Optimizing performance of glycopeptide capture for plasma proteomics

Journal of Proteome Research

Volumn 9, Issue 4, 2010, Pages 1706-1715

  Berven, Frode S ^a,b   Ahmad, Rushdy ^a   Clauser, Karl R ^a   Carr, Steven A ^a  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b UNIVERSITY OF BERGEN   (Norway)

Author keywords

Biomarker discovery; Glycopeptide; Glycoproteins; Hydrazide chemistry; Proteomics; Solid phase extraction of N linked glycoproteins

Indexed keywords

GLYCOPEPTIDE; GLYCOPROTEIN;

ARTICLE; CONTROLLED STUDY; FUNCTIONAL PROTEOMICS; GLYCOSYLATION; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PEPTIDE ANALYSIS; PLASMA; PRIORITY JOURNAL; PROTEIN ANALYSIS; SENSITIVITY AND SPECIFICITY; SOLID PHASE EXTRACTION;

CHROMATOGRAPHY, LIQUID; GLYCOPEPTIDES; GLYCOPROTEINS; HUMANS; HYDRAZINES; MAGNETICS; MASS SPECTROMETRY; MICROSPHERES; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SODIUM ACETATE; SODIUM CHLORIDE; SOLID PHASE EXTRACTION;

EID: 77950662044     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr900845m     Document Type: Article

References (25)

1. Davis, M. A.; Hanash, S. High-throughput genomic technology in research and clinical management of breast cancer. Plasma-based proteomics in early detection and therapy Breast Cancer Res. 2006, 8 (6) 217
2. Geho, D. H.; Liotta, L. A.; Petricoin, E. F.; Zhao, W.; Araujo, R. P. The amplified peptidome: the new treasure chest of candidate biomarkers Curr. Opin. Chem. Biol. 2006, 10 (1) 50 - 5
3. Rifai, N.; Gillette, M. A.; Carr, S. A. Protein biomarker discovery and validation: the long and uncertain path to clinical utility Nat. Biotechnol. 2006, 24 (8) 971 - 83
4. Pitteri, S. J.; Hanash, S. M. Proteomic approaches for cancer biomarker discovery in plasma Expert Rev. Proteomics 2007, 4 (5) 589 - 90
5. Anderson, L. Candidate-based proteomics in the search for biomarkers of cardiovascular disease J. Physiol. 2005, 563 (Pt 1) 23 - 60
6. Schenk, S.; Schoenhals, G. J.; de Souza, G.; Mann, M. A high confidence, manually validated human blood plasma protein reference set BMC Med. Genomics 2008, 1, 41
7. Hu, S.; Loo, J. A.; Wong, D. T. Human body fluid proteome analysis Proteomics 2006, 6 (23) 6326 - 53
8. Rajcevic, U.; Niclou, S. P.; Jimenez, C. R. Proteomics strategies for target identification and biomarker discovery in cancer Front. Biosci. 2009, 14, 3292 - 303
9. 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
10. Freeze, H. H. Update and perspectives on congenital disorders of glycosylation Glycobiology 2001, 11 (12) 129R - 143R
11. Spiro, R. G. Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds Glycobiology 2002, 12 (4) 43R - 56R
12. Van den Steen, P.; Rudd, P. M.; Dwek, R. A.; Opdenakker, G. Concepts and principles of O-linked glycosylation Crit. Rev. Biochem. Mol. Biol. 1998, 33 (3) 151 - 208
13. Helenius, A.; Aebi, M. Intracellular functions of N-linked glycans Science 2001, 291 (5512) 2364 - 9
14. Lowe, J. B. Glycosylation, immunity, and autoimmunity Cell 2001, 104 (6) 809 - 12
15. 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
16. Kobata, A.; Endo, T. Immobilized lectin columns: useful tools for the fractionation and structural analysis of oligosaccharides J. Chromatogr. 1992, 597 (1-2) 111 - 22
17. Yang, Z.; Harris, L. E.; Palmer-Toy, D. E.; Hancock, W. S. Multilectin affinity chromatography for characterization of multiple glycoprotein biomarker candidates in serum from breast cancer patients Clin. Chem. 2006, 52 (10) 1897 - 905
18. Pan, S.; Wang, Y.; Quinn, J. F.; Peskind, E. R.; Waichunas, D.; Wimberger, J. T.; Jin, J.; Li, J. G.; Zhu, D.; Pan, C.; Zhang, J. Identification of glycoproteins in human cerebrospinal fluid with a complementary proteomic approach J. Proteome Res. 2006, 5 (10) 2769 - 79
19. 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
20. Sun, B.; Ranish, J. A.; Utleg, A. G.; White, J. T.; Yan, X.; Lin, B.; Hood, L. Shotgun glycopeptide capture approach coupled with mass spectrometry for comprehensive glycoproteomics Mol. Cell. Proteomics 2007, 6 (1) 141 - 9
21. Tian, Y.; Zhou, Y.; Elliott, S.; Aebersold, R.; Zhang, H. Solid-phase extraction of N-linked glycopeptides Nat. Protoc. 2007, 2 (2) 334 - 9
22. Zhou, Y.; Aebersold, R.; Zhang, H. Isolation of N-linked glycopeptides from plasma Anal. Chem. 2007, 79 (15) 5826 - 37
23. 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
24. Liu, T.; Qian, W. J.; Gritsenko, M. A.; Camp, D. G., 2nd; Monroe, M. E.; Moore, R. J.; Smith, R. D. Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry J. Proteome Res. 2005, 4 (6) 2070 - 80
25. Hortin, G. L.; Sviridov, D.; Anderson, N. L. High-abundance polypeptides of the human plasma proteome comprising the top 4 logs of polypeptide abundance Clin. Chem. 2008, 54 (10) 1608 - 16