This doctoral thesis is designed for graduates who wish to gain research experience in an active laboratory with intent to earn their PhD. The Torres lab’s goal is to understand how protein post-translational modifications (PTMs) regulate protein structure, function, and cell behavior. We approach this challenge using three primary tools, including: Mammalian and Yeast cell systems; Mass spectrometry-based proteomics; Bioinformatics, Structural biology, and Machine learning. We address questions at multiple levels of complexity - from proteome to protein.