ProtView: A versatile tool for in silico protease evaluation and selection in a proteomic and proteogenomic context

Abstract

Tools have been created to generate in silico proteome 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 versatile in-silico protease/protease combination and digest evaluation workflow that maps in silico digested peptides to both protein and genome references, so that the potential observable sections of the proteome, transcriptome and genome can be identified. This supports the identification and quantification of the proteomic evidence of transcriptional, co-transcriptional, post-transcriptional and translational regulations. Benchmarking against biological data comparing multiple proteases shows that ProtView can correctly estimate the relative 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 analysis, in a broader context to optimize proteomic and proteogenomic experiments. ProtView is available at https://github.com/SSPuliasis/ProtView.