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J Proteome Res. 2015 Sep 4;14(9):3583-94. doi: 10.1021/acs.jproteome.5b00435.

Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins.

Zhang Y1,2,3, Li Q4,5,3, Wu F1,6, Zhou R5, Qi Y1, Su N1, Chen L1,7, Xu S5, Jiang T5, Zhang C1, Cheng G5, Chen X8, Kong D9, Wang Y5, Zhang T1, Zi J5, Wei W1, Gao Y1, Zhen B1, Xiong Z6, Wu S1, Yang P10, Wang Q4,5,3, Wen B5, He F1, Xu P1,11, Liu S4,5,3.

Author information

1
State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences, Beijing Institute of Radiation Medicine , Beijing 102206, China.
2
Institute of Microbiology, Chinese Academy of Science , Beijing 100101, China.
3
Graduate University of the Chinese Academy of Sciences , Beijing 100049, China.
4
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101, China.
5
BGI-Shenzhen , Shenzhen 518083, China.
6
Life Science College, Southwest Forestry University , Kunming 650224, P. R, China.
7
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University , Nanning 530005, China.
8
Institute of Organ Transportation, General Hospital of Chinese People's Armed Police Forces , Beijing 100039, China.
9
General Surgery Dept., Capital Medical University Affiliated Beijing YouAn Hospital , Beijing 100069, China.
10
Institutes of Biomedical Sciences, Department of Chemistry and Zhongshan Hospital, Fudan University , 130 DongAn Road, Shanghai 200032, China.
11
Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences , Wuhan 430071, China.

Abstract

Investigations of missing proteins (MPs) are being endorsed by many bioanalytical strategies. We proposed that proteogenomics of testis tissue was a feasible approach to identify more MPs because testis tissues have higher gene expression levels. Here we combined proteomics and transcriptomics to survey gene expression in human testis tissues from three post-mortem individuals. Proteins were extracted and separated with glycine- and tricine-SDS-PAGE. A total of 9597 protein groups were identified; of these, 166 protein groups were listed as MPs, including 138 groups (83.1%) with transcriptional evidence. A total of 2948 proteins are designated as MPs, and 5.6% of these were identified in this study. The high incidence of MPs in testis tissue indicates that this is a rich resource for MPs. Functional category analysis revealed that the biological processes that testis MPs are mainly involved in are sexual reproduction and spermatogenesis. Some of the MPs are potentially involved in tumorgenesis in other tissues. Therefore, this proteogenomics analysis of individual testis tissues provides convincing evidence of the discovery of MPs. All mass spectrometry data from this study have been deposited in the ProteomeXchange (data set identifier PXD002179).

KEYWORDS:

Chromosome-Centric Human Proteome Project; individual; missing proteins; proteome; testis; transcriptome

PMID:
26282447
DOI:
10.1021/acs.jproteome.5b00435
[Indexed for MEDLINE]

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