A method for the detection of analytes using resonant mass sensors or sensor arrays comprises frequency encoding each sensor element, acquiring a time-domain resonance signal from the sensor or sensor array as it is exposed to analyte, detecting change in the frequency or resonant properties of each sensor element using a Fourier transform or other spectral analysis method, and classifying, identifying, and/or quantifying analyte using an appropriate data analysis procedure. Frequency encoded sensors or sensor arrays comprise sensor elements with frequency domain resonance signals that can be uniquely identified under a defined range of operating conditions. Frequency encoding can be realized either by fabricating individual sensor elements with unique resonant frequencies or by tuning or modifying identical resonant devices to unique frequencies by adding or removing mass from individual sensor elements. The array of sensor elements comprises multiple resonant structures that may have identical or unique sensing layers. The sensing layers influence the sensor elements' response to analyte. Time-domain signal is acquired, typically in a single data acquisition channel, and typically using either (1) a pulsed excitation followed by acquisition of the free oscillatory decay of the entire array or (2) a rapid scan acquisition of signal from the entire array in a direct or heterodyne configuration. Spectrum analysis of the time domain data is typically accomplished with Fourier transform analysis. The methods and sensor arrays of the invention enable rapid and sensitive analyte detection, classification and/or identification of complex mixtures and unknown compounds, and quantification of known analytes, using sensor element design and signal detection hardware that are robust, simple and low cost.