{"entity": "researcher", "timestamp": "2026-08-20T21:02:48.714Z", "family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "affiliations": ["Institute for Systems Biology, Seattle, Washington 98109, United States."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4"}}, "publications": [{"entity": "publication", "iuid": "47fd732a27064ac6ad542fa347d7dc8b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/47fd732a27064ac6ad542fa347d7dc8b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/47fd732a27064ac6ad542fa347d7dc8b"}}, "title": "The Circulating Proteome\u2500Technological Developments, Current Challenges, and Future Trends.", "authors": [{"family": "Geyer", "given": "Philipp E", "initials": "PE", "orcid": "0000-0001-7980-4826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d69184685884e28ac1557b8bf354920.json"}}, {"family": "Hornburg", "given": "Daniel", "initials": "D", "orcid": "0000-0002-6618-7774", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0cee5a39e5314a03ab14899eff0f9b11.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M"}, {"family": "Hauck", "given": "Stefanie M", "initials": "SM", "orcid": "0000-0002-1630-6827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c34e958b66ea4d4f90bc5d77a1ef2fbb.json"}}, {"family": "Palaniappan", "given": "Krishnan K", "initials": "KK", "orcid": "0000-0003-0203-9016", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ad180add9d14755b44834d00ea88fb4.json"}}, {"family": "Albrecht", "given": "Vincent", "initials": "V"}, {"family": "Dagley", "given": "Laura F", "initials": "LF", "orcid": "0000-0003-4171-3712", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/37484d809bd244978484d49d685d5520.json"}}, {"family": "Moritz", "given": "Robert L", "initials": "RL"}, {"family": "Yu", "given": "Xiaobo", "initials": "X"}, {"family": "Edfors", "given": "Fredrik", "initials": "F"}, {"family": "Vandenbrouck", "given": "Yves", "initials": "Y", "orcid": "0000-0002-1292-373X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ed616edf97c454aa6b79c56e565ce64.json"}}, {"family": "Mueller-Reif", "given": "Johannes B", "initials": "JB"}, {"family": "Sun", "given": "Zhi", "initials": "Z"}, {"family": "Brun", "given": "Virginie", "initials": "V", "orcid": "0000-0002-9098-8707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/075e825949ea4031bbcf6a2449ce1051.json"}}, {"family": "Ahadi", "given": "Sara", "initials": "S"}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8271c48d1bc6477ca3ba90d05d3854ad.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}], "type": "journal article", "published": "2024-12-06", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "23", "issue": "12", "pages": "5279-5295", "issn-l": "1535-3893"}, "abstract": "Recent improvements in proteomics technologies have fundamentally altered our capacities to characterize human biology. There is an ever-growing interest in using these novel methods for studying the circulating proteome, as blood offers an accessible window into human health. However, every methodological innovation and analytical progress calls for reassessing our existing approaches and routines to ensure that the new data will add value to the greater biomedical research community and avoid previous errors. As representatives of HUPO's Human Plasma Proteome Project (HPPP), we present our 2024 survey of the current progress in our community, including the latest build of the Human Plasma Proteome PeptideAtlas that now comprises 4608 proteins detected in 113 data sets. We then discuss the updates of established proteomics methods, emerging technologies, and investigations of proteoforms, protein networks, extracellualr vesicles, circulating antibodies and microsamples. Finally, we provide a prospective view of using the current and emerging proteomics tools in studies of circulating proteins.", "doi": "10.1021/acs.jproteome.4c00586", "pmid": "39479990", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11629384"}], "notes": [], "created": "2026-08-20T08:11:51.037Z", "modified": "2026-08-20T08:11:51.256Z"}, {"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": "cf131f18e0054b35903421a1b0de6f39", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cf131f18e0054b35903421a1b0de6f39.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cf131f18e0054b35903421a1b0de6f39"}}, "title": "A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics.", "authors": [{"family": "Luo", "given": "Xiyang", "initials": "X"}, {"family": "Bittremieux", "given": "Wout", "initials": "W", "orcid": "0000-0002-3105-1359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e740b95ac84bb6ad8f3ff159aece03.json"}}, {"family": "Griss", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2206-9511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b001048c5a5148bdb9bd16ff46e067db.