ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

ABSTRACT Mass spectrometry (MS)-based proteomics is a well-established strategy for analyzing complex biological mixtures. Many MS instruments and data acquisition strategies are available, and the data they acquire differ substantially, thus requiring tailored analysis algorithms. Hence, many dedicated bioinformatics workflows are developed. These are in constant evolution, and the community lacks a centralized platform for comparing their performance. Here, we propose ProteoBench, a single platform that brings together software developers and software users to provide an ever-evolving comparison of state-of-the-art proteomics data processing tools. ProteoBench is an open-source resource that enables the community to evaluate data analysis workflows, develop benchmarking modules dedicated to specific comparisons, and discuss the best methods to compare software tools. The platform ensures that the benchmark evolves alongside advances in proteomics data analysis workflows. ProteoBench guides researchers towards the best-suited tool and parameters for their specific project and data according to their needs, and developers can test their newly developed tools or workflows privately, before adding them as public references. This community-driven effort will increase transparency and reproducibility between MS data analysis workflows, as well as facilitate the development and publication of software workflows in the field.

Authors 50

1. Robbe Devreese

   Ghent University · VIB-UGent Center for Medical Biotechnology

   Affiliation as printed

   VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;

2. Caroline Jachmann

   Ghent University · VIB-UGent Center for Medical Biotechnology

   Affiliation as printed

   VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;

3. Bart Van Puyvelde
   Affiliation as printed

   ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent, 9000, Belgium;

4. Holda A. Anagho

   University of Copenhagen · Novo Nordisk Foundation

   Affiliation as printed

   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;

5. Witold Wolski

   SIB Swiss Institute of Bioinformatics · University of Zurich · ETH Zurich · Functional Genomics Center Zurich

   Affiliation as printed

   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);

6. Henry Emanuel Webel

   Novo Nordisk Foundation · Technical University of Denmark

   Affiliation as printed

   Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.;

7. Matthias Mattanovich

   University of Copenhagen · Novo Nordisk Foundation Center for Basic Metabolic Research

   Affiliation as printed

   Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark;

8. Wout Bittremieux

   University of Antwerp

   Affiliation as printed

   Department of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium;

9. Karima Chaoui

   Centre National de la Recherche Scientifique · Institut de Pharmacologie et de Biologie Structurale · Université de Toulouse

   Affiliation as printed

   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;

10. Cristina Chiva

    Universitat Pompeu Fabra · Centre for Genomic Regulation

    Affiliation as printed

    Centre for Genomic Regulation, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain;

11. Tine Claeys

    Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;

12. Hector Mauricio Castaneda Cortes

    James Hutton Institute

    Affiliation as printed

    The James Hutton Institute, Errol Road, Invergowrie, DD2 5DA, United Kingdom;

13. Simon Devos

    Vlaams Instituut voor Biotechnologie · Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Center for Medical Biotechnology, VIB, Ghent, Belgium; VIB-Proteomics Core facility; Core for Life (C4L);

14. Maarten Dhaenens

    Ghent University

    Affiliation as printed

    Laboratory of Pharmaceutical Biotechnology, ProGenTomics, Ghent University, Ghent, Belgium;

15. Nadezhda T. Doncheva

    University of Copenhagen · Novo Nordisk Foundation

    Affiliation as printed

    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;

16. Viktoria Dorfer

    University of Applied Sciences Upper Austria

    Affiliation as printed

    University of Applied Sciences Upper Austria, Bioinformatics Research Group, Softwarepark 11, 4232 Hagenberg, Austria;

17. Martin Eisenacher

    Ruhr University Bochum

    Affiliation as printed

    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;

18. Ralf Gabriels

    Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;

19. Quentin Giai Gianetto

    Centre National de la Recherche Scientifique · Institut Pasteur · Université Paris Cité · Spectrométrie de Masse pour la Biologie

    Affiliation as printed

    Institut Pasteur, Universite Paris Cite, Bioinformatics and Biostatistics HUB; Institut Pasteur, Universite Paris Cite, Proteomics Platform, Mass Spectrometry for Biology Unit, UAR CNRS 2024;

20. David Maria Hollenstein

    Max Perutz Labs · Vienna Biocenter

    Affiliation as printed

    Mass Spectrometry Facility, Max Perutz Labs, Vienna Biocenter Campus (VBC), 1030, Vienna, Austria;

21. Lars Juhl Jensen
    Affiliation as printed

    ZS Discovery, Lottenborgvej 26, 2800 Kgs Lyngby, Denmark;

22. Vedran Kasalica

    Netherlands eScience Center

    Affiliation as printed

    Netherlands eScience Center, Netherlands;

23. Olivier Langella

    Centre National de la Recherche Scientifique · AgroParisTech · Université Paris-Saclay · Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Génétique Quantitative et Évolution Le Moulon

