Denaturation of a group of model proteins of diverse size and composition with three branched alkyl surfactants-sodium 2-ethylhexyl sulfate (2-EHS), sodium 3,7-dimethyloctyl sulfate (3,7-DMOS), and sodium 2-butyloctyl sulfate (2-BOS)-has been investigated using circular dichroism (CD), small-angle X-ray scattering, and polyacrylamide gel electrophoresis (PAGE). Circular dichroism reveals that 2-BOS disrupts to a higher extent the secondary structure for most of the proteins. Also, it is found that upon adsorption the shape of the protein-surfactant complexes varies from "pearl necklace" to ellipsoidal depending on the surfactant that is used. Macroscopic separations also reveal that branching sodium alkyl sulfates with n-butyl (2-BOS) and n-methyl (3,7-DMOS) groups significantly affects their performance in PAGE. 3,7-DMOS and 2-BOS result in anomalous migrations that deviate from the expected electrophoretic mobility. A combined interpretation of spectroscopy, scattering, and polyacrylamide gel electrophoresis suggests that 2-BOS promotes stronger modification of proteins during denaturation. The findings in this work aim to improve protein electrophoretic separations and the design of novel surfactants.