Carbohydrate Analysis With Gas Chromatography-Mass Spectrometry Carbohydrates are energy-rich molecules which provide energy for life processes and the building parts of the cellular structure of plants and animals (Lindhorst, 2003). They play crucial roles in the immune system, pathogenesis, blood clotting, fertilization, and protein folding and placement. Apart from this, carbohydrates get added to proteins as a result of post translational modification called glycosylation. Now we know that virtually all extracellular proteins and some cytoplasmic proteins get glycosylated (Oxley et al. 2004). Many analytical techniques have been developed to study the structure of carbohydrates but due to their complexity not a single technique can offer comprehensive information. In most cases the target molecules are modified prior to analysis. The incredible diversity of these carbohydrate molecules can be explained in the following example. Two identical hexoses can generate 20 isomeric glycans and three identical hexoses can form 448 isomers. On comparing this complexity to that of amino acids in proteins, only a single peptide can be formed from three identical amino acid residues (Oxley et al. 2004). Here we will be using GC-MS (Gas Chromatography coupled with Mass Spectrometry) to analyze monosaccharides in the total cell wall extracts of spinach leaves. The extracts will be derivatized by trimethylsilane (TMS) before analysis on the GC-MS instrument. Lindhorst TK. 2003. Essentials of Carbohydrate Chemistry and Biochemistry. Wiley-VCH: Weinheim. Oxley D, Currie G C, Bacic A (2004) Analysis of carbohydrate from glycoproteins. In: Purifying proteins for proteomics: Purifying proteins for proteomics: A laboratory manual. R J Simpson (ed), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NewYork, USA, ch 25, pp 579-636. Cell wall preparation by the Alcohol Insoluble Residue (AIR) method 10 g of Spinach leaves were weighed. Tissue was pulverized in liquid nitrogen to obtain a fine powder. Then it is boiled for 30 min in 96% ethanol. Then it is centrifuged at 10,000g for 5 min. The supernatant was removed and the pellet was retained. The pellet was washed in 70% ethanol and subsequently centrifuged (10,000g at 5mins) until it appears colorless and free from chlorophyll. A final wash with 100% acetone was performed, and the pellet was air dried. 1 The protocol is adapted from Jesper Harholt, Jacob Krüger Jensen,Susanne Oxenbøll Sørensen, Caroline Orfila, Markus Pauly, and Henrik Vibe Scheller (2006) ARABINAN DEFICIENT 1 Is a Putative Arabinosyltransferase Involved in Biosynthesis of Pectic Arabinan in Arabidopsis. Plant Physiol. 140: 49-58. Hydrolysis of glycans from Glycoproteins 1 Add 80 μl of 1 M methanolic HCl followed by 40 μl of methyl acetate to each tube. 2. Seal each tube with a cap, liner, and Teflon tape. 3. Vortex each mixture thoroughly. Heat the samples and standards for 16 hours at 80ºC. 4. Remove the tubes from the heat and cool them to room temperature before opening the vials. 5. Add 500 μl of t-butyl alcohol to each tube and vortex them thoroughly. Immediately evaporate the solvent by passing a stream of argon (or nitrogen) over the solution at room temperature. 6. N-acetylate the samples by adding 50 μl of super-dry methanol, 5 μl of pyridine, and 5 μl of acetic anhydride and mix thoroughly. 7. Incubate the tubes for 15 minutes at room temperature. 8. Evaporate the samples to dryness by passing a stream of argon (or nitrogen) over the solution at room temperature. 9. To a thoroughly dry sample, add 100 μl of Tri-Sil. Incubate the tube for 10 minutes at 70ºC. 10. Resuspend the samples in 1ml of DCM (Dichloromethane) and add it to GC-MS sample vials. This protocol is modified from the protocol in Oxley’s paper. Oxley D, Currie G C, Bacic A (2004) Analysis of carbohydrate from glycoproteins. In: Purifying proteins for proteomics:, Purifying proteins for proteomics: A laboratory manual. R J Simpson (ed), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NewYork, USA, ch 25, pp 579-636. 2