{"entity": "researcher", "timestamp": "2026-10-05T21:48:45.187Z", "family": "Baker", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-5858-4035", "affiliations": ["Faculty of Medicine, Health and Human Sciences, Department of Biomedical Sciences, Macquarie University, North Ryde, NSW, 2109, Australia. mark.baker@mq.edu.au.", "Department of Genetics, Stanford School of Medicine, Stanford, CA, 94305, USA. mark.baker@mq.edu.au."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/c4620f71cdce4e6e91264f96b74c6d84.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/c4620f71cdce4e6e91264f96b74c6d84"}}, "publications": [{"entity": "publication", "iuid": "3b8d1f21730c444f9488bdde02b7966a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3b8d1f21730c444f9488bdde02b7966a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3b8d1f21730c444f9488bdde02b7966a"}}, "title": "A high-stringency blueprint of the human proteome.", "authors": [{"family": "Adhikari", "given": "Subash", "initials": "S"}, {"family": "Nice", "given": "Edouard C", "initials": "EC"}, {"family": "Deutsch", "given": "Eric W", "initials": "EW"}, {"family": "Lane", "given": "Lydie", "initials": "L", "orcid": "0000-0002-9818-3030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0992244993b4f0799f58c63f39a5c5e.json"}}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications.scilifelab.se/researcher/c434ae7226ff49e8b00a33c37a46dd60.json"}}, {"family": "Pennington", "given": "Stephen R", "initials": "SR"}, {"family": "Paik", "given": "Young-Ki", "initials": "YK"}, {"family": "Overall", "given": "Christopher M", "initials": "CM", "orcid": "0000-0001-5844-2731", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f770b082f2447fd96e1daab1b1bc4f1.json"}}, {"family": "Corrales", "given": "Fernando J", "initials": "FJ"}, {"family": "Cristea", "given": "Ileana M", "initials": "IM"}, {"family": "Van Eyk", "given": "Jennifer E", "initials": "JE", "orcid": "0000-0001-9050-148X", "researcher": {"href": "https://publications.scilifelab.se/researcher/9e860403a0224d588958a9c588688ff6.json"}}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Chan", "given": "Daniel W", "initials": "DW"}, {"family": "Bairoch", "given": "Amos", "initials": "A"}, {"family": "Waddington", "given": "James C", "initials": "JC"}, {"family": "Justice", "given": "Joshua L", "initials": "JL"}, {"family": "LaBaer", "given": "Joshua", "initials": "J"}, {"family": "Rodriguez", "given": "Henry", "initials": "H"}, {"family": "He", "given": "Fuchu", "initials": "F"}, {"family": "Kostrzewa", "given": "Markus", "initials": "M"}, {"family": "Ping", "given": "Peipei", "initials": "P"}, {"family": "Gundry", "given": "Rebekah L", "initials": "RL", "orcid": "0000-0002-9263-833X", "researcher": {"href": "https://publications.scilifelab.se/researcher/60163f86086644e9a74a7793d886dd3e.json"}}, {"family": "Stewart", "given": "Peter", "initials": "P"}, {"family": "Srivastava", "given": "Sanjeeva", "initials": "S"}, {"family": "Srivastava", "given": "Sudhir", "initials": "S"}, {"family": "Nogueira", "given": "Fabio C S", "initials": "FCS"}, {"family": "Domont", "given": "Gilberto B", "initials": "GB"}, {"family": "Vandenbrouck", "given": "Yves", "initials": "Y", "orcid": "0000-0002-1292-373X", "researcher": {"href": "https://publications.scilifelab.se/researcher/16eb301087cd46c5b12bdb276fdf561b.json"}}, {"family": "Lam", "given": "Maggie P Y", "initials": "MPY"}, {"family": "Wennersten", "given": "Sara", "initials": "S"}, {"family": "Vizcaino", "given": "Juan Antonio", "initials": "JA", "orcid": "0000-0002-3905-4335", "researcher": {"href": "https://publications.scilifelab.se/researcher/9df36c9559504428a42edba7ba33ec08.json"}}, {"family": "Wilkins", "given": "Marc", "initials": "M", "orcid": "0000-0002-5700-5684", "researcher": {"href": "https://publications.scilifelab.se/researcher/98c5bc0757d145d692312da866ebf51a.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Bandeira", "given": "Nuno", "initials": "N", "orcid": "0000-0001-8385-3655", "researcher": {"href": "https://publications.scilifelab.se/researcher/d6377e04591748fc9450eaff4d41acff.json"}}, {"family": "Marko-Varga", "given": "Gyorgy", "initials": "G"}, {"family": "Weintraub", "given": "Susan T", "initials": "ST"}, {"family": "Pineau", "given": "Charles", "initials": "C"}, {"family": "Kusebauch", "given": "Ulrike", "initials": "U", "orcid": "0000-0001-6162-7577", "researcher": {"href": "https://publications.scilifelab.se/researcher/a0b4bcdb047c4b1fa84e513ea0eddd5e.json"}}, {"family": "Moritz", "given": "Robert L", "initials": "RL", "orcid": "0000-0002-3216-9447", "researcher": {"href": "https://publications.scilifelab.se/researcher/2aaa7d54f7de41cf915b47e8037c15cf.json"}}, {"family": "Ahn", "given": "Seong Beom", "initials": "SB"}, {"family": "Palmblad", "given": "Magnus", "initials": "M"}, {"family": "Snyder", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-0784-7987", "researcher": {"href": "https://publications.scilifelab.se/researcher/a2594af48f3d45e68983030873c06cf5.