#include <OpenMS/APPLICATIONS/SearchEngineBase.h>
#include <OpenMS/ANALYSIS/ID/PeptideIndexing.h>
#include <OpenMS/CHEMISTRY/ProteaseDB.h>
#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/XTandemInfile.h>
#include <OpenMS/FORMAT/XTandemXMLFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/METADATA/SpectrumLookup.h>
#include <OpenMS/SYSTEM/File.h>
#include <fstream>
#include <QStringList>