Quantitative glycoproteomics for N-glycoproteome profiling

Methods in Molecular Biology

Volumn 1156, Issue , 2014, Pages 379-388

  Pan, Sheng ^a  

^a NONE

Author keywords

Glycoprotein; Glycoproteomics; Glycosylation; Glycosylation site occupancy; Hydrazide chemistry; Lectin; Mass spectrometry; Proteomics; Quantifi cation

Indexed keywords

GLYCOPEPTIDE; GLYCOPROTEIN;

ARTICLE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN GLYCOSYLATION; PROTEOMICS; QUANTITATIVE ANALYSIS; SIZE EXCLUSION CHROMATOGRAPHY; SOLID PHASE EXTRACTION; TANDEM MASS SPECTROMETRY; BIOLOGY; CHEMISTRY; GLYCOSYLATION; LIQUID CHROMATOGRAPHY;

CHROMATOGRAPHY, LIQUID; COMPUTATIONAL BIOLOGY; GLYCOPROTEINS; GLYCOSYLATION; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 84922393687     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0685-7_25     Document Type: Article

References (27)

1. Jones J, Krag SS, Betenbaugh MJ (2005) Controlling N-linked glycan site occupancy. Biochim Biophys Acta 1726:121-137
2. Zhao YY, Takahashi M, Gu JG, Miyoshi E, Matsumoto A, Kitazume S, Taniguchi N (2008) Functional roles of N-glycans in cell signaling and cell adhesion in cancer. Cancer Sci 99:1304-1310
3. Wuhrer M (2013) Glycomics using mass spectrometry. Glycoconj J 30:11-22
4. Pan S, Chen R, Aebersold R, Brentnall TA (2011) Mass spectrometry based glycoproteomics— from a proteomics perspective. Mol Cell Proteomics 10:R110
5. Liu T, Qian WJ, Gritsenko MA, Camp DG, Monroe ME, Moore RJ, Smith RD (2005) Human plasma N-glycoproteome analysis by immunoaffi nity subtraction, hydrazide chemistry, and mass spectrometry. J Proteome Res 4:2070-2080
6. Zhang H, Li XJ, Martin DB, Aebersold R (2003) Identifi cation and quantifi cation of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol 21:660-666
7. Kaji H, Saito H, Yamauchi Y, Shinkawa T, Taoka M, Hirabayashi J, Kasai K, Takahashi N, Isobe T (2003) Lectin affi nity capture, isotopecoded tagging and mass spectrometry to identify N-linked glycoproteins. Nat Biotechnol 21:667-672
8. Qiu R, Regnier FE (2005) Use of multidimensional lectin affi nity chromatography in differential glycoproteomics. Anal Chem 77: 2802-2809
9. Yang Z, Hancock WS (2004) Approach to the comprehensive analysis of glycoproteins isolated from human serum using a multilectin affi nity column. J Chromatogr A 1053:79-88
10. Jung K, Cho W, Regnier FE (2009) Glycoproteomics of plasma based on narrow selectivity lectin affi nity chromatography. J Proteome Res 8:643-650
11. Lee HJ, Na K, Choi EY, Kim KS, Kim H, Paik YK (2010) Simple method for quantitative analysis of N-linked glycoproteins in hepatocellular carcinoma specimens. J Proteome Res 9:308-318
12. Lei Z, Beuerman RW, Chew AP, Koh SK, Cafaro TA, Urrets-Zavalia EA, Urrets-Zavalia JA, Li SF, Serra HM (2009) Quantitative analysis of N-linked glycoproteins in tear fl uid of climatic droplet keratopathy by glycopeptide capture and iTRAQ. J Proteome Res 8: 1992-2003
13. Wilson CR, Regnier FE, Knapp DW, Raskin RE, Andrews DA, Hooser SB (2008) Glycoproteomic profi ling of serum peptides in canine lymphoma and transitional cell carcinoma. Vet Comp Oncol 6:171-181
14. Ueda K, Katagiri T, Shimada T, Irie S, Sato TA, Nakamura Y, Daigo Y (2007) Comparative profi ling of serum glycoproteome by sequential purifi cation of glycoproteins and 2-nitrobenzensulfenyl (NBS) stable isotope labeling: a new approach for the novel biomarker discovery for cancer. J Proteome Res 6:3475-3483
15. Liu Z, Cao J, He Y, Qiao L, Xu C, Lu H, Yang P (2010) Tandem 18O stable isotope labeling for quantifi cation of N-glycoproteome. J Proteome Res 9:227-236
16. Wollscheid B, Bausch-Fluck D, Henderson C, O’Brien R, Bibel M, Schiess R, Aebersold R, Watts JD (2009) Mass-spectrometric identifi-cation and relative quantifi cation of N-linked cell surface glycoproteins. Nat Biotechnol 27:378-386
17. Pan S, Tamura Y, Chen R, May D, McIntosh MW, Brentnall TA (2012) Large-scale quantitative glycoproteomics analysis of site-specifi c glycosylation occupancy. Mol Biosyst 8: 2850-2856
18. Hsu JL, Huang SY, Chow NH, Chen SH (2003) Stable-isotope dimethyl labeling for quantitative proteomics. Anal Chem 75: 6843-6852
19. Sparbier K, Koch S, Kessler I, Wenzel T, Kostrzewa M (2005) Selective isolation of glycoproteins and glycopeptides for MALDITOF MS detection supported by magnetic particles. J Biomol Tech 16:407-413
20. Alvarez-Manilla G, Atwood J III, Guo Y, Warren NL, Orlando R, Pierce M (2006) Tools for glycoproteomic analysis: size exclusion chromatography facilitates identifi cation of tryptic glycopeptides with N-linked glycosylation sites. J Proteome Res 5:701-708
21. Hagglund P, Bunkenborg J, Elortza F, Jensen ON, Roepstorff P (2004) A new strategy for identifi cation of N-glycosylated proteins and unambiguous assignment of their glycosylation sites using HILIC enrichment and partial deglycosylation. J Proteome Res 3:556-566
22. Larsen MR, Hojrup P, Roepstorff P (2005) Characterization of gel-separated glycoproteins using two-step proteolytic digestion combined with sequential microcolumns and mass spectrometry. Mol Cell Proteomics 4:107-119
23. Craig R, Beavis RC (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20:1466-1467
24. Keller A, Eng J, Zhang N, Li XJ, Aebersold R (2005) A uniform proteomics MS/MS analysis platform utilizing open XML fi le formats. Mol Syst Biol 1:2005
25. Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifi cations made by MS/MS and database search. Anal Chem 74:5383-5392
26. May D, Law W, Fitzgibbon M, Fang Q, McIntosh M (2009) Software platform for rapidly creating computational tools for mass spectrometry-based proteomics. J Proteome Res 8:3212-3217
27. Nesvizhskii AI, Vitek O, Aebersold R (2007) Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 4:787-797