New Technology for Consistently Identifying Proteins from a Dozen Cells

A new platform melding microfluidics and robotics allows more in-depth bioanalysis with fewer cells than ever before.

The Science

Detailed analysis of proteins, an important building block for understanding how cells are functioning, has only been possible with samples of thousands to millions of cells. Now scientists have developed a robotically controlled processing platform that dramatically enhances the analysis while reducing sample volume by more than two orders of magnitude.

The Impact

Solving energy, environmental, and health challenges hinges on the ability to understand and predict how biological systems function. NanoPOTS (Nanodroplet Processing in One pot for Trace Samples) enables scientists to identify more than 3,000 proteins from as few as 10 cells, a level of coverage only achieved previously from thousands of cells. This analysis power could help identify new sources of clean energy, unlock secrets to keeping agriculture healthy during droughts, and pinpoint disease markers for diabetes and cancer.


Scientists at EMSL, the Environmental Molecular Sciences Laboratory, developed the nanoPOTS platform to minimize sample losses and expand the science of bioanalysis. Until nanoPOTS, the process of collecting samples and delivering them for analysis was a path of losses. A portion of the sample stuck to each of the vials required to mix the sample with processing reagents and to the tubes that carried the prepared sample from vial to vial and the analysis instrument. Because of these losses, analysis required starting with thousands of cells and information was then lost on how the cells were organized in the biological system. The result was a severe limitation on using the measurements to solve energy, environmental, and health problems. The new nanoPOTS platform uses patterned glass slides with “nanowells,” allowing all sample processing to be performed robotically in a droplet smaller than one 10,000th of a teaspoon. This 99.5 percent reduction in surface area results in minimal sample loss and allows analysis in as little as a single cell to yield specific results. In the study reported in Nature Communications, scientists harnessed nanoPOTS using an ultrasensitive Orbitrap mass spectrometer at EMSL, a DOE Office of Science user facility, and worked with the University of Florida to identify how proteins differed between a healthy human pancreas and one from a person with diabetes. The team’s ability to identify approximately 2,400 proteins from a single slice of tissue illustrates nanoPOTS’ ability to be used for clinical applications as well as other scientific studies.

Principal Investigator(s)

Ryan Kelly
Pacific Northwest National Laboratory


This work was supported by the U.S. Department of Energy’s Office of Science, Office of Biological and Environmental Research, including support of the Environmental Molecular Sciences Laboratory (EMSL), a DOE Office of Science user facility, as well as the support of the Network for Pancreatic Organ Donors with Diabetes, sponsored by JDRF.


Zhu, Y., P.D. Piehowski, R. Zhao, J. Chen, Y. Shen, R.J. Moore, A.K. Shukla, V.A. Petyuk, M. Campbell-Thompson, C.E. Mathews, R.D. Smith, W-J. Qian, and R.T. Kelly. “Nanodroplet processing platform for deep, quantitative proteome profiling of 10-100 mammalian cells.” Nature Communications 9, #882 (2018). [DOI:10.1038/s41467-018-03367-w]