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Nanomechanical Mass Spectrometry

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Detecting Proteins

Proteins are the workhorses of the cell, driving all functions necessary for life, such as metabolizing nutrients, and creating enzymes, receptors, and tissues. The specific proteins produced in cells are governed by our DNA (genes).

The double-stranded nature of DNA allows it to be broken into single strands and then rebuilt into two identical copies. Repetition of this process leads to amplification, a process known as polymerase chain reaction (PCR), which enables high signal-to-noise ratio detection of DNA. The PCR technique allowed the Human Genome Project to map 92% of human genes and provides the fastest and most reliable diagnostic test for viral diseases such as COVID-19.

Unfortunately, there is no equivalent to PCR amplification for detecting proteins. Any protein detection technique must be sensitive enough to identify and count them directly.

One can infer the average expression levels for different protein types by sequencing cellular mRNA (’transcriptomics’), but this is not equivalent to counting the proteins produced and cannot measure changes in protein structure with time. Sample data for a mouse cell (averaging over many cells) is seen in Figure 1.

Why single-cell proteomics?

Figure 1 shows that the proteins of a cell span several orders of magnitude in terms of concentration, with some present in only a few copies (one in a billion). Therefore, cataloging the entire protein content of a cell is a massive challenge.

Nevertheless, the dream of single-cell proteomics is to catalog the entire protein content of individual cells to power advances in gene therapy, cancer treatment, and medical diagnostics. Mass spectrometry (MS) is currently the dominant avenue towards realizing single-cell proteomics.

Figure 1: The “dark proteome”. The estimated number of protein types is plotted versus their average number of copies in a mouse cell [1]. Proteins in the shadow evade conventional MS detection.

What is Mass Spectrometry (MS)?

Mass spectrometry encompasses a family of techniques and tools, where the goal is to measure the mass of an unknown object, typically with masses below 10-21 kg, as accurately and quickly as possible. Precise knowledge of the mass of an unknown protein or compound can generally be used to identify its molecular composition.

Conventional Mass Spectrometry (MS) and its Limitations

In modern MS, molecular species gyrating in an electrostatic trap are identified via charge-to-mass ratio (q/m). State-of-the-art MS systems can distinguish species with masses that differ by 1 atomic mass unit (amu), yet they provide only indirect measurements of mass (q/m) and suffer from low throughput (∼ 2 molecules/second). This severely limits their use in proteomics. A single animal cell, for instance, containing a billion proteins (see Fig. 1), would require ~15 years of continuous acquisition time to measure on current systems. Consequently, a human cellular proteome has never been fully characterized. Important proteins present in few copies are practically undetectable.

Mass Spectrometry with Nano-electromechanical Systems (NEMS-MS)

In recent decades, nano-electromechanical systems (NEMS) have emerged as a versatile platform for sensing, enabling advances in areas ranging from consumer electronics to quantum measurement. A new and potentially disruptive application for NEMS is mass spectrometry (MS). In contrast to conventional MS, NEMS-MS provides a direct measurement of mass through the discrete frequency shift of a mechanical resonance upon mass adsorption. The experimenter tracks the mechanical frequency over time, observing frequency jumps when a mass adsorbs (see Fig. 2). The mass responsivity of the mechanical resonator is used to convert the frequency change into a mass sensed [2]. A single millimeter-scale chip with space for upwards of 10,000 NEMS, each acting as an individual mass sensor, could detect up to a million proteins per second. The proteome of a single cell could be fully characterized within an hour.

Figure 2: (a) A simulation of a NEMS mechanical frequency over time showing one mass adsorption event. (b) A COMSOL simulation of a NEMS device oscillation.

In LINQS, we are developing the next generation of nano-electromechanical resonators using a lithium niobate material platform. Metal deposited on the lithium niobate enables excitation and readout of mechanical resonances through the piezoelectric effect. This platform, illustrated in Fig. 3a-c, is naturally amenable to massively scalable high-throughput mass sensing.

In parallel, we are pursuing silicon and heterogenous nano-electromechanical devices for mass spectrometry and massively multiplexed readout schemes.

To differentiate protein species by mass, the main challenge is to remove sources of mechanical frequency noise which obfuscates the frequency jump due to mass adsorption. Nanomechanical devices stand to benefit from operation at millikelvin temperatures where thermal sources of noise [2] are suppressed. Recent studies in our group [3] suggest that energy loss at low temperatures is caused by solid-state material defects, which behave as quantum two-level systems (TLS’s). TLS-induced decoherence constitutes the main obstacle preventing superconducting microwave or acoustic circuits from forming viable quantum transducers, memories, and processors. These same TLS cause frequency fluctuations in our NEMS, limiting the mass sensitivity. A key effort in our group is to understand the fundamental physical models describing the TLS and to remove TLS through improved fabrication and TLS bath engineering.

Another avenue toward lower frequency noise is to leverage advances in quantum sensing. By coupling a mechanical resonator to an electromagnetic field, one can generate a squeezed photon state and then convert it to a squeezed state of mechanical motion. Squeezed light is already being employed by the Laser Interferometer Gravitational Wave Observatory (LIGO) project to detect the position of an interferometer mirror within 10-18 m. Conceptually similar techniques can be employed on-chip by using a superconducting nonlinear microwave circuit coupled to the NEMS. The objective would be to distribute mechanical states in NEMS to squeeze their frequency quadrature, creating an array of integrated quantum-enhanced mass sensors.

All of our efforts are being pursued in collaboration with the Roukes Group at Caltech.

Figure 3: (a) Depiction of an array of NEMS resonators and a COMSOL simulated displacement profile (exaggerated). (b) Microwave reflection spectroscopy data containing 45 mechanical resonances. (c) A 45-degree scanning electron micrograph (SEM) of an array of lithium niobate NEMS. (d) A top-view SEM of two silicon nanomechanical resonators coupled to a lithium niobate transducer. (e) A microscope view of a chip containing arrays of NEMS wire bonded to a printed circuit board.


  1. B. Schwanhäusser, D. Busse, N. Li, G. Dittmar, J. Schuchhardt, J. Wolf, W. Chen, and M. Selbach, “Global quantification of mammalian gene expression control,” Nature 473, 337–342 (2011).
  2. K. Ekinci, Y. T. Yang, and M. Roukes, “Ultimate limits to inertial mass sensing based upon nanoelectromechanical systems,” Journal of Applied Physics 95, 2682–2689 (2004).
  3. A. Wollack, A. Y. Cleland, P. Arrangoiz-Arriola, T. P. McKenna, R. G. Gruenke, R. N. Patel, W. Jiang, C. J. Sarabalis, and A. H. Safavi-Naeini, “Loss channels affecting lithium niobate phononic crystal resonators at cryogenic temperature,” Applied Physics Letters 118, 123501 (2021).

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