{"entity": "researcher", "timestamp": "2026-08-20T20:46:28.008Z", "family": "Martens", "given": "Lennart", "initials": "L", "orcid": "0000-0003-4277-658X", "affiliations": ["VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.", "Department of Biomolecular Medicine, Faculty of Health Sciences and Medicine, Ghent University, 9000 Ghent, Belgium."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/df9a736ba6d04cbdb881a040480bf6f0.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/df9a736ba6d04cbdb881a040480bf6f0"}}, "publications": [{"entity": "publication", "iuid": "ed86cc02c63e46d09350d9ba3702350b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ed86cc02c63e46d09350d9ba3702350b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ed86cc02c63e46d09350d9ba3702350b"}}, "title": "Open-Source and FAIR Research Software for Proteomics.", "authors": [{"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}, {"family": "Bittremieux", "given": "Wout", "initials": "W", "orcid": "0000-0002-3105-1359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e740b95ac84bb6ad8f3ff159aece03.json"}}, {"family": "Noble", "given": "William S", "initials": "WS", "orcid": "0000-0001-7283-4715", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77bfbf9a1a8242b8955c8dd9f5642a8b.json"}}, {"family": "Martens", "given": "Lennart", "initials": "L", "orcid": "0000-0003-4277-658X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df9a736ba6d04cbdb881a040480bf6f0.json"}}, {"family": "Bilbao", "given": "Aivett", "initials": "A", "orcid": "0000-0003-2985-8249", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2939469149284dee8f3b20bf40c9e2e9.json"}}, {"family": "Lazear", "given": "Michael R", "initials": "MR", "orcid": "0000-0001-5313-4262", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ebe2629197bf4b53a53a06244b7f1302.json"}}, {"family": "Gr\u00fcning", "given": "Bjorn", "initials": "B", "orcid": "0000-0002-3079-6586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2539c92f7e2437782cf04c0c9a23fc8.json"}}, {"family": "Katz", "given": "Daniel S", "initials": "DS", "orcid": "0000-0001-5934-7525", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b3f98d2fb8384d4684bd7e9e93dc3ef1.json"}}, {"family": "MacCoss", "given": "Michael J", "initials": "MJ", "orcid": "0000-0003-1853-0256", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b57b50e580b940cba50310ac37e89603.json"}}, {"family": "Dai", "given": "Chengxin", "initials": "C"}, {"family": "Eng", "given": "Jimmy K", "initials": "JK", "orcid": "0000-0001-6352-6737", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d748f8f4b03940ac81712a0910415b8b.json"}}, {"family": "Bouwmeester", "given": "Robbin", "initials": "R", "orcid": "0000-0001-6807-7029", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd945733eeaf46d895f9d8799b430d66.json"}}, {"family": "Shortreed", "given": "Michael R", "initials": "MR", "orcid": "0000-0003-4626-0863", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cf4bd1d3f2ed44bf94983b952500e04d.json"}}, {"family": "Audain", "given": "Enrique", "initials": "E"}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Van Goey", "given": "Jeroen", "initials": "J"}, {"family": "Wallmann", "given": "Georg", "initials": "G"}, {"family": "Wen", "given": "Bo", "initials": "B"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Fondrie", "given": "William E", "initials": "WE", "orcid": "0000-0002-1554-3716", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0605055453fc4d54b057471ae964ca3f.json"}}], "type": "journal article", "published": "2025-05-02", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "24", "issue": "5", "pages": "2222-2234", "issn-l": "1535-3893"}, "abstract": "Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.", "doi": "10.1021/acs.jproteome.4c01079", "pmid": "40267229", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12053954"}], "notes": [], "created": "2026-08-20T08:12:01.116Z", "modified": "2026-08-20T08:12:01.507Z"}, {"entity": "publication", "iuid": "75d22281ae0c460ab81945d4b6549abe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/75d22281ae0c460ab81945d4b6549abe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/75d22281ae0c460ab81945d4b6549abe"}}, "title": "Toward an Integrated Machine Learning Model of a Proteomics Experiment.", "authors": [{"family": "Neely", "given": "Benjamin A", "initials": "BA", "orcid": "0000-0001-6120-7695", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6942cadc06104793927194f19aa57a8d.json"}}, {"family": "Dorfer", "given": "Viktoria", "initials": "V", "orcid": "0000-0002-5332-5701", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2a0a15b0b2945238e7a39343b5c2a29.json"}}, {"family": "Martens", "given": "Lennart", "initials": "L", "orcid": "0000-0003-4277-658X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/df9a736ba6d04cbdb881a040480bf6f0.json"}}, {"family": "Bludau", "given": "Isabell", "initials": "I"}, {"family": "Bouwmeester", "given": "Robbin", "initials": "R", "orcid": "0000-0001-6807-7029", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd945733eeaf46d895f9d8799b430d66.json"}}, {"family": "Degroeve", "given": "Sven", "initials": "S", "orcid": "0000-0001-8349-3370", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/99e10b1c63144945aa258d810ddbb090.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Gessulat", "given": "Siegfried", "initials": "S"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Palczynski", "given": "Pawel", "initials": "P"}, {"family": "Payne", "given": "Samuel H", "initials": "SH", "orcid": "0000-0002-8351-1994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe701ec4cf24456980c1902ec61a0ab1.json"}}, {"family": "Rehfeldt", "given": "Tobias Greisager", "initials": "TG", "orcid": "0000-0002-1190-9485", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9671e5e2b13f40e293e935c355e68d2a.json"}}, {"family": "Schmidt", "given": "Tobias", "initials": "T", "orcid": "0000-0002-1883-6514", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d612bc6bfdce4e968b76abbd88a7603d.json"}}, {"family": "Schw\u00e4mmle", "given": "Veit", "initials": "V", "orcid": "0000-0002-9708-6722", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/158e08b0cfd34f90882f66142d8e62b7.json"}}, {"family": "Uszkoreit", "given": "Julian", "initials": "J", "orcid": "0000-0001-7522-4007", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/97c6efaaa4f045a7a718ca2ba376f641.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": "Wilhelm", "given": "Mathias", "initials": "M", "orcid": "0000-0002-9224-3258", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2eda8473072c48639cbd09676ed17cfe.json"}}, {"family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c.json"}}], "type": "journal article", "published": "2023-03-03", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "22", "issue": "3", "pages": "681-696", "issn-l": "1535-3893"}, "abstract": "In recent years machine learning has made extensive progress in modeling many aspects of mass spectrometry data. We brought together proteomics data generators, repository managers, and machine learning experts in a workshop with the goals to evaluate and explore machine learning applications for realistic modeling of data from multidimensional mass spectrometry-based proteomics analysis of any sample or organism. Following this sample-to-data roadmap helped identify knowledge gaps and define needs. Being able to generate bespoke and realistic synthetic data has legitimate and important uses in system suitability, method development, and algorithm benchmarking, while also posing critical ethical questions. The interdisciplinary nature of the workshop informed discussions of what is currently possible and future opportunities and challenges. In the following perspective we summarize these discussions in the hope of conveying our excitement about the potential of machine learning in proteomics and to inspire future research.", "doi": "10.1021/acs.jproteome.2c00711", "pmid": "36744821", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9990124"}], "notes": [], "created": "2026-08-20T08:11:44.566Z", "modified": "2026-08-20T08:11:45.110Z"}]}