title: Quantitative proteomic survey of endoplasmic reticulum in mouse liver.
abstract: To gain a better understanding of the critical function of the endoplasmic reticulum (ER) in liver, we carried out a proteomic survey of mouse liver ER. The ER proteome was profiled with a new three-dimensional, gel-based strategy. From 6152 and 6935 MS spectra, 903 and 1042 proteins were identified with at least two peptides matches at 95% confidence in the rough (r) and smooth (s) ER, respectively. Comparison of the rER and sER proteomes showed that calcium-binding proteins are significantly enriched in the sER suggesting that the ion-binding function of the ER is compartmentalized. Comparison of the rat and mouse ER proteomes showed that 662 proteins were common to both, comprising 53.5% and 49.3% of those proteomes, respectively. We proposed that these proteins were stably expressed proteins that were essential for the maintenance of ER function. GO annotation with a hypergeometric model proved this hypothesis. Unexpectedly, 210 unknown proteins and some proteins previously reported to occur in the cytosol were highly enriched in the ER. This study provides a reference map for the ER proteome of liver. Identification of new ER proteins will enhance our current understanding of the ER and also suggest new functions for this organelle.
authors.affiliation: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, PR China.
authors.forename: Yanping
authors.initials: Y
authors.lastname: Song
authors.forename: Ying
authors.initials: Y
authors.lastname: Jiang
authors.forename: Wantao
authors.initials: W
authors.lastname: Ying
authors.forename: Yan
authors.initials: Y
authors.lastname: Gong
authors.forename: Yujuan
authors.initials: Y
authors.lastname: Yan
authors.forename: Dong
authors.initials: D
authors.lastname: Yang
authors.forename: Jie
authors.initials: J
authors.lastname: Ma
authors.forename: Xiaofang
authors.initials: X
authors.lastname: Xue
authors.forename: Fan
authors.initials: F
authors.lastname: Zhong
authors.forename: Songfeng
authors.initials: S
authors.lastname: Wu
authors.forename: Yunwei
authors.initials: Y
authors.lastname: Hao
authors.forename: Aihua
authors.initials: A
authors.lastname: Sun
authors.forename: Tao
authors.initials: T
authors.lastname: Li
authors.forename: Wei
authors.initials: W
authors.lastname: Sun
authors.forename: Handong
authors.initials: H
authors.lastname: Wei
authors.forename: Yunping
authors.initials: Y
authors.lastname: Zhu
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Qian
authors.forename: Fuchu
authors.initials: F
authors.lastname: He
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D003577:Cytochrome P-450 Enzyme System / Q000378:metabolism; D057225:Data Mining; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D018870:Endoplasmic Reticulum, Rough / Q000737:chemistry* / Q000378:metabolism; D018871:Endoplasmic Reticulum, Smooth / Q000737:chemistry* / Q000378:metabolism; D008099:Liver / Q000737:chemistry* / Q000378:metabolism; D008297:Male; D051379:Mice; D008810:Mice, Inbred C57BL; D010455:Peptides / Q000737:chemistry; D020543:Proteome / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D051381:Rats; D018709:Statistics, Nonparametric; D013347:Subcellular Fractions / Q000737:chemistry / Q000378:metabolism
chemical_list: D010455:Peptides; D020543:Proteome; D003577:Cytochrome P-450 Enzyme System