ProteoBench: the community-curated platform for comparing proteomics data analysis workflows
Year: 2025
Type: article
Topic: Advanced Proteomics Techniques and Applications
Authors and affiliations:
raw_author_name: Robbe Devreese
raw_affiliation_strings: VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;
raw_author_name: Caroline Jachmann
raw_affiliation_strings: VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;
raw_author_name: Bart Van Puyvelde
raw_affiliation_strings: ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent, 9000, Belgium;
raw_author_name: Holda A. Anagho-Mattanovich
raw_affiliation_strings: Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, Institute for Cellular and Molecular Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark;
raw_author_name: Witold E. Wolski
raw_affiliation_strings: Functional Genomics Center Zurich (FGCZ), ETH Zurich/University of Zurich, Winterthurerstrasse 190, CH- 8057 Zurich, Switzerland; Swiss Institute of Bioinformatics (SIB), Switzerland; Core for Life (C4L);
raw_author_name: Henry Webel
raw_affiliation_strings: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.;
raw_author_name: Matthias Anagho-Mattanovich
raw_affiliation_strings: Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark;
raw_author_name: Wout Bittremieux
raw_affiliation_strings: Department of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium;
raw_author_name: Karima Chaoui
raw_affiliation_strings: Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, Universite de Toulouse (UT), Toulouse, 31077, France; Infrastructure Nationale de Proteomique, ProFI, UAR 2048, Toulouse, France;
raw_author_name: Cristina Chiva
raw_affiliation_strings: Centre for Genomic Regulation, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain;
raw_author_name: Tine Claeys
raw_affiliation_strings: VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;
raw_author_name: Hector Mauricio Castaneda Cortes
raw_affiliation_strings: The James Hutton Institute, Errol Road, Invergowrie, DD2 5DA, United Kingdom;
raw_author_name: Simon Devos
raw_affiliation_strings: Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Center for Medical Biotechnology, VIB, Ghent, Belgium; VIB-Proteomics Core facility; Core for Life (C4L);
raw_author_name: Maarten Dhaenens
raw_affiliation_strings: Laboratory of Pharmaceutical Biotechnology, ProGenTomics, Ghent University, Ghent, Belgium;
raw_author_name: Nadezhda T. Doncheva
raw_affiliation_strings: Novo Nordisk Foundation Center for Protein Research, Institute for Cellular and Molecular Biology, University of Copenhagen, Copenhagen, Denmark; Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University;
raw_author_name: Viktoria Dorfer
raw_affiliation_strings: University of Applied Sciences Upper Austria, Bioinformatics Research Group, Softwarepark 11, 4232 Hagenberg, Austria;
raw_author_name: Martin Eisenacher
raw_affiliation_strings: Medical Faculty, Medizinisches Proteom-Center, Ruhr University Bochum, Bochum, Germany; Medical Faculty, Center for Protein Diagnostics (PRODI), Medical Proteome Analysis, Ruhr-University Bochum, Bochum, Germany; CUBiMed.RUB, Core Unit Bioinformatics, Med;
raw_author_name: Ralf Gabriels
raw_affiliation_strings: VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;
raw_author_name: Quentin Giai Gianetto
raw_affiliation_strings: Institut Pasteur, Universite Paris Cite, Bioinformatics and Biostatistics HUB; Institut Pasteur, Universite Paris Cite, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR CNRS 2024;
raw_author_name: David M. Hollenstein
raw_affiliation_strings: Mass Spectrometry Facility, Max Perutz Labs, Vienna Biocenter Campus (VBC), 1030, Vienna, Austria;
raw_author_name: Lars Juhl Jensen
raw_affiliation_strings: ZS Discovery, Lottenborgvej 26, 2800 Kgs Lyngby, Denmark;
raw_author_name: Vedran Kasalica
raw_affiliation_strings: Netherlands eScience Center, Netherlands;
raw_author_name: Olivier Langella
raw_affiliation_strings: GQE-Le Moulon, Universit Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV-12, route 128, Gif-sur-Yvette F-91272, France;
raw_author_name: Caroline Lennartsson
raw_affiliation_strings: Department of Proteomics, Novo Nordisk Foundation Center for Protein Research, Institute for Cellular and Molecular Biology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark;
