Representing raw MS data visually

The raw data of proteomics analysis is the spectra that's generated by the mass spectrometers. Each type of mass spectrometer has a different native file format in which the spectra are encoded. Examining and analyzing the spectra begins with loading in the files and coercing them into a common object type. In this recipe, we'll look at how to load the varied file types, look at the metadata, and plot the spectra themselves.

Getting ready

For this recipe, we'll need the Bioconductor package, mzR, and some files from this book's data repository, in the datasets/ch6 folder. We'll use three different files, selected not so much for the data in them, but because they each...