MSMSTheoSPectrum - Perl class to represent MS/MS theoretical spectra
use InSilicoSpectro::InSilico::MSMSTheoSpectrum;
MSMSTheoSpectrum class is an object that simplifies the access to the data contained in the data structure returned by function InSilicoSpectro::InSilico::MassCalculator::getFragmentMasses.
Note that there is no analogous class for PMF spectra because the theoretical spectrum in this case is simply the vector of Peptide objects returned by the digestion functions. To define an object to wrap such a simple data structure would be overdue.
A reference to the data structure returned by the function InSilicoSpectro::InSilico::MassCalculator::getFragmentMasses.
Monoisotopic (0) or average (1) masses.
Relative mass error tolerance. Useful for displaying matches with a different tolerance than the one used by the MassCalculator match functions.
Absolute mass error tolerance. Useful for displaying matches with a different tolerance than the one used by the MassCalculator match functions.
Constructor. %h is a hash of attribute=>value pairs, $MSMSTheoSpectrum is a InSilicoSpectro::InSilico::MSMSTheoSpectrum object, from which the attributes are copied.
Example:
getFragmentMasses(pept=>$peptide, fragTypes=>['b','a','b-H2O*-NH3*','b++','y','y-H2O*-NH3*','y++','immo'], spectrum=>\%spectrum); my $theoSpectrum = new InSilicoSpectro::InSilico::MSMSTheoSpectrum(theoSpectrum=>\%spectrum, massType=>getMassType());
Acessor/modifier of attribute theoSpectrum.
Accessor/modifier of the attribute massType.
Accessor/modifier of the attribute tol.
Accessor/modifier of the attribute minTol.
Returns the peptide sequence or the Peptide object stored in the data structure produced by getFragmentMasses.
Returns the length of the fragmented peptide.
Returns a reference to the vector of modifications used for the theoretical masses computation.
Returns the peptide mass.
Returns a vector containing all the terminal ion series sorted with respect to their name by the function InSilicoSpectro::InSilico::MSMSOutput::cmpFragTypes.
Returns a vector containing all the internal ion series sorted with respect to their name by the function InSilicoSpectro::InSilico::MSMSOutput::cmpFragTypes.
See t/InSilico/testCalcFragOOP.pl.
Jacques Colinge, Upper Austria University of Applied Science at Hagenberg
To install InSilicoSpectro, copy and paste the appropriate command in to your terminal.
cpanm
cpanm InSilicoSpectro
CPAN shell
perl -MCPAN -e shell install InSilicoSpectro
For more information on module installation, please visit the detailed CPAN module installation guide.