Mapping tissue-specific expression of extracellular proteins using systematic glycoproteomic analysis of different mouse tissues

Journal of Proteome Research

Volumn 9, Issue 11, 2010, Pages 5837-5847

  Tian, Yuan ^a   Kelly Spratt, Karen S ^b   Kemp, Christopher J ^b   Zhang, Hui ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Fred Hutchinson Cancer Research Center   (United States)

Author keywords

different tissues; extracellular proteins; glycosylation; mass spectrometry; proteomics; skin tumor; solid phase extraction of glycopeptides; tissue specificity

Indexed keywords

BIOLOGICAL MARKER; GLYCOPEPTIDE; GLYCOPROTEIN;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; CELL SURFACE; DRUG TARGETING; FEMALE; LIQUID CHROMATOGRAPHY; MALE; MASS SPECTROMETRY; MOUSE; NONHUMAN; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; QUANTITATIVE ANALYSIS; SKIN TUMOR; SOLID; SOLID PHASE EXTRACTION; TISSUE SPECIFICITY; TUMOR MODEL;

ANIMALS; BIOLOGICAL MARKERS; GENE EXPRESSION REGULATION; GLYCOPROTEINS; MICE; PROTEOMICS; SKIN NEOPLASMS; SOLID PHASE EXTRACTION; TANDEM MASS SPECTROMETRY; TISSUE DISTRIBUTION;

EID: 78149399037     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr1006075     Document Type: Article

References (56)

