Proteomics – Human Diseases and Protein Functions Chapter 19, 2012
Quantitative Proteomics for Investigation of Secreted Factors: Focus on Muscle Secretome
Jeanette Henningsen, Blagoy Blagoev and Irina Kratchmarova
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M Denmark
Clinical Proteomics 2012, 9:2
Characterization of the seminal plasma proteome in men with prostatitis by mass spectrometry
Daniel Kagedan1,2, Irene Lecker1,2, Ihor Batruch3, Christopher Smith3, Ilia Kaploun2, Kirk Lo2,5, Ethan Grober2, Eleftherios P Diamandis1,2,3,4 and Keith A Jarvi1,2,3,5*
1 Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada. 2 Division of Urology,Department of Surgery, Mount Sinai Hospital, University of Toronto, Toronto, Canada. 3 Department of Pathology and Laboratory Medicine, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Canada. 4 Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada. 5 Institute of Medical Sciences,University of Toronto, Toronto, Canada.
Quantitative Methods in Proteomics
Search and Decoy: The Automatic Identification of Mass Spectra
Methods in Molecular Biology, 2012, Volume 893, Part 5
Martin Eisenacher, Michael Kohl, Michael Turewicz, Markus-Hermann Koch, Julian Uszkoreit and Christian Stephan
Journal of General Virology February 2012
E2F1, ARID3A/Bright and Oct-2 factors bind to the Epstein-Barr virus C promoter, EBNA1 and oriP, participating in long-distance promoter-enhancer interactions
Cecilia Boreström, Alma Forsman, Ulla Rüetschi1 and Lars Rymo
Institute of Biomedicine, Sahlgrenska University Hospital, University of Gothenburg, Sweden
Molecular & Cellular Proteomics, February 2012
Characterization of membrane-shed micro-vesicles from cytokine-stimulated beta-cells using proteomics strategies
Giuseppe Palmisano1, Soren Skov Jensen2, Marie Catherine Le Bihan2, Jeanne Laine3, James N. McGuire4, Flemming Pociot5 and Martin Rossel Larsen2
1 University of Southern Denmark, Denmark;
2 University of Southern Denmark,, Denmark;
3 UMR S 974 Inserm, France;
4 Hagedorn Research Institute, Denmark;
5 Glostrup Research Institute, Denmark
Molecular & Cellular Proteomics, March 2012
Proteomic analysis of microvesicles released by the human prostate cancer cell line PC-3
MHC class I target recognition, immunophenotypes and proteomic profiles of natural killer cells within the spleens of day-14 chick embryos
Lei Zhanga,, George S. Katselisb, Roger E. Mooreb, Kossi Lekporb, Ronald M. Gotoa, Henry D. Huntc, Terry D. Leeb, Marcia M. Millera
a Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA b Department of Immunology, Beckman Research Institute, City of Hope, 1500 E. Duarte Road, Duarte, CA 91010-3000, USA c Avian Disease and Oncology Laboratory, USDA-ARS, East Lansing, MI 48823, USA
Journal of Biological Chemistry, April 2012
Quantitative Proteomic Analysis of Eight Cartilaginous Tissues Reveals Characteristic Differences as well as Similarities between Subgroups
Patrik Onnerfjord1, Areej Khabut1, Finn P. Reinholt2, Olle Svensson3 and Dick Heinegard1
1 Lund University, Sweden;
2 University of Oslo, Norway;
3 Umea University, Sweden
Molecular & Cellular Proteomics, April 2012
Tumor proteomics by multivariate analysis on individual pathway data for characterization of vulvar cancer phenotypes
Label-free quantification and shotgun analysis of complex proteomes by 1D SDS-PAGE/nanoLC-MS: evaluation for the large-scale analysis of inflammatory human endothelial cells
Violette Gautier1, Emmanuelle Mouton-Barbosa2, David Bouyssie1, Nicolas Delcourt2, Mathilde Beau1, Jean-Philippe P. Girard1, Corinne Cayrol1, Odile Burlet-Schiltz1, Bernard Monsarrat1 and Anne Gonzalez de Peredo1
1 CNRS / University of Toulouse, France;
2 University of Toulouse, France
Journal of Proteomics, Volume 75, Issue 12, 2012
Tyrosine-dependent capture of CAP-Gly domain‐containing proteins in complex mixture by EB1 C-terminal peptidic probes
David Calligarisa, b, Cristina Manatschald, Marlène Marcelline, f, Claude Villarda, b, Bernard Monsarrate, f, Odile Burlet-Schiltze, f, Michel O. Steinmetzd, Diane Braguera, b, c, Daniel Lafittea, b, Pascal Verdier-Pinarda, b
a Inserm UMR 911, Centre de Recherche en Oncologie biologique et en Oncopharmacologie 27 Boulevard Jean Moulin, 13385 Marseille Cedex 5, France b Université Aix-Marseille, Faculté de Pharmacie, Marseille, France c Assistance Publique-Hôpitaux de Marseille, France d Biomolecular Research, Paul Scherrer Institut, CH-5232 Villigen PSI, Switzerland e CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse, France f Université de Toulouse; UPS, F-31077 Toulouse, France
