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