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.

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

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

Ihor Batruch, Christopher R Smith, Brendan J Mullen, Ethan Grober, Kirk C Lo, Eleftherios P Diamandis, and Keith A Jarvi

Sonja I. Buschow^a, Edwin Lasonder^b, Radek Szklarczyk^b, Machteld M. Oud^a, I. Jolanda M. de Vries^a, Carl G. Figdor^a

^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

S Melnik, B Deng, A Papantonis, S Baboo, IM Carr

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

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

Stéphane D. Galiacy^c, Carine Fromenta^b, Emmanuelle Mouton-Barbosaa^b, Angélique Erraud^c, Karima Chaouia^b, Laurence Desjardins^d, Bernard Monsarrata^b, François Malecaze^c, 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

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

Costel C. Darie, Katrin Deinhardt, Guoan Zhang, Helene S. Cardasis, Moses V. Chao, Thomas A. Neubert

Darko Bozic^, Lovorka Grgurevic^, Igor Erjavec^, Jelena Brkljacic^, Iva Orlic^, Genadij Razdorov^, Ivica Grgurevic^, Slobodan Vukicevic^, Darije Plancak

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

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

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.

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.

Yu CJ, Wang CL, Wang CI, Chen CD, Dan YM, Wu CC, Wu YC, Lee IN, Tsai YH, Chang YS, Yu JS.

Rebekah L. Gundry ^1,2, Paul W. Burridge ³, Kenneth R. Boheler ⁴

B. Kar , B. Liu , Z. Zhou and Y. W. Lam

Jan Martela, ^b, ^c, ⁱ, David Young^a, ^d, ⁱ, Andrew Young^{a, i}, Cheng-Yeu Wu^a, ^c, ^e, Chi-De Chen^b, ^f, Jau-Song Yu^f, ^g and John D. Young^a, ^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

^f Proteomics Core Laboratory, 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

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

J.S. Rees^a,  and K.S. Lilley,^a,

^a Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK

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

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

Sarah Elschenbroich, Vladimir Ignatchenko, Blaise Clarke, Steve Kalloger, Paul Boutros, Anthony Gramolini, Patricia Shaw, Igor Jurisica and Thomas Kislinger

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

Angel Manteca‡§, Jesus Sanchez§, Hye R. Jung‡, Veit Schwämmle‡ and Ole N. Jensen‡

‡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

Sutton CW, Sutherland M, Shnyder S, Patterson LH.

Institute of Cancer Therapeutics, University of Bradford, Bradford, West Yorkshire, BD7 1DP,UK.

Jeanette Henningsen¹, Kristoffer T. G. Rigbolt¹, Blagoy Blagoev¹, Bente Klarlund Pedersen² and Irina Kratchmarova¹ 

¹ Center for Experimental BioInformatics (CEBI), BMB, University of Southern Denmark, Denmark;

² The Centre of Inflammation and Metabolism (CIM), University of Copenhagen, Denmark

Brekke HK, Oveland E, Kollmannskog O, Hammersborg SM, Wiig H, Husby P, Tenstad O, Nedrebø T.
Haukeland University Hospital, Bergen, Norway

Manimalha Balasubramani^a, Emanuel M. Schreiber^a, Joseph Candiello^b, G.K. Balasubramani^c, Justin Kurtz^d and Willi Halfter^d

 a Proteomics Core, Genomics and Proteomics Core Laboratories, University of Pittsburgh, Pittsburgh, PA 15261, United States

 b Department of Biological Engineering, University of Pittsburgh, Pittsburgh, PA 15261, United States

 c Department of Epidemiology, Epidemiology Data Center, University of Pittsburgh, Pittsburgh, PA 15261, United States

 d Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA 15261, United States

Drake RR, Elschenbroich S, Lopez-Perez O, Kim Y, Ignatchenko V, Ignatchenko A, Nyalwidhe JO, Basu G, Wilkins CE, Gjurich B, Lance RS, Semmes OJ, Medin JA, Kislinger T. Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia 23517, USA.

Jose Luis Luque-García¹, Jorge Luis Martínez-Torrecuadrada¹, Carolina Epifano¹, Marta Cañamero², Ingrid Babel^1,3, J. Ignacio Casal^1,3

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

W. Y. Tong¹, Y. M. Liang², Vivian Tam¹, H. K. Yip³, Y. T. Kao¹, KI. M. C. Cheung¹, K. W. K. Yeung4 and Y. W. Lam²,*

¹ The University of Hong Kong, Hong Kong; ² City University of Hong Kong, Hong Kong; ³ James Cook University, Hong Kong; ⁴ HKU, Hong Kong

Alexandra Abramsson, Ann Westman-Brinkmalm, Josef Pannee, Mikael Gustavsson, Malin von Otter, Kaj Blennow, Gunnar Brinkmalm, Petronella Kettunen, Henrik Zetterberg. 

Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.

Frank Schmidt¹, Sandra S. Scharf¹, Petra Hildebrandt¹, Marc Burian¹, Jörg Bernhardt², Vishnu Dhople¹, Julia Kalinka1, Melanie Gutjahr¹, Elke Hammer¹, and Uwe Völker¹

¹ Interfaculty Institute for Genetics and Functional Genomics, Ernst-Moritz- Arndt-University Greifswald, Friedrich-Ludwig-Jahn-Strasse 15a, D-17487 Greifswald, Germany

² Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Friedrich-Ludwig-Jahn-Strasse 15, D-17487 Greifswald, Germany

Gundry RL, Tchernyshyov I, Sheng S, Tarasova Y, Raginski K,  Boheler KR, Van Eyk JE. 

Johns Hopkins University School of Medicine

Alessia Farinazzo^a, Umberto Restuccia^b, Angela Bachi^b, Luc Guerrier^c, Frederic Fortis^c, Egisto Boschetti^c, Elisa Fasoli^a, Attilio Citterio^a and Pier Giorgio Righetti^a,

^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

Chih-Ching Wu1*, Chia-Wei Hsu2*, Chi-De Chen2, Chia-Jung Yu ^1,2,3, Kai-Ping Chang ^4,

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

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

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

Elschenbroich S, Ignatchenko V, Sharma P, Schmitt-Ulms G, Gramolini AO, Kislinger T.

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.

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.

Even Birkeland, Gyrid Nygaard, Eystein Oveland, Olav Mjaavatten, Marie Ljones, Stein Ove Doskeland, Camilla Krakstad and Frode Selheim

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.

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.

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..."

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

38105, USA.

"...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. ..."

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

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."

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.

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.."

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%).

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."

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

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.

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.

Simó C,  Bachi A,  Cattaneo A,  Guerrier L, Fortis F., Boschetti E, Podtelejnikov A, and Righetti PG.

 " 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.

"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

"We used ProteinCenter to compare the results of the two prefractionation methods subcellular fractionation in combination with SDS-gel electrophoresis and isoelectric focusing."

Johannes Graumann^1,4, Nina C. Hubner^1,4, 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

"Gene ontology (GO) analysis was performed using ProteinCenter software package"

L. Grgurevici¹, B. Macek², D. Durdevic^3,, S. Vukicevic¹

¹ Labpratory of Mineralized  Tissues, School of Medicine, University of Zagreb, Salata 11, 10000 Zagreb, Croatia
² Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
³ Cline of Traumatology, Draskoviceva 19, Zagreb, Croatia

"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. Zhang^1,2, 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

"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

Michael J. Rindler, Chong-feng Xu, Iwona Gumper, Nora N. Smith, and Thomas A. Neubert

"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

"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

"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

"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

"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