Combining results from lectin affinity chromatography and glycocapture approaches substantially improves the coverage of the glycoproteome

Molecular and Cellular Proteomics

Volumn 8, Issue 2, 2009, Pages 287-301

  McDonald, Claudia A ^a   Yang, Jane Y ^a   Marathe, Vinita ^a   Yen, Ten Yang ^a   Macher, Bruce A ^a  

^a SAN FRANCISCO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLYCOPROTEIN; HYDRAZIDE; LECTIN; MEMBRANE PROTEIN; PROTEOME; RESIN; SIALIC ACID;

AFFINITY CHROMATOGRAPHY; AMINO ACID SEQUENCE; ARTICLE; CELL CYCLE; CELL LYSATE; CELL MEMBRANE; CONTROLLED STUDY; HELA CELL; HUMAN; HUMAN CELL; HUMAN CELL CULTURE; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN SECRETION; PROTEOMICS; WESTERN BLOTTING;

AMINO ACID SEQUENCE; CELL CYCLE; CELL MEMBRANE; CHROMATOGRAPHY, AFFINITY; GLYCOMICS; GLYCOPEPTIDES; GLYCOPROTEINS; GLYCOSYLATION; HELA CELLS; HUMANS; HYDRAZINES; LECTINS; MAACKIA; MEMBRANE GLYCOPROTEINS; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; PEPTIDE-N4-(N-ACETYL-BETA-GLUCOSAMINYL) ASPARAGINE AMIDASE; PERIODIC ACID; POLYMERS; PROTEOME; SUBCELLULAR FRACTIONS;

EID: 61649103556     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M800272-MCP200     Document Type: Article

References (61)

