For this recipe, we require the mzR package and the threonine_i2_e35_pH_tree.mzXML file from the datasets/ch6 folder of this book's repository. Some of the dependencies rely on encapsulated Java code, so you'll need to install a Java Runtime Environment (JRE) for your system; refer to https://docs.oracle.com/goldengate/1212/gg-winux/GDRAD/java.htm for instructions. Install the JRE before the R packages.