There are several important basic neuropeptides which include Vasoactive intestinal peptide (VIP), Pituitary adenylate cyclase-activating polypeptide (PACAP) and Parathyroid Hormone (PTH). These peptides are generally very basic (with isoelectric points > 10) and are difficult to analyze by LC-MS methods as they bind to auto-sampler components and columns resulting in very poor chromatographic results. CESI is the integration of capillary electrophoresis (CE) and electrospray ionization (ESI) into a single process in a single device. CESI-MS operates at low nL/min flowrates offering several advantages including increased ionization efficiency and a reduction in ion suppression. In this work we describe the use of the electro-kinetic injection technique to improve sensitivity in a CESI-MS method for the analysis of these intact peptides. The data shows CESI is not hampered by hydrophobic absorptive losses and carryover as in conventional LC workflows. The methods demonstrates teh ability to reproducibly analyse and quantify the neuropeptides PACAP-38 and VIP in serum with excellent sensitivity