{"entity": "researcher", "timestamp": "2026-08-20T20:45:18.643Z", "family": "Van Eyk", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0001-9050-148X", "affiliations": ["Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women's Heart Center , Cedars-Sinai Medical Center , Los Angeles , California 90048 , United States."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e2a63243b3f4e14959dad947be60cb2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e2a63243b3f4e14959dad947be60cb2"}}, "publications": [{"entity": "publication", "iuid": "397f4f28164a4198b37916aac346c8cc", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/397f4f28164a4198b37916aac346c8cc.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/397f4f28164a4198b37916aac346c8cc"}}, "title": "A standardized framework for circulating blood proteomics.", "authors": [{"family": "Cai", "given": "Xue", "initials": "X"}, {"family": "Geyer", "given": "Philipp E", "initials": "PE"}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y"}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS"}, {"family": "Dong", "given": "Lianhua", "initials": "L"}, {"family": "Winkler", "given": "Robert", "initials": "R", "orcid": "0000-0001-6732-1958", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/03391a12e21d476daaabc9f0eb4c7d40.json"}}, {"family": "Ahadi", "given": "Sara", "initials": "S"}, {"family": "L\u00f6ssl", "given": "Philip", "initials": "P"}, {"family": "Yu", "given": "Xiaobo", "initials": "X"}, {"family": "Chang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-0361-2438", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6abdb99d9c504d34ac8eb17b5506007d.json"}}, {"family": "Ralser", "given": "Markus", "initials": "M", "orcid": "0000-0001-9535-7413", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3bd2e773cef04695ae85ab6646092c9f.json"}}, {"family": "Jimenez", "given": "Connie R", "initials": "CR"}, {"family": "Zhao", "given": "Yang", "initials": "Y"}, {"family": "Chen", "given": "Yu-Ju", "initials": "YJ"}, {"family": "Poon", "given": "Terence C W", "initials": "TCW"}, {"family": "Bache", "given": "Nicolai", "initials": "N"}, {"family": "Shi", "given": "Leming", "initials": "L", "orcid": "0000-0002-2981-4150", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7eb9403fed44eaa67bebe95b6a5e47.json"}}, {"family": "Dai", "given": "Xinhua", "initials": "X"}, {"family": "Wang", "given": "Ziyue", "initials": "Z"}, {"family": "Zhu", "given": "Yi", "initials": "Y", "orcid": "0000-0003-0429-0802", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccc6070e71c647048cb05efe30756a14.json"}}, {"family": "Fang", "given": "Xiang", "initials": "X"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.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": "V\u00f6lker", "given": "Uwe", "initials": "U", "orcid": "0000-0002-5689-3448", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68bb357d1344475596bf14ca926fdac5.json"}}, {"family": "Guo", "given": "Tiannan", "initials": "T", "orcid": "0000-0003-3869-7651", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/730482798d584ac8b5d30f4450ad24ad.json"}}], "type": "journal article", "published": "2025-10-00", "journal": {"title": "Nat. Genet.", "issn": "1546-1718", "volume": "57", "issue": "10", "pages": "2371-2380", "issn-l": "1061-4036"}, "abstract": "The circulating blood proteome holds immense potential for biomarker discovery and understanding disease mechanisms. Notable advances in mass spectrometry and affinity-based technologies have been made, but data integration across studies and platforms is hindered by the absence of unified analytical standards. This limitation impedes comprehensive exploration of human biology across diverse phenotypes and cohorts as well as the translation of findings into clinical applications. The disparities between datasets, stemming from a combination of factors related to differences in sample collection, pre-analytical handling, measurement methods and instrumentation, further complicate data integration. In this Perspective, we outline key challenges in blood-based proteomics and propose actionable strategies. Central to our recommendations are high-quality, technology-agnostic reference samples, which can bridge disparate datasets and enable robust cross-study comparisons. By fostering interconnected investigations across proteomic technologies, blood sample collections, clinical phenotypes and different populations, these references will accelerate the field and its translation.", "doi": "10.1038/s41588-025-02319-7", "pmid": "40987950", "labels": [], "xrefs": [{"db": "pii", "key": "10.1038/s41588-025-02319-7"}], "notes": [], "created": "2026-08-20T09:00:20.767Z", "modified": "2026-08-20T09:00:21.026Z"}, {"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"}]}