Peer Reviewed - Pressure BioSciences Inc.

Mapping Protein Conformational Heterogeneity Under Pressure with Site-Directed Spin Labeling and Double Electron–Electron Resonance

Michael T. Lerch^a,b; Zhongyu Yangk^a; Evan K. Brooks^a; and Wayne L. Hubbell^a,b

PNAS | Published online March 18, 2014 | E1201–E1210

Quantification of Cotinine in Dried Blood Spots as a Biomarker of Exposure to Tobacco Smoke

Daniel Ladror^a; Bruce Pitt^b and William Funk^a

^aDepartment of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA, ^bDepartment of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA

Confronting high-throughput protein refolding using high pressure and solution screens

M. Walid Qoronfleh^a,*, Lyndal K. Hesterberg^b, Matthew B. Seefeldt^b

^aUniversity of Michigan and Core Technology Alliance-CTA, 1024 Wolverine Tower, 3003 State Street, Ann Arbor, MI 48109-1274, USA

^bBaroFold Inc., 1825 33rd Street, Boulder, CO 80301, USA

Identification of Heat-Induced Proteomes in Tomato Microspores Using LCMProteomics Analysis

Li H¹; Zhu Y¹; Rangu M¹; Wu X¹; Bhatti S¹; Zhou S¹; Yang Y²; Fish T²; and Thannhauser TW²

¹Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, USA, ²R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY, USA

Pressure Cycling Technology (PCT) Reduces Effects of Inhibitors of the PCR - Manuscript

Pamela L. Marshall; Jonathan L. King; Nathan P. Lawrence; Alexander Lazarev; Vera S. Gross; Bruce Budowle

Structure-Relaxation Mechanism for the Response of T4 Lysozyme Cavity Mutants to Hydrostatic Pressure

Michael T. Lerch^a,b; Carlos J. Lopez^a,b; Zhongyu Yanga^b; Margaux J. Kreitman^a,b; Joseph Horwitz^a; and Wayne L. Hubbell^a,b

PNAS | May 12, 2015 112 (19) | E2437-E2446 | first published April 27, 2015

Effects of Plant Species on Stream Bacterial Communities via Leachate from Leaf Litter

Adam S. Wymore; Elena Salpas; Giorgio Casaburi; Cindy M. Liu; Lance B. Price; Bruce A. Hungate; William H. McDowell; Jane C. Marks

High hydrostatic pressure as a tool to study protein aggregation and amyloidosis.

Randolph TW, Seefeldt M, Carpenter JF.

Department of Chemical Engineering, University of Colorado, Boulder, CO 80309, USA.

Improved DNA Profiles from Aged Horse Feces Using Pressure Cycling Technology

K. Deshpande^1,2; M. Villarreal^1,2; D. K. Mills^1,2

¹Department of Biological Sciences, Florida International University, OE 167, 11200 SW 8th Street, Miami, FL 33199, USA, ²International Forensic Research Institute, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA

A Comparative In Vivo Study of Albumin‐Coated Paclitaxel Nanocrystals and Abraxane

Joonyoung Park; Ji Eun Park; Victoria E. Hedrick; Karl V. Wood; Connie Bonham; Wooin Lee; Yoon Yeo

High-pressure refolding of bikunin: efficacy and thermodynamics.

Seefeldt MB¹, Ouyang J, Froland WA, Carpenter JF, Randolph TW.

Department of Chemical and Biological Engineering, Center for Pharmaceutical Biotechnology, ECCH 111, University of Colorado, Boulder, CO 80309-0424, USA.

The LINK-A lncRNA interacts with PtdIns(3,4,5)P3 to hyperactivate AKT and confer resistance to AKT inhibitors

Aifu Lin^1,14,15, Qingsong Hu^1,15, Chunlai Li^1,15, Zhen Xing¹, Guolin Ma², Cheng Wang³, Jun Li^4,5, Yin Ye⁶, Jun Yao¹n Liang4,5, Zhibin Hu3, Hongbing Shen3, David H. Hawke⁵, Leng Han¹², Yubin Zhou2, Chunru Lin^1,10,16 and Liuqing Yang^1,10,13,16

1Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. 2Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, Texas 77030, USA. 3Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China. 4Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. 5Department of System Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. 6Department of Experimental Radiation Oncology, The University of Texas, MD Anderson Cancer Center, Houston, Texas 77030, USA. 7Department of Molecular Cell Biology and Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China. 8Department of Surgery, Division of Surgical Science, Duke University, School of Medicine, Durham, North Carolina 27710, USA. 9Department of Oncology, Yixing People’s Hospital, Yixing 214200, China. 10The Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. 11Graduate Institute of Cancer Biology and Center for Molecular Medicine, China Medical University, Taichung 404, Taiwan. 12Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas 77030, USA. 13Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA. 14Present address: College of Life Sciences, Zhejiang University, Hangzhou 310058, China. 15These authors contributed equally to this work. 16Correspondence should be addressed to C.Li or L.Y.

High-pressure studies of aggregation of recombinant human interleukin-1 receptor antagonist: thermodynamics, kinetics, and application to accelerated formulation studies.

Seefeldt MB¹, Kim YS, Tolley KP, Seely J, Carpenter JF, Randolph TW

Department of Chemical and Biological Engineering, Center for Pharmaceutical Biotechnology, ECCH 111, University of Colorado, Boulder, CO 80309-0242, USA.

Specific volume and adiabatic compressibility measurements of native and aggregated recombinant human interleukin-1 receptor antagonist: density differences enable pressure-modulated refolding.

