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