A fundamental study of peptide transport behavior provides information about length dependent transport and sequence structure relationships. In these highly accurate investigations of peptide electrokinetic properties and peptide conformations using a Micro-Electro-Mechanical Systems (MEMS)-fabricated capillary zone electrophoresis (CZE) platform, we demonstrate accurate and repeatable separations of polyglutamate peptides of two different lengths (10 and 20 amino acids). We investigate this separation phenomenon as a function of electrolyte concentration and ionic composition, counter-ion radius, ionic strength and pH. We report a length-dependent counter-ion species selectivity and enhanced separation at pH much higher than the pKa of the peptides that can aid in understanding the relationship between the function of biological peptides and their microenvironments. The ability of our platform to optimize separation resolution between very similar peptides is promising for distinguishing molecular characteristics of peptides and can contribute to resolving current challenges in peptidomics.