A rapid and simultaneous separation of cationic and anionic peptides and proteins in a glass microfluidic device that has been covalently modified with a neutral poly(ethylene glycol) (PEG) coating to minimize protein adsorption is presented. The features of the device allow samples that contain both anions and cations to be introduced from a central flow stream and separated in different channels with different outlets—all in the presence of low electroosmotic flow (EOF) imparted by the PEG coating. The analytes are electrophoretically extracted from a central hydrodynamic stream and electrophoretically separated in two different channels, in which pressure driven flow has been suppressed through the use of hydrodynamic restrictors. Having different outlets for the electrophoretic separation channels that are spatially separated from the injection enables coupling with further downstream functionalities or off-chip detection, such as mass spectrometry. A plug of charged analyte is hydrodynamically pumped to the sampling intersection and anions from the plug migrate electrophoretically toward the anode in one channel while cations migrate toward the cathode in the other channel due to suppressed EOF from the PEG coating. The separations presented here required less than a minute to complete and produced average separation efficiencies of up to about 3,500 plates from a separation length of 2 cm. The extraction efficiency of both cations and anions from the hydrodynamic stream is determined experimentally and compared with a previously reported model that was used to determine anion extraction efficiency. The extraction efficiency is determined to be 87% and 98% for the two sample mixtures analyzed, and the values predicted by the model are within 3.5% of the experimental data. It is anticipated that this basic approach for simultaneous separation of anions and cations with reduced EOF will be integrated into larger microfluidic systems because the design provides separate outlets that can feed downstream processes or linked to off-chip detection.