Patents by Inventor Jeffrey Cruz Silva
Jeffrey Cruz Silva 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: 9312110Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.Type: GrantFiled: February 4, 2015Date of Patent: April 12, 2016Assignee: Waters Technologies CorporationInventors: Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li, Marc Victor Gorenstein
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Publication number: 20150311052Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.Type: ApplicationFiled: February 4, 2015Publication date: October 29, 2015Inventors: Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li, Marc Victor Gorenstein
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Patent number: 9146213Abstract: A method for matching a precursor ion with one or more related product ions includes providing input data sets obtained from sample injections, each of the data sets including a precursor ion and one or more product ions, normalizing the input data sets in accordance with a single retention time for the precursor ion, determining which product ions are within a predetermined retention time window with respect to the single retention time, and, if a product ion is within the predetermined retention time window for a specified number of the input data sets, determining that the product ion is related to the precursor having the single retention time. An apparatus for analyzing a sample includes a chromatography module, a mass-spectrometry module in communication with the chromatography module, and control unit in communication with the chromatography module and the mass-spectrometry module.Type: GrantFiled: April 15, 2013Date of Patent: September 29, 2015Assignee: Waters Technologies CorporationInventors: Marc Victor Gorenstein, Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li
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Patent number: 8975577Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.Type: GrantFiled: August 8, 2014Date of Patent: March 10, 2015Assignee: Waters Technologies CorporationInventors: Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li, Marc Victor Gorenstein
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Publication number: 20150028199Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.Type: ApplicationFiled: August 8, 2014Publication date: January 29, 2015Inventors: Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li, Marc Victor Gorenstein
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Patent number: 8921773Abstract: Techniques are described for performing mass spectrometry. A stream of one or more ions is generated. The stream is transmitted into a collision cell over a period of time. In accordance with a set of criteria including a retention time of one or more precursor ions, a collision energy of the collision cell is selected to generate one or more product ions for said one or more precursor ions in said stream.Type: GrantFiled: January 19, 2011Date of Patent: December 30, 2014Assignee: Waters Technologies CorporationInventors: Scott J. Geromanos, Johannes P. C. Vissers, Craig A. Dorschel, Asish B. Chakraborty, Welbin Chen, Jeffrey Cruz Silva
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Patent number: 8835837Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.Type: GrantFiled: April 10, 2013Date of Patent: September 16, 2014Assignee: Waters Technologies CorporationInventors: Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li, Marc Victor Gorenstein
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Patent number: 8809062Abstract: A method (100) for analyzing chemicals includes fractionating a complex sample into at least two sample portions that each includes potions of two polypeptides though in different concentration ratios, digesting and performing LC/MS on each of the sample portions (110, and associating precursor ions observed via LC/MS with their corresponding polypeptide in response to LC/MS provided intensity data (170). A set of precursor ions that has substantially similar intensity ratios in both sample portions is determined to be associated with the same polypeptide.Type: GrantFiled: April 16, 2013Date of Patent: August 19, 2014Assignee: Waters Technologies CorporationInventors: Marc Victor Gorenstein, Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li
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Patent number: 8688389Abstract: Absolute quantitation of protein in a sample is provided by comparing a sum or average of the N highest ionization intensities observed for peptides of a particular protein along with a calibration standard. The calibration standard can be in the form of a table generated by prior protein peptide analysis performed using one or more pre-determined proteins. The comparison is used to determine a corresponding absolute quantity of protein based on the observed sum or average of ionization intensities. A simple conversion factor can be applied to the calibration standard value to determine the absolute quantity of protein in the sample.Type: GrantFiled: August 20, 2012Date of Patent: April 1, 2014Assignee: Waters Technologies CorporationInventors: Scott Geromanos, Jeffrey Cruz Silva, Hans Vissers, Guo-Zhong Li
