Tissue-Based Proteogenomics Reveals that Human Testis Endows Plentiful Missing Proteins.
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).
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.|Institute of Microbiology, Chinese Academy of Science , Beijing 100101, China.|Graduate University of the Chinese Academy of Sciences , Beijing 100049, China.
Yao
Y
Zhang
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101, China.|BGI-Shenzhen , Shenzhen 518083, China.|Graduate University of the Chinese Academy of Sciences , Beijing 100049, China.
Qidan
Q
Li
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.|Life Science College, Southwest Forestry University , Kunming 650224, P. R, China.
Feilin
F
Wu
BGI-Shenzhen , Shenzhen 518083, China.
Ruo
R
Zhou
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.
Yingzi
Y
Qi
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.
Na
N
Su
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.|State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University , Nanning 530005, China.
Lingsheng
L
Chen
BGI-Shenzhen , Shenzhen 518083, China.
Shaohang
S
Xu
BGI-Shenzhen , Shenzhen 518083, China.
Tao
T
Jiang
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.
Chengpu
C
Zhang
BGI-Shenzhen , Shenzhen 518083, China.
Gang
G
Cheng
Institute of Organ Transportation, General Hospital of Chinese People's Armed Police Forces , Beijing 100039, China.
Xinguo
X
Chen
General Surgery Dept., Capital Medical University Affiliated Beijing YouAn Hospital , Beijing 100069, China.
Degang
D
Kong
BGI-Shenzhen , Shenzhen 518083, China.
Yujia
Y
Wang
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.
Tao
T
Zhang
BGI-Shenzhen , Shenzhen 518083, China.
Jin
J
Zi
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.
Wei
W
Wei
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.
Yuan
Y
Gao
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.
Bei
B
Zhen
Life Science College, Southwest Forestry University , Kunming 650224, P. R, China.
Zhi
Z
Xiong
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.
Songfeng
S
Wu
Institutes of Biomedical Sciences, Department of Chemistry and Zhongshan Hospital, Fudan University , 130 DongAn Road, Shanghai 200032, China.
Pengyuan
P
Yang
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101, China.|BGI-Shenzhen , Shenzhen 518083, China.|Graduate University of the Chinese Academy of Sciences , Beijing 100049, China.
Quanhui
Q
Wang
BGI-Shenzhen , Shenzhen 518083, China.
Bo
B
Wen
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.
Fuchu
F
He
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.|Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences , Wuhan 430071, China.
Ping
P
Xu
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences , Beijing 100101, China.|BGI-Shenzhen , Shenzhen 518083, China.|Graduate University of the Chinese Academy of Sciences , Beijing 100049, China.
Siqi
S
Liu
D002853:Chromatography, Liquid; D004591:Electrophoresis, Polyacrylamide Gel; D023281:Genomics; D006801:Humans; D008297:Male; D011506:Proteins / Q000302:isolation & purification / Q000378:metabolism*; D040901:Proteomics; D017423:Sequence Analysis, RNA; D053719:Tandem Mass Spectrometry; D013737:Testis / Q000378:metabolism*; D059467:Transcriptome
D011506:Proteins
Chromosome-Centric Human Proteome Project; individual; missing proteins; proteome; testis; transcriptome