Open-pFind Verified Four Missing Proteins from Multi-Tissues
Open-pFind Verified Four Missing Proteins from Multi-Tissues
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Open-pFind 验证了多种组织中的四种缺失蛋白质
DOI：
10.1021/acs.jproteome.0c00370
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发表时间：
2020
影响因子：
4.4
通讯作者：
Xu Ping
中科院分区：
文献类型：
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作者：
Wu Shujia;Sun Jinshuai;Wang Xi;Xu Feng;Chi Hao;Li Yanchang;Zhong Bowen;Xie Yuping;Yan Zhonghua;Chang Lei;Wang Dongxue;He Fuchu;Wu Junzhu;Zhang Yao;Xu Ping
以染色体为中心的人类蛋白质组计划（C-HPP）于2012年启动，旨在通过在蛋白质水平上识别缺失蛋白（MP）表达的更有力证据，完善人类蛋白质存在的注释。经过全球8年的努力，neXtProt数据库中的议员人数从5511人（2012年2月24日）大幅减少到1899人（2020年1月17日）。由于其低丰度、低分子量、非预期修饰、跨膜结构、组织表达特异性等特点，目前已难以提供可靠的证据，而更高分辨率的质谱解释引擎与多组织大规模蛋白质组学相结合，可能为复杂样品中这些埋藏的MP的鉴定提供机会。在该研究中，Wang等人使用open-pFind从20对健康人组织中挖掘MP（Mol. Syst. Biol.2019，15（2），e8503）结合我们的大规模睾丸数据集，该数据集由三种酶（Glu-C，Lys-C和胰蛋白酶）消化，对不同的氨基酸残基具有特异性（J. Proteme Res.2019，18（12），4189−4196）。在PSM、肽和蛋白质水平上，总共将具有17 283 477个肽谱匹配（PSM）的1 535 536个肽映射到14 279个蛋白质条目，错误发现率<1%。共鉴定出103个MP候选物，其中86个候选物与我们的单个睾丸组织相比具有更多的独特肽编号。经过严格的筛选，人工检查，肽合成，并与PeptideAtlas中记录的肽匹配，我们在蛋白质水平上验证了四种MP，P0 C7 T8（十二指肠和小肠），Q8 WWZ 4（胃和直肠），Q8 IV 35（输卵管）和O 14921（扁桃体）。所有MS原始文件均已保存至ProteomeXchange，标识符为PXD 021391。
The Chromosome-Centric Human Proteome Project (C-HPP) was launched in 2012 to perfect the annotation of human protein existence by identifying stronger evidence of the expression of missing proteins (MPs) at the protein level. After an 8 year effort all over the world, the number of MPs in the neXtProt database significantly decreased from 5511 (2012-02-24) to 1899 (2020-01-17). It is now more difficult to provide confident evidence of the remaining MPs because of their specific characteristics, including low abundance, low molecular weight, unexpected modifications, transmembrane structure, tissue-expression specificity, and so on. A higher resolution mass spectrometry (MS) interpretation engine might provide an opportunity to identify these buried MPs in complex samples by the combination with multi-tissue large-scale proteomics. In this study, open-pFind was used to dig MPs from 20 pairs of healthy human tissues by Wang et al. (Mol. Syst. Biol.2019, 15 (2), e8503) combined with our large-scale testis data set digested by three enzymes (Glu-C, Lys-C, and trypsin) with specificity for different amino acid residues (J. Proteme Res.2019, 18 (12), 4189−4196). A total of 1 535 536 peptides with 17 283 477 peptide-spectrum matches (PSMs) were mapped to 14 279 protein entries at a false discovery rate of <1% at the PSM, peptide, and protein levels. A total of 103 MP candidates were identified, among which 86 candidates had more unique peptide numbers compared with our single testis tissue. After rigorous screening, manual checks, peptide synthesis, and matching with documented peptides from PeptideAtlas, we validated four MPs, P0C7T8 (duodenum and small intestine), Q8WWZ4 (stomach and rectum), Q8IV35 (fallopian tube), and O14921 (tonsil), at the protein level. All MS raw files have been deposited to the ProteomeXchange with identifier PXD021391.