Comprehensive and quantitative proteome profiling of the mouse liver and plasma

Hepatology

Volumn 47, Issue 3, 2008, Pages 1043-1051

  Lai, Keane K Y ^a,b   Kolippakkam, Deepak ^a   Beretta, Laura ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

^b VA PUGET SOUND HEALTH CARE SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMOKINE; CYTOKINE; EPIDERMAL GROWTH FACTOR; FATTY ACID; INSULIN; INTERLEUKIN 4; LIVER PROTEIN; PLASMA PROTEIN; PLATELET DERIVED GROWTH FACTOR; PROTEOME; PURINE; PYRUVIC ACID; RECEPTOR;

ACCURACY; ANIMAL TISSUE; ARTICLE; BLOOD CLOTTING; BODY FLUID; COMPARATIVE STUDY; COMPLEMENT SYSTEM; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; FATTY ACID METABOLISM; GENETIC TRANSCRIPTION; GLUCONEOGENESIS; GLYCOLYSIS; LIVER; MAMMAL; MASS SPECTROMETRY; METABOLISM; MOUSE; NONHUMAN; PLASMA; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONTENT; PROTEIN DETERMINATION; PROTEIN ISOLATION; PROTEOMICS; PURINE METABOLISM; QUANTITATIVE ANALYSIS; SEPARATION TECHNIQUE; SIGNAL TRANSDUCTION; TRANSCRIPTOMICS; UBIQUITINATION; ANIMAL; C57BL MOUSE; FRACTIONATION; GENETICS; METHODOLOGY; PROTEIN MICROARRAY; PROTEIN SYNTHESIS; SERUM;

ANIMALS; BLOOD PROTEINS; CHEMICAL FRACTIONATION; LIVER; MICE; MICE, INBRED C57BL; PROTEIN ARRAY ANALYSIS; PROTEIN BIOSYNTHESIS; PROTEOME; PROTEOMICS; SERUM; TRANSCRIPTION, GENETIC;

EID: 40949156210     PISSN: 02709139     EISSN: None     Source Type: Journal    
DOI: 10.1002/hep.22123     Document Type: Article

References (43)