raw_author_name: Dominik Lux
raw_affiliation_strings: Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center, Gesundheitscampus 4, 44801 Bochum, Germany;
raw_author_name: Lennart Martens
raw_affiliation_strings: VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium; BioOrganic Mass Spectrometry Laboratory (LSMBO), IPHC UMR 7178, Universi;
raw_author_name: Mariette Matondo
raw_affiliation_strings: Proteomics Core facility, Mass Spectrometry for Biology, Institut Pasteur, CNRS UAR 2024, Universite Paris Cite, France;
raw_author_name: Teresa Mendes Maia
raw_affiliation_strings: Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Center for Medical Biotechnology, VIB, Ghent, Belgium; VIB-Proteomics Core facility;  Core for Life (C4L);
raw_author_name: Emmanuelle Mouton-Barbosa
raw_affiliation_strings: Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, Universite de Toulouse (UT), Toulouse, 31077, France; Infrastructure Nationale de Proteomique, ProFI, UAR 2048, Toulouse, France;
raw_author_name: Alireza Nameni
raw_affiliation_strings: VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;
raw_author_name: Michael Lund Nielsen
raw_affiliation_strings: Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.;
raw_author_name: Jesper Velgaard Olsen
raw_affiliation_strings: Novo Nordisk Foundation Center for Protein Research, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark;
raw_author_name: Magnus Palmblad
raw_affiliation_strings: Center for Proteomics and Metabolomics, Leiden University Medical Center, Postbus, 9600, 2300 RC Leiden, The Netherlands;
raw_author_name: Christian Panse
raw_affiliation_strings: Functional Genomics Center Zurich (FGCZ), ETH Zurich/University of Zurich, Winterthurerstrasse 190, CH- 8057 Zurich, Switzerland; Swiss Institute of Bioinformatics (SIB), Quartier Sorge - Batiment Amphipole, 1015 Lausanne, Switzerland; Core for Life (C4L);
raw_author_name: Yasset Perez-Riverol
raw_affiliation_strings: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK;
raw_author_name: Marina Pominova
raw_affiliation_strings: Department of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium;
raw_author_name: Martin Rykær
raw_author_name: Eduard Sabidó
raw_affiliation_strings: Centre for Genomic Regulation, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain;
raw_author_name: Julia Schessner
raw_affiliation_strings: Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany;
raw_author_name: Martin Schneider
raw_affiliation_strings: Proteomics Core Facility, German Cancer Research Center (DKFZ),Heidelberg 69120, Germany;
raw_author_name: Veit Schwämmle
raw_affiliation_strings: Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark;
raw_author_name: An Staes
raw_affiliation_strings: Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Center for Medical Biotechnology, VIB, Ghent, Belgium; VIB-Proteomics Core facility; Core for Life (C4L);
raw_author_name: Maximilian T. Strauss
raw_affiliation_strings: Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200, Blegdamsvej 3, 2200 Copenhagen;
raw_author_name: Tim Van Den Bossche
raw_affiliation_strings: VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;
raw_author_name: Sam Van Puyenbroeck
raw_affiliation_strings: VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;
raw_author_name: Kevin Velghe
raw_affiliation_strings: VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;
raw_author_name: Runxuan Zhang
raw_affiliation_strings: The James Hutton Institute, Errol Road, Invergowrie, DD2 5DA, United Kingdom;
raw_author_name: Julian Uszkoreit
raw_affiliation_strings: Ruhr University Bochum, Medical Faculty, Medical Bioinformatics, 44801 Bochum, Germany; Ruhr University Bochum, Medical Faculty, Core Unit Bioinformatics - CUBiMed.RUB, 44801 Bochum, Germany
raw_author_name: Robbin Bouwmeester
raw_affiliation_strings: VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;
raw_author_name: Marie Locard-Paulet
raw_affiliation_strings: Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS, Universite de Toulouse (UT), Toulouse, 31077, France; Infrastructure Nationale de Proteomique, ProFI, UAR 2048, Toulouse, France;