Visualize Casanovo result

Input files

Two files are needed: the MS/MS data in MGF format and the denovo result in mzTab format. For example:

b1906_293T_proteinID_01A_QE3_122212.mgf
dda.mztab

Load the files into PDV:

Click "Denovo Sequencing" in the welcome panel:

Load MS/MS data (.mgf) and identification result (.mztab):

Visualization panel:

After click the "Start" button as shown in the above panel, the visualization panel will be shown in less than 30 seconds for most of datasets:

Validate denovo result using deep learning predicted spectrum

For a denovo peptide, to compare deep learning predicted spectrum (bottom) of this peptide with its associated experimental spectrum (top), PDV could use Prosit or AlphaPeptDeep to predict spectrum and generate a mirror plot like below to facilitate this process. The following tutorial shows how to do this in PDV:

Mirror plot: observed vs predicted spectra