Proteomics June 2012
Quantitative proteomics of primary tumors with varying metastatic capabilities using stable isotope-labeled proteins of multiple histogenic origins
Rikke Raaen Lund1, Mikkel Green Terp1, Anne-Vibeke Lænkholm2, Ole Nørregaard Jensen3, Rikke Leth-Larsen1, Henrik Jørn Ditzel1,4
1 Department of Cancer and Inflammation Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark 2 Department of Pathology, Slagelse Hospital, Slagelse, Denmark 3 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark 4 Department of Oncology, Odense University Hospital, Odense, Denmark
PLoS One, May 2012
Targeting Melanoma Metastasis and Immunosuppression with a New Mode of Melanoma Inhibitory Activity (MIA) Protein Inhibition
Jennifer Schmidt1, Alexander Riechers2, Raphael Stoll3, Thomas Amann4, Florian Fink5, Thilo Spruss6, Wolfram Gronwald5, Burkhard König2, Claus Hellerbrand4, Anja Katrin Bosserhoff1
1 Institute of Pathology, University of Regensburg, Regensburg, Germany 2 Institute of Organic Chemistry, University of Regensburg, Regensburg, Germany 3 Faculty of Chemistry and Biochemistry, Biomolecular NMR, Ruhr University of Bochum, Bochum, Germany 4 Department of Internal Medicine I, University Hospital Regensburg, Regensburg, Germany 5 Institute of Functional Genomics, University of Regensburg, Regensburg, Germany 6 Institute of Pharmacy, University of Regensburg, Regensburg, Germany
Molecular & Cellular Proteomics, May 2012
Proteomic profiling of the planarian Schmidtea mediterranea and its mucous reveals similarities with human secretions and those predicted for parasitic flatworms
Donald G. Bocchinfuso1, Paul Taylor2, Eric Ross3, Alex Ignatchenko4, Vladimir Ignatchenko4, Thomas Kislinger4, Bret J. Pearson2 and Michael F. Moran2
1 University of Toronto, Canada
2 Hospital For Sick Children, Canada
3 Stowers Institute for Medical Research, United States
4 Ontario Cancer Institute, Canada
Journal of Interferon and Cytokine Research 2012
Glomulin: A Permissivity Factor for Vaccinia Virus Infection
Ramtin Rahbar,1,2,3 Erin Rogers,1,2 Thomas Murooka,1,2 Thomas Kislinger,3,4 and Eleanor N. Fish 1,2,3
1 Toronto General Research Institute, University Health Network, Toronto, Ontario, Canada.
2 Department of Immunology, University of Toronto, Toronto, Ontario, Canada.
3 Ontario Cancer Institute, University Health Network, Toronto, Ontario, Canada.
4 Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
Open Biology 2012
Interleukin-2 signalling is modulated by a labile disulfide bond in the CD132 chain of its receptor
Clive Metcalfe1, Peter Cresswell2 and A. Neil Barclay1
1Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
2Department of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine, 300 Cedar Street, New Haven, CT 06520-8011, USA
Journal of Proteomics, 2011
Integrative analysis of the ubiquitin proteome isolated using Tandem Ubiquitin Binding Entities (TUBEs)
Fernando Lopitz-Otsoa a, Eva Rodriguez-Suarez b, Fabienne Aillet a, Juan Casado-Vela b, Valérie Lang a, Rune Matthiesen c, Felix Elortza b, Manuel S. Rodrigueza, d, , a Proteomics Unit, CIC bioGUNE CIBERehd, ProteoRe d, Technology Park of Bizkaia, Building 801A, 48160 Derio, Spain b Proteomics Platform, CIC bioGUNE CIBERehd, ProteoRed, Technology Park of Bizkaia, Building 801A, 48160 Derio, Spain c Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal d Biochemistry Department, University of the Basque Country, 48940, Leioa, Spain
Journal of Proteome Research, 2011
Analysis of Seminal Plasma from Patients with Non-Obstructive Azoospermia and Identification of Candidate Biomarkers of Male Infertility
Ihor Batruch, Christopher R Smith, Brendan J Mullen, Ethan Grober, Kirk C Lo, Eleftherios P Diamandis, and Keith A Jarvi
Journal of Proteomics, 2011
Unraveling the human dendritic cell phagosome proteome by organellar enrichment ranking
Sonja I. Buschowa, Edwin Lasonderb, Radek Szklarczykb, Machteld M. Ouda, I. Jolanda M. de Vriesa, Carl G. Figdora
a Department of Tumor Immunology at the Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Postbox 9101, 6500 HB Nijmegen, The Netherlands
b CMBI at the Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Postbox 9101, 6500 HB Nijmegen, The Netherlands
Nature Methods, 2011
The proteomes of transcription factories containing RNA polymerases I, II or III
S Melnik, B Deng, A Papantonis, S Baboo, IM Carr
J. Proteome Res., 2011