1. Apweiler, R., Hermjakob, H., and Sharon, N. (1999) On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. Biochim. Biophys. Acta 1473, 4-8
2. Schachter, H. (1991) The 'yellow brick road' to branched complex Nglycans. Glycobiology 1, 453-461
3. Kornfeld, S. (1986) Trafficking of lysosomal enzymes in normal and disease states. J. Clin. Investig. 77, 1-6
4. Trombetta, E. S., and Parodi, A. J. (2003) Quality control and protein folding in the secretory pathway. Annu. Rev. Cell Dev. Biol. 19, 649-676
5. Lowe, J. B., and Marth, J. D. (2003) A genetic approach to Mammalian glycan function. Annu. Rev. Biochem. 72, 643-691
6. Hakomori, S. (1996) Tumor malignancy defined by aberrant glycosylation and sphingo(glyco)lipid metabolism. Cancer Res. 56, 5309-5318
7. Haltiwanger, R. S. (2002) Regulation of signal transduction pathways in development by glycosylation. Curr. Opin. Struct. Biol. 12, 593-598
8. Martin, P. T., and Freeze, H. H. (2003) Glycobiology of neuromuscular disorders. Glycobiology 13, 67R-75R
9. Wopereis, S., Lefeber, D. J., Morava, E., and Wevers, R. A. (2006) Mechanisms in protein O-glycan biosynthesis and clinical and molecular aspects of protein O-glycan biosynthesis defects: a review. Clin. Chem. 52, 574-600
10. Bard, F., and Malhotra, V. (2006) The formation of TGN-to-plasma-membrane transport carriers. Annu. Rev. Cell Dev. Biol. 22, 439-455
11. Lippincott-Schwartz, J., Roberts, T. H., and Hirschberg, K. (2000) Secretory protein trafficking and organelle dynamics in living cells. Annu. Rev. Cell Dev. Biol. 16, 557-589
12. Hedlund, M., Ng, E., Varki, A., and Varki, N. M. (2008) α2-6-Linked sialic acids on N-glycans modulate carcinoma differentiation in vivo. Cancer Res. 68, 388-394
13. Roth, J. (1993) Cellular sialoglycoconjugates: a histochernical perspective. Histochem. J. 25, 687-710
14. Schrohl, A. S., Holten-Andersen, M., Sweep, F., Schmitt, M., Harbeck, N., Foekens, J., and Brunner, N. (2003) Tumor markers; from laboratory to clinical utility. Mol. Cell. Proteomics 2, 378-387
15. Zhang, H., Li, X. J., Martin, D. B., and Aebersold, R. (2003) Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat. Biotechnol. 21, 660-666
16. Zhou, Y., Aebersold, R., and Zhang, H. (2007) Isolation of N-linked glycopeptides from plasma. Anal. Chem. 79, 5826-5837
17. Wang, W. C., and Cummings, R. D. (1988) The immobilized leukoagglutinin from the seeds of Maackia amurensis binds with high affinity to complextype Asn-linked oligosaccharides containing terminal sialic acid-linked α-2,3 to penultimate galactose residues. J. Biol. Chem. 263, 4576-4585
18. Konami, Y., Yamamoto, K., Osawa, T., and Irimura, T. (1994) Strong affinity of Maackia amurensis hemagglutinin (MAH) for sialic acid-containing Ser/Thr-linked carbohydrate chains of N-terminal octapeptides from human glycophorin A. FEBS Lett. 342, 334-338
19. Imberty, A., Gautier, C., Lescar, J., Perez, S., Wyns, L., and Loris, R. (2000) An unusual carbohydrate binding site revealed by the structures of two Maackia amurensis lectins complexed with sialic acid-containing oligosaccharides. J. Biol. Chem. 275, 17541-17548
20. Whitfield, M. L., Zheng, L. X., Baldwin, A., Ohta, T., Hurt, M. M., and Marzluff, W. F. (2000) Stem-loop binding protein, the protein that binds the 3′ end of histone mRNA, is cell cycle regulated by both translational and posttranslational mechanisms. Mol. Cell. Biol. 20, 4188-4198
21. Garner, A. E., Smith, D. A., and Hooper, N. M. (2008) Visualization of detergent solubilization of membranes: implications for the isolation of rafts. Biophys. J. 94, 1326-1340
22. Craig, R., and Beavis, R. C. (2003) A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun. Mass Spectrom. 17, 2310-2316
23. Eng, J. K., McCormack, A. L., and Yates, J. R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5, 976-989
24. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567
25. Masters, J. R. (2002) HeLa cells 50 years on: the good, the bad and the ugly. Nat. Rev. 2, 315-319
26. Yi, E. C., Marelli, M., Lee, H., Purvine, S. O., Aebersold, R., Aitchison, J. D., and Goodlett, D. R. (2002) Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis 23, 3205-3216
27. Wolters, D. A., Washburn, M. P., and Yates, J. R., III (2001) An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73, 5683-5690
28. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392
29. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658
30. Millan, J. L. (1988) Oncodevelopmental expression and structure of alkaline phosphatase genes. Anticancer Res. 8, 995-1004
31. Marieb, E. A., Zoltan-Jones, A., Li, R., Misra, S., Ghatak, S., Cao, J., Zucker, S., and Toole, B. P. (2004) Emmprin promotes anchorage-independent growth in human mammary carcinoma cells by stimulating hyaluronan production. Cancer Res. 64, 1229-1232
32. Sleat, D. E., Wang, Y., Sohar, I., Lackland, H., Li, Y., Li, H., Zheng, H., and Lobel, P. (2006) Identification and validation of mannose 6-phosphate glycoproteins in human plasma reveal a wide range of lysosomal and non-lysosomal proteins. Mol. Cell. Proteomics 5, 1942-1956
33. Kornfeld, S., and Mellman, I. (1989) The biogenesis of lysosomes. Annu. Rev. Cell Biol. 5, 483-525
34. van Meel, E., and Klumperman, J. (2008) Imaging and imagination: understanding the endo-lysosomal system. Histochem. Cell Biol. 129, 253-266
35. Schirle, M., Heurtier, M. A., and Kuster, B. (2003) Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 2, 1297-1305
36. Ramachandran, P., Boontheung, P., Xie, Y., Sondej, M., Wong, D. T., and Loo, J. A. (2006) Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry. J. Proteome Res. 5, 1493-1503