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Levitsky", "given": "Lev I", "initials": "LI", "orcid": "0000-0002-4048-0876", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d992ceb2e30945529ee9200b4fe306c9.json"}}, {"family": "Ivanov", "given": "Mark V", "initials": "MV", "orcid": "0000-0003-4762-2846", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd0d8592597c43eea8a122dd2ac128b5.json"}}, {"family": "Bubis", "given": "Julia A", "initials": "JA", "orcid": "0000-0002-4895-6146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1face4f1b57e4bddafffb09013e3e07c.json"}}, {"family": "Gabriels", "given": "Ralf", "initials": "R", "orcid": "0000-0002-1679-1711", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30094adc291549c28c6c74cbeb9aacd2.json"}}, {"family": "Webel", "given": "Henry", "initials": "H"}, {"family": "Sanchez", "given": "Aniel", "initials": "A"}, {"family": "Bai", "given": "Mingze", "initials": "M"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L"}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}], "type": "journal article", "published": "2022-06-03", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "21", "issue": "6", "pages": "1566-1574", "issn-l": "1535-3893"}, "abstract": "Spectrum clustering is a powerful strategy to minimize redundant mass spectra by grouping them based on similarity, with the aim of forming groups of mass spectra from the same repeatedly measured analytes. Each such group of near-identical spectra can be represented by its so-called consensus spectrum for downstream processing. Although several algorithms for spectrum clustering have been adequately benchmarked and tested, the influence of the consensus spectrum generation step is rarely evaluated. Here, we present an implementation and benchmark of common consensus spectrum algorithms, including spectrum averaging, spectrum binning, the most similar spectrum, and the best-identified spectrum. We have analyzed diverse public data sets using two different clustering algorithms (spectra-cluster and MaRaCluster) to evaluate how the consensus spectrum generation procedure influences downstream peptide identification. The BEST and BIN methods were found the most reliable methods for consensus spectrum generation, including for data sets with post-translational modifications (PTM) such as phosphorylation. All source code and data of the present study are freely available on GitHub at https://github.com/statisticalbiotechnology/representative-spectra-benchmark.", "doi": "10.1021/acs.jproteome.2c00069", "pmid": "35549218", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9171829"}], "notes": [], "created": "2026-08-20T08:11:35.592Z", "modified": "2026-08-20T08:11:35.948Z"}, {"entity": "publication", "iuid": "245bd5639e1f4d64ac139e92715c8495", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/245bd5639e1f4d64ac139e92715c8495.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/245bd5639e1f4d64ac139e92715c8495"}}, "title": "A comprehensive evaluation of consensus spectrum generation methods in proteomics", "authors": [{"family": "Luo", "given": "Xiyang", "initials": "X"}, {"family": "Bittremieux", "given": "Wout", "initials": "W", "orcid": "0000-0002-3105-1359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/07e740b95ac84bb6ad8f3ff159aece03.json"}}, {"family": "Griss", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2206-9511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b001048c5a5148bdb9bd16ff46e067db.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Levitsky", "given": "Lev I", "initials": "LI", "orcid": "0000-0002-4048-0876", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d992ceb2e30945529ee9200b4fe306c9.json"}}, {"family": "Ivanov", "given": "Mark V", "initials": "MV", "orcid": "0000-0003-4762-2846", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cd0d8592597c43eea8a122dd2ac128b5.json"}}, {"family": "Bubis", "given": "Julia