Seefeldt MB¹, Crouch C, Kendrick B, Randolph TW.

Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, USA.

Relationships between airborne pollutants, serum albumin adducts and short-term health outcomes in an experimental crossover study

George W.Preston^a, Sonia Dagnino^b, Erica Ponzi^b^c, Osman Sozeri^a, Karin van Veldhoven^b, Benjamin Barratt^a, Sa Liu^d¹, Hasmik Grigoryan^d, Sixin S.Lu^d, Stephen M.Rappaport^d, Kian Fan Chung^e^f, Paul Cullinan^e^f, Rudy Sinharay^g, Frank J.Kelly^a, Marc Chadeau-Hyam^b, Paolo Vineis^b, and David H.Phillips^a

^a: MRC-PHE Centre for Environment & Health, Department of Analytical, Environmental & Forensic Sciences, School of Population Health & Environmental Sciences, Faculty of Life Sciences & Medicine, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK

^b: MRC-PHE Centre for Environment & Health, Department of Epidemiology and Biostatistics, School of Public Health, Faculty of Medicine, Imperial College London, Norfolk Place, London, W2 1PG, UK

^c: Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Hirschengraben 84, 8001, Zurich, Switzerland

^d: Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, 94720, USA

^e: National Heart & Lung Institute, Faculty of Medicine, Imperial College London, Royal Brompton Campus, London, SW3 6LY, UK

^f: NIHR Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, SW3 6NP, UK

^g: Pulmonary, Adult Critical Care and Sleep Directorate, Guy's and St Thomas' NHS Foundation Trust, London, SE1 7EH, UK

Selective Reduction of Ketones Using Water as a Hydrogen Source under high Hydrostatic Pressure

Anna Tomin^a; Alexander Lazarev^b; Matthew P. Bere^a; Hana Redjeb^a; and Bela Torok^a,*

Org. Biomol. Chem., 2012, 10, 7321–7326 | 7321 | DOI: 10.1039/c2ob25941a

Method for Recovery and Immunoaffinity Enrichment of Membrane Proteins Illustrated with Metastatic Ovarian Cancer Tissues

Luke V. Schneider;¹ Varsha Likhte;¹ William H. Wright;¹ Frances Chu;¹ Emma Cambron;¹ Anne Baldwin-Burnett;¹ Jessica Krakow;¹ and Gary B. Smejkal^2,3

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

Application of high hydrostatic pressure to dissociate aggregates and refold proteins.

Seefeldt MB¹, Rosendahl MS, Cleland JL, Hesterberg LK.

BaroFold Inc., Boulder, CO 80301, USA.

Effects of Elevated Hydrostatic Pressure against Mesophilic Background Microflora and Habituated Salmonella Serovars in Orange Juice

Abimbola Allison¹; Edward Daniels¹; Shahid Chowdhury^1,2 and Aliyar Fouladkhah^1,2,*

Microorganisms 2018, 6, 23 | https://doi.org/10.3390/microorganisms6010023

Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156)

Léa Chuzel^1,2, Mehul B. Ganatra¹, Erdmann Rapp^2,3, Bernard Henrissat^4,5,6 and Christopher H. Taron¹*

1New England Biolabs, 240 County Road, Ipswich, MA 01938, USA; 2Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; 3glyXera GmbH, Leipziger Straße 44, 39120 Magdeburg, Germany; 4Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France; 5INRA, USC 1408 AFMB,

13288, Marseille, France; 6Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia

High-Pressure EPR Reveals Conformational Equilibria and Volumetric Properties of Spin-Labeled Proteins

John McCoy and Wayne L. Hubbell

PNAS January 25, 2011 108 (4) 1331-1336; https://doi.org/10.1073/pnas.1017877108

Effects of Conjugated Linoleic Acid (CLA) on Fat Accumulation, Activity, and Proteomics Analysis in Caenorhabditis elegans

Peiyi Shen; Jonathan C. Kershaw; Yiren Yue; Ou Wang; Kee-Hong Kim; Julian McClements; Yeonhwa Park

High Pressure Induced DNA Damage in Escherichia Coli Involves Pressure-Mediated Dissociation of the Tetrameric Mrr Restriction Endonuclease

Anais Bourges; Anirban Ghosh; Nathalie Declerck; Abram Aertsen; Catherine Royer

BIOPHYSICAL JOURNAL | VOLUME 110, ISSUE 3, SUPPLEMENT 1, 316A | FEBRUARY 16, 2016

Mass Spectrometry-Based Proteomic Quest for Diabetes Biomarkers

Shiying Shao^a,b; Tiannan Guo^b; Ruedi Aebersold^b,c

^aDivision of Endocrinology, Tongji Hospital, Huazhong University of Science & Technology, Wuhan 430030, PR China, ^bDepartment of Biology, Institute of Molecular Systems Biology, ETH Zurich, Wolfgang-Pauli-Str. 16, 8093, Switzerland, ^cFaculty of Science, University of Zurich, 8057 Zurich, Switzerland Biochimica et Biophysica Acta 1854 (2015) 519-527

Co-option and Detoxification of a Phage Lysin for Housekeeping Function

Amelia M. Randich¹, David T. Kysela¹, Cécile Morlot², Yves V. Brun¹

¹Indiana University, Bloomington, IN USA, Bloomington, IN USA,

²Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, France

Indiana University, Bloomington, IN USA

Reproducible Tissue Homogenization and Protein Extraction for Quantitative Proteomics using MicroPestle-assisted Pressure Cycling Technology

