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Mass Spectrometry

Mass Spectrometry

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PCT Related Publications


Quantifying cancer related proteins via targeting MS assay resources
Ruedi Aebersold, Ph.D
Institute of Molecular Systems Biology, ETH-Zürich;
Faculty of Science, University of Zürich


Proteomic investigation of intra-tumor heterogeneity
Tiannan Guo, MD, PhD
Ruedi Aebersold lab
Institute of Molecular Systems Biology
ETH Zurich


Proteotypic features of NCI-60 cancer cells obtained by SWATH-MS predicts phenotypes
Tiannan Guo *1; Ching Chiek Koh *1,2, Michael Menden *3, Alessandro Ori 4, Murat Iskar 4, Wilson Wen Bin7, Goh 5, Li Li 6, Qing Zhong 7, Emanuel Gonalves 3, Ludovic Gillet 1, Peng Qiu 8, Andreas Beyer 6, Martin Beck 4, Julio Saez-Rodriguez 3, Ruedi Aebersold1,9
1,Institute of Molecular Systems Biology, ETH Zurich, Zurich, SWITZERLAND; 2, Heidelberg University, Germany; 3, EMBL - EBI European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, Cambridge, UK; 4, EMBL Heidelberg, Heidelberg, Germany; 5, Center for Interdisciplinary Cardiovascular Sciences, Harvard Medical School, USA; 6, University of Cologne, Albertus-Magnus-Platz, Cologne, Germany; 7, Institute of Surgical Pathology, University Hospital Zürich, Zürich, Switzerland; 8, Georgia Tech and Emory University; 9, Faculty of Science, University of Zurich, Zurich, Switzerland

* Equal contribution
Contact: guo@imsb.biol.ethz.ch ; aebersold@imsb.biol.ethz.ch


PCT-SWATH: pressure cycling technology coupled with SWATH mass spectrometry for fast, deep and reproducible proteomic analysis
Tiannan Guo1, Petri Kouvonen1, Chiek Koh Ching1, Ludovic Gillet1, Witold Wolski1, Hannes Rost1, George Rosenberger1, Silke Gillessen2, Markus Jorger2, Ben Collins1, Alexander Leitner1, Ruedi Aebersold1 1Institute of Molecular Systems Biology, ETH Zurich, Switzerland, 2Department of Internal Medicine, Kantonsspital, Switzerland
Abstract Only
Please contact Dr. Tiannan Guo (guo@imsb.biol.ethz.ch) for more information.


Analysis of Tissue Biopsies by PCT-SWATH
Tiannan Guo, MD, PhD, Aebersold Lab, IMSB, ETH Zurich
Presented at International HUPO 2013
Subset of Slides
Please contact Dr. Tiannan Guo (guo@imsb.biol.ethz.ch) for more information.


Fecal Lipidomics Profiling and Structural Identification using High Resolution LC-MS and HCD Fragmentation
Susan S. Bird1, 2; Katherine E. Gregory1, 3; Vera S. Gross4; Vasant R. Marur1; Alexander V. Lazarev4; W. Allen Walker2, 5; Bruce S. Kristal1, 2 1Brigham and Women's Hospital, Boston, MA; 2Harvard Medical School, Boston, MA; 3Boston College, Boston, MA; 4Pressure BioSciences, South Easton, MA; 5Massachusetts General Hospital, Boston, MA
ASMS 2013


Method Development for Fecal Lipidomics Profiling
Katherine E Gregory , Susan Schiavo Bird , Vera S. Gross , Vasant R Marur , Alexander V. Lazarev , W. Allan Walker, and Bruce S. Kristal
Anal. Chem. 2012


Intact protein profiling and deconvolution of bacterial lysates on multiple mass spectrometers
Denis Andrzejewski1; John H. Callahan1; Timothy Croley1; Peter E. Leopold2; Melinda A. McFarland 1 1FDA-CFSAN, College Park , MD; 2BioAnalyte, Inc., Portland, ME
ASMS 2013


Improved proteomic profiling of the cell surface of culture-expanded human bone marrow multipotent stromal cells
Samuel T. Mindayea, Moonjin Raa, Jessica Lo Surdob, Steven Bauerb, and Michail A. Altermana
aTumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD, bCellular and Tissue Therapies Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Bethesda, MD
Journal of Proteomics 2012


Method for Recovery and Immunoaffinity Enrichment of Membrane Proteins Illustrated with Metastatic Ovarian Cancer Tissues
Luke V. Schneider,1 Varsha Likhte,1 WilliamH.Wright,1 Frances Chu,1 Emma Cambron,1 Anne Baldwin-Burnett,1 Jessica Krakow,1 and Gary B. Smejkal2, 3
1Target Discovery, Inc., 4030 Fabian Way, Palo Alto, CA 94030, USA
2Pressure Biosciences, Inc., 14 Norfolk Avenue, South Easton, MA 02375, USA
3Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH 03824, USA


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

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

Innovative Sample Preparation Tools for Proteomics and Analytical Laboratories
Pressure BioSciences, Inc. 14 Norfolk Ave., South Easton, MA 02375

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. Smith1
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

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

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

Intact and Functional Mitochondria from Solid Tissue: Effective Semi-Automated Extraction Using Gentle Mechanical Homogenization and Pressure Cycling Technology
Alexander Lazarev1, Vera S. Gross1, Greta Carlson1, Emily Freeman2, Alexander R. Ivanov2, Heather Greenberg3, Sergei Baranov3, Irina Stavrovskaya3, Bruce Kristal3 1Pressure BioSciences, Inc., South Easton, MA. 2HSPH Proteomics Resource, Harvard School of Public Health, Boston, MA. 3Brigham and Women's Hospital; Harvard University, Boston, MA

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.

