WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract Proteomics research encompasses a wide array of experimental designs, resulting in diverse datasets varying in structure and properties. This diversity has led to a considerable variety of software solutions for data analysis, each of them using multiple tools with different algorithms for operations like peptide-spectrum matching, protein inference, quantification, statistical analysis, and visualization. Computational workflows combine these algorithms to facilitate end-to-end analysis, spanning from raw data to detecting differentially regulated proteins. We introduce WOMBAT-P, a versatile platform designed for the automatic benchmarking and comparison of bottom-up label-free proteomics workflows. By standardizing software parameterization and workflow outputs, WOMBAT-P empowers an objective comparison of four commonly utilized data analysis workflows. Furthermore, WOMBAT-P streamlines the processing of public data based on the provided metadata, with an optional specification of 30 parameters. Wombat-P can use Sample and Data Relationship Format for Proteomics (SDRF-Proteomics) as the file input to simply process annotated local or ProteomeXchange deposited datasets. This feature offers a shortcut for data analysis and facilitates comparisons among diverse outputs. Through an examination of experimental ground truth data and a realistic biological dataset, we unveil significant disparities and a low overlap between identified and quantified proteins. WOMBAT-P not only enables rapid execution and seamless comparison of four workflows (on the same dataset) using a wide range of benchmarking metrics but also provides insights into the capabilities of different software solutions. These metrics support researchers in selecting the most suitable workflow for their specific dataset. The modular architecture of WOMBAT-P promotes extensibility and customization, making it an ideal platform for testing newly developed software tools within a realistic data analysis context.

Authors 18

1. David Bouyssié

   Institut de Pharmacologie et de Biologie Structurale · Université de Toulouse

   Affiliation as printed

   Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse

2. Pınar Altıner

   Institut de Pharmacologie et de Biologie Structurale · Université de Toulouse

   Affiliation as printed

   Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse

3. Salvador Capella-Gutiérrez

   Barcelona Supercomputing Center

   Affiliation as printed

   Barcelona Supercomputing Center (BSC)

4. José M. Fernández

   Barcelona Supercomputing Center

   Affiliation as printed

   Life Sciences Department, Barcelona Supercomputing

5. Yanick Paco Hagemeijer

   University of Groningen

   Affiliation as printed

   University of Groningen

6. Peter L. Horvatovich

   University of Groningen

   Affiliation as printed

   University of Groningen

7. Fredrik Levander

   Lund University

   Affiliation as printed

   Lund University

8. Pierluigi Mauri

   Institute of Biomedical Technologies · National Research Council

   Affiliation as printed

   Istituto di Tecnologie Biomediche Consiglio Nazionale delle Ricerche

9. Magnus Palmblad Aachen

   Leiden University Medical Center

   Affiliation as printed

   Leiden University Medical Center

10. Wolfgang Raffelsberger

    Université de Strasbourg

    Affiliation as printed

    Université de Strasbourg

11. Laura Rodríguez‐Navas

    Barcelona Supercomputing Center

    Affiliation as printed

    Life Sciences Department, Barcelona Supercomputing

12. Dario Di Silvestre

    National Academies of Sciences, Engineering, and Medicine · National Research Council · Institute of Biomedical Technologies · National Research Council

    Affiliation as printed

    Institute for Biomedical Technologies (ITB), Dept. of Biomedical Sciences, National Research Council

13. Balázs Tibor Kunkli

    University of Debrecen

    Affiliation as printed

    University of Debrecen

14. Julian Uszkoreit

    Ruhr University Bochum

    Affiliation as printed

    Ruhr University Bochum

15. Yves Vandenbrouck

    Commissariat à l'Énergie Atomique et aux Énergies Alternatives

    Affiliation as printed

    CEA

16. Juan Antonio Vizcaíno

    European Bioinformatics Institute

    Affiliation as printed

    EMBL-European Bioinformatics Institute

17. Dirk Winkelhardt

    Ruhr University Bochum

    Affiliation as printed

    Ruhr University Bochum

18. Veit Schwämmle corresponding

    University of Southern Denmark

    Affiliation as printed

    University of Southern Denmark