Creating Glycan Isomer Cartoons with Ambiguous Linkages – Protein Metrics

This article explains how to create glycan cartoons with ambiguous linkages (represented with a bracket). This is useful to show represent a glycan assignment where the composition is known, but the exact isomer structure is not known. See the Glycan Cartoon KB article for more general information on Glycan Cartoons in Byos.

Glycan cartoon structures can be manually edited by right-clicking on the Glycan Candidate and selecting Show alternative glycan structures...

This will open the Glycan Structure Selection window. In this example, the IUPAC glycan structure for the currently assigned G1F structure is copied to use as a starting point for creating the glycan cartoon with an ambiguous linkage of the terminal Gal. Then click Add new from IUPAC...

This opens the Glycan Structure from IUPAC dialog to create new glycan structure alternatives. Clicking the Draw button will show you the glycan structure represented by the currently entered IUPAC string. Next we can paste the IUPAC string copied in Step 2 into the IUPAC text box. Find the left-most Gal() residue and delete the text (see figure below). Then add +"Gal()" to the right-end of the IUPAC string. Click Draw to confirm the correct IUPAC text is entered.

In this specific example, here are the IUPAC strings before and after.

Before: Gal()GlcNAc()Man()[GlcNAc()Man()]Man()GlcNAc()[Fuc()]GlcNAc()

After (Ambiguous Linkage): GlcNAc()Man()[GlcNAc()Man()]Man()GlcNAc()[Fuc()]GlcNAc()+"Gal()"

This will add the new glycan alternative structure to the Glycan Structure Selection window. Select the new Glycan Alternative structure and click OK.