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The mid-infrared atmospheric window of 3-5.5 μm holds valuable information regarding molecular composition and function for fundamental and applied spectroscopy. Using a robust, mode-locked fiber-laser source of <11 fs pulses in the near infrared, we explore quadratic (χ(2)) nonlinear optical processes leading to frequency comb generation across this entire mid-infrared atmospheric window. With experiments and modeling, we demonstrate intrapulse difference frequency generation that yields few-cycle mid-infrared pulses in a single pass through periodically poled lithium niobate. Harmonic and cascaded χ(2) nonlinearities further provide direct access to the carrier-envelope offset frequency of the near infrared driving pulse train. The high frequency stability of the mid-infrared frequency comb is exploited for spectroscopy of acetone and carbonyl sulfide with simultaneous bandwidths exceeding 11 THz and with spectral resolution as high as 0.003 cm-1. The combination of low noise and broad spectral coverage enables detection of trace gases with concentrations in the part-per-billion range. [ABSTRACT FROM AUTHOR]