<br>HUPO 人类蛋白质组计划 2023 年蛋白质组报告,Journal of Proteome Research

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HUPO 人类蛋白质组计划 2023 年蛋白质组报告
Journal of Proteome Research ( IF 3.8 ) Pub Date : 2024-01-17 , DOI: 10.1021/acs.jproteome.3c00591
Gilbert S Omenn _{1,

2} , Lydie Lane ₃ , Christopher M Overall _{4,

5} , Cecilia Lindskog ₆ , Charles Pineau ₇ , Nicolle H Packer ₈ , Ileana M Cristea ₉ , Susan T Weintraub ₁₀ , Sandra Orchard ₁₁ , Michael H A Roehrl ₁₂ , Edouard Nice ₁₃ , Tiannan Guo ₁₄ , Jennifer E Van Eyk ₁₅ , Siqi Liu ₁₆ , Nuno Bandeira ₁₇ , Ruedi Aebersold _{18,

19} , Robert L Moritz ₂ , Eric W Deutsch ₂

Affiliation

University of Michigan, Ann Arbor, Michigan 48109, United States.
Institute for Systems Biology, Seattle, Washington 98109, United States.
CALIPHO Group, SIB Swiss Institute of Bioinformatics and University of Geneva, 1015 Lausanne, Switzerland.
University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.
Yonsei University, Seoul 03722, Republic of Korea.
Uppsala Universitet, 752 36 Uppsala, Sweden.
University Rennes, Inserm U1085, Irset, 35042 Rennes, France.
Macquarie University, Sydney, New South Wales 2109, Australia.
Princeton University, Princeton, New Jersey 08544-1014, United States.
University of Texas Health Science Center-San Antonio, San Antonio, Texas 78229-3900, United States.
EMBL-EBI, Hinxton, Cambridgeshire CB10 1SD, United Kingdom.
Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States.
Monash University, Clayton, Victoria 3800, Australia.
Westlake Center for Intelligent Proteomics, Westlake Laboratory, Westlake University, Hangzhou 310024, Zhejiang Province, China.
Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, 127 South San Vicente Boulevard, Pavilion, 9th Floor, Los Angeles, California 90048, United States.
BGI Group, Shenzhen 518083, China.
University of California, San Diego, La Jolla, California 92093, United States.
Institute of Molecular Systems Biology in ETH Zurich, 8092 Zurich, Switzerland.
University of Zurich, 8092 Zurich, Switzerland.

自 2010 年以来，人类蛋白质组计划 (HPP) 作为人类蛋白质组组织 (HUPO) 的旗舰计划，一直追求两个目标：(1) 可靠地识别蛋白质组成部分列表；(2) 使蛋白质组学成为多组学不可或缺的一部分人类健康和疾病的研究。 HPP 依靠国际合作、数据共享、PeptideAtlas 和 MassIVE-KB 对 MS 数据集的标准化再分析，使用 HPP 指南进行质量保证、neXtProt 对 MS 和非 MS 蛋白质数据的整合和管理，以及广泛使用抗体分析由人类蛋白质图谱列出。根据 neXtProt 于 2023 年 4 月 18 日发布的信息，在人类基因组中编码的 19,778 个 neXtProt 预测蛋白中，目前已可靠地检测到了 18,397 个蛋白表达 (PE1) (93%)。在这些 PE1 蛋白中，有 17,453 种是根据 HPP 指南通过质谱 (MS) 检测到的，另外 944 种是通过各种非 MS 方法检测到的。 neXtProt PE2、PE3 和 PE4 缺失蛋白的数量目前为 1381 个。实现对所有染色体编码的 93% 预测蛋白的明确鉴定代表了人类蛋白质组部分列表上的显着实验进展。与此同时，无论使用何种基于蛋白质的方法，有几类预测蛋白质已被证明难以检测。此外，还有一些 PE1-4 蛋白质可能应该重新分类为 PE5，特别是 21 个 LINC 条目和 ∼30 个 HEV 条目；今年正在解决这些问题。将蛋白质组学应用于广泛的生物学和临床研究中，可确保与生物学和疾病驱动的 HPP 团队以及抗体和病理学资源支柱所报告的其他组学平台的集成。目前的进展已使 HPP 过渡到其大挑战项目，重点是确定每种蛋白质本身以及人类健康和疾病背景下的网络和途径的主要功能。

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The 2023 Report on the Proteome from the HUPO Human Proteome Project

Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1–4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

更新日期：2024-01-17

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