#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/ANALYSIS/ID/IDConflictResolverAlgorithm.h>
#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/FORMAT/MzTab.h>
#include <OpenMS/FORMAT/MzTabFile.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/IdentifierMSRunMapper.h>
#include <OpenMS/METADATA/MetaInfoInterfaceUtils.h>
#include "Contaminants.h"
#include "FragmentMassError.h"
#include "FWHM.h"
#include <OpenMS/QC/MissedCleavages.h>
#include <OpenMS/QC/Ms2IdentificationRate.h>
#include "MzCalibration.h"
#include "PeptideMass.h"
#include <OpenMS/QC/PSMExplainedIonCurrent.h>
#include "RTAlignment.h"
#include <OpenMS/QC/TIC.h>
#include "Ms2SpectrumStats.h"
#include "MQEvidenceExporter.h"
#include "MQMsmsExporter.h"
#include "MQExporterHelper.h"
#include <map>