A difference-frequency generation based spectrometer system for simultaneous ultra-sensitive measurements of formaldehyde (CH2O) and Methane (CH4) is presented. A new multiplexing approach using collinear quasi-phase-matching in a single grating period of periodically poled lithium niobate (PPLN) is discussed and demonstrated for two pairs of pump and signal lasers to generate mid-infrared frequencies at 2831.64 cm(-1) and 2916.32 cm(-1), respectively. The corresponding absorption signals are discriminated by modulating the DFB diode lasers at modulation frequencies of 40 kHz and 50 kHz, respectively, and using a computer based modulation and de-modulation scheme. In addition, simultaneous measurements of CH2O, CH4 and H2O are demonstrated utilizing both collinear and non-collinear quasi-phase-matching.