Comprehensive genome-wide proteomic analysis of human placental tissue for the chromosome-centric human proteome project

Hyoung Joo Lee, Seul Ki Jeong, Keun Na, Min Jung Lee, Sun Hee Lee, Jong Sun Lim, Hyun Jeong Cha, Jin Young Cho, Ja Young Kwon, Hoguen Kim, Si Young Song, Jong Shin Yoo, Young Mok Park, Hail Kim, William S. Hancock, Young Ki Paik*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    29 Citations (Scopus)


    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.

    Original languageEnglish
    Pages (from-to)2458-2466
    Number of pages9
    JournalJournal of Proteome Research
    Issue number6
    Publication statusPublished - 2013


    • C-HPP
    • glycosylation
    • phosphorylation
    • preeclampsia
    • quantitation
    • TMT


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