interact-ms was developed at the Quantitative and Systems Biology group at the Max Planck Institute for Multidisciplinary Sciences. We are particulary interested in finding non-canonical peptides in large search spaces. In particular, we are focussed on the identification and characterization of proteasomse catalyzed peptide splicing both in immunopeptidomics data (1, 2, 3) and in in vitro assays (4, 5, 6). The challenges posed by these large search spaces (7, 8) necessitated improvements in peptide identification.

In order to leverage the advances made by Prosit (9, 10) and NetMHCpan (11) we developed inSPIRE (12) as a flexible tool for enhanced peptide identification leveraging these tools. It quickly became apparent that inSPIRE had benefits in many applications beyond non-canonical peptide identification.

One of the most important applications of mass spectrometry on immunopeptidomics is the identifications of epitope candidates as potential targets for vaccine development. To this end, we developed PEPSeek, a tool which selects candidate peptides from immunopeptidomics datasets. PEPSeek filters for peptides detected in control data and pathogen peptides which multi-map to the host proteome. Furthermore, PEPSeek enables quantitative analysis of control and infected immunopeptidomes with the use of Skyline (13).

We provide this interact-ms platform to allow easy access web-server based access for any user. A single installation of interact-ms makes our tools available for a whole lab so that even users with no computational experience can apply our tools to gain insight into their data.

We look forward to further developing our software suite in the future.