A method and apparatus for detecting quadrupole nuclei in motion relative to a search region, during the sensing operation, provides a system for decreasing the throughput time of quadrupole resonance (QR) detection systems. The apparatus uses a single QR probe, or a plurality of QR probes, which may be formed into an array, to remotely and non-invasively generate a QR response from one or more targets containing quadrupole nuclei, as they pass through the probe-sensing region. The method employs an optimized pulse sequence that simultaneously increases the QR signal power while reducing the peak power of the RF pulses. The pulse sequence generates a matrix of signals that are processed to improve detection performance by increasing the signal to noise ratio.