Many proteins are unstable in solution and must be formulated in the solid state. This has led to an increase in the use of lyophilized dosage forms. Lyophilization is a complicated processing method consisting of three major steps: freezing, primary drying, and secondary drying. This can lead to several formulation stability challenges including changes in ionization within the matrix, phase separation of the protein drug from added stabilizers, sufficient mobility within the system for movement of reactive species and protein side chains, and crystallization of excipients upon storage. Solid-State Nuclear Magnetic Resonance Spectroscopy (SSNMR) is used to characterize many important properties of lyophilized formulations including crystalline vs. amorphous content, polymorphic form, ionization profile, interaction between formulation components with domain sizes, and mobility within the cake matrix. In order to study ionization changes in lyophilized solids, SSNMR and UV/Vis Diffuse Reflectance spectroscopy were used. 13C-labeled fumaric, succinic, and butyric acids were added to formulations at various pH levels, and were used to quantify change in the ionization of the matrix by monitoring the ionization ratios of the carboxylic acid peaks using SSNMR. pH indicators were also added to the formulations and their ionization ratio was determined using UV/Visible Diffuse Reflectance Spectroscopy. The ionization profile in the solid state was compared with that in solution before lyophilization. A rank ordering of ionization shift was made in pharmaceutically relevant buffers. SSNMR proton relaxation times (1H T1 and 1H T1rho) for each formulation component can be compared to determine homogeneity within the lyophilized matrix. The concept of spin diffusion is used in order to determine the length scale on which the components are either homogeneous or phase separated. The domain size is typically 20-50 nm or 2-10 nm for 1H T1 and 1H T1rho, respectively. PVP and dextran polymers were phase separated on both domains for physical mixtures and lyophilized mixtures. BSA and lysozyme were both lyophilized with formulations containing sucrose, trehalose, or mannitol as the stabilizer. Mannitol crystallized, and the relaxation times showed phase separation. Sucrose and trehalose both formed homogeneous systems at both length scales when formulated in a 1:1 ratio with BSA or lysozyme. Aspartame was shown to be phase separated from trehalose. The SSNMR proton relaxation times were also used to measure the local mobility in the lyophilized matrix, as a timescale of picoseconds to nanoseconds is associated with the 1H T1 relaxation time. Mobility was monitored in formulations containing a fixed amount of sucrose and mannitol, but with a variable amount of an IgG2 protein. The 1H T1 relaxation times decreased as protein content increased. The formulations with the highest relaxation time (lowest mobility), was the most stable in accelerated temperature conditions as monitored by size exclusion chromatography and capillary isoelectric focusing. This method can be used to rank order the most stable formulations at time-zero. Anti-plasticization was also studied by formulating sorbitol in various ratios with trehalose. The 1H T1 relaxation times increased with increasing sorbitol content, while the glass transition temperature decreased. Sorbitol and trehalose glasses were also exposed to different temperature storage conditions. Sorbitol appears to promote aging, as the formulations with higher sorbitol content showed larger increases in proton relaxation time.