Abstract: Field asymmetric waveform ion mobility spectrometry (FAIMS) is a rapid gas phase ion separation technique that can separate different ions by exploiting the unique ion mobility differences of each ion between the high and low electric fields, and has a great potential to become a portable technology for rapid detection of chemical and biological agents. In this study, a high performance standalone planar FAIMS device was developed, which combined with a denoising algorithm and an overlapping peaks separation algorithm. Instead of using mass spectrometer (MS) to detect ions separated by FAIMS, this device can directly measure the ion current at the exit of the planar FAIMS by using a charge collector and a highly sensitive electrometer. This standalone FAIMS device can effectively separate different ions, filter the noise of FAIMS signal and accurately extract the analyte peaks from the overlapping peaks to achieve an accurate identification of analyte with different isomeric structures. Using sucrose and maltose samples, the performance of this FAIMS device on saccharide isomer separation was systematically evaluated. With 3 L/min pure N₂ as FAIMS carrier gas and 3.8 kV bi-sinusoidal waveform as FAIMS dispersion voltage (DV), the FAIMS could effectively separate two structures of sucrose ions. These two sucrose conformers were not resolved by the direct IMS analysis which implies that the FAIMS is somehow more sensitive to the ion structure variations. The resolving power of the FAIMS can be further improved by using a gas mixture of N2/He as the FAIMS carrier gas. With 40% He as carrier gas, the resolving power of this FAIMS device is about 1.5-fold higher compared to 0% He. Interestingly, the resolution of FAIMS may increase or decrease with the increase of the He percentage in FAIMS carrier gas. The resolution for the peaks of two sucrose conformers decreased from 0.92 at 0% He to about 0 at 40% He, which is mainly due to the structural annealing by the field heating of FAIMS DV. However, the overlap of sucrose and maltose peaks at 40% He has reduced from 77% to 50% and the resolution is improved from 0.36 to 0.67, as compared to the FAIMS spectra at pure N2. Overall, this study demonstrated the effectiveness of this standalone planar FAIMS device in separating ions offered a better understanding towards the performance characteristics of the planar FAIMS and provided a potential method for the qualitative analysis of isomers.