MassSpec::ViewSpectrum::RealVsHypPeptide is a Perl module to view a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico.
open GRAPHIC, ">mygraphic.png" or die "Unable to open output filen";
my @masses = (78.1,81.1,81.7,85.4,86.8,88.8,89.4,97.6,99.0,99.4,108.7,112.1,129.1,
my @intensities = (8.7,7.7,7.3,10.5,7.7,7.3,8.4,8.0,9.1,9.1,7.3,29.0,12.6,7.3,8.0,
my $peptide = "RTSVAR";
my $vs = MassSpec::ViewSpectrum::RealVsHypPeptide->new($peptide, @masses,@intensities);
$vs->set(yaxismultiplier => 1.8); # a sample tweak to adjust the output
$vs->set(title => "BSA-689 -- " . $peptide);
my $output = $vs->plot();
print GRAPHIC $output;
MassSpec::ViewSpectrum::RealVsHypPeptide - View a real mass spectrum on the same graph as a hypothetical spectrum generated by fragmenting a peptide in silico. The in silico fragmention is performed by generating all of the possible peptides which contain either the amino-terminal or carboxyl-terminal amino acids.
Negative peak intensity values are permitted; this permits the drawing of "pseudospectra" which, for example, illustrate peaks present in one spectrum but missing in another. Note that these negative peaks have no true intensities, but in some cases we assign different heights to illustrate the differences among different hypothetical peaks. In addition, pseudocoloring of both positive and negative peaks is performed to illustrate what type of ion that peak represents. In some cases these ions are labelled explicitly, although in practice it is best to minimize this labelling to avoid excessive clutter.