    Affiliation as printed

    GQE-Le Moulon, Universit Paris-Saclay, INRAE, CNRS, AgroParisTech, IDEEV-12, route 128, Gif-sur-Yvette F-91272, France;

24. Caroline Lennartsson

    University of Copenhagen · Novo Nordisk Foundation

    Affiliation as printed

    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;

25. Dominik Lux

    Ruhr University Bochum

    Affiliation as printed

    Ruhr University Bochum, Medical Faculty, Medizinisches Proteom-Center, Gesundheitscampus 4, 44801 Bochum, Germany;

26. Lennart Martens

    Institut Pluridisciplinaire Hubert Curien · Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    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;

27. Mariette Matondo

    Centre National de la Recherche Scientifique · Institut Pasteur · Université Paris Cité · Spectrométrie de Masse pour la Biologie

    Affiliation as printed

    Proteomics Core facility, Mass Spectrometry for Biology, Institut Pasteur, CNRS UAR 2024, Universite Paris Cite, France;

28. Teresa Mendes Maia

    Vlaams Instituut voor Biotechnologie · Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Center for Medical Biotechnology, VIB, Ghent, Belgium; VIB-Proteomics Core facility; Core for Life (C4L);

29. Emmanuelle Mouton‐Barbosa

    Centre National de la Recherche Scientifique · Institut de Pharmacologie et de Biologie Structurale · Université de Toulouse

    Affiliation as printed

    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;

30. Alireza Nameni

    Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;

31. Michael Lund Nielsen

    University of Copenhagen · Novo Nordisk Foundation

    Affiliation as printed

    Novo Nordisk Foundation Center for Protein Research, Proteomics Program, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.;

32. Jesper Velgaard Olsen

    University of Copenhagen · Novo Nordisk Foundation

    Affiliation as printed

    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;

33. Magnus Palmblad Aachen Center for Proteomics and Metabolomics

    Leiden University Medical Center

    Affiliation as printed

    Center for Proteomics and Metabolomics, Leiden University Medical Center, Postbus, 9600, 2300 RC Leiden, The Netherlands;

34. Christian Panse

    SIB Swiss Institute of Bioinformatics · University of Zurich · ETH Zurich · Functional Genomics Center Zurich

    Affiliation as printed

    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);

35. Yasset Pérez‐Riverol

    European Bioinformatics Institute

    Affiliation as printed

    European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK;

36. Marina Pominova

    University of Antwerp

    Affiliation as printed

    Department of Computer Science, University of Antwerp, 2020 Antwerpen, Belgium;

37. Martin Rykær
38. Eduard Sabidó

    Universitat Pompeu Fabra · Centre for Genomic Regulation

    Affiliation as printed

    Centre for Genomic Regulation, Dr Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain;

39. Julia Patricia Schessner

    Max Planck Institute of Biochemistry

    Affiliation as printed

    Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Martinsried, Germany;

40. Martin Schneider

    German Cancer Research Center

    Affiliation as printed

    Proteomics Core Facility, German Cancer Research Center (DKFZ),Heidelberg 69120, Germany;

41. Veit Schwämmle

    University of Southern Denmark

    Affiliation as printed

    Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark;

42. An Staes

    Vlaams Instituut voor Biotechnologie · Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; VIB Center for Medical Biotechnology, VIB, Ghent, Belgium; VIB-Proteomics Core facility; Core for Life (C4L);

43. Maximilian T. Strauss

    University of Copenhagen · Novo Nordisk Foundation

    Affiliation as printed

    Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200, Blegdamsvej 3, 2200 Copenhagen;

44. Tim Van Den Bossche

    Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;

45. Sam van Puyenbroeck

    Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;

46. Kevin Velghe

    Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;

47. Runxuan Zhang

    James Hutton Institute

    Affiliation as printed

    The James Hutton Institute, Errol Road, Invergowrie, DD2 5DA, United Kingdom;

48. Julian Uszkoreit

    Ruhr University Bochum

    Affiliation as printed

    Ruhr University Bochum, Medical Faculty, Medical Bioinformatics, 44801 Bochum, Germany; Ruhr University Bochum, Medical Faculty, Core Unit Bioinformatics - CUBiMed.RUB, 44801 Bochum, Germany

49. Robbin Bouwmeester

    Ghent University · VIB-UGent Center for Medical Biotechnology

    Affiliation as printed

    VIB Center for Medical Biotechnology, VIB, Ghent, 9052, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, 9052, Belgium;

50. Marie Locard‐Paulet corresponding

    Centre National de la Recherche Scientifique · Institut de Pharmacologie et de Biologie Structurale · Université de Toulouse

    Affiliation as printed

    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;