N- and O-glycomics from minor amounts of formalin-fixed, paraffin-embedded tissue samples

Methods in Molecular Biology

Volumn 1503, Issue , 2017, Pages 131-145

  Hinneburg, Hannes ^a,b   Schirmeister, Falko ^a,b   Korać, Petra ^c   Kolarich, Daniel ^a  

^a MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

^c UNIVERSITY OF ZAGREB   (Croatia)

Author keywords

Formalin fixed; Glycomics; Glycoprotein; Laser capture microdissection; Liquid chromatography; Mass spectrometry; N glycan; O glycan; Paraffi n embedded (FFPE); Porous graphitized carbon

Indexed keywords

FORMALDEHYDE; GLYCAN DERIVATIVE; GLYCOPROTEIN; N GLYCAN; O GLYCAN; PARAFFIN; POLYVINYLIDENE FLUORIDE; UNCLASSIFIED DRUG; GRAPHITE; IMMOBILIZED PROTEIN; POLYSACCHARIDE;

BLOTTING; DESALTING; ELECTROSPRAY MASS SPECTROMETRY; ENZYME ACTIVITY; GLYCOBIOLOGY; HUMAN; HUMAN TISSUE; LASER CAPTURE MICRODISSECTION; LIQUID CHROMATOGRAPHY; PRECIPITATION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PURIFICATION; PROTEIN SECRETION; TISSUE SECTION; ANIMAL; ARTIFICIAL MEMBRANE; CHEMISTRY; PROCEDURES; PROTEOMICS; STAINING; TANDEM MASS SPECTROMETRY; TISSUE FIXATION;

ANIMALS; CHROMATOGRAPHY, LIQUID; FORMALDEHYDE; GLYCOMICS; GLYCOPROTEINS; GRAPHITE; HUMANS; IMMOBILIZED PROTEINS; LASER CAPTURE MICRODISSECTION; MEMBRANES, ARTIFICIAL; PARAFFIN EMBEDDING; POLYSACCHARIDES; PROTEOMICS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; STAINING AND LABELING; TANDEM MASS SPECTROMETRY; TISSUE FIXATION;

EID: 84991730503     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-6493-2_11     Document Type: Chapter

References (23)

1. Ohtsubo K, Marth JD (2006) Glycosylation in cellular mechanisms of health and disease. Cell 126:855-867
2. Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR et al (2009) 2 edn. Cold Spring Harbor Laboratory Press, New York
3. Kolarich D, Lepenies B, Seeberger PH (2012) Glycomics, glycoproteomics and the immune system. Curr Opin Chem Biol 16:214-220
4. Almeida A, Kolarich D (2016) The promise of protein glycosylation for personalized medicine. Biochim Biophys Acta 1860:1583-1595
5. Christiansen MN, Chik J, Lee L, Anugraham M, Abrahams JL, Packer NH (2014) Cell surface protein glycosylation in cancer. Proteomics 14:525-546
6. Vasconcelos-Dos-Santos A, Oliveira IA, Lucena MC, Mantuano NR, Whelan SA, Dias WB et al (2015) Biosynthetic machinery involved in aberrant glycosylation: promising targets for developing of drugs against cancer. Front Oncol 5:138
7. Spiro RG (2002) Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds. Glycobiology 12:43R-56R
8. Shade KT, Platzer B, Washburn N, Mani V, Bartsch YC, Conroy M et al (2015) A single glycan on IgE is indispensable for initiation of anaphylaxis. J Exp Med 212:457-467
9. Carvalho S, Catarino TA, Dias AM, Kato M, Almeida A, Hessling B et al (2015) Preventing E-cadherin aberrant N -glycosylation at Asn-554 improves its critical function in gastric cancer. Oncogene 35:1619-1631
10. Thaysen-Andersen M, Venkatakrishnan V, Loke I, Laurini C, Diestel S, Parker BL et al (2015) Human neutrophils secrete bioactive paucimannosidic proteins from azurophilic granules into pathogen-infected sputum. J Biol Chem 290:8789-8802
11. Toghi Eshghi S, Yang S, Wang X, Shah P, Li X, Zhang H (2014) Imaging of N -linked glycans from formalin-fi xed paraffi n-embedded tissue sections using MALDI mass spectrometry. ACS Chem Biol 9:2149-2156
12. Turiak L, Shao C, Meng L, Khatri K, Leymarie N, Wang Q et al (2014) Workfl ow for combined proteomics and glycomics profi ling from histological tissues. Anal Chem 86:9670-9678
13. Ostasiewicz P, Zielinska DF, Mann M, Wisniewski JR (2010) Proteome, phosphoproteome, and N -glycoproteome are quantitatively preserved in formalin-fi xed paraffi n-embedded tissue and analyzable by high-resolution mass spectrometry. J Proteome Res 9:3688-3700
14. Casadonte R, Caprioli RM (2011) Proteomic analysis of formalin-fi xed paraffi n-embedded tissue by MALDI imaging mass spectrometry. Nat Protoc 6:1695-1709
15. Klopfl eisch R, Weiss AT, Gruber AD (2011) Excavation of a buried treasure—DNA, mRNA, miRNA and protein analysis in formalin fi xed, paraffi n embedded tissues. Histol Histopathol 26:797-810
16. Kotorashvili A, Ramnauth A, Liu C, Lin J, Ye K, Kim R et al (2012) Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalinfi xed paraffi n-embedded specimens. PLoS One 7, 34683
17. Gustafsson OJ, Briggs MT, Condina MR, Winderbaum LJ, Pelzing M, McColl SR et al (2015) MALDI imaging mass spectrometry of N -linked glycans on formalin-fi xed paraffi nembedded murine kidney. Anal Bioanal Chem 407:2127-2139
18. Dwek MV, Brooks SA, Streets AJ, Harvey DJ, Leathem AJ (1996) Oligosaccharide release from frozen and paraffi n-wax-embedded archival tissues. Anal Biochem 242:8-14
19. Espina V, Wulfkuhle JD, Calvert VS, VanMeter A, Zhou WD, Coukos G et al (2006) Lasercapture microdissection. Nat Protoc 1:586-603
20. Cheng L, Zhang S, MacLennan GT, Williamson SR, Davidson DD, Wang M et al (2013) Laser-assisted microdissection in translational research: theory, technical considerations, and future applications. Appl Immunohistochem Mol Morphol 21:31-47
21. Jensen PH, Karlsson NG, Kolarich D, Packer NH (2012) Structural analysis of N - and O -glycans released from glycoproteins. Nat Protoc 7:1299-1310
22. Kolarich D, Windwarder M, Alagesan K, Altmann F (2015) Isomer-specifi c analysis of released N -glycans by LC-ESI MS/MS with porous graphitized carbon. Methods Mol Biol 1321:427-435
23. Wessel D, Flügge UI (1984) A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal Biochem 138:141-14