Due to rapid turnover rates of metabolites and relatively low throughput of most ambient SCMS techniques, cell metabolites may change during the extended measurement. To overcome these challenges, we developed a method, which integrates cell quenching, drying, and storage, to preserve cell metabolites for ambient SCMS metabolomics studies. Cells processed under different conditions were analyzed using the Single-probe SCMS technique to evaluate the influence of experimental protocols on cell metabolites.