Archive: 2004-2009

Third Party Publications & Posters

Improved Preparation and Analysis of Biothreat Agents and Infectious Microbial Samples Using Pressure Cycling Technology (PCT)
Bradford Powell, Ph.D., Cernomics Solutions

Comparative Proteomics of Swine Tissue 2DLC/MS of Tissue Digestion Preliminary Protein Analysis
Matthew Lawrence
Human Proteomics Program
University of Wisconsin-Madison

Proteomics under Pressure: Development of Essential Sample Preparation Techniques in Proteomics Using Ultrahigh Hydrostatic Pressure
Emily Freeman and Alexander R. Ivanov*
HSPH Proteomics Resource, Department of Genetics and Complex Diseases, Harvard School of Public Health, Harvard University,
655 Huntington Avenue, SPH-1 Room 409, Boston, Massachusetts 02115, United States

Application of Pressure Cycling Technology (PCT) in Differential Extraction
Deepthi Nori*, MFS; Dr. Bruce R. McCord, PhD International Forensic Research Institute, Department of Chemistry and Biochemistry Florida International University, Miami, FL

DNA recovery by pressure cycling and its potential application to differential extraction
Deepthi Nori and Bruce R. McCord*
Department of Chemistry and Biochemistry
Florida International University
mccordb@fiu.edu

Revisiting Jurassic Park: The Isolation of Proteins from Amber Encapsulated Organisms Millions of Years Old
Gary B. Smejkal, George O. Poinar, Pier Giorgio Righetti and Feixia Chu Sample Preparation in Biological Mass Spectrometry 2011, Part 14, 925-938, DOI: 10.1007/978-94-007-0828-0_45

Global Deglycosylation in High Throughput LC-MS Glycomics: Comparing Microwave, Pressure, and Ultrasound Effects on PNGase F with Human Serum
Scott R. Kronewitter, Gordon W. Slysz, Daniel López-Ferrer, Matthew E. Monroe, Rui Zhao, Thomas L. Fillmore, Karl K. Weitz, Robert A. Heegel, Daniel J. Orton, Brian L. LaMarche, Kevin L. Crowell, Anuj R. Shah, Carrie D. Nicora, Heather M. Brewer, David G. Camp II, Gordon A. Anderson, Ronald J. Moore, and Richard D. Smith

Poster: Improved Tools for Examining Low Copy Number (LCN) DNA Obtained from Challenged or Degraded Samples
Pamela Marshall, Jonathan King, Sarah Schmedes, Meredith Turnbough, Arthur Eisenberg and Bruce Budowle
Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Ft Worth, Texas 76107, USA

Improving the Efficiency and Throughput of an Enzymatic Digestion of Klotho using Pressure Cycling Technology (PCT)
Taha Rezai1, Vera Gross2, Alexander Lazarev2, Mary Lopez1
1Thermo Fisher Scientific, Cambridge, MA; 2Pressure BioSciences Inc., Boston, MA
MSACL 2011

Composition of Microbial Communities in Petroleum Deposits
Jamie Scott, Debarati Paul, Magan Green, Lewis R. Brown, and Mark L. Lawrence.
College of Veterinary Medicine, Biological Sciences, Mississippi State University, Mississippi State, MS-39762
ASM 2011

The Evaluation of Pressure-Assisted Enzymatic Digestion for the Optimal Digestion of Monoclonal Antibodies
Yazen Jmeian; Eric Beil; Dariusz Janecki; Steven C. Pomerantz; Jennifer F. Nemeth
Centocor R&D, a division of J&JPRD LLC, Radnor, PA

Does LC Separation of Intact Proteins Hinder Identification of Bacterial Markers?
Melinda A. McFarland ; Denis Andrzejewski; John H. Callahan; Steven M. Musser
FDA-CFSAN, College Park, MD

