Doppler free two-photon spectroscopy of 87Rb is a leading candidate for a portable frequency standard with instability comparable to a hydrogen maser. The required 778 nm light has been achieved through second-harmonic generation of continuous wave (cw) lasers, due to the availability of compact, narrow linewidth, fiber-coupled telecom diodes at 1556 nm. The cw laser was then compared to a frequency comb to convert the optical frequency into a radio frequency. It is alternatively possible to excite the same transition directly with a frequency comb, removing the need for the cw laser and increasing the efficiency of second-harmonic generation. Previous efforts to utilize direct comb spectroscopy as a frequency standard have shown larger instability than their cw counterparts, due in large part to residual Doppler broadening from pulses lasting less than one ps. Herein are discussed the relevant considerations to make direct comb spectroscopy perform equivalently to cw two-photon spectroscopy, most importantly, narrowly filtering the optical bandwidth. The leading sources of instability are explained and methods for compensation are implemented. Features which distinguish direct comb spectroscopy from cw two-photon spectroscopy, such as spectral aliasing, pulse overlap volume, and the residual Stark shift, are evaluated theoretically and experimentally. Direct comb spectroscopy is shown to be capable of resolving the two photon transitions with equivalent linewidth and equivalent ac-Stark shift compared to cw two-photon spectroscopy, with total fluorescence capture of up to 60%. By recording relative frequency deviations between two nearly identical direct comb clocks, instability rivaling the state-of-the-art compact optical frequency standard is shown, with fractional frequency Allan deviation at 1.7×10−13 at one second averaging down to 3×10−14 at 1000 s before drifting in longer timescales. The drift at times longer than an hour is shown to correlate with room temperature, offering some explanation for its source and solution. Efforts towards miniaturization and packaging and future directions for research are discussed
