plot(itraqdata2[[i]], s, main = s) issues warning

[lgatto]

The changes in how PSMatch::calculateFragments() handles modifications produced an error (now fixes) and still a warning in the plot,MSnExp,character. See the fragplot code chunk in the MSnbase-demo vignette.

[lgatto]

The current fix is quite horrible (calling suppressWarnings() when setting the .plotSingleSpectrum()'s fragments argument.

[lgatto]

This included some additional changes to PTMods.