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The authors developed a temperature-programmed desorption mass spectrometry system equipped with two quadrupole mass spectrometers (QMSs) positioned in the line and out of the line of sight for a sample, respectively. This enables us to directly compare and discuss detection efficiencies and limits of detection of a gas species due to the QMS positions in the same desorption at the same time. Cryopanels are attached to cover the QMS heads, which function as cold traps to decrease interference from unexpected gas species, especially for eliminating the effect of water on hydrogen measurement. The authors evaluated and compared detection efficiencies during hydrogen measurements at room temperature and 50 K using standard hydrogen ion-implanted samples. The cold measurements enhanced detection efficiencies of hydrogen at both QMS positions since ionization efficiencies increased as a result of lowered velocity of the hydrogen molecules after collision with the cryopanels. The authors measured hydrogen content in a steel sample after immersion in an ammonium thiocyanate aqueous solution. The elimination of water effectively resulted in high signal-to-background ratios, which led to low limits of detection and quantitation of hydrogen, rather than enhancement in detection efficiencies.