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications.scilifelab.se/researcher/9222eeba13464c618695f91ea8764abb.json"}}, {"family": "Baker", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-5858-4035", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4620f71cdce4e6e91264f96b74c6d84.json"}}], "type": "journal article", "published": "2020-10-16", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "11", "issue": "1", "pages": "5301", "issn-l": "2041-1723"}, "abstract": "The Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP) in 2010, creating an international framework for global collaboration, data sharing, quality assurance and enhancing accurate annotation of the genome-encoded proteome. During the subsequent decade, the HPP established collaborations, developed guidelines and metrics, and undertook reanalysis of previously deposited community data, continuously increasing the coverage of the human proteome. On the occasion of the HPP's tenth anniversary, we here report a 90.4% complete high-stringency human proteome blueprint. This knowledge is essential for discerning molecular processes in health and disease, as we demonstrate by highlighting potential roles the human proteome plays in our understanding, diagnosis and treatment of cancers, cardiovascular and infectious diseases.", "doi": "10.1038/s41467-020-19045-9", "pmid": "33067450", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-020-19045-9"}, {"db": "pmc", "key": "PMC7568584"}], "notes": [], "created": "2020-12-10T19:07:09.284Z", "modified": "2021-11-10T12:46:20.338Z"}, {"entity": "publication", "iuid": "b62b4fc2be7544fca04f5423b2db9c18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b62b4fc2be7544fca04f5423b2db9c18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b62b4fc2be7544fca04f5423b2db9c18"}}, "title": "Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data.", "authors": [{"family": "Ignjatovic", "given": "Vera", "initials": "V"}, {"family": "Geyer", "given": "Philipp E", "initials": "PE"}, {"family": "Palaniappan", "given": "Krishnan K", "initials": "KK", "orcid": "0000-0003-0203-9016", "researcher": {"href": "https://publications.scilifelab.se/researcher/e9e72f6b9b9f4dcc8aa79af3129a000c.json"}}, {"family": "Chaaban", "given": "Jessica E", "initials": "JE"}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications.scilifelab.se/researcher/c434ae7226ff49e8b00a33c37a46dd60.json"}}, {"family": "Baker", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-5858-4035", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4620f71cdce4e6e91264f96b74c6d84.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications.scilifelab.se/researcher/aada71c99b5b4364855e193e3a719d39.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2019-12-06", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "18", "issue": "12", "pages": "4085-4097", "issn-l": "1535-3893"}, "abstract": "The proteomic analysis of human blood and blood-derived products (e.g., plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g., interindividual variability) and analysis of biospecimens (e.g., sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing, and bioinformatic analysis. With exciting opportunities in studying human health and disease though this plasma proteomics pipeline, a more informed analysis of human plasma will accelerate interest while enhancing possibilities for the incorporation of proteomics-scaled assays into clinical practice.", "doi": "10.1021/acs.jproteome.9b00503", "pmid": "31573204", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6898750"}, {"db": "mid", "key": "NIHMS1055853"}], "notes": [], "created": "2020-01-08T14:59:07.436Z", "modified": "2021-07-08T12:07:33.913Z"}, {"entity": "publication", "iuid": "1263f853e1fc4fe2bbea2d67c6ef7058", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1263f853e1fc4fe2bbea2d67c6ef7058.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1263f853e1fc4fe2bbea2d67c6ef7058"}}, "title": "Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project.", "authors": [{"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications.scilifelab.se/researcher/c434ae7226ff49e8b00a33c37a46dd60.json"}}, {"family": "Lane", "given": "Lydie", "initials": "L", "orcid": "0000-0002-9818-3030", "researcher": {"href": "https://publications.scilifelab.se/researcher/c0992244993b4f0799f58c63f39a5c5e.json"}}, {"family": "Overall", "given": "Christopher M", "initials": "CM", "orcid": "0000-0001-5844-2731", "researcher": {"href": "https://publications.scilifelab.se/researcher/1f770b082f2447fd96e1daab1b1bc4f1.json"}}, {"family": "Corrales", "given": "Fernando J", "initials": "FJ", "orcid": "0000-0002-0231-5159", "researcher": {"href": "https://publications.scilifelab.se/researcher/95df414dbc3a4af48b827ce3bf801565.