Open-pFind Verified Four Missing Proteins from Multi-Tissues

doi:10.1021/acs.jproteome.0c00370

	Open-pFind Verified Four Missing Proteins from Multi-Tissues
	Wu, Shujia 1,2; Sun, Jinshuai 2,3; Wang, Xi 4; Xu, Feng 2; Chi, Hao 4; Li, Yanchang 2; Zhong, Bowen 2; Xie, Yuping 2; Yan, Zhonghua 2; Chang, Lei 2; Wang, Dongxue 2; He, Fuchu 2; Wu, Junzhu 1; Zhang, Yao 2; Xu, Ping 1,2,3
	2020-12-04
发表期刊	JOURNAL OF PROTEOME RESEARCH
ISSN	1535-3893
卷号	19 期号:12 页码:4808-4814
摘要	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.
关键词	Chromosome-Centric Human Proteome Project missing proteins open-pFind multiple tissues
DOI	10.1021/acs.jproteome.0c00370
收录类别	SCI
语种	英语
资助项目	MOST[2017YFD0501500] ; MOST[2017YFC0906700] ; MOST[2017YFA0505700] ; National Natural Science Foundation of China[31901037] ; National Natural Science Foundation of China[31670834] ; National Natural Science Foundation of China[31870824] ; National Natural Science Foundation of China[91839302] ; Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences[2019RU006] ; Foundation of State Key Lab of Proteomics[SKLP-Y201704] ; Foundation of State Key Lab of Proteomics[SKLP-K201901] ; Innovation Foundation of Medicine[16CXZ027] ; Innovation Foundation of Medicine[BWS17J032] ; Innovation Foundation of Medicine[AWS17J008] ; Innovation Foundation of Medicine[19SWAQ17] ; National Megaprojects for Key Infectious Diseases[2018ZX10302302] ; Guangzhou Science and Technology Innovation & Development Project[201802020016] ; Guangzhou Science and Technology Innovation & Development Project[2018A030310257] ; Unilever 21th Century Toxicity Program[MA-2018-02170N]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:000598145200008
出版者	AMER CHEMICAL SOC
引用统计	被引频次：4[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/16630
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	He, Fuchu; Wu, Junzhu; Zhang, Yao; Xu, Ping
作者单位	1.Wuhan Univ, Sch Basic Med Sci, Minist Educ, Key Lab Combinatl Biosynth & Drug Discovery, Wuhan 430072, Peoples R China 2.Chinese Acad Med Sci, Inst Life, Res Unit Prote & Res & Dev New Drug,State Key Lab, Natl Ctr Prot Sci Beijing,Beijing Proteome Res Ct, Beijing 102206, Peoples R China 3.Hebei Univ, Coll Life Sci, Hebei Prov Key Lab Res & Applicat Microbial Diver, Baoding 071002, Hebei, Peoples R China 4.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing 100080, Peoples R China
推荐引用方式 GB/T 7714	Wu, Shujia,Sun, Jinshuai,Wang, Xi,et al. Open-pFind Verified Four Missing Proteins from Multi-Tissues[J]. JOURNAL OF PROTEOME RESEARCH,2020,19(12):4808-4814.
APA	Wu, Shujia.,Sun, Jinshuai.,Wang, Xi.,Xu, Feng.,Chi, Hao.,...&Xu, Ping.(2020).Open-pFind Verified Four Missing Proteins from Multi-Tissues.JOURNAL OF PROTEOME RESEARCH,19(12),4808-4814.
MLA	Wu, Shujia,et al."Open-pFind Verified Four Missing Proteins from Multi-Tissues".JOURNAL OF PROTEOME RESEARCH 19.12(2020):4808-4814.