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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
//! [TSG]
#include <OpenMS/CHEMISTRY/TheoreticalSpectrumGenerator.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <iostream>
using namespace OpenMS;
using namespace std;
int main()
{
// initialize a TheoreticalSpectrumGenerator
TheoreticalSpectrumGenerator tsg;
// get current parameters
// in this case default parameters, since we have not changed any yet
Param tsg_settings = tsg.getParameters();
// with default parameters, only b- and y-ions are generated,
// so we will add a-ions
tsg_settings.setValue("add_a_ions", "true");
// store ion types for each peak
tsg_settings.setValue("add_metainfo", "true");
// set the changed parameters for the TSG
tsg.setParameters(tsg_settings);
PeakSpectrum theoretical_spectrum;
// initialize peptide to be fragmented
AASequence peptide = AASequence::fromString("DEFIANGER");
// generate a-, b- and y- ion spectrum of the peptide
// with all fragment charges from 1 to 2
tsg.getSpectrum(theoretical_spectrum, peptide, 1, 2);
// output of masses and meta information (ion-types) of some peaks
const PeakSpectrum::StringDataArray& ion_types = theoretical_spectrum.getStringDataArrays().at(0);
cout << "Mass of second peak: " << theoretical_spectrum[1].getMZ()
<< " | Ion type of second peak: " << ion_types[1] << endl;
cout << "Mass of tenth peak: " << theoretical_spectrum[9].getMZ()
<< " | Ion type of tenth peak: " << ion_types[9] << endl;
return 0;
} //end of main
//! [TSG]
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