Comprehensive genome-wide proteomic analysis of human placental tissue for the Chromosome-Centric Human Proteome Project.
As a starting point of the Chromosome-Centric Human Proteome Project (C-HPP), we established strategies of genome-wide proteomic analysis, including protein identification, quantitation of disease-specific proteins, and assessment of post-translational modifications, using paired human placental tissues from healthy and preeclampsia patients. This analysis resulted in identification of 4239 unique proteins with high confidence (two or more unique peptides with a false discovery rate less than 1%), covering 21% of approximately 20, 059 (Ensembl v69, Oct 2012) human proteins, among which 28 proteins exhibited differentially expressed preeclampsia-specific proteins. When these proteins are assigned to all human chromosomes, the pattern of the newly identified placental protein population is proportional to that of the gene count distribution of each chromosome. We also identified 219 unique N-linked glycopeptides, 592 unique phosphopeptides, and 66 chromosome 13-specific proteins. In particular, protein evidence of 14 genes previously known to be specifically up-regulated in human placenta was verified by mass spectrometry. With respect to the functional implication of these proteins, 38 proteins were found to be involved in regulatory factor biosynthesis or the immune system in the placenta, but the molecular mechanism of these proteins during pregnancy warrants further investigation. As far as we know, this work produced the highest number of proteins identified in the placenta and will be useful for annotating and mapping all proteins encoded in the human genome.
Yonsei Proteome Research Center and Department of Integrated Omics for Biomedical Science, World Class University Program, Yonsei University, Seoul, Korea.
Hyoung-Joo
HJ
Lee
Seul-Ki
SK
Jeong
Keun
K
Na
Min Jung
MJ
Lee
Sun Hee
SH
Lee
Jong-Sun
JS
Lim
Hyun-Jeong
HJ
Cha
Jin-Young
JY
Cho
Ja-Young
JY
Kwon
Hoguen
H
Kim
Si Young
SY
Song
Jong Shin
JS
Yoo
Young Mok
YM
Park
Hail
H
Kim
William S
WS
Hancock
Young-Ki
YK
Paik
D016022:Case-Control Studies; D002877:Chromosomes, Human / Q000737:chemistry*; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015894:Genome, Human; D055106:Genome-Wide Association Study; D006031:Glycosylation; D016045:Human Genome Project; D006801:Humans; D013058:Mass Spectrometry; D010766:Phosphorylation; D010920:Placenta; D011225:Pre-Eclampsia / Q000235:genetics / Q000378:metabolism*; D011247:Pregnancy; D011499:Protein Processing, Post-Translational; D020543:Proteome / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism
D020543:Proteome