CoMPaseD is a Python-based tool that predicts the optimal selection of protease combinations for specific proteome subsets, such as small proteins, by employing Monte-Carlo-Simulations. The software introduces a novel protease score metric, which enables neutral and comprehensive evaluation of different instruments, sample preparation protocols, or measurement schemes. Designed with a graphical user interface for researchers without programming experience, CoMPaseD facilitates method optimisation before conducting experimental workflows.

Resources and Further Reading:

• Publication DOI:https://doi.org/10.1093/femsml/uqaf043
• Full documentation:https://microbialproteomics.github.io/CoMPaseD/
• GitHub repository:https://github.com/MicrobialProteomics/CoMPaseD
• Mass spectrometric raw data:
  • https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD062213 (B. subtilis, Glu-C and LysArgiNase)
  • https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD017416 (B. subtilis, trypsin, Lys-C, chymotrypsin)
  • https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD023921 (M. mazei, all proteases)

Questions or feedback? Contact us via GitHub Issues or email.