{"entity": "researcher", "timestamp": "2026-09-23T15:38:57.101Z", "family": "Horvatovich", "given": "Peter", "initials": "P", "orcid": "0000-0003-2218-1140", "affiliations": ["Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, 9712 CP Groningen, The Netherlands."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/15ce5ebac4b546679244f69fbcb5f379.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/15ce5ebac4b546679244f69fbcb5f379"}}, "publications": [{"entity": "publication", "iuid": "29f9bd60f9ba4469b1e0a71246022d47", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/29f9bd60f9ba4469b1e0a71246022d47.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/29f9bd60f9ba4469b1e0a71246022d47"}}, "title": "WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.", "authors": [{"family": "Bouyssi\u00e9", "given": "David", "initials": "D", "orcid": "0000-0002-0847-4759", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/877b0a0677fb463b829241dc4fc52203.json"}}, {"family": "Alt\u0131ner", "given": "P\u0131nar", "initials": "P"}, {"family": "Capella-Gutierrez", "given": "Salvador", "initials": "S"}, {"family": "Fern\u00e1ndez", "given": "Jos\u00e9 M", "initials": "JM", "orcid": "0000-0002-4806-5140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3511b21fa18645df8da018bd490e3d20.json"}}, {"family": "Hagemeijer", "given": "Yanick Paco", "initials": "YP", "orcid": "0000-0001-6036-3741", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/76b2c76095b149a89e349830770c5cc7.json"}}, {"family": "Horvatovich", "given": "Peter", "initials": "P", "orcid": "0000-0003-2218-1140", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/15ce5ebac4b546679244f69fbcb5f379.json"}}, {"family": "Hub\u00e1lek", "given": "Martin", "initials": "M", "orcid": "0000-0003-0247-7956", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9f36f0a91f548a6b1013f619e139c9a.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3aaa3dcdb4f4e9f9b4bd44097d85d0c.json"}}, {"family": "Mauri", "given": "Pierluigi", "initials": "P"}, {"family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c.json"}}, {"family": "Raffelsberger", "given": "Wolfgang", "initials": "W"}, {"family": "Rodr\u00edguez-Navas", "given": "Laura", "initials": "L"}, {"family": "Di Silvestre", "given": "Dario", "initials": "D"}, {"family": "Kunkli", "given": "Bal\u00e1zs Tibor", "initials": "BT", "orcid": "0000-0003-1266-2792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bc333a7d2db94a4baa1a05cad9080753.json"}}, {"family": "Uszkoreit", "given": "Julian", "initials": "J", "orcid": "0000-0001-7522-4007", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/97c6efaaa4f045a7a718ca2ba376f641.json"}}, {"family": "Vandenbrouck", "given": "Yves", "initials": "Y", "orcid": "0000-0002-1292-373X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ed616edf97c454aa6b79c56e565ce64.json"}}, {"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81245410f3234e658147bc94f6b3dad2.json"}}, {"family": "Winkelhardt", "given": "Dirk", "initials": "D", "orcid": "0000-0001-8770-2221", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0bc906f12f834e4f8e909a0b8426e0af.json"}}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V", "orcid": "0000-0002-9708-6722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/158e08b0cfd34f90882f66142d8e62b7.json"}}], "type": "journal article", "published": "2024-01-05", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "23", "issue": "1", "pages": "418-429", "issn-l": "1535-3893"}, "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.", "doi": "10.1021/acs.jproteome.3c00636", "pmid": "38038272", "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T13:33:30.019Z", "modified": "2026-09-23T13:33:30.315Z"}]}