This work describes the development of improved surface coating methods for microchip capillary electrophoresis-electrospray ionization-mass spectrometry (CE-ESI-MS) and their application for the analysis of biological analytes. A new coating method based on chemical vapor deposition (CVD) of aminopropyl silane (APS) reagents is demonstrated. The method improved the efficiency of separations over previously used surface coatings while also promoting batch processing of multiple devices at once. The separation performance was quantified using a new efficiency metric based on CE theory. Microchips coated via CVD produced the most efficient liquid phase separations coupled to MS reported to date. The CVD method was found to produce a base layer well suited for subsequent modification. APS surfaces administered via CVD were modified with n-hydroxy succinimide (NHS) esters of polyethylene glycol (PEG) with varying PEG chain lengths. These coatings were found to produce highly efficient separations while offering a range of electroosmotic flow (EOF) values. PEGylation resulted in increased peak capacity and resolution as compared to APS coatings for the separation of intact proteins and digested proteins using CE-ESI microchips coupled with MS. Microfluidic CE-ESI devices with separation channels of 1 cm and 3 cm in length were coated with APS via CVD and used for high speed (HS) CE-ESI-MS of peptides and proteins. These devices were capable of CE separation times ranging from 10 s to < 1 s. To adequately sample the temporally narrow peaks generated by these devices a new MS data collection with increased data acquisition rates was developed. Both MS and tandem MS analyses were demonstrated using this high speed MS data acquisition method. The HSCE-ESI-MS separations performed on the 1 cm microchip are the fastest liquid phase separations coupled to MS reported to date. Finally, the performance limits of both the APS and PEG surface coatings were investigated. APS was applied to a CE-ESI device with a 1 m separation channel to test the ability of the CVD method to coat long channels. This device achieved > 1.4 million theoretical plates for the separation of peptide standards. A PEG surface coating was used to analyze an intact monoclonal antibody to determine structural charge variants as well as variants arising from glycosylation differences. Additionally, this PEG surface was used to inhibit the effects of sample matrix components that were deleterious to CE-ESI-MS through on-chip mobility-based sample clean-up. This approach facilitated the analysis of biological samples in matrices that would otherwise be incompatible with microchip CE-ESI-MS.