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Paik", "given": "Young-Ki", "initials": "YK", "orcid": "0000-0002-8146-1751", "researcher": {"href": "https://publications.scilifelab.se/researcher/2f66698be6ad4916b900d074a0105386.json"}}, {"family": "Van Eyk", "given": "Jennifer E", "initials": "JE"}, {"family": "Liu", "given": "Siqi", "initials": "S", "orcid": "0000-0001-9744-3681", "researcher": {"href": "https://publications.scilifelab.se/researcher/50e0c0c26a474b73b2193ed2f2ec29af.json"}}, {"family": "Snyder", "given": "Michael", "initials": "M"}, {"family": "Baker", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-5858-4035", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4620f71cdce4e6e91264f96b74c6d84.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications.scilifelab.se/researcher/aada71c99b5b4364855e193e3a719d39.json"}}], "type": "journal article", "published": "2018-12-07", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "17", "issue": "12", "pages": "4031-4041", "issn-l": "1535-3893"}, "abstract": "The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the Journal of Proteome Research, contains 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PE1 proteins, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein-protein interaction findings. PeptideAtlas has 15 798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.", "doi": "10.1021/acs.jproteome.8b00441", "pmid": "30099871", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC6387656"}, {"db": "mid", "key": "NIHMS993890"}], "notes": [], "created": "2018-10-31T09:20:52.470Z", "modified": "2021-07-08T11:58:30.742Z"}, {"entity": "publication", "iuid": "f51fe47e221a40f89e4936c9689a725c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f51fe47e221a40f89e4936c9689a725c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f51fe47e221a40f89e4936c9689a725c"}}, "title": "The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Omenn", "given": "Gilbert S", "initials": "GS", "orcid": "0000-0002-8976-6074", "researcher": {"href": "https://publications.scilifelab.se/researcher/c434ae7226ff49e8b00a33c37a46dd60.json"}}, {"family": "Sun", "given": "Zhi", "initials": "Z"}, {"family": "Campbell", "given": "David S", "initials": "DS"}, {"family": "Baker", "given": "Mark S", "initials": "MS", "orcid": "0000-0001-5858-4035", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4620f71cdce4e6e91264f96b74c6d84.json"}}, {"family": "Overall", "given": "Christopher M", "initials": "CM"}, {"family": "Aebersold", "given": "Ruedi", "initials": "R"}, {"family": "Moritz", "given": "Robert L", "initials": "RL", "orcid": "0000-0002-3216-9447", "researcher": {"href": "https://publications.scilifelab.se/researcher/2aaa7d54f7de41cf915b47e8037c15cf.json"}}, {"family": "Deutsch", "given": "Eric W", "initials": "EW", "orcid": "0000-0001-8732-0928", "researcher": {"href": "https://publications.scilifelab.se/researcher/aada71c99b5b4364855e193e3a719d39.json"}}], "type": "historical article", "published": "2017-12-01", "journal": {"title": "J. Proteome Res.", "issn": "1535-3907", "volume": "16", "issue": "12", "pages": "4299-4310", "issn-l": "1535-3893"}, "abstract": "Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome Organization's Human Plasma Proteome Project (HPPP) has been promoting advances in the study and understanding of the full protein complement of human plasma and on determining the abundance and modifications of its components. In 2017, we review the history of the HPPP and the advances of human plasma proteomics in general, including several recent achievements. We then present the latest 2017-04 build of Human Plasma PeptideAtlas, which yields \u223c43 million peptide-spectrum matches and 122,730 distinct peptide sequences from 178 individual experiments at a 1% protein-level FDR globally across all experiments. Applying the latest Human Proteome Project Data Interpretation Guidelines, we catalog 3509 proteins that have at least two non-nested uniquely mapping peptides of nine amino acids or more and >1300 additional proteins with ambiguous evidence. We apply the same two-peptide guideline to historical PeptideAtlas builds going back to 2006 and examine the progress made in the past ten years in plasma proteome coverage. We also compare the distribution of proteins in historical PeptideAtlas builds in various RNA abundance and cellular localization categories. We then discuss advances in plasma proteomics based on targeted mass spectrometry as well as affinity assays, which during early 2017 target \u223c2000 proteins. Finally, we describe considerations about sample handling and study design, concluding with an outlook for future advances in deciphering the human plasma proteome.", "doi": "10.1021/acs.jproteome.7b00467", "pmid": "28938075", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC5864247"}, {"db": "mid", "key": "NIHMS950847"}], "notes": [], "created": "2018-10-31T09:22:30.694Z", "modified": "2021-07-08T12:07:34.326Z"}]}