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 ~43 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 9 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 ~2000 proteins. Finally we describe considerations about sample handling and study design, concluding with an outlook for future advances in deciphering the human plasma proteome.

中文翻译：

---

2017年人类血浆蛋白质组学草案：基于质谱和互补分析的人类血浆肽图集

人体血浆为健康和疾病中任何人的蛋白质组提供了一个高度可访问的窗口。自2002年成立以来，人类蛋白质组组织的人类血浆蛋白质组计划（HPPP）一直在促进研究和了解人类血浆全蛋白补体以及确定其组成的丰度和修饰方面的进展。在2017年，我们回顾了HPPP的历史以及总体人类血浆蛋白质组学的进展，包括最近取得的一些成就。然后，我们介绍了最新的2017-04年构建的人类血浆PeptideAtlas，它从178个单独的实验中产生了约4,300万个肽谱匹配和122,730个不同的肽序列，全球所有实验中蛋白水平为1％。应用最新的人类蛋白质组计划数据解释准则，我们对3509种蛋白质进行了分类，这些蛋白质具有至少两个9个或更多个氨基酸的非嵌套式独特映射肽，以及另外1300种含歧义证据的蛋白质。我们对历史可追溯到2006年的PeptideAtlas构建体使用相同的两肽指南，并研究了过去十年中血浆蛋白质组覆盖率方面的进展。我们还比较了各种RNA丰度和细胞定位类别中历史PeptideAtlas构建中蛋白质的分布。然后，我们将讨论基于靶向质谱法和亲和力测定的血浆蛋白质组学的进展，该技术在2017年初可靶向约2000种蛋白质。最后，我们描述了有关样品处理和研究设计的注意事项，并对解密人类血浆蛋白质组学的未来进展作了展望。