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Characterization at the molecular level establishes X-ray photoelectron spectroscopy (XPS) as a useful technique for determining the extent of proton transfer in molecular crystals by studying theophylline-citric acid co-crystals alongside solid-state nuclear magnetic resonance (ssNMR) and attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR). A complex has been formed by milling theophylline with either anhydrous or monohydrate citric acid and established as a 1:1 co-crystal by a combination of both conventional and novel analytical methods. The absence of peaks from the starting materials in the X-ray diffraction powder pattern indicates that the product was formed quantitatively, with elemental analysis and XPS revealing a 1:1 stoichiometry. Thermogravimetric analysis demonstrated the complex was anhydrous, with differential scanning calorimetry showing a melting temperature different from that of the starting materials. The absence of a CNH+ N1s peak in XPS and the small magnitude of 15N ssNMR and ATR-FTIR shifts relative to anhydrous theophylline revealed that proton transfer, and hence salt formation, had not occurred. The combination of analytical techniques allows the complex to be assigned as a 1:1 co-crystal without the need for a single crystal structure.