A", "initials": "JA", "orcid": "0000-0002-4895-6146", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1face4f1b57e4bddafffb09013e3e07c.json"}}, {"family": "Gabriels", "given": "Ralf", "initials": "R", "orcid": "0000-0002-1679-1711", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/30094adc291549c28c6c74cbeb9aacd2.json"}}, {"family": "Webel", "given": "Henry", "initials": "H", "orcid": "0000-0001-8833-7617", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b16b0288b71a4c37a9d3c0cee30a16bf.json"}}, {"family": "Sanchez", "given": "Aniel", "initials": "A", "orcid": "0000-0002-0278-8802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e38a8f60ffc14ab18499396cbf8595a8.json"}}, {"family": "Bai", "given": "Mingze", "initials": "M", "orcid": "0000-0002-9782-2056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb01c19bbd9c4a96950d782fc71db8b9.json"}}, {"family": "Kall", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}], "type": "posted-content", "published": "2022-01-27", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.01.25.477699", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:09:16.755Z", "modified": "2026-08-20T10:09:17.065Z"}, {"entity": "publication", "iuid": "209b1e6bec59490f9922fab7244b452a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/209b1e6bec59490f9922fab7244b452a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/209b1e6bec59490f9922fab7244b452a"}}, "title": "Advances and Utility of the Human Plasma Proteome.", "authors": [{"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8271c48d1bc6477ca3ba90d05d3854ad.json"}}, {"family": "Sun", "given": "Zhi", "initials": "Z", "orcid": "0000-0003-3324-6851", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5076a80c046441482472dea34610eb6.json"}}, {"family": "Maes", "given": "Michal", "initials": "M", "orcid": "0000-0002-7406-3982", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81e9fc09132c4e5685870c00b35717ea.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c34e0806a3d142019ae8e16de8d720ef.json"}}, {"family": "Palaniappan", "given": "Krishnan K", "initials": "KK", "orcid": "0000-0003-0203-9016", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ad180add9d14755b44834d00ea88fb4.json"}}, {"family": "Letunica", "given": "Natasha", "initials": "N", "orcid": "0000-0003-3604-1536", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ca1b9a786b064d6aa7b8c68331fc25f0.json"}}, {"family": "Vandenbrouck", "given": "Yves", "initials": "Y", "orcid": "0000-0002-1292-373X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1ed616edf97c454aa6b79c56e565ce64.json"}}, {"family": "Brun", "given": "Virginie", "initials": "V", "orcid": "0000-0002-9098-8707", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/075e825949ea4031bbcf6a2449ce1051.json"}}, {"family": "Tao", "given": "Sheng-Ce", "initials": "SC", "orcid": "0000-0002-9210-1823", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95665a9e4ff6496dbe47132ddf08ef3b.json"}}, {"family": "Yu", "given": "Xiaobo", "initials": "X"}, {"family": "Geyer", "given": "Philipp E", "initials": "PE", "orcid": "0000-0001-7980-4826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d69184685884e28ac1557b8bf354920.json"}}, {"family": "Ignjatovic", "given": "Vera", "initials": "V", "orcid": "0000-0002-5548-5813", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8fa9f5752da349a79a4969866f014edb.json"}}, {"family": "Moritz", "given": "Robert L", "initials": "RL", "orcid": "0000-0002-3216-9447", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/505eb37634de49d4b6a29f41c18f142b.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}], "type": "journal article", "published": "2021-12-03", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "20", "issue": "12", "pages": "5241-5263", "issn-l": "1535-3893"}, "abstract": "The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophysiology. Here we provide views and perspectives about technological developments and possible clinical applications that use mass-spectrometry(MS)- or affinity-based methods. We discuss examples where plasma proteomics contributed valuable insights into SARS-CoV-2 infections, aging, and hemostasis and the opportunities offered by combining proteomics with genetic data. As a contribution to the Human Proteome Organization (HUPO) Human Plasma Proteome Project (HPPP), we present the Human Plasma PeptideAtlas build 2021-07 that comprises 4395 canonical and 1482 additional nonredundant human proteins detected in 240 MS-based experiments. In addition, we report the new Human Extracellular Vesicle PeptideAtlas 2021-06, which comprises five studies and 2757 canonical proteins detected in extracellular vesicles circulating in blood, of which 74% (2047) are in common with the plasma PeptideAtlas. Our overview summarizes the recent advances, impactful applications, and ongoing challenges for translating plasma proteomics into utility for precision