Matching spectra to peptides with protViz can be done by using the following steps:

1. Load in the libraries and the MS data:

library(mzR)
library(protViz)
mzml_file <- file.path(getwd(), "datasets", "ch6", "MM8.mzML")
ms <- openMSfile(mzml_file)

2. Extract the peaks and retention time from the spectrum:

p <- peaks(ms,2)
spec <- list(mZ = p[,1], intensity = p[,2])

3. Create a plot of theoretical versus observed ion masses:

m <- psm("PEPTIDESEQ", spec, plot=TRUE)