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An experiment devoted to studies of relativistic effects in the proton-deuteron breakup reaction has been performed at Cyclotron Center Bronowice in Kraków, Poland, with the use of the Kratta detectors and a deuterated polyethylene target (CD2). One of the main sources of background are reactions on carbon. They need to be subtracted from the measured spectra to obtain pure proton-deuteron breakup cross section. In order to determine this component, an additional measurement was carried out using a target made of natural graphite. A procedure of the background subtraction is discussed.