Annotation of a serum N-Glycan library for rapid identification of structures

Journal of Proteome Research

Volumn 11, Issue 3, 2012, Pages 1958-1968

  Aldredge, Danielle ^a   An, Hyun Joo ^b   Tang, Ning ^c   Waddell, Keith ^c   Lebrilla, Carlito B ^a,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Chungnam National University   (South Korea)

^c AGILENT TECHNOLOGIES   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

database library; glycan structures; isomers; N linked glycan; nano HPLC Chip TOF MS; online detection; retention time

Indexed keywords

GLYCAN; GLYCOPROTEIN; GLYCOPROTEIN IGM; GLYCOSIDASE; N GLYCAN; PLASMA PROTEIN; SERUM GLYCAN; UNCLASSIFIED DRUG;

CARBOHYDRATE ANALYSIS; CONFERENCE PAPER; ENZYME MECHANISM; HUMAN; ISOMER; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION MASS SPECTROMETRY; MOLECULAR GENETICS; MOLECULAR LIBRARY; MOLECULAR WEIGHT; NANOLIQUID CHROMATOGRAPHY MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN BLOOD LEVEL; PROTEIN STRUCTURE;

CARBOHYDRATE CONFORMATION; CARBOHYDRATE SEQUENCE; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DATABASES, PROTEIN; GLYCOPROTEINS; GLYCOSIDE HYDROLASES; GLYCOSYLATION; HUMANS; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; POLYSACCHARIDES; PROTEIN ISOFORMS; PROTEIN PROCESSING, POST-TRANSLATIONAL; REFERENCE STANDARDS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TANDEM MASS SPECTROMETRY;

EID: 84857869147     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr2011439     Document Type: Conference Paper

References (43)