Development of a 20 kpsi Enzymatic Digester for High Throughput Proteomic Analysis and Its Application to Membrane Proteomics
Seok-Won Hyung¹; Daniel López-Ferrer¹; Daniel J. Orton¹; Erika Zink¹; Karl K. Weitz¹; Rui Zhao¹; Ronald J. Moore¹; Kim K. Hixson¹; Edmund Y. Ting²; Alexander V. Lazarev²; Richard D. Smith^1
1Pacific Northwest National Laboratory, Richland, WA; 2Pressure Biosciences, Inc, South Easton, MA

Identification and Validation of Vaccine Candidate Proteins by 2-Dimensional Mass Spectrometry Analysis of Group A Streptococcus
Lori C Stansberry; Angela Payne; Julie Skinner; Loren Schultz; Jon Heinrichs; Eberhard Durr
Merck and Co., West Point, PA

Development of Improved Sample Inactivation and Extraction Methods for Systems Biology Analysis
1Bradford S. Powell and 2Loreen L. Lofts
1Bacteriology Division and 2Virology Division, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA

Poster: Application of Pressure Cycling Technology (PCT) in Differential Extraction
Deepthi Nori*, MFS; Dr. Bruce R. McCord, PhD
International Forensic Research Institute, Department of Chemistry and Biochemistry
Florida International University, Miami, FL USA

Seminar : Application of Pressure Cycling Technology (PCT) in Differential Extraction
Deepthi Nori*, MFS; Dr. Bruce R. McCord, PhD
International Forensic Research Institute, Department of Chemistry and Biochemistry
Florida International University, Miami, FL USA

MALDI and LCMS Identifications of Early Protein and LA-ICP-MS Identification of Early Metal Biomarkers of Ionizing Radiation
P. Pevsner1, G. Li2, N. Sobol1, D.C Miller1, D. Robertson2,3
1Department of Pathology and Anatomical Sciences
University of Missouri School of Medicine
2 University of Missouri Department of Chemistry
3University of Missouri Research Reactor (MURR)
Columbia, MO, USA

Rapid Protein Extraction and Trypsin Digestion with Pressure Cycling Technology (PCT)
Paul H Pevsner et al., University of Missouri School of Medicine

Digestion with Pressure Cycling Technology (PCT)
Nicholas Sobol, Jennifer Oprihory*, Tiffany Remsen, A. Yuen, P., Paul Pevsner.
Department of Pathology and Anatomical Sciences
University of Missouri School of Medicine, Columbia, MO

Applications of High Pressure for Automated High Performance Proteomics Capitalizing on thermodynamic principles to reduce sample preparation times from hours to minutes
Daniel López-Ferrer
Caprion Proteomics US LLC

Recovery and Immunoaffinity Mass Spectrometric Analysis of Integral Membrane Proteins from Metastatic Ovarian Cancer Tissue Using PCT™ and ProteoSolve™-TD Buffers
Dr. Luke V. Schneider, CSO, Target Discovery, Inc.

Recovery and Immunoaffinity Mass Spectrometric Analysis of Integral Membrane Proteins from Metastatic Ovarian Cancer Tissue Using PCT™ and ProteoSolve™-TD Buffers
Dr. Luke V. Schneider, CSO, Target Discovery, Inc.

High-pressure EPR reveals conformational equilibria and volumetric properties of spin-labeled proteins
John McCoy and Wayne L. Hubbell1
Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
Contributed by Wayne L. Hubbell, December 6, 2010 (sent for review October 5, 2010)
www.pnas.org/cgi/doi/10.1073/pnas.1017877108

Overcoming Lab Automation Challenges
Flexibility Is Essential as There Is No Such Thing as One-Size-Fits-All Instrumentation
GEN Jan 15 2011 (Vol. 31, No. 2)

Pressure Cycling Technology (PCT) Applications for DNA Extractions from Challenging Forensic Samples
Suzanne Gonzalez, Elizabeth Feller, Dixie Peters, Bruce Budowle, and Arthur Eisenberg
University of North Texas Health Science Center, Institute of Investigative Genetics, UNT Center for Human Identification, 3500 Camp Bowie Blvd., Fort Worth, TX 76107