Shao S; Guo T; Gross V; Lazarev A; Koh CC; Gillessen S; Joerger M; Jochum W; Aebersold R

Green coffee bean extract and 5-O-caffeoylquinic acid regulate fat metabolism in Caenorhabditis elegans (2)

Renalison Farias-Pereira^a; Jordan Oshiro^b; Kee-Hong Kim^bc; Yeonhwa Park^a

^a Department of Food Science, University of Massachusetts, Amherst, MA 01003, USA

^b Department of Food Science, Purdue University, West Lafayette, IN 47907, USA

^c Purdue University Center for Cancer Research, West Lafayette, IN 47907, USA

Intrinsic Allosteric Inhibition of Signaling Proteins by Targeting Rare Interaction States Detected by High-Pressure NMR Spectroscopy

Prof. Dr. Hans Robert Kalbitzer; Dr. Ina C. Rosnizeck; Prof. Dr. Claudia E. Munte; Dr. Sunilkumar Puthenpurackal Narayanan; Veronika Kropf; Priv.-Doz. Dr. Michael Spoerner

Angew. Chem. Int. Ed., 52: 14242-14246. https://doi.org/10.1002/anie.201305741

Minimal Sample Requirement for Highly Multiplexed Protein Quantification in Cell Lines and Tissues by PCT-SWATH Mass Spectrometry

Shao S^1,2; Guo T²; Koh CC²; Gillessen S³; Joerger M³; Jochum W⁴; Aebersold R^2,5
¹Division of Endocrinology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, P. R. China, ²Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH), Zurich, Switzerland, ³Department of Oncology/Hematology, Kantonsspital St. Gallen, St. Gallen, Switzerland, ⁴Institute of Pathology, Kantonsspital St. Gallen, St. Gallen, Switzerland, ⁵Faculty of Science, University of Zurich, Zurich, Switzerland. Proteomics. 2015 Aug 19. doi: 10.1002/pmic.201500161.

The Proteomic Dataset for Bone Marrow Derived Human Mesenchymal Stromal Cells: Effect of in Vitro Passaging

Samuel T. Mindaye^a; Jessica LoSurdo^b; Steven R. Bauer^b; Michail A. Alterman^a

^aTumor Vaccines and Biotechnology Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States, ^bCellular and Tissue Therapies Branch, Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, United States

Rapid Mass Spectrometric Conversion of Tissue Biopsy Samples into Permanent Quantitative Digital Proteome Maps

Tiannan Guo; Petri Kouvonen; Ching Chiek Koh; Ludovic C Gillet; Witold E Wolski; Hannes L Röst; George Rosenberger; Ben C Collins; Lorenz C Blum; Silke Gillessen; Markus Joerger; Wolfram Jochum & Ruedi Aebersold

Improved Protein Extraction and Protein Identification from Archival Formalin-Fixed Paraffin-Embedded Human Aortas

Fu Z; Yan K; Rosenberg A; Jin Z; Crain B; Athas G; Heide RS; Howard T; Everett AD; Herrington D; Van Eyk JE.

Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA. Proteomics Clin Appl. 2013 Apr;7(3-4):217-24. doi: 10.1002/prca.201200064.

Pressure Dependence of Backbone Chemical Shifts in the Model Peptides Ac-Gly-Gly-Xxx-Ala-NH2

Markus Beck Erlach; Joerg Koehler; Edson Crusca Jr.; Werner Kremer; Claudia E. Munte; Hans Robert Kalbitzer

J Biomol NMR 65, 65–77 (2016) | https://doi.org/10.1007/s10858-016-0030-4

Digestion, Purification, and Enrichment of Protein Samples for Mass Spectrometry

Victoria E. Hedrick; Mercedes N. LaLand; Ernesto S. Nakayasu; Lake N. Paul

Quantitative Proteomics Signature Profiling Based on Network Contextualization

Wilson Wen Bin Goh; Tiannan Guo; Ruedi Aebersold and Limsoon Wong

Cosolvent and Crowding Effects on the Temperature and Pressure Dependent Conformational Dynamics and Stability of Globular Actin

Schummel PH; Haag A; Kremer W; Kalbitzer HR; Winter R

J PHYS CHEM B | 2016 Jul 14;120(27):6575-86 | doi: 10.1021/acs.jpcb.6b04738 | Epub 2016 Jun 28

Identification of Salmonella taxon-specific peptide markers to the serovar level by mass spectrometry

Shu-Hua Chen, Christine H. Parker, Timothy R Croley, and Melinda A. McFarland

Multiplex and Label-Free Relative Quantification Approach for Studying Protein Abundance of Drug Metabolizing Enzymes in Human Liver Microsomes Using SWATH-MS

Rohitash Jamwal;† Benjamin J. Barlock;† Sravani Adusumalli;† Ken Ogasawara;† Brigitte L. Simons;‡
and Fatemeh Akhlaghi*;†
†Clinical Pharmacokinetics Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island 02881, United States, ‡SCIEX, 71 Four Valley Drive, Concord, Ontario L4K4 V8, Canada

Interactions of Carvacrol, Caprylic Acid, Habituation, and Mild Heat for Pressure-Based Inactivation of O157 and Non-O157 Serogroups of Shiga Toxin-Producing Escherichia coli in Acidic Environment

Md Niamul Kabir¹, Sadiye Aras¹, Abimbola Allison¹, Jayashan Adhikari¹, Shahid Chowdhury¹ and Aliyar Fouladkhah^1,2

¹Public Health Microbiology Laboratory, Tennessee State University, Nashville, TN 37209, USA;This email address is being protected from spambots. You need JavaScript enabled to view it. (M.N.K.); This email address is being protected from spambots. You need JavaScript enabled to view it. (S.A.); This email address is being protected from spambots. You need JavaScript enabled to view it. (A.A.);This email address is being protected from spambots. You need JavaScript enabled to view it. (J.A.); This email address is being protected from spambots. You need JavaScript enabled to view it. (S.C.)