medicine.", "doi": "10.1021/acs.jproteome.1c00657", "pmid": "34672606", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1833436"}, {"db": "pmc", "key": "PMC9469506"}], "notes": [], "created": "2026-08-20T08:11:22.145Z", "modified": "2026-08-20T08:11:22.712Z"}, {"entity": "publication", "iuid": "3709fd60c019405fa8ed8899d8abaaa1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3709fd60c019405fa8ed8899d8abaaa1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3709fd60c019405fa8ed8899d8abaaa1"}}, "title": "Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project.", "authors": [{"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8271c48d1bc6477ca3ba90d05d3854ad.json"}}, {"family": "Lane", "given": "Lydie", "initials": "L"}, {"family": "Overall", "given": "Christopher M", "initials": "CM", "orcid": "0000-0001-5844-2731", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e5d78d8a93d94dab97f8c5d16406d1e7.json"}}, {"family": "Corrales", "given": "Fernando J", "initials": "FJ"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Paik", "given": "Young-Ki", "initials": "YK", "orcid": "0000-0002-8146-1751", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/24672947114a44b39c30f018bb5aa01d.json"}}, {"family": "Van Eyk", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0001-9050-148X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e2a63243b3f4e14959dad947be60cb2.json"}}, {"family": "Liu", "given": "Siqi", "initials": "S", "orcid": "0000-0001-9744-3681", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ab48f31a2fb843ab9dd6b41cc305acf2.json"}}, {"family": "Pennington", "given": "Stephen", "initials": "S"}, {"family": "Snyder", "given": "Michael P", "initials": "MP"}, {"family": "Baker", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-5858-4035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1128bdda3cb4fababf5a938c2a94c16.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}], "type": "journal article", "published": "2019-12-06", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "18", "issue": "12", "pages": "4098-4107", "issn-l": "1535-3893"}, "abstract": "The Human Proteome Project (HPP) annually reports on progress made throughout the field in credibly identifying and characterizing the complete human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2019-01-11 contains 17 694 proteins with strong protein-level evidence (PE1), compliant with HPP Guidelines for Interpretation of MS Data v2.1; these represent 89% of all 19 823 neXtProt predicted coding genes (all PE1,2,3,4 proteins), up from 17 470 one year earlier. Conversely, the number of neXtProt PE2,3,4 proteins, termed the \"missing proteins\" (MPs), has been reduced from 2949 to 2129 since 2016 through efforts throughout the community, including the chromosome-centric HPP. PeptideAtlas is the source of uniformly reanalyzed raw mass spectrometry data for neXtProt; PeptideAtlas added 495 canonical proteins between 2018 and 2019, especially from studies designed to detect hard-to-identify proteins. Meanwhile, the Human Protein Atlas has released version 18.1 with immunohistochemical evidence of expression of 17 000 proteins and survival plots as part of the Pathology Atlas. Many investigators apply multiplexed SRM-targeted proteomics for quantitation of organ-specific popular proteins in studies of various human diseases. The 19 teams of the Biology and Disease-driven B/D-HPP published a total of 160 publications in 2018, bringing proteomics to a broad array of biomedical research.", "doi": "10.1021/acs.jproteome.9b00434", "pmid": "31430157", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1058401"}, {"db": "pmc", "key": "PMC6898754"}], "notes": [], "created": "2026-08-20T08:12:25.022Z", "modified": "2026-08-20T08:12:25.276Z"}, {"entity": "publication", "iuid": "75426557b80e4c05ade1bd35825841cf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/75426557b80e4c05ade1bd35825841cf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/75426557b80e4c05ade1bd35825841cf"}}, "title": "Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data", "authors": [{"family": "Ignjatovic", "given": "Vera", "initials": "V", "orcid": "0000-0002-5548-5813", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8fa9f5752da349a79a4969866f014edb.json"}}, {"family": "Geyer", "given": "Philipp E", "initials": "PE", "orcid": "0000-0001-7980-4826", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d69184685884e28ac1557b8bf354920.json"}}, {"family": "Palaniappan", "given": "Krishnan K", "initials": "KK", "orcid": "0000-0003-0203-9016", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ad180add9d14755b44834d00ea88fb4.json"}}, {"family": "Chaaban", "given": "Jessica E", "initials": "JE"}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8271c48d1bc6477ca3ba90d05d3854ad.json"}}, {"family": "Baker", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-5858-4035", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1128bdda3cb4fababf5a938c2a94c16.