Many tools have been created to generatein silicoproteome digests with different protease enzymes and provide useful
information for selecting optimal digest schemes for specific needs.
This can save on time and resources and generate insights on the observable
proteome. However, there remains a need for a tool that evaluates
digest schemes beyond protein and amino acid coverages in the proteomic
domain. Here, we present ProtView, a versatilein silicoprotease combination digest evaluation workflow that mapsin silico-digested peptides to both protein and genome references,
so that the potential observable portions of the proteome, transcriptome,
and genome can be identified. The proteomic identification and quantification
of evidence for transcriptional, co-transcriptional, post-transcriptional,
translational, and post-translational regulation can all be examinedin silicowith ProtView prior to an experiment. Benchmarking
against biological data comparing multiple proteases shows that ProtView
can correctly estimate performances among the digest schemes. ProtView
provides this information in a way that is easy to interpret, allowing
for digest schemes to be evaluated before carrying out an experiment,
in context that can optimize both proteomic and proteogenomic experiments.
ProtView is available athttps://github.com/SSPuliasis/ProtView.