The glycofilter: A simple and comprehensive sample preparation platform for proteomics, N-glycomics and glycosylation site assignment

Molecular and Cellular Proteomics

Volumn 12, Issue 10, 2013, Pages 2981-2991

  Zhou, Hui ^a   Froehlich, John W ^a   Briscoe, Andrew C ^a   Lee, Richard S ^a  

^a BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARAGINE; FETUIN; GLYCAN; GLYCAN DERIVATIVE; GLYCOPROTEIN; IMMUNOGLOBULIN G; N ACETYLNEURAMINIC ACID; N GLYCAN; N GLYCOME; N GLYCOPROTEOME; N GLYCOSITE; PROTEIN; PROTEOME; RIBONUCLEASE; SUGAR; TRYPSIN; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DE N GLYCOSYLATION; DEAMINATION; FILTRATION; GLYCOBIOLOGY; GLYCOFILTER; GLYCOSYLATION; GLYCOSYLATION SITE; HUMAN; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MICROWAVE IRRADIATION; N GLYCOMICS; NORMAL HUMAN; PLASMA; PREPROCESSING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN PROCESSING; PROTEOMICS; SEPARATION TECHNIQUE; TANDEM MASS SPECTROMETRY; URINALYSIS;

ANIMALS; CATTLE; CHROMATOGRAPHY, LIQUID; FETUINS; GLYCOMICS; GLYCOPROTEINS; GLYCOSYLATION; HUMANS; IMMUNOGLOBULIN G; POLYSACCHARIDES; PROTEOMICS; RIBONUCLEASES; TANDEM MASS SPECTROMETRY;

EID: 84885163658     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M113.027953     Document Type: Article

References (45)

