Matching spectra to peptides for verification with protViz

Although most spectra/peptide matching is done in high throughput search engines, there are times when you'd like to check the quality of competing ambiguous matches against one another, or against a completely arbitrary sequence of interest. Running the whole search engine pipeline is probably overkill, so, in this recipe, we'll look at a convenient method to run a single spectrum against a single peptide sequence and get a plot of congruence between theoretical ion sizes and those present in the spectrum.

Getting ready

For this recipe, all we need is the protViz package, the mzR package, and the MM8.mzml file from the datasets/ch6 folder of this book&apos...