37. Liu, T., Qian, W. J., Gritsenko, M. A., Camp, D. G., II, Monroe, M. E., Moore, R. J., and Smith, R. D. (2005) Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry. J. Proteome Res. 4, 2070-2080
38. Lewandrowski, U., Moebius, J., Walter, U., and Sickmann, A. (2006) Elucidation of N-glycosylation sites on human platelet proteins: a glycoproteomic approach. Mol. Cell. Proteomics 5, 226-233
39. Robinson, N. E., and Robinson, A. B. (2001) Molecular clocks. Proc. Natl. Acad. Sci. U. S. A. 98, 944-949
40. Fedde, K. N., and Sly, W. S. (1985) Ricin-binding properties of acid hydrolases from isolated lysosomes implies prior processing by terminal transferases of the trans-Golgi apparatus. Biochem. Biophys. Res. Commun. 133, 614-620
41. Foster, L. J., De Hoog, C. L., and Mann, M. (2003) Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors. Proc. Natl. Acad. Sci. U. S. A. 100, 5813-5818
42. Foster, L. J., Zeemann, P. A., Li, C., Mann, M., Jensen, O. N., and Kassem, M. (2005) Differential expression profiling of membrane proteins by quantitative proteomics in a human mesenchymal stem cell line undergoing osteoblast differentiation. Stem Cells 23, 1367-1377
43. Li, H., DeSouza, L. V., Ghanny, S., Li, W., Romaschin, A. D., Colgan, T. J., and Siu, K. W. (2007) Identification of candidate biomarker proteins released by human endometrial and cervical cancer cells using two-dimensional liquid chromatography/tandem mass spectrometry. J. Proteome Res. 6, 2615-2622
44. Masuda, T., Tomita, M., and Ishihama, Y. (2008) Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J. Proteome Res. 7, 731-740
45. Sun, B., Ranish, J. A., Utleg, A. G., White, J. T., Yan, X., Lin, B., and Hood, L. (2007) Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics. Mol. Cell. Proteomics 6, 141-149
46. Elortza, F., Mohammed, S., Bunkenborg, J., Foster, L. J., Nuhse, T. S., Brodbeck, U., Peck, S. C., and Jensen, O. N. (2006) Modification-specific proteomics of plasma membrane proteins: identification and characterization of glycosylphosphatidylinositol-anchored proteins released upon phospholipase D treatment. J. Proteome Res. 5, 935-943
47. Kim, D. D., and Song, W. C. (2006) Membrane complement regulatory proteins. Clin. Immunol. 118, 127-136
48. Bogenrieder, T., and Herlyn, M. (2002) Axis of evil: molecular mechanisms of cancer metastasis. Oncogene 22, 6524-6536
49. Talora, C., Sgroi, D. C., Crum, C. P., and Dotto, G. P. (2002) Specific down-modulation of Notch1 signaling in cervical cancer cells is required for sustained HPV-E6/E7 expression and late steps of malignant transformation. Genes Dev. 16, 2252-2263
50. Haapasalo, A., Kim, D. Y., Carey, B. W., Turunen, M. K., Pettingell, W. H., and Kovacs, D. M. (2007) Presenilin/-secretase-mediated cleavage regulates association of leukocyte-common antigen-related (LAR) receptor tyrosine phosphatase with β-catenin. J. Biol. Chem. 282, 9063-9072
51. Uhlen, M., Bjorling, E., Agaton, C., Szigyarto, C. A., Amini, B., Andersen, E., Andersson, A. C., Angelidou, P., Asplund, A., Asplund, C., Berglund, L., Bergstrom, K., Brumer, H., Cerjan, D., Ekstrom, M., Elobeid, A., Eriksson, C., Fagerberg, L., Falk, R., Fall, J., Forsberg, M., Bjorklund, M. G., Gumbel, K., Halimi, A., Hallin, I., Hamsten, C., Hansson, M., Hedhammar, M., Hercules, G., Kampf, C., Larsson, K., Lindskog, M., Lodewyckx, W., Lund, J., Lundeberg, J., Magnusson, K., Malm, E., Nilsson, P., Odling, J., Oksvold, P., Olsson, I., Oster, E., Ottosson, J., Paavilainen, L., Persson, A., Rimini, R., Rockberg, J., Runeson, M., Sivertsson, A., Skollermo, A., Steen, J., Stenvall, M., Sterky, F., Stromberg, S., Sundberg, M., Tegel, H., Tourle, S., Wahlund, E., Walden, A., Wan, J., Wernerus, H., Westberg, J., Wester, K., Wrethagen, U., Xu, L. L., Hober, S., and Ponten, F. (2005) A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteomics 4, 1920-1932
52. Bai, X., Brown, J. R., Varki, A., and Esko, J. D. (2001) Enhanced 3-O-sulfation of galactose in Asn-linked glycans and Maackia amurensis lectin binding in a new Chinese hamster ovary cell line. Glycobiology 11, 621-632
53. Brinkman-Van der Linden, E. C., Sonnenburg, J. L., and Varki, A. (2002) Effects of sialic acid substitutions on recognition by Sambucus nigra agglutinin and Maackia amurensis hemagglutinin. Anal. Biochem. 303, 98-104
54. Bar-Joseph, Z., Siegfried, Z., Brandeis, M., Brors, B., Lu, Y., Eils, R., Dynlacht, B. D., and Simon, I. (2008) Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells. Proc. Natl. Acad. Sci. U. S. A. 105, 955-960
55. Sandhu, C., Connor, M., Kislinger, T., Slingerland, J., and Emili, A. (2005) Global protein shotgun expression profiling of proliferating mcf-7 breast cancer cells. J. Proteome Res. 4, 674-689
56. Tang, W., Chang, S. B., and Hemler, M. E. (2004) Links between CD147 function, glycosylation, and caveolin-1. Mol. Biol. Cell 15, 4043-4050
57. Chillaron, J., Roca, R., Valencia, A., Zorzano, A., and Palacin, M. (2001) Heteromeric amino acid transporters: biochemistry, genetics, and physiology. Am. J. Physiol. 281, F995-F1018
58. Deves, R., and Boyd, C. A. (2000) Surface antigen CD98(4F2): not a single membrane protein, but a family of proteins with multiple functions. J. Membr. Biol. 173, 165-177
59. Kolesnikova, T. V., Mannion, B. A., Berditchevski, F., and Hemler, M. E. (2001) β1 integrins show specific association with CD98 protein in low density membranes. BMC Biochem. 2, 10
60. Merlin, D., Sitaraman, S., Liu, X., Eastburn, K., Sun, J., Kucharzik, T., Lewis, B., and Madara, J. L. (2001) CD98-mediated links between amino acid transport and β1 integrin distribution in polarized columnar epithelia. J. Biol. Chem. 276, 39282-39289
61. Xu, D., and Hemler, M. E. (2005) Metabolic activation-related CD147-CD98 complex. Mol. Cell. Proteomics 4, 1061-1071