Using proteomescout: A resource of post-translational modifications, their experiments, and the proteins that they annotate

Post-translational modifications (PTMs) of protein amino acids are ubiquitous and important to protein function, localization, degradation, and more. In recent years, there has been an explosion in the discovery of PTMs as a result of improvements in PTM measurement techniques, including quantitative measurements of PTMs across multiple conditions. ProteomeScout is a repository for such discovery and quantitative experiments and provides tools for visualizing PTMs within proteins, including where they are relative to other PTMS, domains, mutations, and structure. ProteomeScout additionally provides analysis tools for identifying statistically significant relationships in experimental datasets. This unit describes four basic protocols for working with the ProteomeScout Web interface or programmatically with the database download.