Faster, better, and cheaper: harnessing microfluidics and mass spectrometry for biotechnology

Emerging biomedical applications of surface-enhanced Raman spectroscopy integrated with artificial intelligence and microfluidic technologies

The integration of surface-enhanced Raman spectroscopy (SERS), artificial intelligence (AI), and microfluidics represent a transformative approach for biomedical applications. By combining the molecular sensitivity of SERS, AI-driven spectral analysis, and the precise sample handling of microfluidics, these novel integrated systems enable ultrasensitive, label-free diagnostics with minimal sample processing. The development of portable, cost-effective platforms could democratize advanced diagnostics for resource-limited settings. However, challenges such as reproducibility, clinical validation, and system integration hinder widespread adoption. This review explores these new integrated platforms, beginning with a discussion of SERS principles, their biomedical applications, and the critical roles of AI and microfluidics in enhancing analytical performance. We evaluate recent advances in the application of these integrated systems, while addressing key challenges such as substrate scalability, biocompatibility, and point-of-care translation, with a focus on nanomaterials, AI models, and lab-on-chip designs. Finally, we outline future directions, including multimodal sensing, sustainable materials, and embedded AI for real-time diagnostics, to bridge the gap between technological innovation and clinical implementation.

Enhancing the Design of Microdevices: The Role of Computational Fluid Dynamics and Experimental Investigation

The growing use of microfluidic-based devices necessitates an analysis of flow characteristics through both experimental methods and computational fluid dynamic (CFD) simulations. CFD simulations facilitate the investigation of various devices, including medical sensors, by providing detailed insights into flow behavior. In this study, we conducted experimental and CFD analysis of the microfluidic flow in three devices: a COVID-19 rapid test kit, a blood glucose kit, and a PDMS kit. Our findings revealed that the changes in wall adhesion (contact angles) during the capillary flow could cause significant deviation from theoretical flow speed predictions. A hemodynamic analysis of the blood glucose kit and PDMS kit showed that capillary filling decreased in length, and flow speed could depend on the microchannel diameter. CFD results indicated the prominent role of porosity in the simulation of porous media material such as the COVID-19 test kit, as well as surface tension coefficients and wall adhesion (contact angles) in blood glucose kits and PDMS kits. Therefore, considering adaptive dynamic contact angles in CFD simulation software such as Ansys-Fluent 2024 could result in a more accurate prediction than simplified theoretical techniques, which is useful for sensor optimization and development.

Advances and challenges in preparing membrane proteins for native mass spectrometry

Native mass spectrometry (nMS) is becoming a crucial tool for analyzing membrane proteins (MPs), yet challenges remain in solubilizing and stabilizing their native conformations while resolving and characterizing the heterogeneity introduced by post-translational modifications and ligand binding. This review highlights recent advancements and persistent challenges in preparing MPs for nMS. Optimizing detergents and additives can significantly reduce sample heterogeneity and surface charge, enhancing MP signal quality and structural preservation in nMS. A strategic workflow incorporating affinity capture, stabilization agents, and size-exclusion chromatography to remove unfolded species demonstrates success in improving nMS characterization. Continued development of customized detergents and reagents tailored for specific MPs may further minimize heterogeneity and boost signals. Instrumental advances are also needed to elucidate more dynamically complex and labile MPs. Effective sample preparation workflows may provide insights into MP structures, dynamics, and interactions underpinning membrane biology. With ongoing methodological innovation, nMS shows promise to complement biophysical studies and facilitate drug discovery targeting this clinically important yet technically demanding protein class.

A prescription for engineering PFAS biodegradation

Per- and polyfluorinated chemicals (PFAS) are of rising concern due to environmental persistence and emerging evidence of health risks to humans. Environmental persistence is largely attributed to a failure of microbes to degrade PFAS. PFAS recalcitrance has been proposed to result from chemistry, specifically C-F bond strength, or biology, largely negative selection from fluoride toxicity. Given natural evolution has many hurdles, this review advocates for a strategy of laboratory engineering and evolution. Enzymes identified to participate in defluorination reactions have been discovered in all Enzyme Commission classes, providing a palette for metabolic engineering. In vivo PFAS biodegradation will require multiple types of reactions and powerful fluoride mitigation mechanisms to act in concert. The necessary steps are to: (1) engineer bacteria that survive very high, unnatural levels of fluoride, (2) design, evolve, and screen for enzymes that cleave C-F bonds in a broader array of substrates, and (3) create overall physiological conditions that make for positive selective pressure with PFAS substrates.