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

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

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.

The Effect of Pressure Cycling on Proteolytic Cleavage Efficiency, Reaction Time and Protein Sequence Coverage
Eric Bonneil1; Roger Biringer2; Julian Saba2; Andreas Huhmer2; Pierre Thibault1 1Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada 2Thermo Fisher Scientific, San Jose, CA


Membrane Protein Extraction and Biomarker Analysis from Solid Metastatic Ovarian Tumors with ProteoSolve™-TD Buffers and Pressure Cycling Technology
Luke V. Schneider, CSO, Target Discovery, Inc.
Harvard Symposium 2010


Elevated Pressure Improves the Extraction and Identification of Proteins Recovered from Formalin-Fixed, Paraffin-Embedded Tissue Surrogates
Carol B. Fowler1,2*, Ingrid E. Chesnick1, Cedric D. Moore1, Timothy J. O'Leary2, Jeffrey T. Mason1
1 Department of Biophysics, Armed Forces Institute of Pathology, Rockville, Maryland, United States of America, 2 Biomedical Laboratory Research and Development Service, Veterans Health Administration, Washington, D.C., United States of America


Strategies to recover proteins from ocular tissues for proteomics
Nikhil Patel1, Ekta Solanki1, Renata Picciani1, Valerie Cavett2, Jennifer A. Caldwell-Busby2, Sanjoy K. Bhattacharya Dr.1,*
PROTEOMICS Volume 8, Issue 5, pages 1055–1070, No. 5 March 2008


Development of Essential Sample Preparation Techniques in Proteomics Using Ultra-high Pressure
Alexander R. Ivanov
HSPH Proteomics Research Department of Genetics and Complex Diseases Harvard School of Public Health


Tissue Fractionation by Hydrostatic Pressure Cycling Technology:
The Unified Sample Preparation Technique for Systems Biology Studies
Vera Gross,1 Greta Carlson,1 Ada T Kwan,1 Gary Smejkal,1 Emily Freeman,2 Alexander R Ivanov,2Alexander Lazarev1
1Pressure BioSciences, Inc., Woburn, MA; 2Harvard School of Public Health, Boston, MA
Journal of Biomolecular Techniques, Volume 19, issue 3, JULY 2008


Unified Sample Preparation Approach Using Hydrostatic Pressure Cycling: Simultaneous Isolation of Proteins, Nucleic Acids and Lipids from a Single Sample
Vera S. Gross; Greta Carlson; Gary B. Smejkal; Ada T. Kwan; Timothy Straub; Alexander V. Lazarev
Pressure BioSciences, Inc., West Bridgewater, MA
USHUPO 2008


Application of Pressurized Solvents for Ultrafast Trypsin Hydrolysis in Proteomics: Proteomics on the Fly
Daniel Lopez-Ferrer,† Konstantinos Petritis,† Kim K. Hixson,‡ Tyler H. Heibeck,† Ronald J. Moore,† Mikhail E. Belov,† David G. Camp II,† and Richard D. Smith*,†
Biological Sciences Division and Environmental Molecular Sciences Laboratory, Paci?c Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352  Journal of Proteome Research


High Pressure Trypsin Digestion of Proteins for Proteomic Analysis
Shane A. Wyatt and Timothy R. Croley
Commonwealth of Virginia; Division of Consolidated Laboratory Services, Richmond, VA Department of Chemistry; Virginia Commonwealth University, Richmond, VA


Ultra-Rapid Pressure Digestion and Label-Free Quantitative Proteomics of Yersiniae Infected Mice Tissues
Kim K. Hixson1, Daniel López-Ferrer1, Matthew Bender2, Patricia L. Worsham3, Karl K. Weitz1, Nate Lawrence4, Amy Rasley5, Therese W. Clauss1, Ljiljana Pasa-Tolió1, Richard D. Smith1, Mary S. Lipton1 1Pacific Northwest National Laboratory, Richland WA; 2NBACC, Washington, DC; 3USAMRIID, Frederick, MD; 4Pressure BioSciences, Inc., South Easton, MA; 5Lawrence Livermore National Lab, Livermore, CA


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
Harvard Symposium 2010


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
1Mass Spectrometry Resource and 2Amyloid Treatment and Research Program, Boston University School of Medicine, Boston, MA USA
USHUPO2008


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
1Thermo Fisher Scientific, San Jose, CA 2Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
ASBMB 2010


