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.

Balázs Tibor Kunkli Department of Biochemistry and Molecular Biology University of Debrecen 4032 Debrecen Hungary

CEA Fundamental Research Division Proteomics French Infrastructure 91191 Gif sur Yvette France

Center for Protein Diagnostics Medical Proteome Analysis Ruhr University Bochum 44801 Bochum Germany

Department of Analytical Biochemistry University of Groningen Groningen Research Institute of Pharmacy 9712 CP Groningen The Netherlands

Department of Biochemistry and Molecular Biology University of Southern Denmark Campusvej 55 5230 Odense M Denmark

European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD U K

European Research Institute for the Biology of Ageing University Medical Center Groningen 9713 GZ Groningen The Netherlands

Institut de Pharmacologie et de Biologie Structurale 31062 Toulouse France

Institute for Biomedical Technologies Segrate 20054 Milan Italy

Institute of Organic Chemistry and Biochemistry CAS 160 00 Prague Czech Republic

Leiden University Medical Center Postbus 9600 2300 RC Leiden The Netherlands

Life Sciences Department Barcelona Supercomputing Center 08034 Barcelona Spain

Medical Faculty Medical Bioinformatics Ruhr University Bochum 44801 Bochum Germany

Medical Faculty Medizinisches Proteom Center Ruhr University Bochum 44801 Bochum Germany

National Bioinformatics Infrastructure Sweden Science for Life Laboratory Department of Immunotechnology Lund University 22100 Lund Sweden

Proteomics French Infrastructure ProFI FR 2048 Toulouse France

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

References provided by Crossref.org

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