The Rappsilber Lab has a number of projects to aid data processing, information exploration and hypothesis generation. Among these are the following tools:

Data processing

xiSEARCH is a mass-spectrometry search engine, specialised for identification of crosslinked peptides

  • usable with any crosslinker/any chemistry that can be used with MS2 (e.g. BS3, DSSO, SDA)
  • scales from single protein to proteome
  • any enzyme or combination of enzymes

xiFDR is a tool for filtering result of a crosslink search to a given level of confidence

  • Calculates FDR on level of interest (i.e. residue-pairs, protein-pairs or both)
  • improves identification of residue pairs by pre-filtering
  • can read and write mzIdentML 1.2
Data visualization

xiVIEW is a web-based visualisation tool for the analysis of cross-linking/mass spectrometry results

  • 2D network (xiNET or circular)
  • the supporting annotated spectra using xiSPEC.
  • 3D structure view using NGL.

xiSPEC is an interactive tool for visualising and analysing mass spectrometry data

  • Analyse mass spectra intuitively and test hypotheses.
  • Upload and share whole MS datasets.
  • Download annotated spectra as vector graphics.

ProteomeHD Web App is a collection of tools for protein co-regulation analysis

  • find novel functional relationships in the human proteome
  • use machine learning on our human proteome dataset
  • soon to be expanded to other species!