²Cooperative Extension Program, Tennessee State University, Nashville, TN 37209, USA

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

Application of SWATH Proteomics to Mouse Biology

Yibo Wu¹; Evan G. Williams¹; Ruedi Aebersold^1,2

¹Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland, ²Faculty of Science, University of Zurich, Zurich

Advances in Prevention of Foodborne Pathogens of Public Health Concern during Manufacturing

Aliyar Cyrus Fouladkhah (Editor), Bledar Bisha (Editor)

Identification of Protein Abundance Changes in Biopsy-Level Hepatocellular Carcinoma Tissues Using PCT-SWATH

Yi Zhu; Jiang Zhu; Cong Lu; Ping Sun; Wei Xie; Qiushi Zhang; Yue Liang; Tiansheng Zhu; Guan Ruan; Ruedi Aebersold; Shiang Hunag; Tiannan Guo

Rapid Release of N-Linked Glycans from Glycoproteins by Pressure-Cycling Technology

Zoltan Szabo; András Guttman and Barry L. Karger*

Barnett Institute, Northeastern University, Boston, Massachusetts 02115

A repository of assays to quantify 10,000 human proteins by SWATH-MS

George Rosenberger, Ching Chiek Koh, Tiannan Guo, Hannes L. Röst, Petri Kouvonen, Ben C. Collins, Moritz Heusel, Yansheng Liu, Etienne Caron, Anton Vichalkovski, Marco Faini, Olga T. Schubert, Pouya Faridi, H. Alexander Ebhardt, Mariette Matondo, Henry Lam, Samuel L. Bader, David S. Campbell, Eric W. Deutsch, Robert L. Moritz, Stephen Tate & Ruedi Aebersold

Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland

Hydrophilic Interaction Liquid Chromatography in the Separation of Glycopeptides and their Isomers

Petr Kozlik; Radoslav Goldman; and Miloslav Sanda

Identification and Evaluation of Galleria mellonella Peptides with Antileishmanial Activity

Isabel A. Patiño-Márquez; Edwin Patiño-González; Laura Hernández-Villa; Blanca Ortíz-Reyes; Marcela Manrique-Moreno

Platform for Identification of Salmonella Serovar Differentiating Bacterial Proteins by Top-Down Mass Spectrometry: S. Typhimurium vs S. Heidelberg

Melinda A. McFarland;* Denis Andrzejewski; Steven M. Musser; and John H. Callahan

Spectroscopy and Mass Spectrometry Branch, Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, 5100 Paint Branch Parkway, College Park, Maryland 20740

Fast and Efficient non-reduced Lys-C digest using pressure cycling technology for antibody disulfide mapping by LC–MS

Ying Cheng*; Yonghong Chen; Christopher Yu

Protein Analytical Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA

The Application of Alkaline Lysis and Pressure Cycling Technology in the Differential Extraction of DNA from Sperm and Epithelial Cells Recovered from Cotton Swabs

Deepthi V. Nori¹ & Bruce R. McCord¹

¹Department of Chemistry CP304, Florida International University, 11200 SW 8th St, Miami, FL 33199, USA This email address is being protected from spambots. You need JavaScript enabled to view it.

Method Development for Fecal Lipidomics Profiling

Katherine E. Gregory;^†,‡ Susan S. Bird;^§,∥ Vera S. Gross;^⊥ Vasant R. Marur;^§ Alexander V. Lazarev;^⊥ W. Allan Walker;^¶,▲ and Bruce S. Kristal^*,§,∥

^†Boston College, W.F. Connell School of Nursing, 140 Commonwealth Avenue, Chestnut Hill, Massachusetts 02467, United States, ^‡Department of Nursing, Brigham and Women’s Hospital, 75 Francis Street, Boston, Massachusetts 02115, United States, ^§Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts 02115, United States, ^∥Department of Surgery, Harvard Medical School, 221 Longwood Avenue, LMRC-322, Boston, Massachusetts 02115, United States, ^⊥Pressure BioSciences, Inc., 14 Norfolk Avenue, South Easton, Massachusetts 02375, United States, ^¶Department of Pediatrics, Massachusetts General Hospital for Children, Boston, Massachusetts, 02115, United States, ^▲Division of Nutrition, Harvard Medical School, Boston, Massachusetts, 02115, United States

Hepatic Effects of Pharmacological Doses of Hydroxy-Cobalamin[c-lactam] in Mice

Haegler P; Grünig D; Berger B; Terracciano L; Krähenbühl S; Bouitbir J

Sex-Specific Differences in Mitochondria Biogenesis, Morphology, Respiratory Function, and ROS Homeostasis in Young Mouse Heart and Brain

Khalifa AR; Abdel-Rahman EA; Mahmoud AM; Ali MH; Noureldin M; Saber SH; Mohsen M; Ali SS

Mitochondrial GSH Replenishment as a Potential Therapeutic Approach for Niemann Pick Type C Disease