1. Parent R, Beretta L. Proteomics in the study of liver pathology. J Hepatol 2005;43:177-183.
2. Liu T, Qian WJ, Gritsenko MA, Xiao W, Moldawer LL, Kaushal A, et al. High dynamic range characterization of the trauma patient plasma proteome. Mol Cell Proteomics 2006;5:1899-1913.
3. Hoffman SA, Joo WA, Echan LA, Speicher DW. Higher dimensional (Hi-D) separation strategies dramatically improve the potential for cancer biomarker detection in serum and plasma. J Chromatogr B Analyt Technol Biomed Life Sci 2007;849:43-52.
4. Qian WJ, Jacobs JM, Liu T, Camp DG II, Smith RD. Advances and challenges in liquid chtomatography-mass spectrometry-based proteomics profiling for clinical applications. Mol Cell Proteomics 2006;5:1727-1744.
5. Faca V, Pitteri SJ, Newcomb L, Glukhova V, Phanstiel D, Krasnoselsky A, et al. Contribution of protein fractionation to depth of analysis of the serum and plasma proteomes. J Proteome Res 2007;6:3558-3565.
6. Liu H, Sadygov RG, Yates JR III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 2004;76:4193-4201.
7. Zybailov BL, Florens L, Washburn MP. Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors. Mol Biosyst 2007;3:354-360.
8. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, et al. Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 2005;4:1487-1502.
9. Gilchrist A, Au CE, Hiding J, Bell AW, Fernandez-Rodriguez J, Lesimple S, et al. Quantitative proteomics analysis of the secretory pathway. Cell 2006;127:1265-1281.
10. States DJ, Omenn GS, Blackwell TW, Fermin D, Eng J, Speicher DW, et al. Challenges in deriving high-confidence protein identifications from data gathered by a HUPO plasma proteome collaborative study. Nat Biotechnol 2006;24:333-338.
11. Nesvizhskii AI, Keller A, Kolker E, Aebersold R. A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 2003;75:4646-4658.
12. Thorgeirsson SS, Lee JS, Grisham JW. Functional genomics of hepatocellular carcinoma. HEPATOLOGY 2006;43(Suppl):S145-S150.
13. Mato JM, Lu SC. Role of S-adenosyl-L-methionine in liver health and injury. HEPATOLOGY 2007;45:1306-1312.
14. Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol Cell Proteomics 2002;1:845-867.
15. Shi R, Kumar C, Zougman A, Zhang Y, Podtelejnikov A, Cox J, et al. Analysis of the mouse liver proteome using advanced mass spectromerry. J Proteome Res 2007;6:2963-2972.
16. Ying W, Jiang Y, Guo L, Hao Y, Zhang Y, Wu S, et al. A dataset of human fetal liver proteome identified by subcellular fractionation and multiple protein separation and identification technology. Mol Cell Proteomics 2006;5:1703-1707.
17. Wang H, Clouthier SG, Galchev V, Misek DE, Duffner U, Min CK, et al. Intact-protein-based high-resolution three-dimensional quantitative analysis system for proteome profiling of biological fluids. Mol Cell Proteomics 2005;4:618-625.
18. Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, et al. Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 2006;125:173-186.
19. Beretta L. Proteomics from the clinical perspective: many hopes and much debate. Nat Methods 2007;4:785-786.
20. Lescuyer P, Hochstrasser D, Rabilloud T. How shall we use the proteomics toolbox for biomarker discovery? J Proteome Res 2007;6:3371-3376.
21. Jitrapakdee S, Vidal-Puig A, Wallace JC. Anaplerotic roles of pyruvate carboxylase in mammalian tissues. Cell Mol Life Sci 2006;63:843-854.
22. Cox KB, Hamm DA, Millington DS, Matern D, Vockley J, Rinaldo P, et al. Gestational, pathologic and biochemical differences between very long-chain acyl-CoA dehydrogenase deficiency and long-chain acyl-CoA dehydrogenase deficiency in the mouse. Hum Mol Genet 2001;10:2069-2077.
23. Fernandez L, Carrasco-Chaumel E, Serafin A, Xaus C, Grande L, Rimola A, et al. Is ischemic preconditioning a useful strategy in steatotic liver transplantation? Am J Transplant 2004;4:888-899.
24. Matsumoto K, Yu S, Jia Y, Ahmed MR, Viswakarma N, Sarkar J, et al. Critical role for transcription coactivator peroxisome proliferator-activated receptor (PPAR)-binding protein/TRAP220 in liver regeneration and PPARalpha ligand-induced liver tumor development. J Biol Chem 2007;282:17053-17060.
25. Argast GM, Campbell JS, Brooling JT, Fausto N. Epidermal growth factor receptor transactivation mediates tumor necrosis factor-induced hepatocyte replication. J Biol Chem 2004;279:34530-34536.
26. Pusl T, Nathanson MH. The role of inositol 1,4,5-trisphosphate receptors in the regulation of bile secretion in health and disease. Biochem Biophys Res Commun 2004;322:1318-1325.
27. Gao B. Cytokines, STATs and liver disease. Cell Mol Immunol 2005;2:92-100.
28. Estrov Z, Talpaz M, Mavligit G, Pazdur R, Harris D, Greenberg SM, et al. Elevated plasma thrombopoietic activity in patients with metastatic cancer-related thrombocytosis. Am J Med 1995;98:551-558.
29. Adam RA, Horowitz IR, Tekmal RR. Serum levels of macrophage colony-stimulating factor-1 in cervical human papillomavirus infection and intraepithelial neoplasia. Am J Obstet Gynecol 1999;180:28-32.
30. Grondahl-Hansen J, Agerlin N, Munkholm-Larsen P, Bach F, Nielsen LS, Dombernowsky P, et al. Sensitive and specific enzyme-linked immunosorbent assay for urokinase-type plasminogen activator and its application to plasma from patients with breast cancer. J Lab Clin Med 1988;111:42-51.
31. Kato K, Okagawa Y, Suzuki F, Shimizu A, Mokuno K, Takahashi Y. Immunoassay of human muscle enolase subunit in serum: a novel marker antigen for muscle diseases. Clin Chim Acta 1983;131:75-85.
32. Kato K, Asai R, Shimizu A, Suzuki F, Ariyoshi Y. Immunoassay of three enolase isozymes in human serum and in blood cells. Clin Chim Acta 1983;127:353-363.
33. Morimoto LM, Newcomb PA, White E, Bigler J, Potter JD. Variation in plasma insulin-like growth factor-1 and insulin-like growth factor binding protein-3: genetic factors. Cancer Epidemiol Biomarkers Prev 2005;14:1394-1401.
34. Dawnay AB, Cattell WR. Serum Tamm-Horsfall glycoprotein levels in health and in renal disease. Clin Nephrol 1981;15:5-8.
35. Hetherington SV, Spitznagel JK, Quie PG. An enzyme-linked immunoassay (ELISA) for measurement of lactoferrin. J Immunol Methods 1983;65:183-190.
36. Kandoussi A, Cachera C, Pagniez D, Saile R, Tacquet A. Quantification of beta 2-microglobulin and albumin in plasma and peritoneal dialysis fluid by a noncompetitive immunoenzymometric assay. Clin Chem 1993;39:93-96.
37. Miletich JP, Broze GJ Jr. Human plasma protein Z antigen: range in normal subjects and effect of warfarin therapy. Blood 1987;69:1580-1586.
38. Suzuki K, Moriguchi A, Nagayoshi A, Mutoh S, Katsuki S, Hashimoto S. Enzyme immunoassay of human protein C by using monoclonal antibodies. Thromb Res 1985;38:611-621.
39. Knipping G, Gogg-Fassolter G, Frohnwieser B, Krempler F, Kostner GM, Malle E. Quantification of apolipoprotein D by an immunoassay with time-resolved fluorescence spectroscopy. J Immunol Methods 1997;202:85-95.
40. Curry MD, McConathy WJ, Fesmire JD, Alaupovic P. Quantitative determination of human apolipoprotein C-III by electroimmunoassay. Biochim Biophys Acta 1980;617:503-513.
41. Al-oanzi ZH, Tuck SP, Raj N, Harrop JS, Summers GD, Cook DB, et al. Assessment of vitamin D status in male osteoporosis. Clin Chem 2006;52:248-254.
42. Stefan N, Hennige AM, Staiger H, Machann J, Schick F, Krober SM, et al. Alpha2-Heremans-Schmid glycoprotein/fetuin-A is associated with insulin resistance and fat accumulation in the liver in humans. Diabetes Care 2006;29:853-857.
43. Bakker WW, van Dael CM, Pierik LJ, van Wijk JA, Nauta J, Borghuis T, et al. Altered activity of plasma hemopexin in patients with minimal change disease in relapse. Pediatr Nephrol 2005;20:1410-1415.