1. Collins, B. E.; Paulson, J. C. Cell surface biology mediated by low affinity multivalent protein-glycan interactions Curr. Opin. Chem. Biol. 2004, 8 (6) 617-25
2. Zheng, C. J.; Han, L. Y.; Yap, C. W.; Ji, Z. L.; Cao, Z. W.; Chen, Y. Z. Therapeutic targets: progress of their exploration and investigation of their characteristics Pharmacol. Rev. 2006, 58 (2) 259-79
3. Sokoll, L. J.; Chan, D. W., Biomarkers for Cancer Diagnostics. In Abeloff's clinical oncology, 4 th ed.; Abeloff, M. D.; Armitage, J. O.; Niederhuber, J. E.; Kastan, M. B.; McKenna, W. G., Eds; Elsevier Inc: Philadelphia, PA, 2008.
4. Hortobagyi, G. N. Treatment of breast cancer N. Engl. J. Med. 1998, 339 (14) 974-84
5. Chen, X.; Ji, Z. L.; Chen, Y. Z. TTD: Therapeutic Target Database Nucleic Acids Res. 2002, 30 (1) 412-5
6. Zhang, H.; Chan, D. W. Cancer Biomarker Discovery in Plasma Using a Tissue-targeted Proteomic Approach Cancer Epidemiol. Biomarkers Prev. 2007, 16 (10) 1915-7
7. Zhang, H.; Loriaux, P.; Eng, J.; Campbell, D.; Keller, A.; Moss, P.; Bonneau, R.; Zhang, N.; Zhou, Y.; Wollscheid, B.; Cooke, K.; Yi, E. C.; Lee, H.; Peskind, E. R.; Zhang, J.; Smith, R. D.; Aebersold, R. UniPep, a database for human N-linked glycosites: A Resource for Biomarker Discovery Genome Biol. 2006, 7 (8) R73
8. Zhang, H.; Liu, A. Y.; Loriaux, P.; Wollscheid, B.; Zhou, Y.; Watts, J. D.; Aebersold, R. Mass spectrometric detection of tissue proteins in plasma Mol. Cell. Proteomics 2007, 6 (1) 64-71
9. Washburn, M. P.; Wolters, D.; Yates, J. R., 3rd Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 2001, 19 (3) 242-7
10. Han, D.; Eng, J.; Zhou, H.; Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. 2001, 19, 946 - 51.
11. Blonder, J.; Yu, L. R.; Radeva, G.; Chan, K. C.; Lucas, D. A.; Waybright, T. J.; Issaq, H. J.; Sharom, F. J.; Veenstra, T. D. Combined chemical and enzymatic stable isotope labeling for quantitative profiling of detergent-insoluble membrane proteins isolated using Triton X-100 and Brij-96 J. Proteome Res. 2006, 5 (2) 349-60
12. Blonder, J.; Conrads, T. P.; Yu, L. R.; Terunuma, A.; Janini, G. M.; Issaq, H. J.; Vogel, J. C.; Veenstra, T. D. A detergent- and cyanogen bromide-free method for integral membrane proteomics: application to Halobacterium purple membranes and the human epidermal membrane proteome Proteomics 2004, 4 (1) 31-45
13. Wu, C. C.; MacCoss, M. J.; Howell, K. E.; Yates, J. R., 3rd A method for the comprehensive proteomic analysis of membrane proteins Nat. Biotechnol. 2003, 21 (5) 532-8
14. Mirza, S. P.; Halligan, B. D.; Greene, A. S.; Olivier, M. Improved method for the analysis of membrane proteins by mass spectrometry Physiol. Genomics 2007, 30 (1) 89-94
15. Pellitteri-Hahn, M. C.; Warren, M. C.; Didier, D. N.; Winkler, E. L.; Mirza, S. P.; Greene, A. S.; Olivier, M. Improved mass spectrometric proteomic profiling of the secretome of rat vascular endothelial cells J. Proteome Res. 2006, 5 (10) 2861-4
16. Kratchmarova, I.; Kalume, D. E.; Blagoev, B.; Scherer, P. E.; Podtelejnikov, A. V.; Molina, H.; Bickel, P. E.; Andersen, J. S.; Fernandez, M. M.; Bunkenborg, J.; Roepstorff, P.; Kristiansen, K.; Lodish, H. F.; Mann, M.; Pandey, A. A proteomic approach for identification of secreted proteins during the differentiation of 3T3-L1 preadipocytes to adipocytes Mol. Cell. Proteomics 2002, 1 (3) 213-22
17. Roth, J. Protein N-glycosylation along the secretory pathway: relationship to organelle topography and function, protein quality control, and cell interactions Chem. Rev. 2002, 102 (2) 285-303
18. Zhang, H.; Li, X. J.; Martin, D. B.; Aebersold, R. Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry Nat. Biotechnol. 2003, 21 (6) 660-6
