Oral Presentation HUPO 2019 - 18th Human Proteome Organization World Congress

Glycoproteomics goes visual, interactive and analytical (64895)

Frederique Lisacek 1 2 , Julien Mariethoz 1 2 , Thibault Robin 1 2 , Niclas Karlsson 3 , Daniel Kolarich 4 , Nicolle Packer 4 5
  1. University of Geneva, Geneva, Switzerland
  2. SIB Swiss Institute of Bioinformatics, Geneva, GENEVA, Switzerland
  3. Gothenburg University, Gothenburg, Sweden
  4. Griffith University, Gold Coast, Queensland, Australia
  5. Macquarie University, Sydney, New South Wales, Australia

Glycomics@ExPASy the glycomics tab of the Swiss Institute of Bioinformatics server (www.expasy.org/glycomics) was created in 2016 to centralise web-based glycoinformatics resources developed within an international network of glycoscientists. The philosophy of this toolbox is to be {glycoscientist AND protein scientist}–friendly with the aim of popularising (a) the use of bioinformatics in glycobiology and (b) the relation between glycobiology and protein-oriented bioinformatics resources [1]. In 2018, we released GlyConnect as the power engine of the toolbox [2].

GlyConnect was designed to (i) centralise curated data collected from selected items listed in the Glycomics@ExPASy database section as well as supplementary material of large-scale glycoproteomics experiments and (ii) integrate several tools listed in the Glycomics@ExPASy tool section. The latest addition is GlyConnect Compozitor that manages the growing set of glycan compositions accumulated in glycoproteomics data. Supported by precise and flexible tissue controlled vocabularies (Gene Ontology for subcellular location, UBERON for anatomy and Cellosaurus for cell lines) and based on the database glyco-content, Compozitor suggests a custom selection of glycan compositions suited to a glycoproteomics experiment and readily available for commonly used identification software.

In this presentation, we show the impact of increasing the database by 35% in glycoproteins and refining site-specific information, on query results. We highlight the advantages of improved connectivity within and across GlyConnect that cross-references reciprocally with several external databases such as GlyTouCan (the unique glycan repository), UniProt, PDB, GeneCards and neXtprot.

  1. Mariethoz J, Alocci D, Gastaldello A, Horlacher O, Gasteiger E, Rojas-Macias MA, Karlsson NG, Packer NH, Lisacek F (2018) Glycomics@ExPASy: Bridging the gap, Mol Cell Proteomics 17: 2164–2176
  2. Alocci D, Mariethoz J, Gastaldello A, Gasteiger E, Karlsson NG, Kolarich D, Packer NH, Lisacek F (2019) GlyConnect: glycoproteomics goes visual, interactive and analytical, J Prot Research 18(2):664-677