1. Apweiler, R.; Hermjakob, H.; Sharon, N. On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database Biochim. Biophys. Acta: Gen. Subj. 1999, 1473 (1) 4-8
2. Morelle, W.; Canis, K.; Chirat, F.; Faid, V.; Michalski, J. C. The use of mass spectrometry for the proteomic analysis of glycosylation Proteomics 2006, 6 (14) 3993-4015
3. Dwek, R. A. Glycobiology: toward understanding the function of sugars Chem. Rev. 1996, 96 (2) 683-720
4. Varki, A.; Cummings, R.; Esko, J.; Freeze, H.; Essentials of Glycobiology; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 1999.
5. Ratner, D. M.; Adams, E. W.; Disney, M. D.; Seeberger, P. H. Tools for Glycomics: Mapping Interactions of Carbohydrates in Biological Systems ChemBioChem 2004, 5 (10) 1375-1383
6. Alavi, A.; Axford, J. S. Sweet and sour: the impact of sugars on disease Rheumatology 2008, 47 (6) 760-770
7. Varki, A. Sialic acids in human health and disease Trends Mol. Med. 2008, 14 (8) 351-360
8. Callesen, A. K.; Madsen, J. S.; Vach, W.; Kruse, T. A.; Mogensen, O.; Jensen, O. N. Serum protein profiling by solid phase extraction and mass spectrometry: A future diagnostics tool? Proteomics 2009, 9 (6) 1428-1441
9. Abbott, K. L.; Aoki, K.; Lim, J.-M.; Porterfield, M.; Johnson, R.; O'Regan, R. M.; Wells, L.; Tiemeyer, M.; Pierce, M. Targeted glycoproteomic identification of biomarkers for human breast carcinoma J. Proteome Res. 2008, 7 (4) 1470-1480
10. Zhang, X. L. Roles of glycans and glycopeptides in immune system and immune-related diseases Curr. Med. Chem. 2006, 13, 1141-1147
11. Srivastava, S. Move over proteomics, here comes glycomics J. Proteome Res. 2008, 7 (5) 1799
12. Packer, N. H.; von der Lieth, C.-W.; Aoki-Kinoshita, K. F.; Lebrilla, C. B.; Paulson, J. C.; Raman, R.; Rudd, P.; Sasisekharan, R.; Taniguchi, N.; York, W. S. Frontiers in glycomics: Bioinformatics and biomarkers in disease An NIH White Paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11-13, 2006) Proteomics 2008, 8 (1) 8-20
13. Gagneux, P.; Varki, A. Evolutionary considerations in relating oligosaccharide diversity to biological function Glycobiology 1999, 9 (8) 747-755
14. Willy Morelle, J.-C. M. The mass spectrometric analysis of glycoproteins and their glycan structures Curr. Anal. Chem. 2005, 1, 29-57
15. Laine, R. A. Invited Commentary: A calculation of all possible oligosaccharide isomers both branched and linear yields 1.05-1012 structures for a reducing hexasaccharide: the Isomer Barrier to development of single-method saccharide sequencing or synthesis systems Glycobiology 1994, 4 (6) 759-767
16. Arnold, J. N.; Saldova, R.; Hamid, U. M. A.; Rudd, P. M. Evaluation of the serum N-linked glycome for the diagnosis of cancer and chronic inflammation Proteomics 2008, 8 (16) 3284-3293
17. Brooks, S. A.; Dwek, M. V.; Schumacher, U. Functional and Molecular Glycobiology; BIOS Scientific Publishers Limited: Oxford, U.K., 2002.
18. Lis, H.; Sharon, N. Protein glycosylation Eur. J. Biochem. 1993, 218 (1) 1-27
19. Kronewitter, S. R.; An, H. J.; de Leoz, M. L.; Lebrilla, C. B.; Miyamoto, S.; Leiserowitz, G. S. The development of retrosynthetic glycan libraries to profile and classify the human serum N-linked glycome Proteomics 2009, 9 (11) 2986-2994
20. Chu, C. S.; Ninonuevo, M. R.; Clowers, B. H.; Perkins, P. D.; An, H. J.; Yin, H.; Killeen, K.; Miyamoto, S.; Grimm, R.; Lebrilla, C. B. Profile of native N-linked glycan structures from human serum using high performance liquid chromatography on a microfluidic chip and time-of-flight mass spectrometry Proteomics 2009, 9 (7) 1939-1951
21. Joshi, H. J.; Harrison, M. J.; Schulz, B. L.; Cooper, C. A.; Packer, N. H.; Karlsson, N. G. Development of a mass fingerprinting tool for automated interpretation of oligosaccharide fragmentation data Proteomics 2004, 4 (6) 1650-1664
22. Raman, R.; Raguram, S.; Venkataraman, G.; Paulson, J. C.; Sasisekharan, R. Glycomics: an integrated systems approach to structure-function relationships of glycans Nat. Methods 2005, 2 (11) 817-824
23. Ceroni, A.; Maass, K.; Geyer, H.; Geyer, R.; Dell, A.; Haslam, S. M. GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans J. Proteome Res. 2008, 7 (4) 1650-1659
