Patents by Inventor James Alexander Apffel, Jr.

James Alexander Apffel, 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).

  • Patent number: 10012574
    Abstract: Provided herein is a method comprising one or more of the following steps: (a) lysing cells of a biological sample and contacting the biological sample with an amount of ionic liquid sufficient to denature intracellular metabolic enzymes in the biological sample to produce a contacted cellular sample; (b) mixing the contacted cellular sample with an organic solvent to produce an ionic liquid-organic solvent composition; (c) mixing the contacted cellular sample with the organic solvent to produce a dispersed microdroplet ionic liquid-organic solvent composition; (d) contacting the ionic liquid-organic solvent composition with an ion exchange composition to produce a second ionic liquid-organic solvent composition; (d) separating the ionic liquid from the organic solvent; and (e) extracting metabolites from the ionic liquid. Kits and systems for practicing the subject methods are also provided.
    Type: Grant
    Filed: March 11, 2014
    Date of Patent: July 3, 2018
    Assignee: Agilent Technologies, Inc.
    Inventor: James Alexander Apffel, Jr.
  • Patent number: 9958363
    Abstract: A method for removing an ionic liquid from an aqueous sample is provided. In some embodiments, the method includes: (a) combining an aqueous sample including an ionic liquid with an ion exchanger composition including an ion exchanger counterion to produce a solution including a fluorous salt of the ionic liquid, where at least one of the ionic liquid and the ion exchanger counterion is fluorinated; (b) contacting the solution with a fluorous affinity material, thereby removing fluorous salt from the solution and producing an aqueous eluate; and (c) collecting the aqueous eluate. In certain embodiments, the method further includes: contacting a cell with an ionic liquid composition to lyse the cell and produce an aqueous sample; and contacting the aqueous sample with a reverse phase substrate, thereby adsorbing proteins and/or lipids of the cell on the substrate. Compositions, kits and systems for practicing the subject methods are also provided.
    Type: Grant
    Filed: May 28, 2015
    Date of Patent: May 1, 2018
    Assignee: Agilent Technologies, Inc.
    Inventors: Brian Phillip Smart, Brooks Bond-Watts, James Alexander Apffel, Jr.
  • Publication number: 20150369711
    Abstract: A method for removing an ionic liquid from an aqueous sample is provided. In some embodiments, the method includes: (a) combining an aqueous sample including an ionic liquid with an ion exchanger composition including an ion exchanger counterion to produce a solution including a fluorous salt of the ionic liquid, where at least one of the ionic liquid and the ion exchanger counterion is fluorinated; (b) contacting the solution with a fluorous affinity material, thereby removing fluorous salt from the solution and producing an aqueous eluate; and (c) collecting the aqueous eluate. In certain embodiments, the method further includes: contacting a cell with an ionic liquid composition to lyse the cell and produce an aqueous sample; and contacting the aqueous sample with a reverse phase substrate, thereby adsorbing proteins and/or lipids of the cell on the substrate. Compositions, kits and systems for practicing the subject methods are also provided.
    Type: Application
    Filed: May 28, 2015
    Publication date: December 24, 2015
    Inventors: Brian Phillip Smart, Brooks Bond-Watts, James Alexander Apffel, Jr.
  • Publication number: 20140273080
    Abstract: Provided herein is a method comprising one or more of the following steps: (a) lysing cells of a biological sample and contacting the biological sample with an amount of ionic liquid sufficient to denature intracellular metabolic enzymes in the biological sample to produce a contacted cellular sample; (b) mixing the contacted cellular sample with an organic solvent to produce an ionic liquid-organic solvent composition; (c) mixing the contacted cellular sample with the organic solvent to produce a dispersed microdroplet ionic liquid-organic solvent composition; (d) contacting the ionic liquid-organic solvent composition with an ion exchange composition to produce a second ionic liquid-organic solvent composition; (d) separating the ionic liquid from the organic solvent; and (e) extracting metabolites from the ionic liquid. Kits and systems for practicing the subject methods are also provided.
    Type: Application
    Filed: March 11, 2014
    Publication date: September 18, 2014
    Applicant: Agilent Technologies, Inc.
    Inventor: James Alexander Apffel, JR.
  • Patent number: 8642744
    Abstract: Crosslinking reagents and methods for using the same for analysis of protein-protein interactions, are provided. The crosslinking reagents include a trifunctional scaffold that links two protein linking groups to each other and branches to link an affinity tag, where the protein linking groups can be fragmented from the scaffold. The distance between the two protein linking groups can be selected to crosslink two proteins of a protein complex via accessible amino acid residues. Also provided are crosslinked polypeptide compounds and kits that include crosslinking reagents. These reagents and methods find use in a variety of applications in which crosslinking of proteins in desired.
    Type: Grant
    Filed: October 28, 2010
    Date of Patent: February 4, 2014
    Assignee: Agilent Technologies, Inc.
    Inventors: Brian Phillip Smart, James Alexander Apffel, Jr.
  • Publication number: 20120107855
    Abstract: Crosslinking reagents and methods for using the same for analysis of protein-protein interactions, are provided. The crosslinking reagents include a trifunctional scaffold that links two protein linking groups to each other and branches to link an affinity tag, where the protein linking groups can be fragmented from the scaffold. The distance between the two protein linking groups can be selected to crosslink two proteins of a protein complex via accessible amino acid residues. Also provided are crosslinked polypeptide compounds and kits that include crosslinking reagents. These reagents and methods find use in a variety of applications in which crosslinking of proteins in desired.
    Type: Application
    Filed: October 28, 2010
    Publication date: May 3, 2012
    Inventors: Brian Phillip Smart, James Alexander Apffel, JR.
  • Patent number: 7425451
    Abstract: Compounds, compositions, methods for sequencing proteins and peptides, and methods for identifying proteins and peptides in a mixture, are disclosed. Compounds of formula A-B-C wherein A is a nucleophilic reactive group, B is a detectable moiety capable of being isotopically labeled, and C is a charge replacement group, are used to label the peptides at the N-terminus or the C-terminus. The tagged peptides can then be analyzed by mass spectroscopy.
    Type: Grant
    Filed: December 13, 2002
    Date of Patent: September 16, 2008
    Assignee: Agilent Technologies, Inc.
    Inventors: Karla M. Robotti, James Alexander Apffel, Jr.
  • Patent number: 7109040
    Abstract: The present invention provides methods for analyzing a peptide or peptides of interest in a protein sample using a combination of a relatively generic isotope tag with a decoupled selection process, allowing simplified customization of the application with a single reagent. These methods comprise providing a first and a second protein sample; labeling the first protein sample with a first Universal Peptide Isotope Tag (U-PIT) reagent and the second protein sample with a second U-PIT reagent; separating the peptide of interest from the combined first and second protein samples; and determining the relative amount of the first U-PIT reagent and the second U-PIT reagent bound to the peptide or peptides of interest. The U-PIT label of the present inventive methods has the following general formula A-B-C wherein A is a nucleophilic reactive group, B is a detectable moiety that can be isotopically labeled, and C is a charge replacement group.
    Type: Grant
    Filed: December 13, 2002
    Date of Patent: September 19, 2006
    Assignee: Agilent Technologies, Inc.
    Inventors: James Alexander Apffel, Jr., Karla M. Robotti