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Glycan analysis

One of the most important classes of posttranslational modifications is glycosylation. Glycans are very difficult to investigate manually so ProteinScape provides the following analysis and automation tools:

  • the search engine GlycoQuest
  • Glycan search result tables
  • Spectrum viewer for glycan annotation
  • Glycan Structure Editor
ProteinScape Viewers
All required viewers for glycan analysis are provided in the Glycan
perspective (click to enlarge).

GlycoQuest, the integrated search engine for glycans

GlycoQuest supports several kinds of glycans:

  • Released glycans, free or reduced
  • Labeled glycans
  • Derivatized glycans e.g. by permethylation
  • Glycan moieties of glycopeptides

As with protein database searches, search parameters like glycan composition range, mass tolerances, databases, etc. are defined and stored in a search method.

Strategies Glycoprotein Analysis
Several strategies for glycoprotein analysis are supported (click to enlarge).

Databases

Data are searched against a database, which can be:

  • the meta-database GlycomeDB
  • Databases included in the GlycomeDB like GlycO
  • User-defined which are quick and easy to design with the Glycan Structure Editor

 

Glycan search results

The presentation is similar to that of protein search results: a table of glycans is displayed above a table of fragments. Selecting an entry automatically updates the integrated Glycan Structure viewer displaying structural and chemical information, as well as the Spectrum viewer showing the glycan fragment annotation.

N Glycan MS MS Spectrum
N-glycan MS/MS spectrum obtained after tryptic digestion and PGC-LC
separation. The spectrum was acquired on an amaZon speed ETD in
negative mode (click to enlarge).
Related Information