GAG-ID: Heparan sulfate (HS) and heparin glycosaminoglycan high-throughput identification software

Molecular and Cellular Proteomics

Volumn 14, Issue 6, 2015, Pages 1720-1730

  Chiu, Yulun ^a   Huang, Rongrong ^a   Orlando, Ron ^a   Sharp, Joshua S ^a  

^a UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID DERIVATIVE; GLYCOSAMINOGLYCAN; HEPARAN SULFATE; HEPARIN DERIVATIVE; TETRASACCHARIDE; HEPARIN; OLIGOSACCHARIDE;

ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; DERIVATIZATION; DRUG DISCRIMINATION; HIGH THROUGHPUT SEQUENCING; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MOLECULAR WEIGHT; PRIORITY JOURNAL; SCORING SYSTEM; GLYCOBIOLOGY; SOFTWARE; TANDEM MASS SPECTROMETRY;

CHROMATOGRAPHY, LIQUID; GLYCOMICS; HEPARIN; HEPARITIN SULFATE; OLIGOSACCHARIDES; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 84930454215     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M114.045856     Document Type: Article

References (43)

1. Tumova, S., Woods, A., and Couchman, J. R. (2000) Heparan sulfate proteoglycans on the cell surface: versatile coordinators of cellular functions. Int. J. Biochem. Cell Biol. 32, 269-288
2. Sassaki, G. L., Riter, D. S., Santana Filho, A. P., Guerrini, M., Lima, M. A., Cosentino, C., Souza, L. M., Cipriani, T. R., Rudd, T. R., Nader, H. B., Yates, E. A., Gorin, P. A., Torri, G., and Iacomini, M. (2011) A robust method to quantify low molecular weight contaminants in heparin: detection of tris(2-n-butoxyethyl) phosphate. Analyst 136, 2330-2338
3. Mitsiadis, T. A., Salmivirta, M., Muramatsu, T., Muramatsu, H., Rauvala, H., Lehtonen, E., Jalkanen, M., and Thesleff, I. (1995) Expression of the heparin-binding cytokines, midkine (MK), and HB-GAM (pleiotrophin) is associated with epithelial-mesenchymal interactions during fetal development and organogenesis. Development 121, 37-51
4. Makarenkova, H. P., Hoffman, M. P., Beenken, A., Eliseenkova, A. V., Meech, R., Tsau, C., Patel, V. N., Lang, R. A., and Mohammadi, M. (2009) Differential interactions of FGFs with heparan sulfate control gradient formation and branching morphogenesis. Sci. Signal. 2, ra55
5. Muramatsu, T., and Muramatsu, H. (2008) Glycosaminoglycan-binding cytokines as tumor markers. Proteomics 8, 3350-3359
6. Knelson, E. H., Nee, J. C., and Blobe, G. C. (2014) Heparan sulfate signaling in cancer. Trends Biochem. Sci. 39, 277-288
7. Iozzo, R. V., and San Antonio, J. D. (2001) Heparan sulfate proteoglycans: heavy hitters in the angiogenesis arena. J. Clin. Invest. 108, 349-355
8. Kresse, H., and Schonherr, E. (2001) Proteoglycans of the extracellular matrix and growth control. J. Cell. Physiol. 189, 266-274
9. Lyon, M., and Gallagher, J. T. (1998) Bio-specific sequences and domains in heparan sulphate and the regulation of cell growth and adhesion. Matrix Biol. 17, 485-493
10. Li, J. P., and Vlodavsky, I. (2009) Heparin, heparan sulfate, and heparanase in inflammatory reactions. Thromb. Haemost. 102, 823-828
11. Holt, C. E., and Dickson, B. J. (2005) Sugar codes for axons? Neuron 46, 169-172
12. Dityatev, A., and Schachner, M. (2003) Extracellular matrix molecules and synaptic plasticity. Nat. Rev. Neurosci. 4, 456-468
13. De Mattos, D. A., Stelling, M. P., Tovar, A. M., and Mourao, P. A. (2008) Heparan sulfates from arteries and veins differ in their antithrombinmediated anticoagulant activity. J. Thromb. Haemost. 6, 1987-1990
14. Jones, C. J., Beni, S., Limtiaco, J. F., Langeslay, D. J., and Larive, C. K. (2011) Heparin characterization: challenges and solutions. Annu. Rev. Anal. Chem. 4, 439-465
15. Esko, J. D., Kimata, K., and Lindahl, U. (2009) in Essentials of Glycobiology, eds Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, Hart GW, Etzler ME (Cold Spring Harbor (NY)). 2nd Ed.
16. Hirabayashi, J., Hashidate, T., Arata, Y., Nishi, N., Nakamura, T., Hirashima, M., Urashima, T., Oka, T., Futai, M., Muller, W. E., Yagi, F., and Kasai, K. (2002) Oligosaccharide specificity of galectins: a search by frontal affinity chromatography. Biochim. Biophys. Acta 1572, 232-254
17. Wuhrer, M., Deelder, A. M., and Hokke, C. H. (2005) Protein glycosylation analysis by liquid chromatography-mass spectrometry. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 825, 124-133
18. Zaia, J., and Costello, C. E. (2003) Tandem mass spectrometry of sulfated heparin-like glycosaminoglycan oligosaccharides. Anal. Chem. 75, 2445-2455