Torres S; Matías N; Baulies A; Nuñez S; Alarcon-Vila C; Martinez L; Nuño N; Fernandez A; Caballeria J; Levade T; Gonzalez-Franquesa A; Garcia-Rovés P; Balboa E; Zanlungo S; Fabrías G; Casas J; Enrich C; Garcia-Ruiz C; Fernández-Checa JC

Dietary Betaine Supplementation Increases Fgf21 Levels to Improve Glucose Homeostasis and Reduce Hepatic Lipid Accumulation in Mice

Ejaz A; Martinez-Guino L; Goldfine AB; Ribas-Aulinas F; De Nigris V; Ribó S; Gonzalez-Franquesa A; Garcia-Roves PM; Li E; Dreyfuss JM; Gall W; Kim JK; Bottiglieri T; Villarroya F; Gerszten RE; Patti ME; Lerin C

Pressure-Based Alkaline Lysis with Immunocapture, a Method for Enhanced Recovery in Differential Extraction

Vanesa Marinez; Deepthi Nori; Pero Dimimsoski; and Bruce McCord

Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA

Exploring Simvastatin, an Antihyperlipidemic Drug, as a Potential Topical Antibacterial Agent

Shankar Thangamani¹; Haroon Mohammad¹; Mostafa F.N. Abushahba^1,2; Maha I. Hamed^1,2;
Tiago J. P. Sobreira³; Victoria E. Hedrick³; Lake N. Paul³ & Mohamed N. Seleem¹

¹Department of Comparative Pathobiology, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA, ²Faculty of Veterinary Medicine, Assiut University, Assiut, Egypt, ³Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA. Correspondence and requests for materials should be addressed to M.N.S.

Cys34 Adducts of Reactive Oxygen Species in Human Serum Albumin

Hasmik Grigoryan; He Li; Anthony T. Iavarone; Evan R. Williams; and Stephen M. Rappaport

High-Resolution Physicochemical Characterization of Different Intravenous Immunoglobulin Products

Nathaniel Washburn; ¹ Robin Meccariello; ¹ Shaohui Hu; ² Maurice Hains; ¹ Naveen Bhatnagar; ¹ Hetal Sarvaiya; ¹ Bulbul Kapoor; ¹ John Schaeck; ¹ Ignacio Pino; ³ Anthony Manning; ¹ Jonathan C. Lansing; ¹ and Carlos J. Bosques

Profiling the Serum Albumin Cys34 Adductome of Solid Fuel Users in Xuanwei and Fuyuan, China

Sixin S. Lu^†; Hasmik Grigoryan^¶; William M.B. Edmands^¶; Wei Hu^§; Anthony T. Iavarone^║; Alan Hubbard^‡; Nathaniel Rothman^§; Roel Vermeulen^¦; Qing Lan^§; and Stephen M. Rappaport^¶,*

^†Department of Nutritional Sciences and Toxicology, College of Natural Resources, University of California, Berkeley, CA 94720, USA, ^¶Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA 94720, USA, ^§Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Service, Rockville, MD 20850, USA, ^║California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA, ^‡Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA, ^¦Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, 3508 TD Utrecht, The Netherlands

Using Lysine Adducts of Human Serum Albumin to Investigate the Disposition of Exogenous Formaldehyde in Human Blood

Luca G. Regazzoni¹; Hasmik Grigoryan¹; Zhiying Ji¹; Xi Chen²; Sarah I. Daniels¹; Deyin Huang³; Sylvia Sanchez¹; Naijun Tang²; Fenna C. M. Sillé¹; Anthony T. Iavarone⁴; Evan R. Williams⁴; Luoping Zhang¹; and Stephen M. Rappaport^1,*

¹Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, United States, ²Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, China, ³Institute of Occupational Health, School of Public Health, Tianjin Bohai Chemical Industry Group Co. Ltd., Tianjin, China, ⁴California Institute for Quantitative Biosciences and Department of Chemistry, University of California, Berkeley, CA, United States

An Adductomics Pipeline for Untargeted Analysis of Modifications to Cys34 of Human Serum Albumin

Hasmik Grigoryan¹; William Edmands¹; Sixin S. Lu¹; Yukiko Yano¹; Luca Regazzoni¹; Anthony T. Iavarone²; Evan R. Williams³; and Stephen M. Rappaport^1,*

¹School of Public Health, University of California, Berkeley, California 94720-7356, United States, ²California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720, United States, ³College of Chemistry, University of California, Berkeley, California 94720, United States

Elevated Pressure Improves the Extraction and Identification of Proteins Recovered from Formalin-Fixed, Paraffin-Embedded Tissue Surrogates

Carol B. Fowler; Ingrid E. Chesnick; Cedric D. Moore; Timothy J. O'Leary; Jeffrey T. Mason

Elevated Pressure Improves the Rate of Formalin Penetration while Preserving Tissue Morphology

Ingrid E. Chesnick¹; Jeffrey T. Mason¹; Timothy J. O'Leary²; Carol B. Fowler^1,2

¹Department of Biophysics, Armed Forces Institute of Pathology, Rockville, Maryland, USA, ²Biomedical Laboratory Research and Development Service, Veterans Health Administration, Washington, DC, USA

Improved Extraction of Rhizoctonia and Pythium DNA from Wheat Root and Soil Samples Using Pressure Cycling Technology

Patricia A. Okubara; Chunqin Li; Kurtis Schroeder; Richard T. Schumacher; and Nathan P. Lawrence

Rapid Processing of Archival Tissue Samples for Proteomic Analysis Using Pressure-Cycling Technology

