Searching HCD data with pepNovo

[Ryan]

As far as I can tell, PepNovo only has a model for CID data. Can HCD data be searched with PepNovo despite this, and if so what effect does this have on the peptide sequencing?

[Harald Barsnes]

Hi Ryan,

I would recommend that you contact the PepNovo developers directly (see http://proteomics.ucsd.edu/Software/PepNovo).

DeNovoGUI is simply a wrapper around the command lines for the included de novo algorithms, and we therefore do not have access to the details about how the models are created or how much of a difference there would be between CID and HCD fragmentation models.

Best regards,

Harald