Single-cell heterogeneity can arise in both physiological and pathophysiological states of the cell. For example, placing cells in culture can influence both enzymatic and non-enzymatic reactions that lead to the synthesis of diverse bioactive lipids that exhibit either beneficial or detrimental effects on cell survival and/or function. Moreover, a tumor microenvironment consists of cancer and normal cells, with the combination of the two dictating the rate of disease progression and response to therapeutic treatment. However, deciphering which chemical cell-to-cell differences are responsible for contributing to different cell phenotypes is challenging. Here, we present matrix-assisted laser desorption/ionization Fourier-transform ion cyclotron resonance mass spectrometry approaches for characterizing two single-cell systems: cultured versus uncultured cells and GFP-labeled medulloblastoma tumor cells. The approaches used both mass spectrometry imaging where a laser is rastered across the cells on the microscope slide generating spatially resolved chemical maps, or the microMS approach where selected cells are targeted with the laser. For the latter case, the acquisitions are more efficient as the empty space between cells is not probed, allowing a greater number of cells to be characterized in a given time.

Characterizing physiological and pathophysiological chemical heterogeneity in single cells using MALDI FTICR mass spectrometry

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