{"entity": "researcher", "timestamp": "2026-03-05T07:39:53.469Z", "family": "Winkelhardt", "given": "Dirk", "initials": "D", "orcid": "0000-0001-8770-2221", "affiliations": ["Medical Faculty, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/f3b903cf66c34e7b91d1874f603871d3.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/f3b903cf66c34e7b91d1874f603871d3"}}, "publications": [{"entity": "publication", "iuid": "b5b24e2a7739434ca716501314c53d37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5b24e2a7739434ca716501314c53d37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5b24e2a7739434ca716501314c53d37"}}, "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.scilifelab.se/researcher/b950842e8fc94c19b0c3a1872f17c9d8.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.scilifelab.se/researcher/0046e5c6e6e34a9f977710d58eb6b075.json"}}, {"family": "Hagemeijer", "given": "Yanick Paco", "initials": "YP", "orcid": "0000-0001-6036-3741", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3c9fe93b0e04102b0298e2d08a7503c.json"}}, {"family": "Horvatovich", "given": "Peter", "initials": "P", "orcid": "0000-0003-2218-1140", "researcher": {"href": "https://publications.scilifelab.se/researcher/c84f23a68b0b43e4a27655074264342a.json"}}, {"family": "Hub\u00e1lek", "given": "Martin", "initials": "M", "orcid": "0000-0003-0247-7956", "researcher": {"href": "https://publications.scilifelab.se/researcher/19ce60090e42431eb950dc94297fc3ea.json"}}, {"family": "Levander", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0710-9792", "researcher": {"href": "https://publications.scilifelab.se/researcher/1b7add45d810457eb84a72aebbc7b82c.json"}}, {"family": "Mauri", "given": "Pierluigi", "initials": "P"}, {"family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "researcher": {"href": "https://publications.scilifelab.se/researcher/ffa138f687ff406182d87d36d79d5b22.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.scilifelab.se/researcher/9fdcb049f2db4a748e6e31d014a2b55d.json"}}, {"family": "Uszkoreit", "given": "Julian", "initials": "J", "orcid": "0000-0001-7522-4007", "researcher": {"href": "https://publications.scilifelab.se/researcher/9f080e7e9c614db5b49708956a84323a.json"}}, {"family": "Vandenbrouck", "given": "Yves", "initials": "Y", "orcid": "0000-0002-1292-373X", "researcher": {"href": "https://publications.scilifelab.se/researcher/16eb301087cd46c5b12bdb276fdf561b.json"}}, {"family": "Vizca\u00edno", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df36c9559504428a42edba7ba33ec08.json"}}, {"family": "Winkelhardt", "given": "Dirk", "initials": "D", "orcid": "0000-0001-8770-2221", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3b903cf66c34e7b91d1874f603871d3.json"}}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V", "orcid": "0000-0002-9708-6722", "researcher": {"href": "https://publications.scilifelab.se/researcher/5bba954d2b294ec2a917cea775510a55.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": {"Bioinformatics Support, Infrastructure and Training": "Technology development", "Bioinformatics (NBIS)": "Technology development"}, "xrefs": [], "notes": [], "created": "2023-12-11T08:02:08.825Z", "modified": "2024-11-12T13:03:30.548Z"}]}