Okumus, B. et al. Nat. Commun. 7, 11641 (2016).

Detecting individual proteins in cells is very challenging, especially when attempting to count those with very low copy numbers. To aid in the detection of these elusive molecules, Okumus et al. present microfluidics-assisted cell screening, a method that facilitates the counting of fluorescently tagged, low-abundance protein copies using total internal reflection fluorescence (TIRF) microscopy. In this approach, individual bacterial cells are squeezed through narrow microfluidic channels. This process of mechanical compression slows down protein diffusion in the cytoplasm and enhances the spatial separation of the target protein copies. The compression process also has the benefit of reducing autofluorescence and keeping all target protein copies within the objective depth of focus. The authors applied the method to study the effect of the low-abundance adaptor protein SprE on the stress-response regulator RpoS in Escherichia coli.