Mechanical loading-induced TGF-ß1 mediates cartilage degradation caused by upregulation of HTRA1/DDR2
Li, YF;1, Li, Y;2* Xu, L;1* Servais, J;1 Frank, E;2 Lazarev, A;3 Olsen, BR;1 Grodzinsky, AJ;2 Medici, D;1,4
1Harvard School of Dental Medicine and Harvard Medical School, Boston, MA, 2MIT, Cambridge, MA, 3 Pressure BioSciences, Inc, 4BIDMC, Boston, MA
Orthopedic Research Society (ORS) 2011 ORS Annual Meeting

Rapid and efficient protein digestion using trypsin-coated magnetic nanoparticles under pressure cycles.
Lee B, Lopez-Ferrer D, Kim BC, Na HB, Park YI, Weitz KK, Warner MG, Hyeon T, Lee SW, Smith RD, Kim J.
1 Department of Chemical and Biological Engineering, Korea University, Seoul, Korea, 2 Pacific Northwest National Laboratory, Richland, WA, USA 3 Environment Division, Korea
Institute of Science and Technology, Seoul, Korea, 4 National Creative Research Initiative Center for Oxide Nanocrystalline Materials, World Class University (WCU), program of Chemical
Convergence for Energy & Environment (C2E2), School of Chemical and Biological Engineering, Seoul National University, Seoul, Korea, 5 Department of Chemistry, Korea University, Seoul, Korea
Proteomics. 2010 Dec 3

Video Seminar: Exploring Post-translational Modification of the Mitochondrial Subproteome: an Expanding Role in Heart Disease
Jennifer E. Van Eyk, Ph.D., Professor of Medicine, Biological Chemistry and Biomedical Engineering
Director, JHU Bayview Proteomics Center
Director, JHU NHLBI Proteomics Innovation Center on Heart Failure
Director, JHU ICTR/CTSA Biomarker Development Group

Elevated Pressure Improves the Rate of Formalin Penetration while Preserving Tissue Morphology
Ingrid E. Chesnick1, Jeffrey T. Mason1, Timothy J. O'Leary2, Carol B. Fowler1,2
1. Department of Biophysics, Armed Forces Institute of Pathology, Rockville, Maryland, USA;
2. Biomedical Laboratory Research and Development Service, Veterans Health Administration, Washington, DC, USA

Label-free mass spectrometry-based relative quantification of proteins separated by one-dimensional gel electrophoresis
Melkamu Getie-Kebtiea, Alexander Lazarevb, Maryna Eichelbergerc and Michail Altermana,
a Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA b Pressure BioSciences, South Easton, MA 02375, USAc Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA

PRESSURE CYCLING TECHNOLOGY (PCT) APPLICATIONS FOR FORENSIC DNA ANALYSIS
Pam Marshall, MS; Jonathan King, MS; Meredith Turnbough, PhD; Arthur J. Eisenberg, PhD; Bruce Budowle, PhD
Institute of Investigative Genetics, Department of Forensics and Investigative Genetics,
University of North Texas Health Science Center, Fort Worth, Texas

Application of Pressure Cycling Technology (PCT) in Differential Extraction
Deepthi Nori, MFS** Bruce R. McCord, PhD
International Forensic Research Institute, Department of Chemistry and Biochemistry
Florida International University, Miami, FL 33199

A Proteomics Jurassic Park: The isolation of proteins from microorganisms encapsulated in amber from the Oligo-Miocene epoch 30-40 million years ago
Gary B. Smejkal1,3, George O. Poinar Jr.2, Feixia Chu3 and Pier Giorgio Righetti4
1 Harvard Catalyst, Harvard Clinical and Translational Science Center, Laboratory for Innovative
Translational Technologies, Boston, MA, USA. 2 Oregon State University, Department of Zoology, Corvallis, OR, USA.
3 University of New Hampshire, Hubbard Center for Genome Studies, Durham, NH, USA.
4 Politecnico di Milano, Department of Chemistry, Materials, and Chemical Engineering, Milan, Italy.

