A high precision GC system with a pulsed discharge helium ionization detector was set up based on the commercial Agilent 7890A gas chromatography. The gas is identified by retention time and the concentration is calculated through the peak height. Detection limit of the system is about 1 x 10(-9) (mole fraction, the same as below). The standard deviation of 140 continuous injections with a standard cylinder( concentration is roughly 600 x 10(-9)) is better than 0.3 x 10(-9). Between 409.30 x 10(-9) and 867.74 x 10(-9) molecular hydrogen mole fractions and peak height have good linear response. By using two standards to quantify the air sample, the precision meets the background molecular hydrogen compatibility goal within the World Meteorological Organization/Global Atmosphere Watch (WMO/GAW) program. Atmospheric molecular hydrogen concentration at Guangzhou urban area was preliminarily measured by this method from January to November 2013. The results show that the atmospheric molecular hydrogen mole fraction varies from 450 x 10(-9) to 700 x 10(-9) during the observation period, with the lowest value at 14:00 (Beijing time, the same as below) and the peak value at 20:00. The seasonal variation of atmospheric hydrogen at Guangzhou area was similar with that of the same latitude stations in northern hemisphere.

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