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WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows
D. Bouyssié, P. Altıner, S. Capella-Gutierrez, JM. Fernández, YP. Hagemeijer, P. Horvatovich, M. Hubálek, F. Levander, P. Mauri, M. Palmblad, W. Raffelsberger, L. Rodríguez-Navas, D. Di Silvestre, BT. Kunkli, J. Uszkoreit, Y. Vandenbrouck, JA....
Jazyk angličtina Země Spojené státy americké
Typ dokumentu časopisecké články, práce podpořená grantem
- MeSH
- analýza dat MeSH
- benchmarking * MeSH
- proteiny MeSH
- proteomika * MeSH
- průběh práce MeSH
- software MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
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.
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
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
Proteomics French Infrastructure ProFI FR 2048 Toulouse France
Citace poskytuje Crossref.org
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