Computational Pipelines for Protein Ubiquitylation Analysis and Prediction.

Ubiquitylation is a crucial posttranslational modification that regulates cellular homeostasis and has been linked to a range of diseases. Identification and analysis of ubiquitylated proteins and ubiquitylation sites have historically been successfully performed by mass spectrometry from in vitro and in vivo samples. However, to address some of the challenges and improve the efficiency of ubiquitylation analysis by mass spectrometry, computational tools have been developed and are becoming increasingly popular. In this chapter, we summarize the available computational tools for predicting ubiquitylation in silico and the common approaches used to enrich ubiquitylation in samples for mass spectrometry and computational analysis. We subsequently provide simple steps for molecular biologists to follow for predicting ubiquitylation sites on proteins in silico, and we provide a computational approach to identify average ubiquitin branch sites across samples from ubiquitin-enriched mass spectrometry data.