saturated or interfered peaks of the experimental isotopic cluster, wherein at least one of the peaks of the experimental isotopic cluster is un-saturated and un-interfered.Type: GrantFiled: October 29, 2018Date of Patent: June 23, 2020Assignee: Waters Technologies CorporationInventors: Scott J. Geromanos, Marc V. Gorenstein, Daniel Golick, Steven J. Ciavarini
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Patent number: 10573501Abstract: Techniques for performing data acquisition and analysis are described. A multi-mode acquisition strategy may be performed which iteratively selects mass isolation windows of different sizes in different scan cycles to acquire experimental data. The mass isolation windows selected may provide for acquiring elevated energy scan data for a defined set of m/z values. Single scan data analysis may be performed. Data analysis may include forming precursor charge clusters, chaining precursor charge clusters having the same mass to charge ratio to form peaks profiles, and using criteria to align precursor and product ions of the experimental data. Unsupervised and supervised clustering may be performed using a database and composite ion spectra formed from experimental data. Also described are a small molecule acquisition enhancement and additional techniques applicable for biopharmaceutical and other applications.Type: GrantFiled: May 31, 2016Date of Patent: February 25, 2020Assignee: WATERS TECHNOLOGIES CORPORATIONInventors: Scott J. Geromanos, Steven J. Ciavarini, Curt Devlin
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Patent number: 10495647Abstract: A method of mass spectrometry comprises ionising a sample eluting from a separation device in order to generate a plurality of parent ions. Multiple cycles of operation are performed as the sample elutes from the separation device. Each cycle of operation comprises mass analysing the parent ions to obtain parent ion mass spectral data, and mass analysing fragment or product ions derived from the parent ion to obtain fragment or product ion mass spectral data. Each cycle of operation also comprises mass analysing fragment or product ions derived from parent ions having mass to charge ratios within a first range to obtain first fragment or product ion mass spectral data, and mass analysing fragment or product ions derived from parent ions having mass to charge ratios within a second different range to obtain second fragment or product ion mass spectral data. The method can provide a hybrid data independent acquisition (DIA) and data dependent acquisition (DDA) approach.Type: GrantFiled: June 12, 2015Date of Patent: December 3, 2019Assignee: Waters Technologies CorporationInventors: Scott J Geromanos, Steven J Ciavarini, James I. Langridge, Brad J Williams, Michael J Nold
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Publication number: 20190131117Abstract: A method of analyzing a complex sample includes performing a sequential chromatographic-IMS-MS analysis of a sample to obtain a plurality of experimental mass spectra having isotopic clusters, wherein each spectrum of the plurality of spectra is associated with a chromatographic retention time and an ion-mobility drift time. The method also includes calculating a model isotopic cluster of a precursor or product ion associated with a candidate compound in the sample, in correspondence to the natural isotopic-abundance ratios of elements composing the compound. The method further includes comparing peaks of the model isotopic cluster to corresponding peaks of an isotopic cluster of one of the experimental mass spectra to extract one or more saturated or interfered peaks of the experimental isotopic cluster, wherein at least one of the peaks of the experimental isotopic cluster is un-saturated and un-interfered.Type: ApplicationFiled: October 29, 2018Publication date: May 2, 2019Inventors: Scott J. Geromanos, Marc V. Gorenstein, Daniel Golick, Steven J. Ciavarini
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Patent number: 10242853Abstract: A method of mass spectrometry comprises ionizing a sample eluting from a separation device in order to generate a plurality of parent ions. The method further comprises generating a target list of ions, which includes a predicted mass to charge ratio, a predicted chromatographic retention or elution time, and a predicted ion mobility drift time, derived from a model. Multiple cycles of operation are then performed as the sample elutes from the separation device. Each cycle of operation includes mass filtering the parent ions so that selected ions having mass to charge ratios within a first mass to charge ratio range are onwardly transmitted to a fragmentation or reaction device. The target list is then checked and the model is updated accordingly. The first mass to charge ratio range can then be adjusted in response to the updated model.Type: GrantFiled: June 12, 2015Date of Patent: March 26, 2019Assignee: Waters Technologies CorporationInventors: Scott J Geromanos, Steven J Ciavarini, Weibin Chen, Stephane Houel
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Publication number: 20180321198Abstract: The present disclosure relates generally to a system and a method for improving performance of a chromatography system using a highly-compressible fluid based mobile phase (e.g., CO2). In particular, the present disclosure relates to a system that uses a conduit, such as a convergent-divergent nozzle, for reducing pressure noise in a chromatography system using a highly-compressible fluid based mobile phase. The chromatography system can include a conduit, such as a convergent-divergent nozzle, disposed downstream of the column to reduce or prevent the propagation of pressure or density pulses from a back pressure regulator.Type: ApplicationFiled: May 1, 2018Publication date: November 8, 2018Inventors: Abhijit Tarafder, Michael O. Fogwill, Joshua A. Shreve, Joseph D. Michienzi, Steven J. Ciavarini
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Patent number: 10115576Abstract: A method of analyzing a complex sample includes performing a sequential chromatographic-IMS-MS analysis of a sample to obtain a plurality of experimental mass spectra having isotopic clusters, wherein each spectrum of the plurality of spectra is associated with a chromatographic retention time and an ion-mobility drift time. The method also includes calculating a model isotopic cluster of a precursor or product ion associated with a candidate compound in the sample, in correspondence to the natural isotopic-abundance ratios of elements composing the compound. The method further includes comparing peaks of the model isotopic cluster to corresponding peaks of an isotopic cluster of one of the experimental mass spectra to extract one or more saturated or interfered peaks of the experimental isotopic cluster, wherein at least one of the peaks of the experimental isotopic cluster is un-saturated and un-interfered.Type: GrantFiled: December 8, 2014Date of Patent: October 30, 2018Assignee: WATERS TECHNOLOGIES CORPORATIONInventors: Scott J. Geromanos, Marc V. Gorenstein, Daniel Golick, Steven J. Ciavarini
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Publication number: 20180231988Abstract: Exemplary embodiments of the present disclosure are directed to manipulating pressure-related hysteresis in a pressurized flow system by setting the pressure of the system to a predetermined location in the hysteresis band to advantageously minimize an effect of the pressure related hysteresis on the pressure of the system or to advantageously benefit from the effects of the hysteresis on the pressure of the system.Type: ApplicationFiled: April 13, 2018Publication date: August 16, 2018Inventors: Joshua A. Shreve, Paul Keenan, Steven J. Ciavarini
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Publication number: 20180166265Abstract: Techniques for performing data acquisition and analysis are described. A multi-mode acquisition strategy may be performed which iteratively selects mass isolation windows of different sizes in different scan cycles to acquire experimental data. The mass isolation windows selected may provide for acquiring elevated energy scan data for a defined set of m/z values. Single scan data analysis may be performed. Data analysis may include forming precursor charge clusters, chaining precursor charge clusters having the same mass to charge ratio to form peaks profiles, and using criteria to align precursor and product ions of the experimental data. Unsupervised and supervised clustering may be performed using a database and composite ion spectra formed from experimental data. Also described are a small molecule acquisition enhancement and additional techniques applicable for biopharmaceutical and other applications.Type: ApplicationFiled: May 31, 2016Publication date: June 14, 2018Inventors: Scott J. Geromanos, Steven J. Ciavarini, Curt Devlin