A Comparative Study of In-Gel Digestions Using Microwave and Pressure-Accelerated Technologies
Rudy Alvarado, Diana Tran, Bonnie Ching, and Brett S. Phinney*
UC Davis Proteomics Core Facility, University of California Davis Genome Center, Davis, CA 95616, USA

Pressurized Pepsin Digestion in Proteomics: An Automatable Alternative to Trypsin for Integrated Top-down Bottom-up Proteomics
Daniel López-Ferrer1*, Konstantinos Petritis1#, Errol W. Robinson2, Kim K. Hixson2, Zhixin, Tian1, Jung Hwa Lee3, Sang-Won Lee3, Nikola Tolic2, Karl K. Weitz1, Mikhail E. Belov1, Richard D. Smith1 and Ljiljana Paša-Tolic2*
1Biological Science Division, 2Environmental Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, WA, USA and 3Department of Chemistry, Korea University,
Seoul, Korea

Improved Extraction of DNA of Ca. Liberibacter Species from Plants and Cultivated Cells Using Pressure Cycling Technology
A. Sechler1, A Marques2, N. Lawrence3, N. W. Schaad1
1FDWSRU, USDA-ARS, Fort Detrick, MD USA
2EMBRAPA, Brasilia, Brasil
3Pressure BioSciences Inc., South Easton, MA, USA

A Comparison of Methods for Efficient Digestion of Protein Therapeutics
Lorna L. Maheu, Heather M. Connelly, Adam G. Harder, and Steven L. Cockrill
Analytical Sciences, Amgen Inc., Longmont, CO 80503

Soluble Forms of the Notch Ligands Delta1 and Jagged1 Promote in Vivo Tumorigenicity in NIH3T3 Fibroblasts with Distinct Phenotypes
Sumithra Urs, Alice Roudabush, Christine F. O’Neill, Ilka Pinz, Igor Prudovsky, Doreen Kacer, Yuefang Tang, Lucy Liaw, and Deena Small

Novel efficient alternatives for essential sample preparation techniques in functional proteomics
Emily Freeman and Alexander R. Ivanov
Harvard School of Public Health, Department of Genetics and Complex Diseases

Tandem Mass Spectrometry Analysis of Ex Vivo Amyloid Fibril and Tissue Samples
Zhenning Hong,1Giuseppe Infusini,1Lawreen H. Connors,2Martha Skinner,2Catherine E. Costello1,2
Mass Spectrometry Resource and 2Amyloid Treatment and Research Program, Boston University School of Medicine, Boston, MA USA

Geographic distribution of Rhizoctonia and Pythium species in soils from dryland cereal cropping systems in eastern Washington
K. L. SCHROEDER, P. A. Okubara, and T. C. Paulitz
USDA-ARS, Washington State University, Pullman, WA 99164-6430

Proteomic Comparison of Sun-protected vs -Exposed and Young vs Gently-Aged Human Epithelium
1 Facility Center California R.A. Eigenheer1, J.T. Smilowitz2 and B.S. Phinney1
1. Proteomics Core Facility, Genome Center, University of California, Davis
2. Department of Food Science and Technology, University of California, Davis

Screening for Drug-Drug Interactions Using a Targeted Proteomics Strategy
Daniel B. Kassel1; Kheng B. Lim1; Melinda Manuel1;
Teruaki Okuda2; Naomi Kamiguchi2; Christie L Hunter3; Brian Williamson3; Lydia Nuwaysir3
1Takeda San Diego, Inc, San Diego, CA; 2Takeda Pharmaceutical Company, Limited, Osaka, Japan;
3AB Sciex, Foster City, CA

