Formaldehyde Fixation Helps Preserve the Proteome State during Single-Cell Proteomics Sample Processing and Analysis

Mass spectrometry-based single-cell proteomics (SCP) is gaining momentum but remains limited to a few laboratories due to the high costs and specialized expertise required. The ability to send samples to specialized core facilities would benefit nonspecialist laboratories and popularize SCP for biological applications. However, no methods have been tested in SCP to “freeze” the proteome state while maintaining cell integrity for transfer between laboratories or prolonged sorting using fluorescence-activated cell sorting (FACS). This study evaluates whether short-term formaldehyde (FA) fixation can maintain the cell states. We demonstrate that short-term FA fixation does not substantially affect protein recovery, even without heating and strong detergents, and maintains analytical depth compared with classical workflows. Fixation also preserves drug-induced specific perturbations of the protein abundance during cell sorting and sample preparation for SCP analysis. Our findings suggest that FA fixation can facilitate SCP by enabling sample shipping and prolonged sorting, potentially democratizing access to SCP technology and expanding its application in biological research, thereby accelerating discoveries in cell biology and personalized medicine.