19. Tian, Y.; Zhou, Y.; Elliott, S.; Aebersold, R.; Zhang, H. Solid-phase extraction of N-linked glycopeptides Nat. Protocols 2007, 2, 334-9
20. Zhou, Y.; Aebersold, R.; Zhang, H. Isolation of N-linked glycopeptides from plasma Anal. Chem. 2007, 79 (15) 5826-37
21. Zou, Z.; Ibisate, M.; Zhou, Y.; Aebersold, R.; Xia, Y.; Zhang, H. Synthesis and evaluation of superparamagnetic silica particles for extraction of glycopeptides in the microtiter plate format Anal. Chem. 2008, 80 (4) 1228-34
22. Zhang, H.; Yi, E. C.; Li, X. J.; Mallick, P.; Kelly-Spratt, K. S.; Masselon, C. D.; Camp, D. G., 2nd; Smith, R. D.; Kemp, C. J.; Aebersold, R. High throughput quantitative analysis of serum proteins using glycopeptide capture and liquid chromatography mass spectrometry Mol. Cell. Proteomics 2005, 4 (2) 144-55
23. Durand, G.; Seta, N. Protein glycosylation and diseases: blood and urinary oligosaccharides as markers for diagnosis and therapeutic monitoring Clin. Chem. 2000, 46 (6 Pt 1) 795-805
24. Li, X. J.; Yi, E. C.; Kemp, C. J.; Zhang, H.; Aebersold, R. A software suite for the generation and comparison of Peptide arrays from sets of data collected by liquid chromatography-mass spectrometry Mol. Cell. Proteomics 2005, 4 (9) 1328-40
25. Li, X. J.; Zhang, H.; Ranish, J. A.; Aebersold, R. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry Anal. Chem. 2003, 75 (23) 6648-57
26. Eng, J.; McCormack, A. L.; Yates, J. R., 3rd An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database J. Am. Soc. Mass Spectrom. 1994, 5, 976-89
27. Han, D. K.; Eng, J.; Zhou, H.; Aebersold, R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry Nat. Biotechnol. 2001, 19 (10) 946-51
28. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search Anal. Chem. 2002, 74 (20) 5383-92
29. Tian, Y.; Tan, A.; Sun, X.; Olson, M. T.; Xie, Z.; Jinawath, N.; Chan, D. W.; Shih Ie, M.; Zhang, Z.; Zhang, H. Quantitative Proteomic Analysis of Ovarian Cancer Cells Identified Mitochondrial Proteins Associated with Paclitaxel Resistance Proteomics: Clin. Appl. 2009, 3 (11) 1288-95
30. Nielsen, H.; Engelbrecht, J.; Brunak, S.; von Heijne, G. A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Int. J. Neural Syst. 1997, 8 (5-6) 581-99
31. Krogh, A.; Larsson, B.; von Heijne, G.; Sonnhammer, E. L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes J. Mol. Biol. 2001, 305 (3) 567-80
32. Su, A. I.; Wiltshire, T.; Batalov, S.; Lapp, H.; Ching, K. A.; Block, D.; Zhang, J.; Soden, R.; Hayakawa, M.; Kreiman, G.; Cooke, M. P.; Walker, J. R.; Hogenesch, J. B. A gene atlas of the mouse and human protein-encoding transcriptomes Proc. Natl. Acad. Sci. U.S.A. 2004, 101 (16) 6062-7
33. Tian, Y.; Kelly-Spratt, K. S.; Kemp, K. S.; Zhang, H. Identification of glycoproteins from mouse skin tumors and plasma Clin. Proteomics 2008, 4 (2) XXX
34. Bause, E. Structural requirements of N-glycosylation of proteins. Studies with proline peptides as conformational probes Biochem. J. 1983, 209 (2) 331-6
35. Nielsen, H.; Engelbrecht, J.; Brunak, S.; von Heijne, G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Protein Eng. 1997, 10 (1) 1-6
36. Liu, H.; Sadygov, R. G.; Yates, J. R., 3rd A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal. Chem. 2004, 76 (14) 4193-201
37. Li, X.-J.; Pedrioli, P.; Eng, J.; Martin, D.; Yi, E.; Lee, H.; Aebersold, R. A tool to visualize and evaluate data obtained by liquid chromatography/electrospray ionization/mass spectrometry 2004, 76, 3856-60
