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IP Update: Recent Patents Awarded to Harvard, Cell Signaling Technology, and More

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Recent Patents of Interest in Proteomics

US Patent No. 8,620,595. Methods for determining the retention of peptides in reverse phase chromatography using linear solvent strength theory. Inventors: Oleg Krokhin, Vic Spicer. Assignee: University of Manitoba

Covers methods using reverse phase chromatography to separate or isolate peptides, including methods for calculating the slope of peptides.


US Patent No. 8,618,475. Ion mobility spectrometer with one or more integral ion activation regions. Inventors: David Clemmer, Stormy Koeniger, Stephen Valentin. Assignee: Indiana University

Covers an ion mobility spectrometer with a drift tube configured to separate ions in time according to their ion mobility. Also includes an ion activation region to selectively induce structural changes in some of the ions.


US Patent No. 8,618,260. Tyrosine, serine and threonine phosphorylation sites. Inventors: Peter Hornbeck, Albrecht Moritz, John Rush, Steven Gygi. Assignee: Cell Signaling Technology

Covers 155 novel phosphorylation sites identified in carcinoma and leukemia as well as peptides with these sites, antibodies to them, and diagnostic and therapeutic uses of them.


US Patent No. 8,618,248. Phosphopeptide compositions and anti-phosphopeptide antibody compositions and methods of detecting phosphorylated peptides. Inventors: Steven Gygi, Judit Villen, Sean Beausoleil. Assignee: Harvard College

Covers phosphopeptide compositions and anti-phosphopeptide antibody compositions.


US Patent No. 8,614,303. Diagnostic methods for ubiquinated protein profiling. Inventors: Kiran Madura, Li Chen. Assignee: University of Medicine and Dentistry

Covers a method of establishing a protein expression profile of a sample by contacting it with a ubiquitin-binding protein such that ubquitinated and specific non-ubiquitinated proteins bind to this protein, allowing for the analysis of the isolated non-ubiquitinated proteins.


US Patent No. 8,609,437. Biomarkers for the diagnosis and treatment of pancreatic cancer. Inventors: Anthony Yeung, Jeffrey Tokar. Assignee: The Institue for Cancer Research

Covers detection of at least three of the following markers mucin 1, mucin 2, mucin 5AC, mucin 5B, mucin 6, CEA CAM 1, CEACAM 5, CEACAM 6, CEACAM 7, CEACAM 8, S100-A6, S100-A8, S100-A9 and S100-A11, to asses a patient's risk of pancreatic cancer.


US Patent No. 8,609,344. Nucleic-acid programmable protein arrays. Inventors: Joshua Labaer, Albert Lau. Assignee: Harvard College

Covers a system in which arrays of polypeptides are generated by translation of nucleic acid sequences encoding the polypeptides at a plurality of addresses on the array.


US Patent No. 8,604,692. Mass spectrometry assay for eIF4E and eIF4E regulon activity. Inventor: Gordon Jamieson. Assignee: Translational Therapeutics

Covers a mass spec assay for quantitation of 4E/4E regulon pathway proteins and their phosphorylation states.


US Patent No. 8,603,752. Methods for identifying and monitoring drug side effects. Inventors: Leroy Hood, Biaoyang Lin. Assignee: Institute for Systems Biology

Covers methods for identifying drug side effects by detecting changes in organ specific molecular blood fingerprints, including proteins and reagents for detecting them.


US Patent No. 8,603,734. Biomarkers for prostate cancer. Inventors: Hui Zhang, Yan Li, Lori Sokoll, Zhen Zhang, Daniel Chan. Assignee: The Johns Hopkins University

Covers methods of detecting prostate cancer by measuring protein biomarkers in a serum sample.


US Patent No. 8,598,515. Mass spectrometry systems. Inventors: Robert Grothe. Assignee: Cedars-Sinai Medical Center.

Covers methods of mass spectrometry including a phase-modeling analysis method for identification of proteins or peptides.