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. Stanley, P., Schachter, H., and Taniguchi, N. (2009) N-Glycans. In: Varki, A., Cummings, R. D., Esko, J. D., Freeze, H. H., Stanley, P., Bertozzi, C. R., Hart, G. W., and Etzler, M. E., eds. Essentials of Glycobiology, 2nd Ed., Cold Spring Harbor (NY)
3. Mariño, K., Bones, J., Kattla, J. J., and Rudd, P. M. (2010) A systematic approach to protein glycosylation analysis: a path through the maze. Nat. Chem. Biol. 6, 713-723
4. Ghaderi, D., Taylor, R. E., Padler-Karavani, V., Diaz, S., and Varki, A. (2010) Implications of the presence of N-glycolylneuraminic acid in recombinant therapeutic glycoproteins. Nat. Biotechnol. 28, 863-867
5. Bosques, C. J., Collins, B. E., Meador, J. W., 3rd, Sarvaiya, H., Murphy, J. L., Dellorusso, G., Bulik, D. A., Hsu, I. H., Washburn, N., Sipsey, S. F., Myette, J. R., Raman, R., Shriver, Z., Sasisekharan, R., and Venkataraman, G. (2010) Chinese hamster ovary cells can produce galactosealpha-1, 3-galactose antigens on proteins. Nat. Biotechnol. 28, 1153-1156
6. Hart, G. W., and Copeland, R. J. (2010) Glycomics hits the big time. Cell 143, 672-676
7. Steentoft, C., Vakhrushev, S. Y., Vester-Christensen, M. B., Schjoldager, K. T., Kong, Y., Bennett, E. P., Mandel, U., Wandall, H., Levery, S. B., and Clausen, H. (2011) Mining the O-glycoproteome using zinc-finger nuclease-glycoengineered SimpleCell lines. Nat. Methods 8, 977-982
8. 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
9. Kaji, H., Saito, H., Yamauchi, Y., Shinkawa, T., Taoka, M., Hirabayashi, J., Kasai, K., Takahashi, N., and Isobe, T. (2003) Lectin affinity capture, isotope-coded tagging and mass spectrometry to identify N-linked glycoproteins. Nat. Biotechnol. 21, 667-672
10. Pan, S., Chen, R., Aebersold, R., and Brentnall, T. A. (2011) Mass spectrometry based glycoproteomics-from a proteomics perspective. Mol. Cell. Proteomics 10, R110.003251
11. Wiśniewski, J. R., Zougman, A., Nagaraj, N., and Mann, M. (2009) Universal sample preparation method for proteome analysis. Nat. Methods 6, 359-362
12. Zielinska, D. F., Gnad, F., Wiśniewski, J. R., and Mann, M. (2010) Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 141, 897-907
13. Liu, T., Qian, W. J., Gritsenko, M. A., Camp, D. G., 2nd, 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
14. Walsh, C. T., Garneau-Tsodikova, S., and Gatto, G. J., Jr. (2005) Protein posttranslational modifications: the chemistry of proteome diversifications. Angew Chem. Int. Ed. Engl. 44, 7342-7372
15. Petrescu, A. J., Milac, A. L., Petrescu, S. M., Dwek, R. A., and Wormald, M. R. (2004) Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding. Glycobiology 14, 103-114
16. Sumer-Bayraktar, Z., Kolarich, D., Campbell, M. P., Ali, S., Packer, N. H., and Thaysen-Andersen, M. (2011) N-glycans modulate the function of human corticosteroid-binding globulin. Mol. Cell. Proteomics 10, M111.009100
17. Vaezzadeh, A. R., Briscoe, A. C., Steen, H., and Lee, R. S. (2010) One-step sample concentration, purification, and albumin depletion method for urinary proteomics. J. Proteome Res. 9, 6082-6089
18. Zhou, H., Briscoe, A. C., Froehlich, J. W., and Lee, R. S. (2012) PNGase F catalyzes de-N-glycosylation in a domestic microwave. Anal. Biochem. 427, 33-35
19. Vaezzadeh, A. R., Deshusses, J. M., Waridel, P., François, P., Zimmermann-Ivol, C. G., Lescuyer, P., Schrenzel, J., and Hochstrasser, D. F. (2010) Accelerated digestion for high-throughput proteomics analysis of whole bacterial proteomes. J. Microbiol. Methods 80, 56-62
20. Ciucanu, I., and Costello, C. E. (2003) Elimination of oxidative degradation during the per-O-methylation of carbohydrates. J. Am. Chem. Soc. 125, 16213-16219
21. Kang, P., Mechref, Y., Klouckova, I., and Novotny, M. V. (2005) Solid-phase permethylation of glycans for mass spectrometric analysis. Rapid Commun. Mass Spectrom. 19, 3421-3428
22. 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
23. Choi, H., Ghosh, D., and Nesvizhskii, A. I. (2008) Statistical validation of peptide identifications in large-scale proteomics using the target-decoy database search strategy and flexible mixture modeling. J. Proteome Res. 7, 286-292
24. Qin, H., Zhao, L., Li, R., Wu, R., and Zou, H. (2011) Size-selective enrichment of N-linked glycans using highly ordered mesoporous carbon material and detection by MALDI-TOF MS. Anal. Chem. 83, 7721-7728
25. Green, E. D., Adelt, G., Baenziger, J. U., Wilson, S., and Van Halbeek, H. (1988) The asparagine-linked oligosaccharides on bovine fetuin. Structural analysis of N-glycanase-released oligosaccharides by 500-megahertz 1H NMR spectroscopy. J. Biol. Chem. 263, 18253-18268