Vinuth N. Puttamallesh^1,2; Krishna Patel^1,2 and Harsha Gowda^1,3,*
¹Institute of Bioinformatics, International Tech Park, Bangalore 560066, India, ²Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India, ³Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore 575018, India

Proteogenomic Analysis of a Thermophilic Bacterial Consortium Adapted to Deconstruct Switchgrass

Patrik D'haeseleer; John M. Gladden; Martin Allgaier; Patrik S. G. Chain; Susannah G. Tringe; Stephanie A. Malfatti; Joshua T. Aldrich; Carrie D. Nicora; Errol W. Robinson; Philip Hugenholtz; Blake A. Simmons; AffiliationsSteven W. Singer

Proteomic Stratification of HPV(+) Oropharyngeal Squamous Cell Carcinoma Identifies Targets in Insulin Receptor Signaling within Nonresponders

Aaron Robinson; Sarah J. Parker; Shiao L. Stephen; Beatrice S. Knudsen; Zachary S. Zumsteg; Jennifer E. Van Eyk and Allen S. Ho

Cedars-Sinai Medical Center, Los Angeles, CA

Fluctuations in Species-Level Protein Expression Occur during Element and Nutrient Cycling in the Subsurface

Michael J. Wilkins; Kelly C. Wrighton; Carrie D. Nicora; Kenneth H. Williams; Lee Ann McCue; Kim M. Handley; Chris S. Miller; Ludovic Giloteaux; Alison P. Montgomery; Derek R. Lovley; Jillian F. Philip; E. Long; Mary S. Lipton

Transcriptome-Based Differentiation of Closely-Related Miscanthus Lines

Philippe Chouvarine; Amanda M. Cooksey; Fiona M. McCarthy; David A. Ray; Brian S. Baldwin; Shane C. Burgess; Daniel G. Peterson

Characterizing the Escherichia coli O157:H7 Proteome Including Protein Associations with Higher Order Assemblies

Rembert Pieper; Quanshun Zhang; David J. Clark; Shih-Ting Huang; Moo-Jin Suh; John C. Braisted; Samuel H. Payne; Robert D. Fleischmann; Scott N. Peterson; Saul Tzipori

A Photoaffinity Labeling-Based Chemoproteomics Strategy for Unbiased Target Deconvolution of Small Molecule Drug Candidates

Jason R. Thomas; Scott M. Brittain; Jennifer Lipps; Luis Llamas; Rishi K. Jain; Markus Schirle

Novartis Institutes for Biomedical Research Cambridge USA

Examining the Influence of Specificity Ligands and ATP-Competitive Ligands on the Overall Effectiveness of Bivalent Kinase Inhibitors

Margaret L. Wong; Jason Murphy; Edmund Harrington; Carrie M. Gower; Rishi K. Jain; Markus Schirle; Jason R. Thomas

Integrated Stress Response and Decreased ECM in Cultured Stromal Cells from Keratoconus Corneas

James W. Foster; Vishal Shinde; Uri S. Soiberman; Gajanan Sathe; Sheng Liu; Julius Wan; Jiang Qian; Yassine Dauoud; Akhilesh Pandey; Albert S. Jun; Shukti Chakravarti

Cys34 Adductomes Differ between Patients with Chronic Lung or Heart Disease and Healthy Controls in Central London

Sa Liu;^† Hasmik Grigoryan;^† William M. B. Edmands;^† Sonia Dagnino;^‡ Rudy Sinharay;^§,∥ Paul Cullinan;^§,∥ Peter Collins;^§,∥ Kian Fan Chung;^§,∥ Benjamin Barratt;^⊥ Frank J. Kelly;^⊥ Paolo Vineis;^‡ and Stephen M. Rappaport*

^†Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, California 94720, United States, ^‡MRC-PHE Centre for Environment and Health, Imperial College, Norfolk Place London W2 1PG, U.K., ^§National Heart & Lung Institute, Imperial College, London SW3 6LY, U.K., ^∥NIHR Biomedical Research Unit, Royal Brompton & Harefield NHS Trust, London, SW3 6NP, U.K., ^⊥MRC-PHE Centre for Environment and Health, King’s College London, London SE1 9NH, U.K.

Proteomics Reveals Rictor as a Non-Canonical TGFB Signaling Target During Aneurysm Progression in Marfan Mice

Sarah J Parker Ph.D.*; Aleksandr Stotland; Elena MacFarlane; Nicole Wilson; Amanda Orosco; Vidya Venkatraman; Kyle Madrid; Roberta A. Gottlieb; Harry C. Dietz; and Jennifer E Van Eyk

Surface Modification of Polymer Nanoparticles with Native Albumin for Enhancing Drug Delivery to Solid Tumors

Hyesun Hyun^a; Joonyoung Park^a; Kiela Willis^b; Ji Eun Park^c;L. Tiffany Lyle^d; Wooin Lee^c; Yoon Yeo^a,e

^aDepartment of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN, 47907, USA, ^bSchool of Chemical Engineering, Purdue University, 480 West Stadium Avenue, West Lafayette, IN, 47907, USA, ^cCollege of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea, ^dDepartment of Comparative Pathobiology, Purdue University, West Lafayette, IN, 47907, USA, ^eWeldon School of Biomedical Engineering, Purdue University, 206 South Martin Jischke Drive, West Lafayette, IN, 47907, USA

Integrated Stress Response and Decreased ECM in Cultured Stromal Cells from Keratoconus Corneas

