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Metabolomics: where seeing is believing.

Pop quiz: What's the best molecular indicator of the status of a cell? It isn't the genome, which remains more or less unchanged during growth, development, and disease. Nor is it the proteome or the transcriptome; though protein abundance and mRNA expression do serve as molecular bellwethers of the cellular condition, these biomolecules turn over far too slowly. When it comes to cellular status, the molecular canary-in-the-mineshaft that researchers should look to is small molecules—or metabolites—says Renato Zenobi, professor of chemistry and applied biosciences at ETH Zurich. " The metab-olome is arguably the most sensitive measure of a cellular phenotype, " he and Matthias Heinemann of the University of Groningen, the Netherlands, wrote in 2010 (1). Whereas proteins and mRNA turn over in minutes to hours, Zenobi says, the metabolome " changes on the time scale of seconds. " To measure those changes, researchers typically use nuclear magnetic resonance (NMR) or mass spectrometry (MS), both of which, generally speaking, assess the bulk abundance of metabolites in populations of cells. Increasingly, though, such population-based approaches are proving unsatisfactory. studies neurotransmitters and neuropep-tides. According to him, some neurons express molecules at high abundance, while others don't express them at all. Homoge-nizing brain tissue and analyzing it directly would produce data representing an average over all the cells in a sample. Interrogating cells one by one, on the other hand, leads to a very different picture. Today, Sweedler can focus on those individual cells, thanks to a technique called MS imaging (MSI) that couples the exquisite sensitivity and mass accuracy of MS with the cellular (or nearly cellular) spatial resolution of imaging. MSI is not without issues; not all molecules ionize equally well, for instance, and mass spectrometers struggle to capture the less-abundant molecules in a sample. But the approach is quickly evolving, and researchers can now apply MSI to living samples in the lab or clinic, as well as in the 3-D molecular reconstruction of biological samples, among other things. While several forms of MSI exist, all share certain key features: A tissue sample is repeatedly interrogated by an MS ionization source point by point, resulting in a multidimensional dataset in which each x-y coordinate (or pixel) is associated with a mass spectrum. Those spectra may themselves contain hundreds or even thousands of peaks, each of which can be represented graphically by a distinct color. kind of representation to the color channels …