Rapid and efficient protein digestion using trypsin-coated magnetic nanoparticles under pressure cycles
Byoungsoo Lee1,, Daniel Lopez-Ferrer2,, Byoung Chan Kim3, Hyon Bin Na4, Yong Il Park4, Karl K. Weitz2, Marvin G. Warner2, Taeghwan Hyeon4, Sang-Won Lee5, Richard D. Smith2, Jungbae Kim1,*
PROTEOMICS Volume 11, Issue 2, pages 309–318, No. 2 January 2011


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
J Biomol Tech. 2010 September; 21(3): 148–155


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          
Harvard Symposium 2010


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


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


Optimization of high pressure-assisted methods for proteomic sample preparation
Alexander V. Lazarev1*; Vera S. Gross1; Greta Carlson1; Edmund Ting1; Emily Freeman2; Alexander R. Ivanov2; Melkamu Getie-Kebtie3; Michail Alterman3
1Pressure BioSciences, South Easton, MA, USA; 2Harvard School of Public Health, Boston, MA, USA; 3FDA, CBER, Rockville , MD, USA


Novel efficient alternatives for essential sample preparation techniques in functional proteomics
Freeman and Alexander R. Ivanov
Harvard School of Public Health, Department of Genetics and Complex Diseases
ASMS 2010


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
ASMS 2010


Application of mass spectrometry-based proteomics in influenza virus research and vaccine manufacturing
Melkamu Getie-Kebtie1; Maryna Eichelberger2; Michail Alterman1
1FDA/CBER/OCTGT/TVBB, Bethesda, MD; 2FDA/CBER/OVRR/DVP, Bethesda, MD
USHUPO  2010


Rapid Release of N-Linked Glycans from Glycoproteins by Pressure-Cycling Technology
Zoltan Szabo, Andrs Guttman and Barry L. Karger*
Barnett Institute, Northeastern University, Boston, Massachusetts 02115
Anal. Chem., 2010, 82 (6), pp 2588–2593

IMAGING MALDI of Colorectal Carcinoma - Field Defects in Satellite Tissue
1Tiffany Remsen , 2M Momeni, 1P Kessler , 3F Francois , 1A Stern , 2S. Anand and 1P. Pevsner  
1Dept of Pharmacology New York University School of Medicine, New York, NY, USA 2Brooklyn Hospital Center, Brooklyn, NY, USA
3Dept of Medicine, New York University School of Medicine, New York, NY, USA


Mass Spectrometry of Buccal Mucosa -Biomarkers for Biodosimetry in Radiation Incidents
1P.H. Pevsner, 2S. Formenti, 1T. Remsen, 1G. Kruppa, 1 P. Kessler, 4G. Rothschild
3Jorge Ghiso, 3J. Melamed, 2B. S. Rosenstein, 4R. Schneider, 5F. Naftolin and 1A. Stern
New York University School of Medicine 1Department of Pharmacology, 2Department of Radiation Oncology, 3Department of Pathology, 4Department of Microbiology, 5Department of Obstetrics and Gynecology- Reproductive Biology
550 1st Avenue New York, NY 10016
AFRRI 2008


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
ASMS 2010


Discovery of Mitochondrial Protein Biomarkers of Atrial Fibrillation Using Unique Human Tissue Samples
Maryam Goudarzi1, Mark M. Ross1, Weidong Zhou1, Amy Van Meter1, Emanuel Petricoin1, Lance Liotta1, Lisa Martin2, Chidima Martin2 and Niv Ad2
1George Mason University, Manassas, VA; 2Inova Heart & Vascular Institute, Falls Church, VA


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
MCP Papers in Press. Published on July 12, 2010 as Manuscript M110.001479


Development of new technology approaches for high-throughput proteome analysis
Daniel López-Ferrer
Biological Separations & Mass Spectrometry Group
Pacific Northwest National Laboratory
Harvard Symposium May 21, 2010


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
ASMS 2010

Improved Protein Coverage and Throughput in Proteomics using On-Line Multiplexed Enzyme Digestions and Targeted MS/MS with a Modified LTQ-FTICR
Daniel López-Ferrer1, Konstantinos Petritis1, Andrey Liyu1,Jung Hwa Lee2, Sang-Won Lee2, Benito Cañas3, Kim K. Hixson1, Richard D. Smith1 and Mikhail E. Belov1
1Pacific Northwest National Laboratory, Richland, WA; Korea University, 2Seoul, Korea; 3Universidad Complutense de Madrid, Madrid, Spain
ASMS 2009


Proteomics Under Pressure: Rapid Extraction and Digestion in a Single Tube
Alexander V. Lazarev1; Emily Freeman2; Vera S. Gross1; Greta Carlson1; Edmund Ting1; Alexander R. Ivanov2
1Pressure BioSciences, South Easton, MA ; 2Harvard School of Public Health, Boston, MA
ASMS 2009


Intact Protein Liquid Chromatography Mass Spectrometry for Bacteria Strain Differentiation and Bacterial Toxin Detection
JOHN H. CALLAHAN; Denis Andrzejewski; Rebecca Bell; Eric Brown; Steve Musser
FDA/CFSAN, College Park, MD