James W. Foster; Vishal Shinde; Uri S. Soiberman; Gajanan Sathe; Sheng Liu; Julius Wan; Jiang Qian; Yassine Dauoud; Akhilesh Pandey; Albert S. Jun; Shukti Chakravarti

Pressure‐ and Heat‐Induced Protein Unfolding in Bacterial Cells: Crowding vs. Sticking

Timothy Chen; Kapil Dave; Martin Gruebele

The consequences of cavity creation on the folding landscape of a repeat protein depend upon context

Kelly A. Jenkins, Martin J. Fossat, Siwen Zhang, Durgesh K. Rai, Sean Klein, Richard Gillilan, Zackary White, Grayson Gerlich, Scott A. McCallum, Roland Winter, Sol M. Gruner, Doug Barrick, and Catherine A. Royer

PNAS August 28, 2018 115 (35) | E8153-E8161 | https://doi.org/10.1073/pnas.1807379115

Pressure response of amide one-bond J-couplings in model peptides and proteins

Joerg Koehler, Markus Beck Erlach, Edson Crusca Jr., Werner Kremer, Claudia E. Munte, Alexander Meier, Hans Robert Kalbitzer

Journal of Biomolecular NMR | 60 | 45–50(2014)

N-Glycosylation Characterization by Liquid Chromatography with Mass Spectrometry

Song Klapoetke

KBI Biopharma, Durham, USA

An Ixodes scapularis cell line with a predominantly neuron-like phenotype

Jonathan D. Oliver, Adela S. Oliva Chávez, Roderick F. Felsheim, Timothy J. Kurtti, Ulrike G. Munderloh

Department of Entomology, University of Minnesota, St. Paul, USA

UMR CMAEE, Agricultural Research Centre for International Development - Control of Animal Diseases, Emerging and Exotic, CIRAD, Petit-Bourg, France

Identification of Protein Abundance Changes in Hepatocellular Carcinoma Tissues using PCT-SWATH.

Zhu Y^1,², Zhu J³, Lu C³, Zhang Q¹, Xie W³, Sun P⁴, Dong X⁵, Yue L¹, Sun Y¹, Yi X¹, Zhu T¹, Ruan G¹, Aebersold R^2,⁶, Huang S³, Guo T^1,².

Quantitative analysis of the murine lipid droplet-associated proteome during diet-induced hepatic steatosis

Salmaan A. Khan, Edith E. Wollaston-Hayden, Todd W. Markowski, LeeAnn Higgins and Douglas G. Mashek

University of Minnesota, United States

The pressure and temperature perturbation approach reveals a whole variety of conformational substates of amyloidogenic hIAPP monitored by 2D NMR spectroscopy

Markus Beck Erlach^a; Hans Robert Kalbitzer^a; Roland Winter^b; Werner Kremer^a

Biophysical Chemistry | Volume 254 | 2019 | https://doi.org/10.1016/j.bpc.2019.106239

Quantitative Liquid Chromatography-Mass Spectrometry-Multiple Reaction Monitoring (LC-MS-MRM) Analysis of Site-specific Glycoforms of Haptoglobin in Liver Disease

Miloslav Sanda, Petr Pompach, Zuzana Brnakova, Jing Wu, Kepher Makambi and Radoslav Goldman

Departments of Oncology and Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, D.C. 20057

High-pressure EPR spectroscopy studies of the E. coli lipopolysaccharide transport proteins LptA and Lpt

Schultz KM1, Klug CS1

Appl Magn Reson | 2017 Dec;48(11-12):1341-1353 | doi: 10.1007/s00723-017-0948-z

Proteomic analysis reveals an extract of the plant Lippia origanoides suppresses mitochondrial metabolism in triple-negative breast cancer cells.

Vishak Raman, Uma K. Aryal, Victoria Hedrick, Rodrigo Mohallem Ferreira, Jorge Luis Fuentes Lorenzo, Elena E. Stashenko, Morris Levy, Maria M. Levy, and Ignacio G. Camarillo

Purdue University

Characterization of longitudinal canal tissue in the acorn barnacle Amphibalanus amphitrite

Chenyue Wang ,
Janna N. Schultzhaus ,
Chris R. Taitt,
Dagmar H. Leary,
Lisa C. Shriver-Lake,
Daniel Snellings,
Samantha Sturiale,
Stella H. North,
Beatriz Orihuela,
Daniel Rittschof,
Kathryn J. Wahl,
Christopher M. Spillmann

Accelerated Barocycler Lysis and Extraction (ABLE) sample preparation for clinical proteomics by mass spectrometry.

Lucas N, Robinson AB, Marcker Espersen M, Mahboob S, Xavier D, Xue J, Balleine RL, deFazio A, Hains PG, Robinson PJ

Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways

Stephanie J. Valberg,1,2Sudeep Perumbakkam,3Erica C. McKenzie,4 and Carrie J. Finno5

Isolation and characterization of Lactobacillus-derived membrane vesicles

¹Scott N. Dean, ²Dagmar H. Leary, ³Claretta J. Sullivan, ⁴Eunkeu Oh and ²Scott A. Walper

¹National Research Council Associate, Washington, DC, USA, Center for Bio/Molecular Science & Engineering (Code 6900), ²US Naval Research Laboratory, Washington, DC, USA, ³Air Force Research Laboratory, Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Ohio, USA, ⁴Sotera Defense Solutions, Inc, Columbia, MD, USA

