Glycoproteomics finally unravelled

- fully integrated workflow in ProteinScape

Protein glycosylation is the most challenging PTM in proteomics studies, due to its complexity and lack of dedicated post-processing tools. Bruker`s ProteinScape software now enables the detection, classification and identification of glycopeptides. The peptide moiety is identified by the usual protein DB search. In addition, ProteinScape’s novel proprietary GlycoQuest™ glycan DB search engine retrieves the glycan structure. The result is a complete glycopeptide elucidation from tryptic protein digests without the need for any glycan modification chemistry.

The task of finding glycopeptide and glycan spectra in an LC-MS/MS dataset of a digested glycoprotein sample is extremely demanding. ProteinScape simplifies this task by searching for characteristic patterns in the MS/MS spectra and only submitting relevant spectra to the database search. For glycopeptides the peptide masses are determined in the same course. ProteinScape comes with a built-in glycan search engine, GlycoQuest. As with protein database searches, search parameters are defined and stored in a search method. Data are then searched against the meta-database GlycomeDB (, which is hosted at the German Cancer Research Center in Heidelberg and currently contains around 35,000 glycan structures. GlycomeDB is regularly updated and automatically synchronized with GlycoQuest.

Familiar search result reporting with comprehensive annotation

The presentation of glycan search results is analogous to that of protein search results in that a table of glycans is displayed above a table of fragments. Selecting a table entry automatically updates the integrated Glycan Structure viewer that display structural and chemical information, and the Spectrum viewer showing the glycan annotation.

Structure editor for customized searches

A glycan editor enables manual editing of glycan structures that can be saved to the database for glycan searches. This means that you can tailor a search to any specific glycan, regardless of its complexity