38. Su, A. I.; Cooke, M. P.; Ching, K. A.; Hakak, Y.; Walker, J. R.; Wiltshire, T.; Orth, A. P.; Vega, R. G.; Sapinoso, L. M.; Moqrich, A.; Patapoutian, A.; Hampton, G. M.; Schultz, P. G.; Hogenesch, J. B. Large-scale analysis of the human and mouse transcriptomes Proc Natl. Acad. Sci. U.S.A. 2002, 99 (7) 4465-70
39. Jongeneel, C. V.; Delorenzi, M.; Iseli, C.; Zhou, D.; Haudenschild, C. D.; Khrebtukova, I.; Kuznetsov, D.; Stevenson, B. J.; Strausberg, R. L.; Simpson, A. J.; Vasicek, T. J. An atlas of human gene expression from massively parallel signature sequencing (MPSS) Genome Res. 2005, 15 (7) 1007-14
40. Egland, K. A.; Vincent, J. J.; Strausberg, R.; Lee, B.; Pastan, I. Discovery of the breast cancer gene BASE using a molecular approach to enrich for genes encoding membrane and secreted proteins Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (3) 1099-104
41. Oda, Y.; Huang, K.; Cross, F. R.; Cowburn, D.; Chait, B. T. Accurate quantitation of protein expression and site-specific phosphorylation Proc. Natl. Acad. Sci. U.S.A. 1999, 96 (12) 6591-6
42. Veenstra, T. D.; Martinovic, S.; Anderson, G. A.; Pasa-Tolic, L.; Smith, R. D. Proteome analysis using selective incorporation of isotopically labeled amino acids J. Am. Soc. Mass Spectrom. 2000, 11 (1) 78-82
43. Gygi, S. P.; Aebersold, R. Absolute quantitation of 2-D protein spots Methods Mol. Biol. 1999, 112, 417-21
44. Link, A. J.; Eng, J.; Schieltz, D. M.; Carmack, E.; Mize, G. J.; Morris, D. R.; Garvik, B. M.; Yates, J. R. 3rd, Direct analysis of protein complexes using mass spectrometry Nat. Biotechnol. 1999, 17 (7) 676-82
45. Wu, C. C.; Yates, J. R. 3rd, The application of mass spectrometry to membrane proteomics Nat. Biotechnol. 2003, 21 (3) 262-7
46. Zhang, H.; Loriaux, P.; Eng, J.; Campbell, D.; Keller, A.; Moss, P.; Bonneau, R.; Zhang, N.; Zhou, Y.; Wollscheid, B.; Cooke, K.; Yi, E. C.; Lee, H.; Peskind, E. R.; Zhang, J.; Smith, R. D.; Aebersold, R. UniPep - a database for human N-linked glycosites: a resource for biomarker discovery Genome Biol. 2006, 7 (8) R73
47. Tian, Y.; Gurley, K.; Meany, D. L.; Kemp, C. J.; Zhang, H. N-linked glycoproteomic analysis of formalin-fixed and paraffin-embedded tissues J. Proteome Res. 2009, 8 (4) 1657-62
48. Marshak-Rothstein, A. Toll-like receptors in systemic autoimmune disease Nat. Rev. Immunol. 2006, 6 (11) 823-35
49. von Heijne, G. Membrane-protein topology Nat. Rev. Mol. Cell Biol. 2006, 7 (12) 909-18
50. Melen, K.; Krogh, A.; von Heijne, G. Reliability measures for membrane protein topology prediction algorithms J. Mol. Biol. 2003, 327 (3) 735-44
51. Ikeda, M.; Arai, M.; Okuno, T.; Shimizu, T. TMPDB: a database of experimentally-characterized transmembrane topologies Nucleic Acids Res. 2003, 31 (1) 406-9
52. Kornfeld, R.; Kornfeld, S. Assembly of asparagine-linked oligosaccharides Annu. Rev. Biochem. 1985, 54, 631-64
53. Kaji, H.; Saito, H.; Yamauchi, Y.; Shinkawa, T.; Taoka, M.; Hirabayashi, J.; Kasai, K.; Takahashi, N.; Isobe, T. Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins Nat. Biotechnol. 2003, 21 (6) 667-72
54. Ghesquiere, B.; Van Damme, J.; Martens, L.; Vandekerckhove, J.; Gevaert, K. Proteome-wide characterization of N-glycosylation events by diagonal chromatography J. Proteome Res. 2006, 5 (9) 2438-47
55. Bernhard, O. K.; Kapp, E. A.; Simpson, R. J. Enhanced analysis of the mouse plasma proteome using cysteine-containing tryptic glycopeptides J. Proteome Res. 2007, 6 (3) 987-95
56. Gundry, R. L.; Raginski, K.; Tarasova, Y.; Tchernyshyov, I.; Bausch-Fluck, D.; Elliott, S. T.; Boheler, K. R.; Van Eyk, J. E.; Wollscheid, B. The mouse C2C12 myoblast cell surface N-linked glycoproteome: identification, glycosite occupancy, and membrane orientation Mol. Cell. Proteomics 2009, 8 (11) 2555-69