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David Charbonneau detected atmospheric absorption in a transiting exoplanet by comparing the transit depth in different wavelength bands. His team's observations of HD 209458 b found extra dimming near the sodium resonance lines relative to adjacent spectral bands.

During an exoplanet transit, a small fraction of the stellar light passes through the planetary limb. Absorbing atmospheric gas therefore changes the apparent blocking area with wavelength. The observed feature was weaker than a particular cloud-free model predicted, illustrating why detecting an atmospheric species and uniquely determining the atmospheric structure are different inference problems.^[ref]

HD 209458 b is a transiting hot Jupiter that illustrates how an unresolved exoplanet atmosphere can be measured. In the sodium experiment reported in 2002, four exoplanet transits were observed around the sodium doublet near $589.3\mathrm{nm}$. The exoplanet transit depth in that narrow band exceeded the depth in neighbouring bands by approximately $2.3\times 10^{-4}$, interpreted as additional sodium absorption in the planetary limb.^[ref]

The observable is a difference in blocked area with wavelength, rather than an isolated planetary emission spectrum. Its interpretation requires radiative transfer through the limb and a model of the illuminating star. The original sodium signal was weaker than a simple clear-atmosphere prediction, already illustrating why exoplanet clouds, composition and photoionization matter.