CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.

ABSTRACT: In proteome studies, the application of alternative proteases, exclusively or in addition to trypsin, often increases protein sequence or proteome coverage. It has recently been shown that, in particular, the analysis of small proteins benefits from such multi-protease approaches. However, selecting the most optimal combination of proteases either requires laboursome experiments or the decision of an experienced user, which might be biased. In this manuscript, we present a protease score that enables the objective comparison of multiple-protease digestions and a Python-based tool named CoMPaseD (Comparison of Multiple Protease  Digestions), which utilizes Monte-Carlo simulations to predict this score for a user-defined set of proteases and any combination of these. By analysis of the small

SUBMITTER: Bartel J 

PROVIDER: S-EPMC12802878 | biostudies-literature | 2026

REPOSITORIES: biostudies-literature