The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.
The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.
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DOI：
10.1021/acs.jproteome.7b00467
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发表时间：
2017-12-01
影响因子：
4.4
通讯作者：
Deutsch EW
中科院分区：
文献类型：
--
作者：
Schwenk JM;Omenn GS;Sun Z;Campbell DS;Baker MS;Overall CM;Aebersold R;Moritz RL;Deutsch EW
人类血浆为任何健康和疾病个体的蛋白质组提供了一个高度可及的窗口。自2002年成立以来，人类蛋白质组组织的人血浆蛋白质组计划（HPPP）一直在促进研究和了解人血浆的完整蛋白质补充以及确定其组分的丰度和修饰方面的进展。在2017年，我们回顾了HPPP的历史和人类血浆蛋白质组学的总体进展，包括最近的几项成就。然后，我们展示了最新的2017-04版Human Plasma PeptideAtlas，它在所有实验中以1%的蛋白质水平FDR从178个单独的实验中产生了约4300万个肽谱匹配和122，730个不同的肽序列。应用最新的人类蛋白质组项目数据解释指南，我们对3509种蛋白质进行了编目，这些蛋白质至少有两个9个氨基酸或更多的非嵌套的同源映射肽，以及>1300种其他蛋白质，这些蛋白质的证据不明确。我们将相同的双肽指南应用于历史PeptideAtlas构建，可以追溯到2006年，并检查了过去十年在血浆蛋白质组覆盖方面取得的进展。我们还比较了历史PeptideAtlas构建中蛋白质在各种RNA丰度和细胞定位类别中的分布。然后，我们讨论了血浆蛋白质组学的进展，基于靶向质谱以及亲和分析，在2017年初针对约2000种蛋白质。最后，我们描述了有关样品处理和研究设计的考虑，最后展望了未来破译人类血浆蛋白质组的进展。
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.
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影响因子：
3.4
作者：
Deutsch, Eric W.;Mendoza, Luis;Shteynberg, David;Farrah, Terry;Lam, Henry;Tasman, Natalie;Sun, Zhi;Nilsson, Erik;Pratt, Brian;Prazen, Bryan;Eng, Jimmy K.;Martin, Daniel B.;Nesvizhskii, Alexey I.;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi
DOI：
10.1007/978-1-61779-068-3_23
发表时间：
2011-01-01
期刊：
SERUM/PLASMA PROTEOMICS: METHODS AND PROTOCOLS
影响因子：
--
作者：
Farrah, Terry;Deutsch, Eric W.;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi
影响因子：
4.4
作者：
Anderson, NL;Anderson, NG;Pearson, TW
通讯作者：
Pearson, TW
影响因子：
3.4
作者：
Deutsch, EW;Eng, JK;Aebersold, R
通讯作者：
Aebersold, R
人蛋白质组项目质谱数据解释指南2.1。
影响因子：
4.4
作者：
Deutsch EW;Overall CM;Van Eyk JE;Baker MS;Paik YK;Weintraub ST;Lane L;Martens L;Vandenbrouck Y;Kusebauch U;Hancock WS;Hermjakob H;Aebersold R;Moritz RL;Omenn GS
通讯作者：
Omenn GS