Our Studies

Cormican, J. A., Horokhovskyi, Y., Soh, W. T., Mishto, M., and Liepe, J. (2022) inSPIRE: An open-source tool for increased mass spectrometry identification rates using Prosit spectral prediction. Mol Cell Proteomics. (doi: doi.org/10.1016/j.mcpro.2022.100432)

John A. Cormican, Lobna Medfai, Magdalena Wawrzyniuk, Martin Pasen, Hassnae Afrache, Constance Fourny, Sahil Khan, Pascal Gneiße, Wai Tuck Soh, Arianna Timelli, Emanuele Nolfi, Yvonne Pannekoek, Andrew Cope, Henning Urlaub, Alice J. A. M. Sijts, Michele Mishto, and Juliane Liepe (2025) PEPSeek-Mediated Identification of Novel Epitopes From Viral and Bacterial Pathogens and the Impact on Host Cell Immunopeptidomes (doi: 10.1016/j.mcpro.2025.100937)

Tools used within interact-ms

Please also cite the relevant publications of the rescoring tools used, see details on Percolator and Mokapot.

Please also cite the relevant publications of the spectral predictors, see details on Prosit.

If using binding affinity please also cite the relevant publications for NetMHCpan binding affinity predictions.

If using MSFragger via interact-ms, please also cite the relevant publications listed on the MSFragger github.

If you are uploading raw files, please also cite the ThermoRawFileParser.