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Publication number: 20130282293Abstract: Protein identification in a complex sample begins by selecting a database having proteins likely to be in the sample. In-silico digestion is performed and a target peptide is selected from produced peptides. The masses of the Y- and B-ion fragments of the target peptide are determined. These masses are used to search previously obtained low- and high-energy AMRTs obtained from LC/MS analysis of the complex sample for masses on the list. Any mass observed in the data within a detection threshold are considered a hit. If enough hits accumulate in a given retention time, the target peptide is identified as being in the sample. The list of peptides identified in the complex sample can be used to identify the proteins present in the sample, track the chromatographic retention times of peptides between samples, and quantitate the peptides and proteins present in complex samples.Type: ApplicationFiled: January 8, 2013Publication date: October 24, 2013Inventors: Scott J. GEROMANOS, Marc Victor Gorenstein, Jeffrey Cruz Silva, Guo-Zhong Li
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Patent number: 8447527Abstract: A method for matching a precursor ion with one or more related product ions includes providing input data sets obtained from sample injections, each of the data sets including a precursor ion and one or more product ions, normalizing the input data sets in accordance with a single retention time for the precursor ion, determining which product ions are within a predetermined retention time window with respect to the single retention time, and, if a product ion is within the predetermined retention time window for a specified number of the input data sets, determining that the product ion is related to the precursor having the single retention time. An apparatus for analyzing a sample includes a chromatography module, a mass-spectrometry module in communication with the chromatography module, and control unit in communication with the chromatography module and the mass-spectrometry module.Type: GrantFiled: March 14, 2012Date of Patent: May 21, 2013Assignee: Waters Technologies CorporationInventors: Marc V. Gorenstein, Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li
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Patent number: 8440465Abstract: A method for analyzing chemicals includes fractionating a complex sample into at least two sample portions that each include portions of two polypeptides though in different concentration ratios, digesting and performing LC/MS on each of the sample portions, and associating precursor ions observed via LC/MS with their corresponding polypeptide in response to LC/MS-provided intensity data. A set of precursor-ions that has substantially similar intensity ratios in both sample portions is determined to be associated with the same polypeptide.Type: GrantFiled: February 24, 2012Date of Patent: May 14, 2013Assignee: Waters Technologies CorporationInventors: Marc V. Gorenstein, Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li
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Patent number: 8436298Abstract: LC/MS data generated by an LC/MS system is analyzed to determine groupings of ions associated with originating molecules. Ions are grouped initially according to retention time, for example, using retention time or chromatographic peaks in mass chromatograms. After initial groupings are determined based on retention time, ion peak shapes are compared to determine whether ions should be excluded. Ions having peak shapes not matching other ions, or alternatively a reference peak shape, are excluded from the group.Type: GrantFiled: August 24, 2010Date of Patent: May 7, 2013Assignee: Waters Technologies CorporationInventors: Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li, Marc Victor Gorenstein
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Publication number: 20130105682Abstract: Techniques are described for performing mass spectrometry. A stream of one or more ions is generated. The stream is transmitted into a collision cell over a period of time. In accordance with a set of criteria including a retention time of one or more precursor ions, a collision energy of the collision cell is selected to generate one or more product ions for said one or more precursor ions in said stream.Type: ApplicationFiled: January 19, 2011Publication date: May 2, 2013Applicant: Waters Technologies CorporationInventors: Scott J. Geromanos, Johannes P.C. Vissers, Craig A. Dorschel, Asish B. Chakraborty, Welbin Chen, Jeffrey Cruz Silva
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Publication number: 20130054149Abstract: Absolute quantitation of protein in a sample is provided by comparing a sum or average of the N highest ionization intensities observed for peptides of a particular protein along with a calibration standard. The calibration standard can be in the form of a table generated by prior protein peptide analysis performed using one or more pre-determined proteins. The comparison is used to determine a corresponding absolute quantity of protein based on the observed sum or average of ionization intensities. A simple conversion factor can be applied to the calibration standard value to determine the absolute quantity of protein in the sample.Type: ApplicationFiled: August 20, 2012Publication date: February 28, 2013Inventors: Scott Geromanos, Jeffrey Cruz Silva, Hans Vissers, Guo-Zhong Li