Phosphoproteome Analysis of Streptomyces Development Reveals Extensive Protein Phosphorylation Accompanying Bacterial Differentiation
Angel Manteca, Juanying Ye, Jesús Sánchez, and Ole Nørregaard Jensen
Area de Microbiologia, Departamento de Biologia Funcional and IUBA, Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
J. Agric. Food Chem., 2011
Identification by Proteomic Analysis of Early Post-mortem Markers Involved in the Variability in Fat Loss during Cooking of Mule Duck “Foie Gras”
Laetitia Theron, Xavier Fernandez, Nathalie Marty-Gasset, Carole Pichereaux, Michel Rossignol, Christophe Chambon, Didier Viala, Thierry Astruc, and Caroline Molette
INRA, UMR 1289 Tissus Animaux Nutrition Digestion Ecosystème Métabolisme, F-31326 Castanet-Tolosan, France
Université de Toulouse, INPT, UMR 1289 Tissus Animaux Nutrition Digestion Ecosystème Métabolisme, ENSAT, F-31326 Castanet-Tolosan, France
ENVT, UMR 1289 Tissus Animaux Nutrition Digestion Ecosystème Métabolisme, F-31076 Toulouse, France
Plateforme Protéomique de la Génopole Toulouse Midi-Pyrénées, IPBS-FR3450, 205 route de Narbonne, 31077 Toulouse, France
IPBS, Université de Toulouse, Université Paul Sabatier, F-31077 Toulouse, France,
PFEM, Composante Protéomique, INRA de Theix, F-63122 Saint Genès Champanelle, France
INRA, UR 370 QuaPA, F-63122 Saint Genès Champanelle, France
J. Proteomics, 2011
Deeper in the human cornea proteome using nanoLC–Orbitrap MS/MS: An improvement for future studies on cornea homeostasis and pathophysiology
Stéphane D. Galiacyc, Carine Fromentab, Emmanuelle Mouton-Barbosaab, Angélique Erraudc, Karima Chaouiab, Laurence Desjardinsd, Bernard Monsarratab, François Malecazec, Odile Burlet-Schiltza b
a CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, F-31077 Toulouse, France
b Université de Toulouse; UPS; IPBS; F-31077 Toulouse, France
c INSERM U563, Université Toulouse III Paul Sabatier, Toulouse, F-31300 France
d Institut Curie, Paris, France
J. Proteome Res. 2011
Multidimensional Strategy for Sensitive Phosphoproteomics Incorporating Protein Prefractionation Combined with SIMAC, HILIC, and TiO2 Chromatography Applied to Proximal EGF Signaling
Kasper Engholm-Keller, Thomas Aarup Hansen, Giuseppe Palmisano, and Martin R. Larsen*
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense, Denmark
Identifying transient protein–protein interactions in EphB2 signaling by blue native PAGE and mass spectrometry
Costel C. Darie, Katrin Deinhardt, Guoan Zhang, Helene S. Cardasis, Moses V. Chao, Thomas A. Neubert
Journal of Clinical Periodontology, 2011
The proteome and gene expression profile of cementoblastic cells treated by bone morphogenetic protein‐7 in vitro
Darko Bozic, Lovorka Grgurevic, Igor Erjavec, Jelena Brkljacic, Iva Orlic, Genadij Razdorov, Ivica Grgurevic, Slobodan Vukicevic, Darije Plancak
J. Proteome Res. 2011
Relative Quantitation of Proteins in Expressed Prostatic Secretion with a Stable Isotope Labeled Secretome Standard
Ting Zhao , Xuemei Zeng , Nicholas W. Bateman , Mai Sun , Pang-ning Teng , William L. Bigbee , Rajiv Dhir , Joel B. Nelson , Thomas P. Conrads , and Brian L. Hood
Anal. Methods, 2012, Advance Article
Evaluation of label-free quantitative proteomics in a plant matrix: A case study of the night-to-day transition in corn leaf
Leah S. Riter, Pamela K. Jensen, Joan M. Ballam, Ewa Urbanczyk-Wochniak, Timothy Clough, Olga Vitek, Jennifer Sutton, Michael Athanas, Mary F. Lopez and Susan MacIsaac
PLoS One. 2011;6(7) 2011
Decellularized matrix from tumorigenic human mesenchymal stem cells promotes neovascularization with Galectin-1 dependent endothelial interaction
Burns JS, Kristiansen M, Kristensen LP, Larsen KH, Nielsen MO, Christiansen H, Nehlin J, Andersen JS, Kassem M.
Molecular Endocrinology Laboratory KMEB, Department of Endocrinology and Metabolism, Odense University Hospital, University of Southern Denmark, Odense, Denmark.
J. Proteome Research 2011
Proteomic analysis of surface and endosomal membrane proteins from the avian LMH epithelial cell line
Zhang L, Katselis GS, Moore RE, Lekpor K, Goto RM, Lee TD, Miller MM.
Department of Molecular and Cellular Biology and ‡Department of Immunology, Beckman Research Institute , City of Hope, 1500 E. Duarte Road, Duarte, California 91010-3000, United States.
J. Proteome Research, 2011
Comprehensive proteome analysis of malignant pleural effusion for lung cancer biomarker discovery by using multidimensional protein identification technology
Yu CJ, Wang CL, Wang CI, Chen CD, Dan YM, Wu CC, Wu YC, Lee IN, Tsai YH, Chang YS, Yu JS.
