{"entity": "researcher", "timestamp": "2026-08-20T21:15:11.858Z", "family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "affiliations": ["Institute for Systems Biology, Seattle, Washington 98109, United States.", "Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109-2218, United States."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8271c48d1bc6477ca3ba90d05d3854ad.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8271c48d1bc6477ca3ba90d05d3854ad"}}, "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": "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": "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"}]}