Alexandre Masselot
and 1 contributors

NAME

MSMSTheoSPectrum - Perl class to represent MS/MS theoretical spectra

SYNOPSIS

use InSilicoSpectro::InSilico::MSMSTheoSpectrum;

DESCRIPTION

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.

ATTRIBUTES

theoSpectrum

A reference to the data structure returned by the function InSilicoSpectro::InSilico::MassCalculator::getFragmentMasses.

massType

Monoisotopic (0) or average (1) masses.

tol

Relative mass error tolerance. Useful for displaying matches with a different tolerance than the one used by the MassCalculator match functions.

minTol

Absolute mass error tolerance. Useful for displaying matches with a different tolerance than the one used by the MassCalculator match functions.

METHODS

new([%h|$MSMSTheoSpectrum])

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());

theoSpectrum([$theoSpectrum])

Acessor/modifier of attribute theoSpectrum.

massType([$mt])

Accessor/modifier of the attribute massType.

tol([$mt])

Accessor/modifier of the attribute tol.

minTol([$mt])

Accessor/modifier of the attribute minTol.

getPeptide

Returns the peptide sequence or the Peptide object stored in the data structure produced by getFragmentMasses.

getPeptideLength

Returns the length of the fragmented peptide.

getModif

Returns a reference to the vector of modifications used for the theoretical masses computation.

getPeptideMass

Returns the peptide mass.

getTermIons

Returns a vector containing all the terminal ion series sorted with respect to their name by the function InSilicoSpectro::InSilico::MSMSOutput::cmpFragTypes.

getInternIons

Returns a vector containing all the internal ion series sorted with respect to their name by the function InSilicoSpectro::InSilico::MSMSOutput::cmpFragTypes.

EXAMPLES

See t/InSilico/testCalcFragOOP.pl.

AUTHORS

Jacques Colinge, Upper Austria University of Applied Science at Hagenberg