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Differential Proteomic Analysis of Mammalian Tissues Using SILAM

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  • Daniel B McClatchy
  • Lujian Liao
  • Sung Kyu Park
  • Tao Xu
  • Bingwen Lu
  • John R Yates III

Abstract

Differential expression of proteins between tissues underlies organ-specific functions. Under certain pathological conditions, this may also lead to tissue vulnerability. Furthermore, post-translational modifications exist between different cell types and pathological conditions. We employed SILAM (Stable Isotope Labeling in Mammals) combined with mass spectrometry to quantify the proteome between mammalian tissues. Using 15N labeled rat tissue, we quantified 3742 phosphorylated peptides in nuclear extracts from liver and brain tissue. Analysis of the phosphorylation sites revealed tissue specific kinase motifs. Although these tissues are quite different in their composition and function, more than 500 protein identifications were common to both tissues. Specifically, we identified an up-regulation in the brain of the phosphoprotein, ZFHX1B, in which a genetic deletion causes the neurological disorder Mowat–Wilson syndrome. Finally, pathway analysis revealed distinct nuclear pathways enriched in each tissue. Our findings provide a valuable resource as a starting point for further understanding of tissue specific gene regulation and demonstrate SILAM as a useful strategy for the differential proteomic analysis of mammalian tissues.

Suggested Citation

  • Daniel B McClatchy & Lujian Liao & Sung Kyu Park & Tao Xu & Bingwen Lu & John R Yates III, 2011. "Differential Proteomic Analysis of Mammalian Tissues Using SILAM," PLOS ONE, Public Library of Science, vol. 6(1), pages 1-10, January.
    • Handle: RePEc:plo:pone00:0016039
    DOI: 10.1371/journal.pone.0016039
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    1. Steve E. Calvano & Wenzhong Xiao & Daniel R. Richards & Ramon M. Felciano & Henry V. Baker & Raymond J. Cho & Richard O. Chen & Bernard H. Brownstein & J. Perren Cobb & S. Kevin Tschoeke & Carol Mille, 2005. "A network-based analysis of systemic inflammation in humans," Nature, Nature, vol. 437(7061), pages 1032-1037, October.
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