Abstract
The Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT) strategy for the sample preparation, data analysis, and relative quantification of N-linked glycans is presented. Glycans are derivatized with either natural (L) or stable-isotope labeled (H) hydrazide reagents and analyzed using reversed phase liquid chromatography coupled online to a Q Exactive mass spectrometer. A simple glycan ladder, maltodextrin, is first used to demonstrate the relative quantification strategy in samples with negligible analytical and biological variability. It is shown that after a molecular weight correction attributable to isotopic overlap and a post-acquisition normalization of the data to account for any systematic bias, a plot of the experimental H:L ratio versus the calculated H:L ratio exhibits a correlation of unity for maltodextrin samples mixed in different ratios. We also demonstrate that the INLIGHT approach can quantify species over four orders of magnitude in ion abundance. The INLIGHT strategy is further demonstrated in pooled human plasma, where it is shown that the post-acquisition normalization is more effective than using a single spiked-in internal standard. Finally, changes in glycosylation are able to be detected in complex biological matrices, when spiked with a glycoprotein. The ability to spike in a glycoprotein and detect change at the glycan level validates both the sample preparation and data analysis strategy, making INLIGHT an invaluable relative quantification strategy for the field of glycomics.
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References
Apweiler, R., Hermjakob, H., Sharon, N.: On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database. BBA-Gen. Subjects 1473(1), 4–8 (1999)
Begley, T.P.: Wiley Encyclopedia of Chemical Biology. John Wiley and Sons, Inc.: Hoboken, NJ, vol. 2, p. 785 (2009)
Varki, A., Cummings, R.D., Esko, J.D., Freeze, H.H., Stanley, P., Bertozzi, C.R., Hart, G.W., Etzler, M.E.: Essentials of Glycobiology, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (2009)
Orlando, R., Lim, J.M., Atwood, J.A., Angel, P.M., Fang, M., Aoki, K., Alvarez-Manilla, G., Moremen, K.W., York, W.S., Tiemeyer, M., Pierce, M., Dalton, S., Wells, L.: IDAWG: metabolic incorporation of stable isotope labels for quantitative glycomics of cultured cells. J. Proteome Res. 4, 3816–3823 (2009)
Atwood, J.A., Cheng, L., Alvarez-Manilla, G., Warren, N.L., York, W.S., Orlando, R.: Quantitation by isobaric labeling: applications to glycomics. J. Proteome Res. 7, 367–374 (2008)
Xia, B.Y., Feasley, C.L., Sachdev, G.P., Smith, D.F., Cummings, R.D.: Glycan reductive isotope labeling for quantitative glycomics. Anal. Biochem. 387(2), 162–170 (2009)
Kang, P., Mechref, Y., Kyselova, Z., Goetz, J.A., Novotny, M.V.: Comparative glycomic mapping through quantitative permethylation and stable-isotope labeling. Anal. Chem. 79, 6064–6073 (2007)
Zhang, P., Zhang, Y., Xue, X.D., Wang, C.J., Wang, Z.F., Huang, L.J.: Relative quantitation of glycans using stable isotopic labels 1-(d 0/d 5) phenyl-3-methyl-5-pyrazolone by mass spectrometry. Anal. Biochem. 418(1), 1–9 (2011)
Walker, S.H., Budhathoki-Uprety, J., Novak, B.M., Muddiman, D.C.: Stable-isotope labeled hydrophobic hydrazide reagents for the relative quantification of N-linked glycans by electrospray ionization mass spectrometry. Anal. Chem. 83(17), 6738–6745 (2011)
Bowman, M.J., Zaia, J.: Comparative glycomics using a tetraplex stable-isotope coded tag. Anal. Chem. 82(7), 3023–3031 (2010)
Alvarez-Manilla, G., Warren, N.L., Abney, T., Atwood, J., Azadi, P., York, W.S., Pierce, M., Orlando, R.: Tools for glycomics: relative quantitation of glycans by isotopic permethylation using (CH3I)-C-13. Glycobiology 17, 677–687 (2007)
Kobata, A., Amano, J.: Altered glycosylation of proteins produced by malignant cells, and application for the diagnosis and immunotherapyof tumors. Immunol. Cell Biol. 3(4), 429–439 (2005)
Filer, C.N.: Isotopic fractionation of organic compounds in chromatography. J. Labeled Compounds Radiopharmaceut. 42, 169–197 (1999)
Filer, C. N., Fazio, R., Ahern, D. G.: (+/−)-[methyl-H-3 and methyl-H-2]mianserin— participants in a dramatic instance of HPLC isotopic fractionation. J. Org. Chem. 46, 3344–3346 (1981)
Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M.H., Aebersold, R.: Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994–999 (1999)
Dixon, R.B., Bereman, M.S., Petitte, J.N., Hawkridge, A.M., Muddiman, D.C.: One-year plasma N-linked glycome intra-individual and inter-individual variability in the chicken model of spontaneous ovarian adenocarcinoma. Int. J. Mass Spectrom. 305(2/3), 79–86 (2011)
de Leoz, M.L.A., Young, L.J.T., An, H.J., Kronewitter, S.R., Kim, J.H., Miyamoto, S., Borowsky, A.D., Chew, H.K., Lebrilla, C.B.: High-mannose glycans are elevated during breast cancer progression. Mol. Cell. Proteom. 10(1), 1–9 (2011)
