Pharmaceutical process development generates thousands of samples in crude matrix within a very short period of time, which requires rapid result turnout from a robust high-throughput analytical method. Microchip-based gel electrophoresis was evaluated as a high-throughput alternative to conventional capillary electrophoresis sodium dodecyl sulfate (CE-SDS) for monitoring quality attributes of process development samples. Separation in CE-SDS is based on apparent molecular size. One application is the separation and quantitation of the degree of glycosylation under reducing conditions. In this study, HT LabChip® GXII Touch system was used to monitor the aglycosyated species for a heavily sialylated protein. Some challenges were encountered using the standard conditions with Protein Express LabChip® for this heavily sialylated protein. A progressively deteriorated electrophoretic profile was observed with the accumulation of replicate injections, for the same sample preparation (< n=10). While investigating the atypical profiles, several critical parameters were identified and optimized to obtain stable and reproducible resolution. In this presentation, we will discuss those critical parameters which are important for separation of heavily sialylated proteins using the LabChip® system. Additionally, the optimized method was further evaluated for specificity, linearity, precision, and limit of quantitation, as compared with conventional CE-SDS. The LabChip® method has been established for monitoring aglycosylated species for this heavily sialylated protein, in either pure or crude in-process sample media with sufficient resolution and sensitivity, but on a time scale of approximately 20 times faster (2 min versus 40 min per sample) than conventional CE-SDS separations.