#include <OpenMS/APPLICATIONS/TOPPBase.h>
#include <OpenMS/ANALYSIS/ID/FalseDiscoveryRate.h>
#include <OpenMS/PROCESSING/ID/IDFilter.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/ProteinIdentification.h>