Unipep is a project to provide access to proteomics data from the Serum Biomarker group at the Swiss Federal Institute of Technology (ETH) in Zurich Switzerland, and the Institute for Systems Biology (ISB) in Seattle, Washington USA.

In the initial phase, we provide a searchable interface to a library of putative glycopeptides, i.e. those containing a concensus NxS/T motif. The database maps peptides observed in a series of LC/MSMS experiments to a library of theoretical glycopeptides. The theoretical peptides are derived from an 'electronic' tryptic digestion of the IPI protein database (version 2.28). The observed peptides are obtained from glycocapture experiments in which whole cell lysates are covalently bound to beads which preferentially bind sugar moieties. The bound proteins are tryptically cleaved and the beads washed to remove non-glycosylated peptides, then the glycopeptides are eluted by enzymatic deglycosylation.

The next phase of the project will be to bring online a similar repository of proteotypic peptides seen in a variety of LC/MSMS experiments. These will also be compared to a library of theoretical peptides which have been scored for their proteotypic potential (i.e. the likelihood of detection in such an experiment).