24. Campbell, M. P.; Royle, L.; Radcliffe, C. M.; Dwek, R. A.; Rudd, P. M. GlycoBase and autoGU: tools for HPLC-based glycan analysis Bioinformatics 2008, 24 (9) 1214-1216
25. Royle, L.; Campbell, M. P.; Radcliffe, C. M.; White, D. M.; Harvey, D. J.; Abrahams, J. L.; Kim, Y. G.; Henry, G. W.; Shadick, N. A.; Weinblatt, M. E.; Lee, D. M.; Rudd, P. M.; Dwek, R. A. HPLC-based analysis of serum N-glycans on a 96-well plate platform with dedicated database software Anal. Biochem. 2008, 376 (1) 1-12
26. Hua, S.; An, H. J.; Ozcan, S.; Ro, G. S.; Soares, S.; DeVere-White, R.; Lebrilla, C. B. Comprehensive native glycan profiling with isomer separation and quantitation for the discovery of cancer biomarkers Analyst 2011, 136 (18) 3663-3671
27. Hua, S.; Lebrilla, C.; An, H. J. Application of nano-LC-based glycomics towards biomarker discovery Bioanalysis 2011, 3 (22) 2573-2585
28. Wu, S.; Tao, N.; German, J. B.; Grimm, R.; Lebrilla, C. B. Development of an annotated library of neutral human milk oligosaccharides J. Proteome Res. 2010, 9 (8) 4138-4151
29. Zhang, J.; Lindsay, L. L.; Hedrick, J. L.; Lebrilla, C. B. Strategy for Profiling and Structure Elucidation of Mucin-Type Oligosaccharides by Mass Spectrometry Anal. Chem. 2004, 76 (20) 5990-6001
30. Arnold, J. N.; Wormald, M. R.; Suter, D. M.; Radcliffe, C. M.; Harvey, D. J.; Dwek, R. A.; Rudd, P. M.; Sim, R. B. Human Serum IgM Glycosylation J. Biol. Chem. 2005, 280 (32) 29080-29087
31. Field, M. C.; Amatayakul-Chantler, S.; Rademacher, T. W.; Rudd, P. M.; Dwek, R. A. Structural analysis of the N-glycans from human immunoglobulin A1: comparison of normal human serum immunoglobulin A1 with that isolated from patients with rheumatoid arthritis Biochem. J. 1994, 299 (Pt 1) 261-275
32. Stadlmann, J.; Pabst, M.; Kolarich, D.; Kunert, R.; Altmann, F. Analysis of immunoglobulin glycosylation by LC-ESI-MS of glycopeptides and oligosaccharides Proteomics 2008, 8 (14) 2858-2871
33. Karlsson, N. G.; Wilson, N. L.; Wirth, H.-J.; Dawes, P.; Joshi, H.; Packer, N. H. Negative ion graphitised carbon nano-liquid chromatography/mass spectrometry increases sensitivity for glycoprotein oligosaccharide analysis Rapid Commun. Mass Spectrom. 2004, 18 (19) 2282-2292
34. Thomsson, K. A.; Backstroàm, M.; Holmen Larsson, J. M.; Hansson, G. C.; Karlsson, H. Enhanced detection of sialylated and sulfated glycans with negative ion mode nanoliquid chromatography/mass spectrometry at high pH Anal. Chem. 2010, 82 (4) 1470-1477
35. Ninonuevo, M. R.; Park, Y.; Yin, H.; Zhang, J.; Ward, R. E.; Clowers, B. H.; German, J. B.; Freeman, S. L.; Killeen, K.; Grimm, R.; Lebrilla, C. B. A Strategy for Annotating the Human Milk Glycome J. Agric. Food Chem. 2006, 54 (20) 7471-7480
36. Knox, J. H.; Carbon-based Packing Materials for Liquid Chromatography-Structure, Performance, and Retention Mechanisms; Marcel Dekker: New York, 1997; Vol. 37.
37. Ross, P.; Carbon-based Packing Materials for Liquid Chromatography: Applications; Marcel Dekker: New York, 1997; Vol. 37.
38. Davies, M.; Smith, K. D.; Harbin, A.-M.; Hounsell, E. F. High-performance liquid chromatography of oligosaccharide alditols and glycopeptides on a graphitized carbon column J. Chromatogr., A 1992, 609 (1-2) 125-131
39. Annesley, T. M. Ion Suppression in Mass Spectrometry Clin. Chem. 2003, 49 (7) 1041-1044
40. Koizumi, K. High-performance liquid chromatographic separation of carbohydrates on graphitized carbon columns J. Chromatogr., A 1996, 720 (1-2) 119-126
41. Koizumi, K.; Okada, Y.; Fukuda, M. High-performance liquid chromatography of mono- and oligo-saccharides on a graphitized carbon column Carbohydr. Res. 1991, 215 (1) 67-80
42. Itoh, S.; Kawasaki, N.; Ohta, M.; Hyuga, M.; Hyuga, S.; Hayakawa, T. Simultaneous microanalysis of N-linked oligosaccharides in a glycoprotein using microbore graphitized carbon column liquid chromatography-mass spectrometry J. Chromatogr., A 2002, 968 (1-2) 89-100
43. Li, B.; Russell, S. C.; Zhang, J.; Hedrick, J. L.; Lebrilla, C. B. Structure determination by MALDI-IRMPD mass spectrometry and exoglycosidase digestions of O-linked oligosaccharides from Xenopus borealis egg jelly Glycobiology 2011, 21 (7) 877-894