Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy

Shaohui Sui, Jinglan Wang, Bing Yang, Lina Song, Jiyang Zhang, Ming Chen, Jinfeng Liu, Zhuang Lu, Yun Cai, Shuo Chen, Wei Bi, Yunping Zhu, Fuchu He, Xiaohong Qian

Research output: Contribution to journalArticlepeer-review

52 Scopus citations

Abstract

The liver is the largest organ in the body, with many complex, essential functions, such as metabolism, deintoxication, and secretion, often regulated via post-translational modifications, especially phosphorylation. Thus, the detection of phosphoproteins and phosphorylation sites is important to comprehensively explore human liver biological function. The human Chang liver cell line is among the first derived from non-malignant tissue, and its phosphoproteome profile has never been globally analyzed. To develop the complete phosphoproteome and probe the roles of protein phosphorylation in normal human liver, we adopted a shotgun strategy based on strong cation exchange chromatograph, titanium dioxide and LC-MS/MS to isolate and identify phosphorylated proteins. Two types of MS approach, Q-TOF and IT, were used and compared to identify phosphosites from complex protein mixtures of these cells. A total of 1035 phosphorylation sites and 686 phosphorylated peptides were identified from 607 phosphoproteins. A search using the public database of PhosphoSite showed that approximately 344 phosphoproteins and 760 phosphorylation sites appeared to be novel. In addition, N-terminal phosphorylated peptides were a greater fraction of all identified phosphopeptides. With GOfact analysis, we found that most of the identified phosphoproteins are involved in regulating metabolism, consistent with the liver's role as a key metabolic organ.

Original languageEnglish (US)
Pages (from-to)2024-2034
Number of pages11
JournalProteomics
Volume8
Issue number10
DOIs
StatePublished - May 2008
Externally publishedYes

Keywords

  • Human Chang liver cells
  • Mass spectrometry
  • Phosphoproteome
  • Phosphorylation site
  • SCX

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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