Proteomics Vol. 11, 2011
Pluripotent stem cell heterogeneity and the evolving role of proteomic technologies in stem cell biology
Rebekah L. Gundry 1,2, Paul W. Burridge 3, Kenneth R. Boheler 4
BMC Cell Biology 2011, 12:33
Quantitative nucleolar proteomics reveals nuclear re-organization during stress-induced senescence in mouse fibroblast
B. Kar , B. Liu , Z. Zhou and Y. W. Lam
Analytical Biochemistry, June 2011
Comprehensive proteomic analysis of mineral nanoparticles derived from human body fluids and analyzed by liquid chromatography–tandem mass spectrometry
Jan Martela, b, c, i, David Younga, d, i, Andrew Younga, i, Cheng-Yeu Wua, c, e, Chi-De Chenb, f, Jau-Song Yuf, g and John D. Younga, c, h, i,
a Laboratory of Nanomaterials, Chang Gung University, Gueishan, Taoyuan 333, Taiwan, ROC
b Graduate Institute of Biomedical Sciences, Chang Gung University, Gueishan, Taoyuan 333, Taiwan, ROC
c Center for Molecular and Clinical Immunology, Chang Gung University, Gueishan, Taoyuan 333, Taiwan, ROC
d Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
e Research Center of Bacterial Pathogenesis, Chang Gung University, Gueishan, Taoyuan 333, Taiwan, ROC
g Department of Cell and Molecular Biology, Chang Gung University, Gueishan, Taoyuan 333, Taiwan, ROC
h Laboratory of Cellular Physiology and Immunology, Rockefeller University, New York, NY 10021, USA
i Biochemical Engineering Research Center, Mingchi University of Technology, Taishan, Taipei 24301, Taiwan, ROC
Molecular & Cellular Proteomics, June 2010
Characterization of human myotubes from type 2 diabetic and non-diabetic subjects using complementary quantitative mass spectrometric methods
Tine E. Thingholm1, Steffen Bak2, Henning Beck-Nielsen2, Ole N. Jensen3 and Michael Gaster2
1 Lund University, Sweden; 2 Odense University Hospital, Denmark; 3 University of Southern Denmark, Denmark
Journal of Proteomics, June 2011
Interleukin-2 signaling pathway analysis by quantitative phosphoproteomics
Nerea Osinaldea, Helle M. Hollegaardb, Onetsine Arrizabalagac, Miren J. Omaetxebarriaa, Blagoy Blagoevb, Ana M. Zubiagac, Asier Fullaondoc, Jesus M. Arizmendia and Irina Kratchmarovab,
a Department of Biochemistry and Molecular Biology, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain
b Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
c Department of Genetics, Physical Anthropology & Animal Physiology, University of the Basque Country, UPV/EHU, 48940 Leioa, Spain
Methods, June 2011
Method for suppressing non-specific protein interactions observed with affinity resins
J.S. Reesa, and K.S. Lilley,a,
a Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
PLoS ONE 6(4): e18497, 2011
A Mighty Small Heart: The Cardiac Proteome of Adult Drosophila melanogaster
Anthony Cammarato1,2, Christian H. Ahrens3, Nakissa N. Alayari1,2, Ermir Qeli3, Jasma Rucker4, Mary C. Reedy5, Christian M. Zmasek6, Marjan Gucek7, Robert N. Cole7, Jennifer E. Van Eyk8, Rolf Bodmer1, Brian O'Rourke4, Sanford I. Bernstein2, D. Brian Foster4*
1 Development and Aging Program, NASCR Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America, 2 Department of Biology and the Heart Institute, San Diego State University, San Diego, California, United States of America, 3 Quantitative Model Organism Proteomics, Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland, 4 Division of Cardiology, Institute of Molecular Cardiobiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America, 5 Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America, 6 Bioinformatics and Systems Biology Program, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America, 7 Johns Hopkins Proteomics Core, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America, 8 Division of Cardiology, Departments of Biological Chemistry and Biomedical Engineering, Johns Hopkins Bayview Medical Center, Baltimore, Maryland, United States of America
PLoS ONE 6(4): e19217, 2011
A New Method for Isolation of Interstitial Fluid from Human Solid Tumors Applied to Proteomic Analysis of Ovarian Carcinoma Tissue
Hanne Haslene-Hox1, Eystein Oveland1, Kaja C. Berg1, Odd Kolmannskog1, Kathrine Woie2, Helga B. Salvesen2,3, Olav Tenstad1#, Helge Wiig1#*
1 Department of Biomedicine, University of Bergen, Bergen, Norway, 2 Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway, 3 Department of Clinical Medicine, University of Bergen, Bergen, Norway
Journal of Proteome Research, 2011
In-depth Proteomics of Ovarian Cancer Ascites: Combining Shotgun Proteomics and Selected Reaction Monitoring Mass Spectrometry
Sarah Elschenbroich, Vladimir Ignatchenko, Blaise Clarke, Steve Kalloger, Paul Boutros, Anthony Gramolini, Patricia Shaw, Igor Jurisica and Thomas Kislinger
Analytical and Bioanalytical Chemistry , 2010
Altered Mascot search results by changing the m/z range of MS/MS spectra: analysis and potential applications
Thomas Köcher1, Peter Pichler2, Michael Mazanek4, Remco Swart3 and Karl Mechtler1, 4
1. Research Institute of Molecular Pathology (IMP), Dr. Bohrgasse 7, 1030 Vienna, Austria, 2. Christian Doppler Laboratory for Proteome Analysis, Dr. Bohrgasse 3, 1030 Vienna, Austria, 3. Dionex Corporation, Abberdaan 114, 1046 AA Amsterdam, Netherlands, 4. Institute of Molecular Biotechnology (IMBA), Dr. Bohrgasse 3, 1030 Vienna, Austria
