In this study, functionalized multi-walled carbon nanotubes (MWCNTs), namely hydroxylated MWCNTs (MWCNT-OH), carboxylated MWCNTs (MWCNT-COOH) and sulfonated MWCNTs (MWCNT-SO3H) coated with sodium dodecyl sulfate (SDS) were demonstrated as effective pseudo-stationary phases (PSPs) in the separation of various species by the nanoparticle capillary electrokinetic chromatography (NPEKC) mode of capillary electrophoresis (CE). Due to the significant increase in their surface charge density in the presence of SDS, the three SDS coated MWCNTs yielded high performance separation for herbicides, barbiturates, dansyl-DL-amino acids (Dns-AAs), dipeptides and proteins by NPEKC. In addition, high resolution tryptic peptide maps of three standard proteins including myoglobin, cytochrome C and lysozyme were readily obtained. The three PSPs systems yielded high plate numbers that spanned a wide range of values depending on the type of species. The values of the observed selectivity factors (i.e., α values) were significantly different among the three PSPs for solutes that underwent strong interactions with the SDS coated functionalized MWCNTs while for negatively charged solutes (e.g., Dns-AAs) of the same charge sign as the PSPs the α values were about the same on the three different PSPs indicating weak association with the PSPs and signaling separation based chiefly on the differences in electro-migration arising from differences in charge-to-mass ratios.