WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows
Journal of Proteome Research, vol. 23, pp. 418–429
Abstract
The inherent diversity of approaches in proteomics research has led to a wide range of software solutions for data analysis. These software solutions encompass multiple tools, each employing different algorithms for various tasks such as peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. To enable an unbiased comparison of commonly used bottom-up label-free proteomics workflows, we introduce WOMBAT-P, a versatile platform designed for automated benchmarking and comparison. WOMBAT-P simplifies the processing of public data by utilizing the sample and data relationship format for proteomics (SDRF-Proteomics) as input. This feature streamlines the analysis of annotated local or public ProteomeXchange data sets, promoting efficient comparisons among diverse outputs. Through an evaluation using experimental ground truth data and a realistic biological data set, we uncover significant disparities and a limited overlap in the quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of workflows but also provides valuable insights into the capabilities of different software solutions. These benchmarking metrics are a valuable resource for researchers in selecting the most suitable workflow for their specific data sets. The modular architecture of WOMBAT-P promotes extensibility and customization. The software is available at https://github.com/wombat-p/WOMBAT-Pipelines.
Authors 19
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Centre National de la Recherche Scientifique · Université Toulouse III - Paul Sabatier · Institut de Pharmacologie et de Biologie Structurale · Université de Toulouse
Affiliation as printed
Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III─Paul Sabatier (UT3), 31062 Toulouse, France
Proteomics French Infrastructure, ProFI, FR 2048 Toulouse, France
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Centre National de la Recherche Scientifique · Université Toulouse III - Paul Sabatier · Institut de Pharmacologie et de Biologie Structurale · Université de Toulouse
Affiliation as printed
Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III─Paul Sabatier (UT3), 31062 Toulouse, France
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Barcelona Supercomputing Center
Affiliation as printed
Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
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Barcelona Supercomputing Center
Affiliation as printed
Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
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University Medical Center Groningen · University of Groningen
Affiliation as printed
Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, 9712 CP Groningen, The Netherlands
European Research Institute for the Biology of Ageing, University Medical Center Groningen, 9713 GZ Groningen, The Netherlands
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Affiliation as printed
Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, 9712 CP Groningen, The Netherlands
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Czech Academy of Sciences, Institute of Organic Chemistry and Biochemistry
Affiliation as printed
Institute of Organic Chemistry and Biochemistry, CAS, 160 00 Prague, Czech Republic
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Lund University · Science for Life Laboratory · National Bioinformatics Infrastructure Sweden
Affiliation as printed
National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Department of Immunotechnology, Lund University, 22100 Lund, Sweden
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Institute of Biomedical Technologies · National Research Council
Affiliation as printed
Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), Segrate, 20054 Milan, Italy
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Magnus Palmblad Aachen
Leiden University Medical Center
Affiliation as printed
Leiden University Medical Center, Postbus 9600, 2300 RC Leiden, The Netherlands
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Centre National de la Recherche Scientifique · Inserm · Institut de génétique et de biologie moléculaire et cellulaire · Université de Strasbourg
Affiliation as printed
Wolfgang Raffelsberger: Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, 1 Rue Laurent Fries, 67404 Illkirch, France
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Barcelona Supercomputing Center
Affiliation as printed
Life Sciences Department, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
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Institute of Biomedical Technologies · National Research Council
Affiliation as printed
Institute for Biomedical Technologies (ITB), Department of Biomedical Sciences, National Research Council (CNR), Segrate, 20054 Milan, Italy
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Affiliation as printed
Balázs Tibor Kunkli: Department of Biochemistry and Molecular Biology, University of Debrecen, 4032 Debrecen, Hungary
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Affiliation as printed
Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany
Medical Faculty, Medical Bioinformatics, Ruhr University Bochum, 44801 Bochum, Germany
Medical Faculty, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
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Commissariat à l'Énergie Atomique et aux Énergies Alternatives
Affiliation as printed
CEA, Fundamental Research Division, Proteomics French Infrastructure, 91191 Gif-sur-Yvette, France
Proteomics French Infrastructure, ProFI, FR 2048 Toulouse, France
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European Bioinformatics Institute · Wellcome Trust
Affiliation as printed
European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Trust, Genome Campus, Hinxton, Cambridge CB10 1SD, U.K
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Affiliation as printed
Medical Faculty, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
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Veit Schwämmle corresponding
University of Southern Denmark
Affiliation as printed
Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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