26. Huhn, C., Selman, M. H., Ruhaak, L. R., Deelder, A. M., and Wuhrer, M. (2009) IgG glycosylation analysis. Proteomics 9, 882-913
27. Wada, Y., Azadi, P., Costello, C. E., Dell, A., Dwek, R. A., Geyer, H., Geyer, R., Kakehi, K., Karlsson, N. G., Kato, K., Kawasaki, N., Khoo, K. H., Kim, S., Kondo, A., Lattova, E., Mechref, Y., Miyoshi, E., Nakamura, K., Narimatsu, H., Novotny, M. V., Packer, N. H., Perreault, H., Peter-Katalinic, J., Pohlentz, G., Reinhold, V. N., Rudd, P. M., Suzuki, A., and Taniguchi, N. (2007) Comparison of the methods for profiling glycoprotein glycans-HUPO Human Disease Glycomics/Proteome Initiative multiinstitutional study. Glycobiology 17, 411-422
28. Palmisano, G., Melo-Braga, M. N., Engholm-Keller, K., Parker, B. L., and Larsen, M. R. (2012) Chemical deamidation: a common pitfall in largescale N-linked glycoproteomic mass spectrometry-based analyses. J. Proteome Res. 11, 1949-1957
29. Chen, R., Jiang, X., Sun, D., Han, G., Wang, F., Ye, M., Wang, L., and Zou, H. (2009) Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry. J. Proteome Res. 8, 651-661
30. Tu, C., Rudnick, P. A., Martinez, M. Y., Cheek, K. L., Stein, S. E., Slebos, R. J., and Liebler, D. C. (2010) Depletion of abundant plasma proteins and limitations of plasma proteomics. J. Proteome Res. 9, 4982-4991
31. Addona, T. A., Shi, X., Keshishian, H., Mani, D. R., Burgess, M., Gillette, M. A., Clauser, K. R., Shen, D., Lewis, G. D., Farrell, L. A., Fifer, M. A., Sabatine, M. S., Gerszten, R. E., and Carr, S. A. (2011) A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease. Nat. Biotechnol. 29, 635-643
32. Carlson, D. M. (1968) Structures and immunochemical properties of oligosaccharides isolated from pig submaxillary mucins. J. Biol. Chem. 243, 616-626
33. Xia, B., Kawar, Z. S., Ju, T., Alvarez, R. A., Sachdev, G. P., and Cummings, R. D. (2005) Versatile fluorescent derivatization of glycans for glycomic analysis. Nat. Methods 2, 845-850
34. Halim, A., Nilsson, J., Ruetschi, U., Hesse, C., and Larson, G. (2012) Human urinary glycoproteomics; attachment site specific analysis of N-and O-linked glycosylations by CID and ECD. Mol. Cell. Proteomics 11, M111.013649
35. Ruhaak, L. R., Zauner, G., Huhn, C., Bruggink, C., Deelder, A. M., and Wuhrer, M. (2010) Glycan labeling strategies and their use in identification and quantification. Anal. Bioanal. Chem. 397, 3457-3481
36. Boersema, P. J., Geiger, T., Wisniewski, J. R., and Mann, M. (2013) Quantification of the N-glycosylated Secretome by Super-SILAC During Breast Cancer Progression and in Human Blood Samples. Mol. Cell. Proteomics 12, 158-171
37. Wada, Y., Gu, J., Okamoto, N., and Inui, K. (1994) Diagnosis of carbohydrate-deficient glycoprotein syndrome by matrix-assisted laser desorption time-of-flight mass spectrometry. Biol. Mass Spectrom. 23, 108-109
38. Domon, B., and Aebersold, R. (2010) Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 28, 710-721
39. Hülsmeier, A. J., Paesold-Burda, P., and Hennet, T. (2007) N-glycosylation site occupancy in serum glycoproteins using multiple reaction monitoring liquid chromatography-mass spectrometry. Mol. Cell. Proteomics 6, 2132-2138
40. Sturiale, L., Barone, R., and Garozzo, D. (2011) The impact of mass spectrometry in the diagnosis of congenital disorders of glycosylation. J. Inherited Metabolic Dis. 34, 891-899
41. Liu, Z., Cao, J., He, Y., Qiao, L., Xu, C., Lu, H., and Yang, P. (2010) Tandem 18O stable isotope labeling for quantification of N-glycoproteome. J. Proteome Res. 9, 227-236
42. Ueda, K., Takami, S., Saichi, N., Daigo, Y., Ishikawa, N., Kohno, N., Katsumata, M., Yamane, A., Ota, M., Sato, T. A., Nakamura, Y., and Nakagawa, H. (2010) Development of serum glycoproteomic profiling technique; simultaneous identification of glycosylation sites and site-specific quantification of glycan structure changes. Mol. Cell. Proteomics 9, 1819-1828
43. Pan, S., Tamura, Y., Chen, R., May, D., McIntosh, M. W., and Brentnall, T. A. (2012) Large-scale quantitative glycoproteomics analysis of sitespecific glycosylation occupancy. Mol. Biosyst. 8, 2850-2856
44. Wu, R., Haas, W., Dephoure, N., Huttlin, E. L., Zhai, B., Sowa, M. E., and Gygi, S. P. (2011) A large-scale method to measure absolute protein phosphorylation stoichiometries. Nat. Methods 8, 677-683
45. Roepstorff, P., and Fohlman, J. (1984) Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed. Mass Spectrom. 11, 601