Overcoming challenges and opening new opportunities in glycoproteomics

Biomolecules

Volumn 3, Issue 2, 2013, Pages 270-286

  Yen, Ten Yang ^a   Dutta, Sucharita M ^b   Litsakos Cheung, Christina ^a   Corona, Alejandro A ^a   Timpe, Leslie C ^a   Macher, Bruce A ^a  

^a SAN FRANCISCO STATE UNIVERSITY   (United States)

^b Thermo Fisher Scientific   (United States)

Author keywords

Deamidation; Glycoproteomics; Hydrazide modified magnetic beads; N linked glycosites; Orbitrap; Tandem mass spectrometry

Indexed keywords

GLYCOPEPTIDE; TRYPSIN;

ALKYLATION; ARTICLE; CELL LYSATE; ELECTROSPRAY MASS SPECTROMETRY; GLYCOPROTEOMICS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; HUMAN CELL; OXIDATION; PROTEIN ANALYSIS; PROTEIN DENATURATION; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 85016374791     PISSN: None     EISSN: 2218273X     Source Type: Journal    
DOI: 10.3390/biom3020270     Document Type: Article

References (30)

1. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
2. Cravatt, B.F.; Simon, G.M.; Yates, J.R., 3rd. The biological impact of mass-spectrometry-based proteomics. Nature 2007, 450, 991-1000.
3. Andersen, J.S.; Mann, M. Organellar proteomics: Turning inventories into insights. EMBO Rep. 2006, 7, 874-879.
4. Pan, S.; Chen, R.; Aebersold, R.; Brentnall, T.A. Mass spectrometry based glycoproteomics-from a proteomics perspective. Mol. Cell. Proteomics 2011, 10, R110.003251.
5. Anderson, N.L.; Anderson, N.G. The human plasma proteome. Mol. Cell. Proteomics 2002, 1, 845-867.
6. Anderson, N.L. The clinical plasma proteome: A survey of clinical assays for proteins in plasma and serum. Clin. Chem. 2010, 56, 177-185.
7. Thaysen-Andersen, M.; Packer, N.H. Site-Specific glycoproteomics confirms that protein structure dictates formation of N-glycan type, core fucosylation and branching. Glycobiology 2012, 22, 1440-1452.
8. Ramachandran, P.; Boontheung, P.; Xie, Y.; Sondej, M.; Wong, D.T.; Loo, J.A. Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry. J. Proteome Res. 2006, 5, 1493-1503.
9. Tu, C.; Rudnick, P.A.; Martinez, M.Y.; Cheek, K.L.; Stein, S.E.; Slebos, R.J.; Liebler, D.C. Depletion of abundant plasma proteins and limitations of plasma proteomics. J. Proteome Res. 2010, 9, 4982-4991.
10. Chen, R.; Jiang, X.; Sun, D.; Han, G.; Wang, F.; Ye, M.; Wang, L.; Zou, H. Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry. J. Proteome Res. 2009, 8, 651-661.
11. Gonzalez, J.; Takao, T.; Hori, H.; Besada, V.; Rodriguez, R.; Padron, G.; Shimonishi, Y. A method for determination of N-glycosylation sites in glycoproteins by collision-induced dissociation analysis in fast atom bombardment mass spectrometry: Identification of the positions of carbohydrate-linked asparagine in recombinant alpha-amylase by treatment with peptide-N-glycosidase F in 18O-labeled water. Anal. Biochem. 1992, 205, 151-158.
12. Wright, T.H. Nonenzymatic deamidation of asparaginyl and glutaminyl residues in protein. Crit. Rev. Biochem. Mol. Biol. 1991, 26, 1-52.
13. Palmisano, G.; Melo-Braga, M.N.; Engholm-Keller, K.; Parker, B.L.; Larsen, M.R. Chemical deamidation: A common pitfall in large-scale N-linked glycoproteomic mass spectrometry-based analyses. J. Proteome Res. 2012, 11, 1949-1957.
14. Hao, P.; Ren, Y.; Alpert, A.J.; Sze, S.K. Detection, evaluation and minimization of nonenzymatic deamidation in proteomic sample preparation. Mol. Cell. Proteomics 2011, 10, O111.009381.
15. Robinson, N.E.; Robinson, A.B. Molecular clocks. Proc. Natl. Acad. Sci. USA 2001, 98, 944-949.
16. Kuster, B.; Mann, M. 18O-Labeling of N-glycosylation sites to improve the identification of gel-separated glycoproteins using peptide mass mapping and database searching. Anal. Chem. 1999, 71, 1431-1440
17. 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. Biotech. 2003, 21, 660-666.
18. McDonald, C.A.; Yang, J.Y.; Marathe, V.; Yen, T.Y.; Macher, B.A. Combining results from lectin affinity chromatography and glycocapture approaches substantially improves the coverage of the glycoproteome. Mol. Cell. Proteomics 2009, 8, 287-301.
19. Arcinas, A.; Yen, T.Y.; Kebebew, E.; Macher, B.A. Cell surface and secreted protein profiles of human thyroid cancer cell lines reveal distinct glycoprotein patterns. J. Proteome Res. 2009, 8, 3958-3968.
20. Yen, T.Y.; Macher, B.A.; McDonald, C.A.; Alleyne-Chin, C.; Timpe, L.C. Glycoprotein profiles of human breast cells demonstrate a clear clustering of normal/benign versus malignant cell lines and basal versus luminal cell lines. J. Proteome Res. 2012, 11, 656-667.
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, 1228-1234.
22. Michalski, A.; Damoc, E.; Hauschild, J.P.; Lange, O.; Wieghaus, A.; Makarov, A.; Nagaraj, N.; Cox, J.; Mann, M.; Horning, S. Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer. Mol. Cell. Proteomics 2011, 10, M111.011015.
23. Johnson, R.S.; Martin, S.A.; Biemann, K.; Stults, J.T.; Watson, J.T. Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: Differentiation of leucine and isoleucine. Anal. Chem. 1987, 59, 2621-2625.
24. Schwartz, J.C.; Senko, M.W.; Syka, J.E.P. A two-dimensional quadrupole ion trap mass spectrometer. J. Am. Soc. Mass Spectrom. 2002, 13, 659-669.
25. Boersema, P.J.; Geiger, T.; Wiśniewski, J.R.; Mann, M. Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples. Mol. Cell. Proteomics 2012, 12, 158-171.
26. Drake, P.M.; Schilling, B.; Niles, R.K.; Prakobphol, A.; Li, B.; Jung, K.; Cho, W.; Braten, M.; Inerowicz, H.D.; Williams, K et al. Lectin chromatography/mass spectrometry discovery workflow identifies putative biomarkers of aggressive breast cancers. J. Proteome Res. 2012, 11, 2508-2520.
27. Zhang, Y.; Wen, Z.; Washburn, M.P.; Florens, L. Effect of dynamic exclusion duration on spectral count based quantitative proteomics. Anal. Chem. 2009, 81, 6317-6326.
28. Perkins, D.N.; Pappin, D.J.; Creasy, D.M.; Cottrell, J.S. Probability-Based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
29. Nesvizhskii, A.I.; Keller, A.; Kolker, E.; Aebersold, R. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 2003, 75, 4646-4658.
30. 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, 5383-5392.