The Brown team was inspired by nanopore sequencing in DNA and envisions commercializing their idea for widespread use by protein researchers, including for the long-sought goal of sequencing proteins one amino acid at a time.

“Mass spectrometry is the best way to look at proteins, which are made up of amino acids that have all sorts of different chemical and physical properties, because it can tell them apart by the mass of their ions with high certainty,” said Derek Stein, a professor of physics at Brown and author on the paper. “Proteomics have not seen the same advances as genomics in the last two decades, and so there's been this this hunger for a technology that can improve analysis of proteins. By getting rid of that sample loss problem, it should enable these much more sensitive analyses to be possible, like sequencing the amino acids in a protein molecule one-by-one and in sequential order. This is the blue-sky idea that has motivated our work.”

The team spent the past 10 years working on the new method. They started by custom designing their own mass spectrometer that could house the unique ion source in a vacuum, unlike traditional designs where the ion source is separate from the device and sits in open air. The team built the key component of their transfer device by using a special machine to heat a glass tube in the middle and then delicately pull it apart to create an extremely small opening at the tip invisible to the naked eye.

Trial and error played a significant role in the process, often leading to weeks of frustration as they worked to get everything functioning consistently at the tip of capillary, which is far too tiny to inspect by eye.

“There were some weeks we didn’t know if we were cursed by God himself or something — things just stopped working,” Stein said. “Other weeks, everything worked brilliantly.”

The team’s persistence paid off. They successfully demonstrated that ion analysis with their new transfer method matches detections done using traditional methods but with far less sample loss, offering a more efficient and accurate way to analyze tiny particles.

“We needed to convince people in the proteomics field that we can generate the same kind of ions that they are used to generating by conventional electrospray — and that we can do it in this different and, we believe, better way,” Drachman said.

The analysis described in the paper serves as a proof of concept for the method. Next, the researchers aim to unlock the full potential of their nanopore ion source.

“We need to show that this can improve the workflow of proteomic analyses,” Drachman said. “We'd like to take that to the next level and make it something that will improve the science of researchers throughout the field.”

Other Brown authors include former Ph.D. students and postdoctoral researchers Mathilde LePoitevin, Hannah Szapary, Benjamin Wiener and William Maulbetsch. Stein, Drachman, LePoitevin and Wiener are listed as inventors on patents and patent applications that are licensed to Oxford Nanopore Technologies, in which they declare a financial interest. The work was supported by Oxford Nanopore Technologies, the National Institutes of Health and the National Science Foundation.