US Patent No. 8,592,216. Labeling peptides with tertiary amines and other basic functional groups for improved mass spectrometric analysis. Inventors: Brian Frey; L. (Madison, WI), Apri Jue, Casey Krusemark, Lloyd Smith, Joshua Coon. Assignee: Wisconsin Alumni Research Foundation

Covers a method of enhancing fragmentation of peptides for mass spec by modifying them with a tagging reagent with greater gas-phase basicity than the amide backbone of the peptide, which leads to higher charge state ions from electrospray ionization mass spec.


US Patent No. 8,591,899. Diagnosis of Bacillus anthracis infection based on detection of bacterial secreted biomarkers. Inventors: Avigdor Shafferman, Ofer Cohen, Theodor Chitlaru, Sagit Sela-Abramovich, Orit Gat. Assignee: Israel Institute for Biological Research

Covers a method of diagnosis anthrax infection by detecting three anthrax proteins.


US Patent No. 8,586,379. Monitoring treatment of colorectal cancer patients with drugs targeting EGFR pathway using mass spectrometry of patient samples. Inventors: Heinrich Roder, Maxim Tsypin, Julia Grigorieva. Assignee: Biodesix

Covers mass spec based measurement of proteins and a classification algorithm to determine whether a non-small cell lung cancer patient, head and neck squamous cell carcinoma, or colorectal cancer patient has likely developed a non-responsiveness to treatment with a drug targeting an epidermal growth factor receptor pathway.


US Patent No. 8,586,340. Selective posttranslational modification of phage-displayed polypeptides. Inventors: Meng-Lin Tsao, Feng Tian, Peter Schultz. Assignee: The Scripps Research Institute

Covers posttranslational modification of phage-displayed polypeptides using unnatural amino acids introduced into the polypeptide using an in vivo orthogonal translation system comprising a suitable orthogonal aminoacyl-tRNA synthetase and a suitable orthogonal tRNA species.


US Patent No. 8,586,320. Methods for prognosing the recurrence of gastrointestinal and other cancers using the Shc proteins. Inventors: Raymond Frackleton, Laurie Hafer. Assignee: Catalyst Oncology.

Covers methods of prognosing the recurrence of gastrointestinal and other cancers using tyrosine phosphorylated Shc (PY-Shc) and/or p66-Shc.


US Patent No. 8,586,006. Organ-specific proteins and methods of their use. Inventors: Leroy Hood, Patricia Beckmann, Richard Johnson, Marcello Marelli, Xiaojun Li. Assignees: Institute for Systems Biology, Integrated Diagnostics

Covers methods of identifying and using organ-specific proteins and transcripts along with diagnostic kits for measuring them in biological samples.


US Patent No. 8,585,884. Apparatus for protein separation using capillary isoelectric focusing--hollow fiber flow field flow fractionation and method thereof. Inventors: Myeong Moon, Duk Kang. Assignee: Industry-Academic Cooperation Foundation, Yonsei University

Covers a device for separating proteins consisting of a capillary isoelectric focusing units and a hollow fiber flow field flow fractionation unit for secondary separation.


US Patent No. 8,580,570. Narrow bore porous layer open tube capillary column and uses thereof. Inventors: Barry Karger, Jian Zhang. Assignee: Northeastern University

Covers a polymer-based PLOT capillary column prepared by in situ copolymerization of a functional monomer which enhances the strength of the polymer matrix and use of such columns for LC analysis, including LC/MS proteomic analysis.


US Patent No. 8,580,534. Method for incorporation of two oxygen atoms into digested peptides using peptidases. Inventor: Masaru Miyagi. Assignee: University of North Dakota

Covers a method for comparative proteomics using a peptidase under enzymatic conditions that permits the optimal incorporation of oxygen isotopes into a digested peptide. Target peptides can then be quantified based on the content of these oxygen isotopes.


US Patent No. 8,580,519. Use of plasma HSP90 related to malignancy. Inventors: Angelika Burger, Edward Sausville. Assignee: University of Maryland, Baltimore

Covers methods of diagnosing and prognosticating cancer by tracking levels of Hsp90-alpha in plasma and determining levels of associated molecules.


US Patent No. 8,580,491. Cancer diagnosis marker using the aberrant glycosylation of a protein. Inventors: Yeong Ahn, Jong Yoo. Assignee: Korea Basic Science Institute

Covers a method of diagnosing cancer based on aberrant glycosylation of a glycoprotein.

The Scan

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.