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}], "type": "posted-content", "published": "2019-07-26", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/716563", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:14:30.875Z", "modified": "2026-08-20T11:14:30.958Z"}, {"entity": "publication", "iuid": "ea525cca041145b7bdfe210040715780", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ea525cca041145b7bdfe210040715780.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ea525cca041145b7bdfe210040715780"}}, "title": "Expanding the Use of Spectral Libraries in Proteomics.", "authors": [{"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}, {"family": "Chalkley", "given": "Robert J", "initials": "RJ"}, {"family": "Wilhelm", "given": "Mathias", "initials": "M", "orcid": "0000-0002-9224-3258", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2eda8473072c48639cbd09676ed17cfe.json"}}, {"family": "Tate", "given": "Stephen", "initials": "S"}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Walzer", "given": "Mathias", "initials": "M"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4464f2bf868498fa6d149a4a6d60e8b.json"}}, {"family": "Delanghe", "given": "Bernard", "initials": "B"}, {"family": "B\u00f6cker", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-9304-8091", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c71ab14b72a540f3be202f873d6c7dea.json"}}, {"family": "Schymanski", "given": "Emma L", "initials": "EL", "orcid": "0000-0001-6868-8145", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc533a4744624b80960f4cf28cabdd64.json"}}, {"family": "Wilmes", "given": "Paul", "initials": "P", "orcid": "0000-0002-6478-2924", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e169727cc0f9482baf98944388a77b24.json"}}, {"family": "Dorfer", "given": "Viktoria", "initials": "V", "orcid": "0000-0002-5332-5701", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b2a0a15b0b2945238e7a39343b5c2a29.json"}}, {"family": "Kuster", "given": "Bernhard", "initials": "B", "orcid": "0000-0002-9094-1677", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5196477f29b345ccb3f4a8fc32c9fac4.json"}}, {"family": "Volders", "given": "Pieter-Jan", "initials": "PJ", "orcid": "0000-0002-2685-2637", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6fac44563b164dae90052b9764a8f9ab.json"}}, {"family": "Jehmlich", "given": "Nico", "initials": "N", "orcid": "0000-0002-5638-6868", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1c3e5702c6740c6a4d553b60eee62e3.json"}}, {"family": "Vissers", "given": "Johannes P C", "initials": "JPC", "orcid": "0000-0001-6283-8456", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3cde55fba2234534a8ce709f13478e42.json"}}, {"family": "Wolan", "given": "Dennis W", "initials": "DW", "orcid": "0000-0001-9879-8353", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/635cea76374a4c90a9514aa845b7f59c.json"}}, {"family": "Wang", "given": "Ana Y", "initials": "AY"}, {"family": "Mendoza", "given": "Luis", "initials": "L", "orcid": "0000-0003-0128-8643", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b6e8a7feab0f481eaf6acd7ec097c5c5.json"}}, {"family": "Shofstahl", "given": "Jim", "initials": "J"}, {"family": "Dowsey", "given": "Andrew W", "initials": "AW", "orcid": "0000-0002-7404-9128", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a1cb70e527d84d32b1e995014007efb8.json"}}, {"family": "Griss", "given": "Johannes", "initials": "J", "orcid": "0000-0003-2206-9511", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b001048c5a5148bdb9bd16ff46e067db.json"}}, {"family": "Salek", "given": "Reza M", "initials": "RM", "orcid": "0000-0001-8604-1732", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/62799f5748ef484b816827380b723b2c.json"}}, {"family": "Neumann", "given": "Steffen", "initials": "S", "orcid": "0000-0002-7899-7192", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3fd85c99a6364305ba466010ed3012ec.json"}}, {"family": "Binz", "given": "Pierre-Alain", "initials": "PA", "orcid": "0000-0002-0045-7698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f857e16ce82b4242ab0e780c8bec9539.json"}}, {"family": "Lam", "given": "Henry", "initials": "H", "orcid": "0000-0001-7928-0364", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5f27cfbc77fe4122977457e89968814c.