{"entity": "researcher", "timestamp": "2026-08-20T20:48:37.960Z", "family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "affiliations": ["Center for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c"}}, "publications": [{"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"}, {"entity": "publication", "iuid": "6b3c9d1faf054f2caf91c423ec008722", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6b3c9d1faf054f2caf91c423ec008722.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6b3c9d1faf054f2caf91c423ec008722"}}, "title": "Interpretation of the DOME Recommendations for Machine Learning in Proteomics and Metabolomics.", "authors": [{"family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c.json"}}, {"family": "B\u00f6cker", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-9304-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c71ab14b72a540f3be202f873d6c7dea.json"}}, {"family": "Degroeve", "given": "Sven", "initials": "S"}, {"family": "Kohlbacher", "given": "Oliver", "initials": "O", "orcid": "0000-0003-1739-4598", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9317a8da5d9d4df782158d7555f229eb.json"}}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Noble", "given": "William Stafford", "initials": "WS", "orcid": "0000-0001-7283-4715", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/77bfbf9a1a8242b8955c8dd9f5642a8b.json"}}, {"family": "Wilhelm", "given": "Mathias", "initials": "M", "orcid": "0000-0002-9224-3258", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2eda8473072c48639cbd09676ed17cfe.json"}}], "type": "journal article", "published": "2022-04-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "21", "issue": "4", "pages": "1204-1207", "issn-l": "1535-3893"}, "abstract": "Machine learning is increasingly applied in proteomics and metabolomics to predict molecular structure, function, and physicochemical properties, including behavior in chromatography, ion mobility, and tandem mass spectrometry. These must be described in sufficient detail to apply or evaluate the performance of trained models. Here we look at and interpret the recently published and general DOME (Data, Optimization, Model, Evaluation) recommendations for conducting and reporting on machine learning in the specific context of proteomics and metabolomics.", "doi": "10.1021/acs.jproteome.1c00900", "pmid": "35119864", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8981311"}], "notes": [], "created": "2026-08-20T08:11:33.301Z", "modified": "2026-08-20T08:11:33.445Z"}, {"entity": "publication", "iuid": "bcc3ce0b92d346ef938cd492f9ee633e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bcc3ce0b92d346ef938cd492f9ee633e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bcc3ce0b92d346ef938cd492f9ee633e"}}, "title": "A protein standard that emulates homology for the characterization of protein inference algorithms", "authors": [{"family": "The", "given": "Matthew", "initials": "M", "orcid": "0000-0002-5401-5553", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8d7d850ed24f92b9506b203ca63ed1.json"}}, {"family": "Edfors", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0017-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9e213b04f8984c8eb00c68f5bc2f6a36.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}, {"family": "Payne", "given": "Samuel H", "initials": "SH", "orcid": "0000-0002-8351-1994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fe701ec4cf24456980c1902ec61a0ab1.json"}}, {"family": "Hoopmann", "given": "Michael R", "initials": "MR", "orcid": "0000-0001-7029-7792", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/04f75056428f499d9806d2fd85d50e9a.json"}}, {"family": "Palmblad", "given": "Magnus", "initials": "M", "orcid": "0000-0002-5865-8994", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80053e2256cd4e55afc7ba916821602c.json"}}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}], "type": "posted-content", "published": "2017-12-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/236471", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:08:00.975Z", "modified": "2026-08-20T11:08:01.125Z"}]}