Molecular & Cellular Proteomics, 2010
Quantitative Proteomics Analysis of Streptomyces coelicolor Development Demonstrates That Onset of Secondary Metabolism Coincides with Hypha Differentiation
‡Protein Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark and §Area de Microbiologia, Departamento de Biologia Funcional and Instituto Universitario de Biotecnología de Asturias (IUBA), Facultad de Medicina, Universidad de Oviedo, 33006 Oviedo, Spain
Jose Luis Luque-García1, Jorge Luis Martínez-Torrecuadrada1, Carolina Epifano1, Marta Cañamero2, Ingrid Babel1,3, J. Ignacio Casal1,3
1 Protein Technology Unit, Biotechnology Programme, Spanish National Cancer Centre (CNIO), Madrid, Spain 2 Comparative Pathology Unit, Biotechnology Programme, Spanish National Cancer Centre, (CNIO), Madrid, Spain 3 Functional Proteomics Laboratory, Centro de Investigaciones Biológicas (CIB-CSIC), Madrid, Spain
aDepartment of Chemistry, Materials and Chemical Egineering "Giulio Natta", Politecnico di Milano, Via Mancinelli 7, 20131 Milan, Italy bSan Raffaele Scientific Institute, 20132 Milan, Italy cBio-Rad Laboratories, C/o CEA-Saclay-DSV, iBiTec-S, 91191 Gif-sur-Yvette, France
Molecular and Cellular Proteomics, 2010 Feb 1. [Epub ahead of print]
Candidate Serological Biomarkers for Cancer Identified from the Secretomes of 23 Cancer Cell Lines and the Human Protein Atlas
Dar-In Tai 5, Hao-Ping Liu 1, Wen-Hui Su 1, Yu-Sun Chang 1,2, and Jau-Song Yu 1,2,3
1 Molecular Medicine Research Center, 2 Graduate Institute of Biomedical Sciences, and 3 Department of Cell and Molecular Biology, Chang Gung University, Tao-Yuan, Taiwan,Republic of China; 4 Department of Otolaryngology-Head and Neck Surgery, and 5 Department of Hepatogastroenterology, Chang Gung Memorial Hospital, Tao-Yuan,
Taiwan, Republic of China
Molecular and Cellular Proteomics., 2010 Feb 5 [Epub ahead of print]
Differential protein expression profiling by iTRAQ-2DLC-MS/MS of human bladder cancer EJ138 cells transfected with the metastasis suppressor KiSS-1 gene
Isabel Ruppen, Laura Grau, Esteban Orenes-Piñero, Keith Ashman, Marta Gil, Ferran Algaba, Joaquim Bellmunt, and Marta Sánchez-Carbayo
Tumor Markers Group, Spanish National Cancer Research Center, Madrid, Madrid E-28029
Molecular and Cellular Proteomics,2010 Feb;9(2):351-61.
Detection of Differentially Expressed Basal Cell Proteins by Mass Spectrometry
Viktor Todorovi, Bhushan V. Desai, Richard A. Eigenheer, Taofei Yin, Evangeline V. Amargo, Milan Mrksich¶, Kathleen J. Green and Melanie J. Schroeder Patterson||,**
From the Departments of Pathology and Dermatology and the R. H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, Proteomics Core Facility, University of California Davis Genome Center, University of California, Davis, California 95616, ¶Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, Illinois 60637, and ||Department of Chemistry, DePaul University, Chicago, Illinois 60614
Ontario Cancer Institute, University Health Network, Canada.
Molecular and Cellular Proteomics, August 2009
Rebekah L. Gundry, Kimberly Raginski, Yelena Tarasova, Irina Tchernyshyov, Damaris Bausch-Fluck, Steven T. Elliott, Kenneth R. Boheler, Jennifer E. Van Eyk, and Bernd Wollscheid
Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21224, USA.
Journal of Virology, July 2009
Dynamic Host Energetics and Cytoskeletal Proteomes in HIV-1-Infected Human Primary CD4 Cells: Analysis by Multiplexed Label-free Mass Spectrometry.
Eric Y. Chan, Jennifer N. Sutton, Jon M. Jacobs, Andrey Bondarenko, Richard D. Smith, and Michael G. Katze.
Department of Microbiology, University of Washington, Seattle, 98195-8070, USA.
Journal of Proteomics Bioinform, June 2009
Epac-induced Alterations in the Proteome of Human SH-SY5Y Neuroblastoma Cells
Even Birkeland, Gyrid Nygaard, Eystein Oveland, Olav Mjaavatten, Marie Ljones, Stein Ove Doskeland, Camilla Krakstad and Frode Selheim
Molecular Systems Biology, June 2009
Comparative systems biology of human and mouse as a tool to guide the modeling of human placental pathology
Brian Cox, Max Kotlyar, Andreas I Evangelou, Vladimir Ignatchenko, Alex Ignatchenko, Kathie Whiteley, Igor Jurisica, S Lee Adamson, Janet Rossant and Thomas Kislinger
The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, Ontario, Canada.
Molecular & Cellular Proteomics, June 2009
Stable Isotopic Labeling by Amino Acids in Cultured Primary Neurons
Daniel S. Spellman, Katrin Deinhardt, Costel C. Darie, Moses V. Chao, and Thomas A. Neubert
Department of Pharmacology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New
York, New York 10016, USA.
Journal of Proteome Research, April 2009
Efficient Isolation and Quantitative Proteomic Analysis of Cancer Cell Plasma Membrane Proteins for Identification of Metastasis-Associated Cell Surface Markers
Rikke Lund, Rikke Leth-Larsen, Ole N. Jensen and Henrik J. Ditzel
Medical Biotechnology Center, Institute of Medical Biology, University of Southern Denmark, Winsloewparken 25. 3, DK-5000
Odense C, Denmark.