19. Ly, M., Leach, 3rd, F. E., Laremore, T. N., Toida, T., Amster, I. J., and Linhardt, R. J. (2011) The proteoglycan bikunin has a defined sequence. Nat. Chem. Biol. 7, 827-833
20. Kailemia, M. J., Li, L., Ly, M., Linhardt, R. J., and Amster, I. J. (2012) Complete mass spectral characterization of a synthetic ultralow-molecular- weight heparin using collision-induced dissociation. Anal. Chem. 84, 5475-5478
21. Ceroni, A., Maass, K., Geyer, H., Geyer, R., Dell, A., and Haslam, S. M. (2008) GlycoWorkbench: a tool for the computer-assisted annotation of mass spectra of glycans. J. Proteome Res. 7, 1650-1659
22. Damerell, D., Ceroni, A., Maass, K., Ranzinger, R., Dell, A., and Haslam, S. M. (2012) The GlycanBuilder and GlycoWorkbench glycoinformatics tools: updates and new developments. Biol. Chem. 393, 1357-1362
23. Tissot, B., Ceroni, A., Powell, A. K., Morris, H. R., Yates, E. A., Turnbull, J. E., Gallagher, J. T., Dell, A., and Haslam, S. M. (2008) Software tool for the structural determination of glycosaminoglycans by mass spectrometry. Anal. Chem. 80, 9204-9212
24. Eng, J. K., McCormack, A. L., and Yates, J. R. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass. Spectrom. 5, 976-989
25. Fridman, T., Razumovskaya, J., Verberkmoes, N., Hurst, G., Protopopescu, V., and Xu, Y. (2005) The probability distribution for a random match between an experimental-theoretical spectral pair in tandem mass spectrometry. J. Bioinform. Comput. Biol. 3, 455-476
26. Sadygov, R. G., Liu, H., and Yates, J. R. (2004) Statistical models for protein validation using tandem mass spectral data and protein amino acid sequence databases. Anal. Chem. 76, 1664-1671
27. Geer, L. Y., Markey, S. P., Kowalak, J. A., Wagner, L., Xu, M., Maynard, D. M., Yang, X., Shi, W., and Bryant, S. H. (2004) Open mass spectrometry search algorithm. J. Proteome Res. 3, 958-964
28. 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
29. Zhang, N., Aebersold, R., and Schwikowski, B. (2002) ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data. Proteomics 2, 1406-1412
30. Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics 20, 1466-1467
31. Tabb, D. L., Fernando, C. G., and Chambers, M. C. (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. J. Proteome Res. 6, 654-661
32. Kailemia, M. J., Ruhaak, L. R., Lebrilla, C. B., and Amster, I. J. (2014) Oligosaccharide analysis by mass spectrometry: a review of recent developments. Anal. Chem. 86, 196-212
33. Venkataraman, G., Shriver, Z., Raman, R., and Sasisekharan, R. (1999) Sequencing complex polysaccharides. Science 286, 537-542
34. Saad, O. M., and Leary, J. A. (2005) Heparin sequencing using enzymatic digestion and ESI-MSn with HOST: a heparin/HS oligosaccharide sequencing tool. Anal. Chem. 77, 5902-5911
35. Maxwell, E., Tan, Y., Tan, Y., Hu, H., Benson, G., Aizikov, K., Conley, S., Staples, G. O., Slysz, G. W., Smith, R. D., and Zaia, J. (2012) GlycReSoft: a software package for automated recognition of glycans from LC/MS data. PLoS One 7, e45474
36. Hu, H., Huang, Y., Mao, Y., Yu, X., Xu, Y., Liu, J., Zong, C., Boons, G. J., Lin, C., Xia, Y., and Zaia, J. (2014) A Computational framework for heparan sulfate sequencing using high-resolution tandem mass spectra. Mol. Cell. Proteomics 13, 2490-2502
37. Arungundram, S., Al-Mafraji, K., Asong, J., Leach, 3rd, F. E., Amster, I. J., Venot, A., Turnbull, J. E., and Boons, G. J. (2009) Modular synthesis of heparan sulfate oligosaccharides for structure-activity relationship studies. J. Am. Chem. Soc. 131, 17394-17405
38. Huang, R., Liu, J., and Sharp, J. S. (2013) An approach for separation and complete structural sequencing of heparin/heparan sulfate-like oligosaccharides. Anal. Chem. 85, 5787-5795
39. Domon, B., and Costello, C. E. (1988) A systematic nomenclature for carbohydrate fragmentations in FAB-MS/MS spectra of glycoconjugates. Glycoconj. J. 5, 397-409
40. Kessner, D., Chambers, M., Burke, R., Agus, D., and Mallick, P. (2008) ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534-2536
41. Nesvizhskii, A. I., and Aebersold, R. (2004) Analysis, statistical validation, and dissemination of large-scale proteomics datasets generated by tandem MS. Drug Discov. Today 9, 173-181
42. Nesvizhskii, A. I., Keller, A., Kolker, E., and Aebersold, R. (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75, 4646-4658
43. Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 74, 5383-5392