Generation of a zebrafish SWATH-MS spectral library to quantify 10,000 proteins

Peter Blattmann,^a,1,* Vivienne Stutz,^1,* Giulia Lizzo,² Joy Richard,² Philipp Gut,² and Ruedi Aebersold^b,1,3

¹Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland

²Nestlé Institute of Health Sciences, EPFL Innovation Park, Bâtiment H, 1015 Lausanne, Switzerland

³Faculty of Science, University of Zurich, Zurich, Switzerland

Epitope Ligand Binding Sites of Blood Group Oligosaccharides in Lectins Revealed by Pressure-Assisted Proteolytic Excision Affinity Mass Spectrometry

Baschung Y^1,², Lupu L¹, Moise A³, Glocker M², Rawer S⁴, Lazarev A⁵, Przybylski M^6,⁷

1: Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße, 29, 65428, Rüsselsheim am Main, Germany.
2: Department of Immunology, University of Rostock, Rostock, Germany.
3: Department of Chemistry and Steinbeis Center for Biopolymer Analysis and Biomedical Mass Spectrometry, University of Konstanz, 78457, Konstanz, Germany.
4: Thermofisher Scientific, Frankfurter Straße 134, Darmstadt, Germany.
5: Pressure BioSciences, Inc., 14 Norfolk Ave., South Easton, MA, USA.
6: Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße, 29, 65428, Rüsselsheim am Main, Germany. This email address is being protected from spambots. You need JavaScript enabled to view it..
7: Department of Chemistry and Steinbeis Center for Biopolymer Analysis and Biomedical Mass Spectrometry, University of Konstanz, 78457, Konstanz, Germany. This email address is being protected from spambots. You need JavaScript enabled to view it..

Addressing the challenges of high-throughput cancer tissue proteomics for clinical application: ProCan®

Brett Tully, Rosemary L. Balleine, Peter G. Hains, Qing Zhong, Roger R. Reddel, Phillip J. Robinson

ProCan®, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead NSW 2145, Australia

A Barocycler-based Concurrent Multi-Omics Method to Assess Molecular Changes Associated with Atherosclerosis using Small Amounts of Arterial Tissue from a Single Mouse

- Jihan Talib,
- Peter G Hains,
- Sergey Tumanov,
- Mark P. Hodson,
- Phillip J. J Robinson, and
- Roland Stocker

Oncoproteomics: Current status and future opportunities

Yujia He^a1Abidali Mohamedali^b1Canhua Huang^a Mark S.Baker^c Edouard C.Nice^acd

^aWest China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China

^bDepartment of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, New South Wales 2109, Australia

^cDepartment of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia

^dDepartment of Biochemistry and Molecular Biology, Monash University, Clayton, Australia

Extensive Intratumor Proteogenomic Heterogeneity Revealed by Multiregion Sampling in a High-Grade Serous Ovarian Tumor Specimen

Allison L. Hunt, Nicholas W. Bateman, Brian L. Hood, Kelly A. Conrads, Ming Zhou, Tracy J. Litzi, Julie Oliver, Dave Mitchell, Glenn Gist, Brian Blanton, Kunle Odunsi, Anil K. Sood, Yovanni Casablanca, Kathleen M. Darcy, Craig D. Shriver, Uma N. M. Rao, G. Larry Maxwell, Thomas P. Conrads

Quantitative proteome landscape of the NCI-60 cancer cell lines

Tiannan Guo, Augustin Luna, Vinodh N. Rajapakse, Ching Chiek Koh, Zhicheng Wu, Wei Liu, Yaoting Sun, Huanhuan Gao, Michael P. Menden, Chao Xu, Laurence Calzone, Loredana Martignetti, Chiara Auwerx, Marija Buljan, Amir Banaei-Esfahani, Alessandro Ori, Murat Iskar, Ludovic Gillet, Ran Bi, Jiangnan Zhang, Huanhuan Zhang, Chenhuan Yu, Qing Zhong, Sudhir Varma, Uwe Schmitt, Peng Qiu, Qiushi Zhang, Yi Zhu, Peter J. Wild, Mathew J. Garnett, Peer Bork, Martin Beck, Kexin Liu, Julio Saez-Rodriguez, Fathi Elloumi, William C. Reinhold, Chris Sander, Yves Pommier, Ruedi Aebersold

Accelerated Protein Biomarker Discovery from FFPE tissue samples using Single-shot, Short Gradient Microflow SWATH MS

Rui Sun, Christie Hunter, Chen Chen, Weigang Ge, Nick Morrice, Shuang Liang, Chunhui Yuan, Qiushi Zhang, Xue Cai, Xiaoyan Yu, Lirong Chen, Shaozheng Dai, Zhongzhi Luan, Ruedi Aebersold, Yi Zhu, Tiannan Guo

ACE over expression in myeloid cells increases oxidative metabolism and cellular ATP

Duo-Yao Cao¹, Weston R. Spivia², Luciana C. Veiras¹, Zakir Khan^1,3, Zhenzi Peng¹, Anthony E. Jones⁴, Ellen A. Bernstein¹, Suguru Saito¹, Derick Okwan-Duodu^1,3, Sarah J. Parker^2,5, Jorge F. Giani^1,3, Ajit S. Divakarun⁴, Jennifer E. Van Eyk², Kenneth E. Bernstein^1,3

¹Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048

²The Smidt Heart Institute and Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048.

³Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048

⁴Department of Molecular and Medical Pharmacology; UCLA David Geffen School of Medicine; Los Angeles CA 90095.

⁵Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048.