#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/CHEMISTRY/ModificationsDB.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/CONCEPT/Factory.h>
#include <OpenMS/COMPARISON/SPECTRA/BinnedSpectrum.h>
#include <OpenMS/COMPARISON/SPECTRA/SpectraSTSimilarityScore.h>
#include <OpenMS/COMPARISON/SPECTRA/ZhangSimilarityScore.h>
#include <OpenMS/FORMAT/IdXMLFile.h>
#include <OpenMS/FORMAT/MSPFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/MATH/MISC/MathFunctions.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <ctime>
#include <vector>
#include <map>
#include <cmath>