"The protein lists generated by VEMS was transferred to ProteinCenter (Professional Edition, version 1.1.2-1 ... To compare the different methods, the proteins were sorted in ProteinCenter according to cellular localization (membrane and ER, Golgi, and mitochondria (EGM), based on gene ontologies) and descriptive statistics were obtained..."
Journal of Proteome Research, December 2008
Large-Scale Analysis of Thermostable, Mammalian Proteins Provides Insights into the Intrinsically Disordered Proteome
Charles A. Galea, Anthony A. High, John C. Obenauer, Ashutosh Mishra, Cheon-Gil Park, Marco Punta, Avner Schlessinger, Jing Ma, Burkhard Rost, Clive A. Slaughter and Richard W. Kriwacki
Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee
"...information on the occurrence of known sites of post-translational modification and alternative splicing for proteins in the TS data set was obtained using the proteomics software suite ProteinCenter.
Analysis using ProteinCenter software indicated that 347 of the 1320 TS proteins (26%) are known to experience alternative splicing. ..."
Journal of Proteome Research, October 2008
Temporal Profiling of the Adipocyte Proteome during Differentiation Using a Five-Plex SILAC Based Strategy
Henrik Molina, Yi Yang, Travis Ruch, Jae-Woo Kim, Peter Mortensen, Tamara Otto, Anuradha Nalli, Qi-Qun Tang, M. Daniel Lane, Raghothama Chaerkady and Akhilesh Pandey
McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University, Baltimore, Maryland 21205, USA.
Data from the MSQuant analyses were imported via a CSV format to ProteinCenter 1.2 for a bioinformatics statistical analysis.
Gene Ontology analysis for identified nuclear and secreted proteins was performed using ProteinCenter version 1.2
Journal of Cell Biology, October 2008
Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes
Laura Trinkle-Mulcahy, Séverine Boulon, Yun Wah Lam, Roby Urcia, François-Michel Boisvert, Franck Vandermoere, Nick A. Morrice, Sam Swift, Ulrich Rothbauer, Heinrich Leonhardt, and Angus Lamond
Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, UK.
"ProteinCenter proteomics data mining and management software was used to eliminate redundancy and compare datasets, and to convert protein IDs to gene symbols and perform initial Gene Ontology characterization."
Journal of Proteome Research, August 2008
Proteome Analysis of Membrane Fractions in Colorectal Carcinomas by Using 2D-DIGE Saturation Labeling
Patricia Alfonso, Marta Caamero, Francisco Fernndez-Carboni, Antonio Nez and J. Ignacio Casal
Protein Technology Unit and Comparative Pathology Unit, Biotechnology Programme, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain.
Leukemia Research, August 2008
Ligand-induced Flt3-downregulation modulates cell death associated proteins and enhances chemosensitivity to idarubicin in THP-1 acute myeloid leukemia cells
Eystein Oveland, Bjørn Tore Gjertsen, Line Wergeland, Frode Selheim, Kari E. Fladmark, Randi Hovland
Proteomic Unit at University of Bergen, Bergen, Norway
Alzheimer's & Dementia: The Journal of the Alzheimer's Association, July 2008
P1-350: Red blood cell membrane proteome is altered in Alzheimer's subjects
Joy G. Mohanty, Hemant D. Shukla, Satya Saxena, Jefferey D. Williamson, Lenore J. Launer, Joseph M. Rifkind
"Protein identification was performed via Bioworks Browser 3.3.1 (Thermo Finnigan, San Jose, CA) with the NCBI non-redundant database. Resultant protein lists of three different runs were compared and annotated using ProteinCenter software.."
Journal of Proteome Research, June 2008
Isocratic Solid Phase Extraction-Liquid Chromatography (SPE-LC) Interfaced to High-Performance Tandem Mass Spectrometry for Rapid Protein Identification
Ole B. Hørning, Frank Kjeldsen, Søren Theodorsen, Ole Vorm and Ole N. Jensen
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M, Denmark.
"Identified proteins with more than 95% sequence similarity were clustered to remove redundancy by using ProteinCenter. ....Annotated peptide fragment ion spectra with Mascot score of 24 or above (p < 0.05) were exported to ProteinCenter
Proteins with shared peptides were collapsed into one group and reported as a single identification, with the highest-scoring protein entry as the anchor (sequence similarity 95%).
Journal of Proteome Research, June 2008
TiO2-Based Phosphoproteomic Analysis of the Plasma Membrane and the Effects of Phosphatase Inhibitor Treatment
Tine E. Thingholm, Martin R. Larsen, Christian R. Ingrell, Moustapha Kassem and Ole N. Jensen
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
"ProteinCenter was used to analyze the cellular components and molecular function as well as the level of transmembrane domains in the proteins identified and for comparison of the different phosphatase inhibitor experiments."
Nephrology dialysis transplantation, April 2008
Proteomic profiling and identification in peritoneal fluid of children treated by peritoneal dialysis
Renske Raaijmakers, Wendy Pluk, Cornelis H. Schröder, Jolein Gloerich, Elisabeth A.M. Cornelissen, Hans J.C.T. Wessels, Johannes L. Willems, Leo A.H. Monnens and Lambert P.W.J. van den Heuvel
Department of Paediatric Nephrology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
Journal of Proteome Research, April 2008
Hepatocystin Is Not Secreted in Cyst Fluid of Hepatocystin Mutant Polycystic Liver Patients
Esm Waanders, Anke L. L. Lameris, Huub J. M. Op den Camp, Wendy Pluk, Jolein Gloerich, Simon P. Strijk and Joost P. H. Drenth
Department of Gastroenterology and Hepatology, Radboud University Nijmegen Medical Center, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.
