In the current work, we developed a new protocol, which combines cell washing by nonvolatile salt solution, LN2 quenching, freeze drying in vacuum, and low-temperature storage, for sensitive ambient SCMS analysis. An advantage of our method is to incorporate a rapid washing utilizing the solution containing ammonium formate (AF), which is compatible with live cells and MS analysis , prior to rapid LN2 quenching to minimize cell membrane damage. Quenched cells are then rapidly dried in a vacuum with the presence of residual LN2 to efficiently remove water molecules from cells, allowing for minimized metabolic activities and degradation of metabolites of cells during SCMS measurement in ambient environment. We also evaluated the influence of storage in a -80 °C freezer on cells' metabolites. Our methods can be readily adopted by researchers for robust SCMS metabolomics studies using other types of techniques.