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": "Bandeira", "given": "Nuno", "initials": "N"}, {"family": "R\u00f6st", "given": "Hannes", "initials": "H", "orcid": "0000-0003-0990-7488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4579af772375404da76c447b23c658a3.json"}}], "type": "journal article", "published": "2018-12-07", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "17", "issue": "12", "pages": "4051-4060", "issn-l": "1535-3893"}, "abstract": "The 2017 Dagstuhl Seminar on Computational Proteomics provided an opportunity for a broad discussion on the current state and future directions of the generation and use of peptide tandem mass spectrometry spectral libraries. Their use in proteomics is growing slowly, but there are multiple challenges in the field that must be addressed to further increase the adoption of spectral libraries and related techniques. The primary bottlenecks are the paucity of high quality and comprehensive libraries and the general difficulty of adopting spectral library searching into existing workflows. There are several existing spectral library formats, but none captures a satisfactory level of metadata; therefore, a logical next improvement is to design a more advanced, Proteomics Standards Initiative-approved spectral library format that can encode all of the desired metadata. The group discussed a series of metadata requirements organized into three designations of completeness or quality, tentatively dubbed bronze, silver, and gold. The metadata can be organized at four different levels of granularity: at the collection (library) level, at the individual entry (peptide ion) level, at the peak (fragment ion) level, and at the peak annotation level. Strategies for encoding mass modifications in a consistent manner and the requirement for encoding high-quality and commonly seen but as-yet-unidentified spectra were discussed. The group also discussed related topics, including strategies for comparing two spectra, techniques for generating representative spectra for a library, approaches for selection of optimal signature ions for targeted workflows, and issues surrounding the merging of two or more libraries into one. We present here a review of this field and the challenges that the community must address in order to accelerate the adoption of spectral libraries in routine analysis of proteomics datasets.", "doi": "10.1021/acs.jproteome.8b00485", "pmid": "30270626", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS1015163"}, {"db": "pmc", "key": "PMC6443480"}], "notes": [], "created": "2026-08-20T08:12:14.655Z", "modified": "2026-08-20T08:12:15.306Z"}, {"entity": "publication", "iuid": "3aeab20114a3467483643835ca64047f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3aeab20114a3467483643835ca64047f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3aeab20114a3467483643835ca64047f"}}, "title": "Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project.", "authors": [{"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8271c48d1bc6477ca3ba90d05d3854ad.json"}}, {"family": "Lane", "given": "Lydie", "initials": "L"}, {"family": "Lundberg", "given": "Emma K", "initials": "EK"}, {"family": "Overall", "given": "Christopher M", "initials": "CM"}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2463c206245a4dbb979cad9d201d73c4.json"}}], "type": "journal article", "published": "2017-12-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "16", "issue": "12", "pages": "4281-4287", "issn-l": "1535-3893"}, "abstract": "The Human Proteome Organization (HUPO) Human Proteome Project (HPP) continues to make progress on its two overall goals: (1) completing the protein parts list, with an annual update of the HUPO draft human proteome, and (2) making proteomics an integrated complement to genomics and transcriptomics throughout biomedical and life sciences research. neXtProt version 2017-01-23 has 17 008 confident protein identifications (Protein Existence [PE] level 1) that are compliant with the HPP Guidelines v2.1 ( https://hupo.org/Guidelines ), up from 13 664 in 2012-12 and 16 518 in 2016-04. Remaining to be found by mass spectrometry and other methods are 2579 \"missing proteins\" (PE2+3+4), down from 2949 in 2016. PeptideAtlas 2017-01 has 15 173 canonical proteins, accounting for nearly all of the 15 290 PE1 proteins based on MS data. These resources have extensive data on PTMs, single amino acid variants, and splice isoforms. The Human Protein Atlas v16 has 10 492 highly curated protein entries with tissue and subcellular spatial localization of proteins and transcript expression. Organ-specific popular protein lists have been generated for broad use in quantitative targeted proteomics using SRM-MS or DIA-SWATH-MS studies of biology and disease.", "doi": "10.1021/acs.jproteome.7b00375", "pmid": "28853897", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS950868"}, {"db": "pmc", "key": "PMC5872831"}], "notes": [], "created": "2026-08-20T08:12:10.737Z", "modified": "2026-08-20T08:12:10.808Z"}]}