In 2017, we published a new Cytoscape App (PTMOracle) that allows the integration and sophisticated analysis of protein-protein interaction networks and post-translational modifications. A few years early, we published PG nexus software platform – a means to co-analyse and co-visualise proteomic data in the context of the IGV genome browser. This paper has been amongst the top accessed papers of the Journal of Proteome Research in 2017.

PTMOracle is a Cytoscape app that allows users to co-visualize and co-analyze post-translational modifications (PTMs) in the context of protein-protein interaction (PPI) networks. By using PTMOracle, users will be able to:

  • Co-visualize and co-analyse PTMs in the context of PPI Networks.
  • Explore the role of domains, motifs and disordered regions in PPIs.
  • Identify proteins of interest and explore network visualisations that address complex PTM-associated relationships.

Proteomic-Genomic Nexus is a tool for integrating proteomics data with genomics and transcriptomics data. It can be used to maps peptide hits from MS/MS ions search to their corresponding location in the genome.

GEOMI allows co-visualisation of interaction data with other proteomic characteristics.

GlycoViewer is a web-based tool that can visualise, summarise and compare up to hundreds of glycan structures.

MethylQuant is a tool that allows accurate and sensitive detection of heavy and light peptide pairs (methyl-SILAC pairs) from heavy-methyl SILAC experiments.