Journal of Proteome Research, April 2008
Screening for EphB Signaling Effectors Using SILAC with a Linear Ion Trap-Orbitrap Mass Spectrometer
Guoan Zhang, David Fenyo, and Thomas A. Neubert
Department of Pharmacology and Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA.
Analytical Chemistry, April 2008
Performance of Combinatorial Peptide Libraries in Capturing the Low-Abundance Proteome of Red Blood Cells. 1. Behavior of Mono- to Hexapeptides.
Simó C, Bachi A, Cattaneo A, Guerrier L, Fortis F., Boschetti E, Podtelejnikov A, and Righetti PG.
Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Polytechnic of Milano, 20131 Milano, Italy.
Journal of Proteome Research, January 2008
A Proteome Resource of Ovarian Cancer Ascites: Integrated Proteomic and Bioinformatic Analyses To Identify Putative Biomarkers
" Comparison of our ascites proteome resource to the HUPO plasma proteome data (3020 proteins and a recently published urine proteome data set (1543 proteins) was performed using ProteinCenter"
Limor Gortzak-Uzan 1,2,', Alex Ignatchenko 1,', Andreas I. Evangelou 1,', Mahima Agochiya 3, Kevin A. Brown 3, Peter St.Onge 5 Inga Kireeva 1, Gerold Schmitt-Ulms6, Theodore J. Brown 4,7, Joan Murphy 2,7, Barry Rosen 2,7, Patricia Shaw 6, Igor Jurisica 1,8,9 and Thomas Kislinger 1,8,*
' Authors contributed equally to this work. 1 Ontario Cancer Institute, Division of Cancer Genomics and Proteomics. 2 Division of Gynecological Oncology, Princess Margaret Hospital. 3 Ontario Cancer Institute, Division of Signaling Biology.
4 Samuel Lunenfeld Research Institute. 5 Department of Cell and Systems Biology, University of Toronto. 6 Department of Laboratory Medicine and Pathology, University of Toronto. 7 Department of Obstetrics and Gynecology, University of Toronto. 8 Department of Medical Biophysics, University of Toronto. 9 Department of Computer Science, University of Toronto.
Journal of Proteome Research, December 2007
Integrated Analysis of the Cerebrospinal Fluid Peptidome and Proteome
"Due to support of major protein sequence databases and computational enrichment, ProteinCenter decreases the redundancy of the databases and significantly improves protein annotation."
Alexandre Zougman1, Bartosz Pilch,1, 2, Alexandre Podtelejnikov 3, Michael Kiehntopf 4, Claudia Schnabel 5, Chanchal Kumar 1 and Matthias Mann 1
1 Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry Am Klopferspitz 18, 82152 Martinsried, Germany 2 Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark 3 Proxeon Bioinformatics A/S, Staermosegaardsvej 6, DK-5230, Denmark 4 Institute of Clinical Chemistry and Laboratory Medecine, University of Jena, Germany 5 Department of Clinical Chemistry, Center for Clinical Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
Molecular & Cellular Proteomics, November 2007
SILAC-labeling and proteome quantitation of mouse embryonic stem cells to a depth of 5111 proteins
"We used ProteinCenter to compare the results of the two prefractionation methods subcellular fractionation in combination with SDS-gel electrophoresis and isoelectric focusing."
Johannes Graumann1,4, Nina C. Hubner1,4, Jeong Beom Kim2, Kinarm Ko2, Markus Moser3 Chanchal Kumar1, Jürgen Cox1, Hans Schöler2 and Matthias Mann1
1 Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz, D-82152 Martinsried, Germany 2 Department of Cell and Development Biology, Max-Planck-Institute for Molecular Biomedicine, Roentgenstr. 20, 48149 Münster, Germany 3 Department of Molecular Medicine, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany 4 These authors contributed equally
International Orthopaedics (SICOT), In press, October 2007
Detection of bone and cartilage-related proteins in plasma of patients with a bone fracture using liquid chromatography-mass spectrometry
"Gene ontology (GO) analysis was performed using ProteinCenter software package"
L. Grgurevici1, B. Macek2, D. Durdevic3,, S. Vukicevic1
1 Labpratory of Mineralized Tissues, School of Medicine, University of Zagreb, Salata 11, 10000 Zagreb, Croatia 2 Department of Proteomicsand Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany 3 Cline of Traumatology, Draskoviceva 19, Zagreb, Croatia
Journal of Proteome Research, July 2007
Analysis of the Mouse Liver Proteome Using Advanced Mass Spectrometry
"ProteinCenter was used to compare experimental data sets with previously published HUPO plasma data sets. The similarity threshold of 70 % was chosen as the cutoff to define clusters of sequences. The liver proteins belonging to the clusters of at least two proteins with at least one identifier from the HUPO data set were deemed overlapping."
R. Shi1, C. Kumar1, A. Zougman1, Y. Zhang1,2, A. Podtelejnikov3, J. Cox1, J.R. Wisniewski1, M. Mann1.
1 Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany 2 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China 3 Proxeon Biosystems A/S, Stærmosegårdsvej 6, 5230 Odense, Denmark
Molecular & Cellular Proteomics, April 2007
In-depth analysis of the adipocyte proteome by mass spectrometry and bioinformatics
"Adipocyte proteome comparison with previous human cell line and drosphila lipid droplet proteomics studies. We used ProteinCenter (Proxeon, Denmark), which is proteomic data mining and management software, to compare our datasets with previously published datasets of 6 human cell lines, and drosophila lipid droplet proteome. Briefly for mapping our dataset to any other dataset we loaded the datasets as two groups in ProteinCenter. The datasets were then clustered based on the sequence similarity, and the optimization criterion used was "most homogeneous groups" wherein protein sequences are clustered to make the individual groups as homogeneous as possible."