Snovida, S.I., Perreault, H.: A 2,5-dihydroxybenzoic acid/N, N-dimethylaniline matrix for the analysis of oligosaccharides by matrix-assisted laser desorption/ionization mass spectrometry. Rapid Commun. Mass Spectrom. 21(22), 3711–3715 (2007)
Kaneshiro, K., Watanabe, M., Terasawa, K., Uchimura, H., Fukuyama, Y., Iwamoto, S., Sato, T.A., Shimizu, K., Tsujimoto, G., Tanaka, K.: Rapid quantitative profiling of N-glycan by the glycan-labeling method using 3-aminoquinoline/alpha-cyano-4-hydroxycinnamic acid. Anal. Chem. 84(16), 7146–7151 (2012)
Walker, S.H., Taylor, A.D., Muddiman, D.C.: The use of a xylosylated plant glycoprotein as an internal standard accounting for N-linked glycan cleavage and sample preparation variability. Rapid Commun. Mass Spectrom. 27(12), 1354–1358 (2013)
Bereman, M.S., Young, D.D., Deiters, A., Muddiman, D.C.: Development of a robust and high throughput method for profiling N-linked glycans derived from plasma glycoproteins by NanoLC-FTICR mass spectrometry. J. Proteome Res. 8(7), 3764–3770 (2009)
Harris, E.K.: Effects of intraindividual and interindividual variation on appropriate use of normal ranges. Clin. Chem. 20(12), 1535–1542 (1974)
Hawkridge, A.M., Muddiman, D.C.: Mass spectrometry-based biomarker discovery: toward a global proteome index of individuality. Ann. Rev. Anal. Chem. 2, 265–277 (2009)
Carvalho, P.C., Fischer, J.S., Chen, E.I., Yates, J.R., Barbosa, V.C.: PatternLab for proteomics: a tool for differential shotgun proteomics. BMC Bioinformatics (9), 316–329 (2008)
Dong, M.Q., Venable, J.D., Au, N., Xu, T., Park, S.K., Cociorva, D., Johnson, J.R., Dillin, A., Yates, J.R.: Quantitative mass spectrometry identifies insulin signaling targets in C-elegans. Science 317(5838), 660–663 (2007)
Zybailov, B., Mosley, A.L., Sardiu, M.E., Coleman, M.K., Florens, L., Washburn, M.P.: Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J. Proteome Res. 5(9), 2339–2347 (2006)
Florens, L., Carozza, M.J., Swanson, S.K., Fournier, M., Coleman, M.K., Workman, J.L., Washburn, M.P.: Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 40(4), 303–311 (2006)
Sardiu, M.E., Cai, Y., Jin, J.J., Swanson, S.K., Conaway, R.C., Conaway, J.W., Florens, L., Washburn, M.P.: Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc. Natl. Acad. Sci. U.S.A. 105(5), 1454–1459 (2008)
Gokce, E., Shuford, C.M., Franck, W.L., Dean, R.A., Muddiman, D.C.: Evaluation of normalization methods on GeLC-MS/MS label-free spectral counting data to correct for variation during proteomic workflows. J. Am. Soc. Mass Spectrom. 22(12), 2199–2208 (2011)
Collier, T.S., Randall, S.M., Sarkar, P., Rao, B.M., Dean, R.A., Muddiman, D.C.: Comparison of stable-isotope labeling with amino acids in cell culture and spectral counting for relative quantification of protein expression. Rapid Commun. Mass Spectrom. 25(17), 2524–2532 (2011)
Walker, S.H., Papas, B.N., Comins, D.L., Muddiman, D.C.: Interplay of permanent charge and hydrophobicity in the electrospray ionization of glycans. Anal. Chem. 82(15), 6636–6642 (2010)
Walker, S.H., Lilley, L.M., Enamorado, M.F., Comins, D.L., Muddiman, D.C.: Hydrophobic derivatization of N-linked glycans for increased ion abundance in electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 22(8), 1309–1317 (2011)
Walker, S.H., Carlisle, B.C., Muddiman, D.C.: Systematic comparison of reverse phase and hydrophilic interaction liquid chromatography platforms for the analysis of N-linked glycans. Anal. Chem. 84(19), 8198–8206 (2012)
Andrews, G.L., Shuford, C.M., Burnett, J.C., Hawkridge, A.M., Muddiman, D.C.: Coupling of a vented column with splitless nanoRPLC-ESI-MS for the improved separation and detection of brain natriuretic peptide-32 and its proteolytic peptides. J. Chromatogr. B 877(10), 948–954 (2009)
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. Proteom. (2011). doi:10.1074/mcp.M111.011015
Imre, T., Schlosser, G., Pocsfalvi, G., Siciliano, R., Molnar-Szollosi, E., Kremmer, T., Malorni, A., Vekey, K.: Glycosylation site analysis of human alpha-1-acid glycoprotein (AGP) by capillary liquid chromatography-electrospray mass spectrometry. J. Mass Spectrom. 40(11), 1472–1483 (2005)
Fournier, T., Medjoubi, N.N., Porquet, D.: Alpha-1-acid glycoprotein. Biochim. Biophys. Acta - Prot. Struct. Mol. Enzymol. 1482(1/2), 157–171 (2000)
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The authors gratefully acknowledge financial support received from the NIH – NCI IMAT Program (grant #R33 CA147988-02), the W. M. Keck Foundation, and North Carolina State University.
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Walker, S.H., Taylor, A.D. & Muddiman, D.C. Individuality Normalization when Labeling with Isotopic Glycan Hydrazide Tags (INLIGHT): A Novel Glycan-Relative Quantification Strategy. J. Am. Soc. Mass Spectrom. 24, 1376–1384 (2013). https://doi.org/10.1007/s13361-013-0681-2
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DOI: https://doi.org/10.1007/s13361-013-0681-2