Quantum coherent oscillations in the electric charge passing through a mesoscopic conductor can give rise to a current noise spectrum which is strongly asymmetric in frequency. The asymmetry reveals the fundamental difference between quantum and classical fluctuations in the current. We show how the quantum current noise can be obtained starting from a Born-Markov master equation, an approach which is applicable to a wide class of systems. Our method enables us to analyze the rich behavior of the current noise associated with the double Josephson quasiparticle resonance in a superconducting single-electron transistor (SSET). The asymmetric part of the noise is found to be strongly dependent on the choice of operating point for the SSET and can be either positive or negative. Our results are in good agreement with recent measurements.