Noncovalent interactions of peptides and proteins with carbon nanotubes play a key role in sensing， dispersion， and biocompatibility. Advances in these areas require that the forces which contribute to physical adsorption are understood in order that the carbon nanotubes present a degree of functionalization appropriate to the desired application. Affinity analyses of peptides are employed to evaluate the role of tryptophan and arginine residues in physical adsorption to carboxylated multiwalled carbon nanotubes. Peptides containing arginine and tryptophan， WR(W) ， are used with affinity capillary electrophoresis to identify factors that lead to the formation of peptide-carbon nanotube complexes. The effects of changing the amino acid composition and residue length are evaluated by measuring dissociation constants. Electrostatic interactions contribute significantly to complexation， with the strongest interaction observed using the peptide WRWWWW and carboxylated carbon nanotube. Stronger interaction is observed when the tryptophan content is successively increased as follows: WR(W) > WR(W) > WR(W) > WRW > WR. However， as observed with polytryptophan (W， W， W， and W)， removing the arginine residue significantly reduces the interaction with carbon nanotubes. Increasing the arginine content to WRWWRW does not improve binding， whereas replacing the arginine residue in WRWWWW with lysine (WKWWWW) reveals that lysine also contributes to surface adsorption， but not as effectively as arginine. These observations are used to guide a search of the primary sequence of lysozyme to identify short regions in the peptide that contain a single cationic residue and two aromatic residues. One candidate peptide sequence (WMCLAKW) from this search is analyzed by capillary electrophoresis. The dissociation constant of carboxylated multiwalled carbon nanotubes is measured for the peptide， WMCLAKW， to demonstrate the utility of affinity capillary electrophoresis analysis.