Examples
Sassi A, Lazaroski S, Wu G, Haslam SM, Fliegauf M, Mellouli F, Patiroglu T, Unal E, Ozdemir MA, Jouhadi Z, Khadir K et al. Hypomorphic homozygous mutations in phosphoglucomutase 3 (PGM3) impair immunity and increase serum IgE levels. J Allergy Clin Immunol. 2014 May;133(5):1410-9, 1419.e1-13. doi: 10.1016/j.jaci.2014.02.025. Epub 2014 Apr 1. PMID: 24698316; PMCID: PMC4825677.
This is a good example presenting the capability of the tool. Majority of the Glycans are annotated correctly because they are presented very similarity to the Standardized Nomenclature for Glycans (SNFG).
Hong Q, Ruhaak LR, Stroble C, Parker E, Huang J, Maverakis E, Lebrilla CB. A Method for Comprehensive Glycosite-Mapping and Direct Quantitation of Serum Glycoproteins. J Proteome Res. 2015 Dec 4;14(12):5179-92. doi: 10.1021/acs.jproteome.5b00756. Epub 2015 Nov 9. PMID: 26510530; PMCID: PMC4670571.
In this example the Glycan format is typical. The tool were able to correctly predict the structure composition; however, because some are presented with very short linkages GlycoCT prediction is inaccurate on some MS table.
Wang C, Qiang S, Jin W, Song X, Zhang Y, Huang L, Wang Z. Reductive chemical release of N-glycans as 1-amino-alditols and subsequent 9-fluorenylmethyloxycarbonyl labeling for MS and LC/MS analysis. J Proteomics. 2018 Sep 15;187:47-58. doi: 10.1016/j.jprot.2018.06.002. Epub 2018 Jun 6. PMID: 29885470.
This example show potential fault in our current tool which failed to detect correct neighbor if two monosaccharides on different brand are placed too close to one another.
Beth McLeod. Characterization of Glycans from Erbitux®, Rituxan® and Enbrel® using PNGase F (Glycerol-free), Recombinant. GLYCOBIOLOGY & PROTEIN TOOLS. Protein Expression and Analysis Manual. New England Biolabs, Inc. www.neb.com.
This example has their glycan presented similar to SNFG yet their linkages are colored red instead of black. As a result, some glycan are not being recognized by the GlycoCT predictor algorithm.
Go EP, Ding H, Zhang S, Ringe RP, Nicely N, Hua D, Steinbock RT, Golabek M, Alin J, Alam SM, Cupo A, Haynes BF, Kappes JC, et al. Glycosylation Benchmark Profile for HIV-1 Envelope Glycoprotein Production Based on Eleven Env Trimers. J Virol. 2017 Apr 13;91(9):e02428-16. doi: 10.1128/JVI.02428-16. PMID: 28202756; PMCID: PMC5391476.
This example has their glycan presented similar to SNFG yet their linkages are colored red instead of black. As a result, some glycan are not being recognized by the GlycoCT predictor algorithm.
Parker BL, Thaysen-Andersen M, Solis N, Scott NE, Larsen MR, Graham ME, Packer NH, Cordwell SJ. Site-specific glycan-peptide analysis for determination of N-glycoproteome heterogeneity. J Proteome Res. 2013 Dec 6;12(12):5791-800. doi: 10.1021/pr400783j. Epub 2013 Nov 1. PMID: 24090084.
This example shown good example of glycan format yet due to low resolution, our tool prediction are thrown off significantly.
Supplementary data (PDF):
This is a document attachment that came with the study by Parker BL et al. which shown the potential for the use of our tool to predict multiple glycan images.
Supplementary Figures of Mass Spec contain Glycans. (Original)