Application of High Pressure and Highly Stable Trypsin Aggregate Coating on Superparamagnetic Magnetite/Silica Nanoparticles for High Performance Proteomics
Daniel López-Ferrer1, Byoungsoo Lee2, Jungbae Kim2 and Richard D. Smith1
1Pacific Northwest National Laboratory, Richland, WA 99352; 2Korea University, Seoul, Korea

A separation-free quantitative MS-based profiling approach using 2-AA isotopically labeled substrates for high-throughput glycan screening
Justin M. Prien1, Lorna Maheu1, Brad Prater1, and Steve Cockrill1
1Analytical Science, Amgen, Longmont, Colorado 80503

New Strategies for High Pressure-Assisted Digestion in Proteomics
Kim K. Hixson1,2, Daniel López-Ferrer1, Karl K. Weitz1, Ronald J. Moore1, Scott R. Kronewitter1, Heather H. Smallwood3, Mikhail E. Belov1, and Richard D. Smith1
1Pacific Northwest National Laboratory, Richland, WA; 2Washington State University, Pullman, WA; St. Jude Children’s Research Hospital, Memphis, TN

Rapid Release of N-Linked Glycans from Glycoproteins by Pressure-Cycling Technology
Zoltan Szabo, Andras Guttman and Barry L. Karger
Barnett Institute, Northeastern University, Boston

The Effect of Pressure Cycling on Proteolytic Cleavage Efficiency, Reaction Time and Protein Sequence Coverage
Roger Biringer1, Eric Bonneil2, Julian Saba1, Andreas Huhmer1, Pierre Thibault2

Role of luxS in Bacillus Anthracis Growth and Virulence Factor Expression
Marcus B. Jones,1-3,* Scott N. Peterson,1 Rosslyn Benn,1 John C. Braisted,1 Behnam Jarrahi,1 Kenneth Shatzkes,1 Dacheng Ren,4 Thomas K. Wood5 and Martin J. Blaser2,3
1Thermo Fisher Scientific, San Jose, CA 2Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada

PRESSURE CYCLING TECHNOLOGY (PCT): APPLICATIONS FOR FORENSIC DNA ANALYSIS
Pam Marshall
University of North Texas Health Science Center, Center for Human Identification

MALDI and LCMS Protein Biomarkers of Ionizing Radiation
Tiffany Remsen, Vladamir Kachalov, Parth Kothiya, Zeineen A. Momin*, Naresh Vasani, Jason Chouake, Douglas C. Miller, Paul Pevsner
Department of Pathology, University of Missouri School of Medicine Columbia, MO

High-Pressure Assisted In-Gel Tryptic Digestion for Qualitative and Quantitative Characterization of Protein Mixtures
Melkamu Getie-Kebtie and Michael Alterman
FDA-CBER-NIH, Rockville Pike, HFM – 735 Bldg 29A rm 2B20, Bethesda, MD 20892

High Pressure Direct Protein Extraction from Tissue – Trypsin Digest with Pressure Cycling Technology (PCT)
Nicholas Sobol, Jennifer Oprihory*, Parth Kothiya, Zeineen A. Momin, Naresh Vasani, Vladamir Kachalov, Tiffany Remsen, Faraj Al Qaraghuli, Paul H. Pevsner
Department of Pathology University of Missouri School of Medicine, Columbia, MO

A Comparative Study of In-gel Digestions Using Microwave and Pressure Accelerated Technologies
Alvarado, Diana Tran, Bonnie Ching and Brett S. Phinney
University of California Davis

Label-free mass spectrometry-based relative quantitation of proteins separated by 1DE
Melkamu Getie-Kebtie1; Maryna Eichelberger2, Manju B. Joshi13, Rajesh Gupta3, Michail A. Alterman1
1FDA/CBER/OCTGT/TVBB; 2FDA/CBER/OVRR/LPRVD; 3FDA/CBER/OVRR/PQLS

Integral Membrane Protein Extraction and Biomarker Analysis from Solid Metastatic Ovarian Tumors
L.V. Schneider¹, V. Likhte¹, W. Wright¹, F. Chu¹, E. Cambron¹, A. Baldwin¹, J. Krakow¹, A. Lazarev², G. Smejkal^3
1Target Discovery, Inc. 2Pressure BioSciences, Inc., 3Harvard LITT

