Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

How To Use Advanced Glycan Search Tutorial

509 views

Published on


You can search for glycans by specifying their chemical features of biological context. In many cases, you may not have this information but will have other information about the glycan or collection of glycans that makes them interesting to you.

This tutorial was created using a portal version: 1.0.1 (09/19/2018).

Published in: Education
  • Be the first to comment

  • Be the first to like this

How To Use Advanced Glycan Search Tutorial

  1. 1. How to use Advanced Glycan Search By GlyGen.org This tutorial was created using a portal version: 1.0.1 (09/19/2018).
  2. 2. You can search for glycans by specifying their GlyTouCan accession numbers, their specific structures or the specific biochemical contexts within which they are found.
  3. 3. You can search for glycans by specifying their GlyTouCan accession number and retrieve a single glycan structure. You can click on the "Search Glycan" button. All of the other search terms become irrelevant at this time.
  4. 4. Glycan Search without knowing the GlyTouCan Accession • A field near the top of this page should be left blank, and you should enter information in the other search fields on this page. • The information you specify in each form field defines a subset of glycans in the GlyGen Data store. Filling in more than one field will instruct GlyGen to find all glycans that simultaneously fulfill all of the criteria that you specify. • It is very important to note that increasing the number of filtering criteria increases the likelihood that no matches will be found. • However, sometimes no matches will be found simply due to the fact that GlyGen does not contain all possible information.
  5. 5. You can search for a glycan according to its molecular mass. The Monoisotopic Mass section allows you to manipulate slider bars or type in the minimum and maximum mass of the interesting glycans. Only glycans within this mass range will be returned when the search is invoked.
  6. 6. At the time this tutorial was made, using the search terms described above will return a list of 2558 glycan structures. Select the GlyTouCan Accession from the list to see details of your glycan.
  7. 7. You can select the minimum and maximum number of sugar residues in the glycan by manipulating slider bars or by typing in these values.
  8. 8. This more limited search returned 1831 glycans. This list is still probably too long to read, so click on the Modify Search Button again to further limit the results Select the GlyTouCan Accession from the list to see details of your glycan.
  9. 9. Let's say you are most interested in human N-glycans. Select Homo Sapiens and N-glycans. You can enter this information in the Organism and Glycan Type fields.
  10. 10. Clicking on the Search Glycan button now returns a list containing 285 glycans. To further limit this result, click the Modify Search button. Select the GlyTouCan Accession from the list to see details of your glycan.
  11. 11. Suppose you are most interested in so-called hybrid N- glycans. You can add this restriction to your search by selecting "hybrid" from the Glycan Subtype pulldown
  12. 12. Select the GlyTouCan Accession from the list to see details of your glycan. This returns a list containing only 19 glycans. Let's pare down this list a bit more. Click the Modify Search button.
  13. 13. Say you are interested in whether the glycans in your list are attached to a particular glycoprotein, for example, an elastase called CELA3B. This has the UniProt Accession "P08861", so type that into the UniProt Accession field.
  14. 14. Select the GlyTouCan Accession from the list to see details of your glycan. The result is a single glycan with the GlyTouCan accession G53962WT.
  15. 15. Suppose you have learned that the enzyme called ST3GAL3 is implicated in the biosynthesis of the glycans you are studying. Enter that into the Biosynthetic Enzyme field.
  16. 16. Select the GlyTouCan Accession from the list to see details of your glycan. This returns a different list containing only four glycans, which bears a sialic acid that has been transferred to the glycan by the ST3GAL3 enzyme.

×