Jun Adachi 1,3, Chanchal Kumar 1, Yanling Zhang 1,2 and Matthias Mann 1
1 Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry Am Klopferspitz 18, 82152 Martinsried, Germany 2 Beijing Institute of Genomics, Chinese Academy of Sciences Beijing 101300, China 3 Graduate School of Global Environmental Studies, Kyoto University Yoshida-Honmachi Sakyo-Ku, Kyoto 606-8501, Japan
Journal of Proteome Research, January 2007
Proteomic Analysis of Pancreatic Zymogen Granules: Identification of New Granule Proteins
Michael J. Rindler, Chong-feng Xu, Iwona Gumper, Nora N. Smith, and Thomas A. Neubert
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes
"Depending on the project, datasets are joined and checked for overlap using ProteinCenter, a proteomics software suite developed by Proxeon. ProteinCenter also allows us to directly distinguish which isoforms of a protein are present in a proteome, provided that distinguishing peptide sequences have been detected."
Yanling Zhang 1,2, Yong Zhang 1,2, Jun Adachi 1,3, Jesper V. Olsen 1, Rong Shi 1, Gustavo de Souza 1, Erica Pasini 4, Leonard J. Foster 5, Boris Macek 1, Alexandre Zougman 1, Chanchal Kumar 1, Jacek R. Winiewski 1, Wang Jun 2,6 and Matthias Mann 1
1 Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry Am Klopferspitz 18, 82152 Martinsried, Germany 2 Beijing Institute of Genomics, Chinese Academy of Sciences Beijing 101300, China 3 Graduate School of Global Environmental Studi, Kyoto University Yoshida- Honmachi Sakyo-Ku, Kyoto 606-8501, Japan 4 Biomedical Primate Research Centre, Lange Kleiweg 139 2288 GJ Rijswijk, The Netherlands 5 Department of Biochemistry and Molecular Biology, Centre for Proteomics, University of British Columbia Vancouver, BC V6T 1Z4, USA 6 Department of Biochemistry and Molecular Biology, University of Southern Denmark DK-5230 Odense M, Denmark
Genome Biology, Volume 7, 2006
Large-scale and high-confidence proteomic analysis of human seminal Plasma
"To prepare a final list of proteins, we used ProteinCenter, a program to analyze the results of proteomic experiments bioinformatically. In particular, ProteinCenter assigns peptide identifications to proteins, resolving ambiguities resulting from peptides matching different members of protein families. Information about which protein was identified in which sample is also kept. ProteinCenter also curates the identified proteome for signal peptides, transmembrane regions, and alternative splicing, and allows analysis of biological function and cellular roles. Results of ProteinCenter analysis, including the occurrence of proteins in one, two, or three samples and bioinformatic annotation, can be found in Additional data file 1."
"A comparison between our data and previously described proteomes using ProteinCenter is presented."
"The merging of data was performed with ProteinCenter, which collapses entries with at least 98% sequence homology and groups homologous sequences."
Bartosz Pilch 1,2 and Matthias Mann 1,2
1 Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK- 5230 Odense M, Denmark 2 Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
Genome Biology, Volume 7, 2006
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins
"In order to compare the different protein identifiers, protein IDs in each dataset were converted to gene symbols using ProteinCenter."
"For counting the number of identified proteins across each experiment, redundant protein identification was removed using Blast search function of ProteinCenter and manual check."
Jun Adachi 1,2,3, Chanchal Kumar 1, Yanling Zhang 1,4, Jesper V Olsen 1,2 and Matthias Mann 1,2
1 Department of Proteomics and Signal Transduction, Max-Planck Institute for Biochemistry, Am Klopferspitz, D-82152 Martinsried, Germany 2 Center for Experimental Bioinformatics, University of Southern Denmark, Campusvej, DK-5230 Odense M, Denmark 3 Current address: Graduate School of Global Environmental Studies, Kyoto University, Yoshida-Honmachi Sakyo-Ku, Kyoto, Japan 4 Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
Genome Biology, Volume 7, 2006
Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors
"The 491 proteins identified in the in-gel analysis were functionally classified using the ProteinCenter Tool"
"Identified proteins were combined in a larger data set and initial GO characterization was done using the ProteinCenter tool"
Gustavo A de Souza 1,2, Lyris MF Godoy 1,2 and Matthias Mann 1,2
1 Center for Experimental BioInformatics (CEBI), Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, DK-5230 Odense M, Denmark 2 Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz, D-82152 Martinsried, Germany
Cell, November 2006
Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks
"Alexandre Podtelejnikov and Søren Gade of Proxeon A/S are acknowledged for their help with bioinformatic analysis using ProteinCenter."
Jesper V. Olsen 1,2,3, Blagoy Blagoev 1,3, Florian Gnad 2,3, Boris Macek 1,2, Chanchal Kumar 2, Peter Mortensen 1 and Matthias Mann 1,2
1 Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense, Denmark 2 Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, D-82152 Martinsried, Germany