Pressure Cycling Technology Research at UNTCHI
Elizabeth Feller

Pressure enhanced processes (PrEP) enabling high quality two-dimensional gel electrophoresis of Frankia mycelia and vesicle structures
Louis S. Tisa, Gary B. Smejkal Tom Berkelma, Chiara Rivas-Morello, Alexander Trachtenberg and Winston P. Kuo

Pressure Cycling Technology (PCT) Applications for DNA Extractions from Challenging Forensic Samples
Suzanne Gonzalez, Elizabeth Feller, Dixie Peters, Bruce Budowle, and Arthur Eisenberg

Presentations

HIGH PRESSURE MEDIATED SAMPLE PREPARATION FOR CAPILLARY ELECTROPHORESIS ANALYSIS OF N-LINKED GLYCANS
András Guttman1,2, Zoltán Szabó1 and Barry L. Karger1 1 Barnett Institute, Northeastern University, Boston, MA 02115 2 HLBS, University of Debrecen, Hungary 49th EHPRG, Aug 28-Sept 2, 2011 Budapest, Hungary

Environmentally Benign Reduction of Organic Compounds in Water under High Hydrostatic Pressure
Anna Tomin, Alexander Lazarev, Bela Torok Pressure BioSciences, Inc. 14 Norfolk Ave., South Easton, MA 02375, USA

A Need for Improved Sample Inactivation and Extraction Methods to Support Systems Biology Analysis of Biological Threat Organisms
1 Bradford S. Powell and 2 Loreen L. Lofts
1 Bacteriology Division, 2 Virology Division
U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD 21702

Comparison between ultra-high pressure and atmospheric tryptic digestion for proteomic analyses
E. Bonneil1, R. Biringer2, C. Bell1, P. Thibault1
1Institute for Research in Immunology and Cancer Université de Montréal; 2Thermo Fisher Scientific

Pressure Cycling Technology (PCT) Augments Sensitivity of Detection and Robustness in Forensic DNA Analyses
Bruce Budowle
Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Ft. Worth, Texas

Convenient and Reliable Extraction of Borrelia burgdorferi from Ticks Using Pressure Cycling Technology and the PCT Shredder
Richard C. Tilton, Ph.D.
Medical Diagnostics Laboratories

RAPID SAMPLE PREPARATION METHODS FOR THE ANALYSIS OF N-LINKED GLYCANS
Zoltan Szabo, András Guttman, Tomas Rejtar and Barry L. Karger
Barnett Institute, Boston, MA, USA

Development of Essential Sample Preparation Techniques in Proteomics Using Ultra-High Pressure
Emily Freeman and Alexander R. Ivanov
Harvard School of Public Health, HSPH Proteomics Resource, Department of Genetics and Complex Diseases, Boston, MA 2115

Development of new technology approaches for high-throughput proteome analysis
Capitalizing on thermodynamic principles to reduce sample preparation times from hours to minutes
Daniel López-Ferrer, Biological Separations & Mass Spectrometry Group, Pacific Northwest National Laboratory

High Pressure Direct Protein Extraction from Tissue – Trypsin Digest with Pressure Cycling Technology (PCT)
Paul H. Pevsner, Jennifer Oprihory, Nicholas Sobol, Parth Kothiya, Zeineen A. Momin, Naresh Vasani, and Tiffany Remsen
Department of Pathology, University of Missouri School of Medicine, Columbia, MO

Membrane Protein Extraction and Biomarker Analysis from Solid Metastatic Ovarian Tumors with ProteoSolve™-TD Buffers and Pressure Cycling Technology
Dr. Luke V. Schneider, CSO, Target Discovery, Inc.

(Fundamentals of) High-pressure Instruments for Innovation and Discovery
Edmund Ting, Sc.D., Pressure BioSciences