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Patent number: 8373115Abstract: Protein identification in a complex sample begins by selecting a database having proteins likely to be in the sample. In-silico digestion is performed and a target peptide is selected from produced peptides. The masses of the Y- and B-ion fragments of the target peptide are determined. These masses are used to search previously obtained low- and high-energy AMRTs obtained from LC/MS analysis of the complex sample for masses on the list. Any mass observed in the data within a detection threshold are considered a hit. If enough hits accumulate in a given retention time, the target peptide is identified as being in the sample. The list of peptides identified in the complex sample can be used to identify the proteins present in the sample, track the chromatographic retention times of peptides between samples, and quantitate the peptides and proteins present in complex samples.Type: GrantFiled: April 30, 2012Date of Patent: February 12, 2013Assignee: Waters Technologies CorporationInventors: Scott J. Geromanos, Marc Victor Gorenstein, Jeffrey Cruz Silva, Guo-Zhong Li
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Publication number: 20120267522Abstract: Protein identification in a complex sample begins by selecting a database having proteins likely to be in the sample. In-silico digestion is performed and a target peptide is selected from produced peptides. The masses of the Y- and B-ion fragments of the target peptide are determined. These masses are used to search previously obtained low- and high-energy AMRTs obtained from LC/MS analysis of the complex sample for masses on the list. Any mass observed in the data within a detection threshold are considered a hit. If enough hits accumulate in a given retention time, the target peptide is identified as being in the sample. The list of peptides identified in the complex sample can be used to identify the proteins present in the sample, track the chromatographic retention times of peptides between samples, and quantitate the peptides and proteins present in complex samples.Type: ApplicationFiled: April 30, 2012Publication date: October 25, 2012Inventors: Scott J. GEROMANOS, Marc Victor GORENSTEIN, Jeffrey Cruz Silva, Guo-Zhong Li
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Publication number: 20120253684Abstract: A method for matching a precursor ion with one or more related product ions includes providing input data sets obtained from sample injections, each of the data sets including a precursor ion and one or more product ions, normalizing the input data sets in accordance with a single retention time for the precursor ion, determining which product ions are within a predetermined retention time window with respect to the single retention time, and, if a product ion is within the predetermined retention time window for a specified number of the input data sets, determining that the product ion is related to the precursor having the single retention time. An apparatus for analyzing a sample includes a chromatography module, a mass-spectrometry module in communication with the chromatography module, and control unit in communication with the chromatography module and the mass-spectrometry module.Type: ApplicationFiled: March 14, 2012Publication date: October 4, 2012Applicant: Waters Technologies CorporationInventors: Marc V. GORENSTEIN, Scott Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li
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Patent number: 8271207Abstract: Absolute quantitation of protein in a sample is provided by comparing a sum or average of the N highest ionization intensities observed for peptides of a particular protein along with a calibration standard. The calibration standard can be in the form of a table generated by prior protein peptide analysis performed using one or more pre-determined proteins. The comparison is used to determine a corresponding absolute quantity of protein based on the observed sum or average of ionization intensities. A simple conversion factor can be applied to the calibration standard value to determine the absolute quantity of protein in the sample.Type: GrantFiled: June 2, 2006Date of Patent: September 18, 2012Assignee: Waters Technologies CorporationInventors: Scott Geromanos, Jeffrey Cruz Silva, Hans Vissers, Guo-Zhong Li
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Publication number: 20120225444Abstract: A method for analyzing chemicals includes fractionating a complex sample into at least two sample portions that each include portions of two polypeptides though in different concentration ratios, digesting and performing LC/MS on each of the sample portions, and associating precursor ions observed via LC/MS with their corresponding polypeptide in response to LC/MS-provided intensity data. A set of precursor-ions that has substantially similar intensity ratios in both sample portions is determined to be associated with the same polypeptide.Type: ApplicationFiled: February 24, 2012Publication date: September 6, 2012Applicant: Waters Technologies CorporationInventors: Marc V. GORENSTEIN, Scott J. Geromanos, Jeffrey Cruz Silva, Guo-Zhong Li