3D printed microfluidic devices with electrodes for electrochemical analysis

A review with 93 references describing various 3D printing approaches that have been used to create microfluidic devices containing electrodes for electrochemical detection. The use of 3D printing to fabricate microfluidic devices is a rapidly growing area. One significant research area is how to detect analytes in the devices for quantitation purposes. This review article is focused on methods used to integrate electrodes into the devices for electrochemical detection. The review is organized in terms of the methodology for integrating the electrode within the device. This includes (1) external coupling of traditional electrode materials with 3D printed devices; (2) printing conductive electrode materials as part of device printing; and (3) integrating traditional electrodes into the device as part of the print process. Example applications are given and some future directions are also outlined.

1-Octanol-assisted ultra-small volume droplet microfluidics with nanoelectrospray ionization mass spectrometry

BACKGROUND

Droplet microfluidics with push-pull and microdialysis sampling from brain slices, cultured cells and engineered tissues produce low volume mass limited samples containing analytes sampled from the extracellular space. This sampling approach coupled to mass spectrometry (MS) detection allows evaluation of time-dependent chemical changes. Our goal is an approach for continuous sampling and segregation of extracellular samples into picoliter droplets followed by the characterization of the droplets using nanoelectrospray ionization (nESI) MS. The main focus here is the optimization of the carrier oil for the microfluidic device that neither affects the stability of picoliter droplets nor compatibility with MS detection of a range of analytes.

RESULTS

We developed and characterized a 1-octanol-assisted ultra-small volume droplet microfluidic nESI MS system for the analysis of neurotransmitters in distinct samples including cerebrospinal fluid (CSF). The use of a 1-octanol oil phase was effective for generation of aqueous droplets as small as 65 pL and enabled detection of acetylcholine (ACh) and gamma-aminobutyric acid (GABA) in water and artificial CSF. Continuous MS analysis of droplets for extended periods up to 220 min validated the long-term stability of droplet generation and analyte detection by nESI-MS. As an example, ACh response demonstrated a linear working range (R2 = 0.99) between 0.4 μM and 25 μM with a limit of detection of 370 nM (24 amol), enabling its quantitation in rodent CSF.

SIGNIFICANCE

The established droplet microfluidics - nESI MS approach allows the analysis of microenvironments at high spatiotemporal resolution. The approach may allow microsampling and monitoring of spatiotemporal dynamics of neurochemicals and drugs in the brain and spinal cord of live animals.

Photosubstitution and photoreduction of a diazido platinum(IV) anticancer complex

The hyphenation of HPLC with its high separation ability and ICP-MS with its excellent sensitivity, allows the analysis of Pt drugs in biological samples at the low nanomolar concentration levels. On the other hand, LC-MS provides molecular structural confirmation for each species. Using a combination of these methods, we have investigated the speciation of the photoactive anticancer complex diazido Pt(IV) complex trans, trans, trans-[Pt(N3)2(OH)2(py)2] (FM-190) in aqueous solution and biofluids at single-digit nanomolar concentrations before and after irradiation. FM-190 displays high stability in human blood plasma in the dark at 37 °C. Interestingly, the polyhydroxido species [{PtIV(py)2(OH)4} + Na]+ and [{PtIV(py)2(N3)(OH)3} + Na]+ resulting from the replacement of azido ligands, as determined by LC-MS, were the major products after photoirradiation of FM-190 with blue light (463 nm). This finding suggests that such photosubstituted Pt(IV) tri- and tetra-hydroxido species could play important roles in the biological activity of this anticancer complex. Density Functional Theory (DFT) and Time-Dependent DFT (TDDFT) calculations show that these Pt(IV) species arising from FM-190 in aqueous media can be formed directly from a singlet excited state. The results highlight how speciation analysis (metallomics) can shed light on photoactivation pathways for FM-190 and formation of potential excited-state pharmacophores. The ability to detect and identify photoproducts at physiologically-relevant concentrations in cells and tissues will be important for preclinical development studies of this class of photoactivatable platinum drugs.

Liquid phase detection in the miniature scale. Microfluidic and capillary scale measurement and separation systems. A tutorial review

Microfluidic and capillary devices are increasingly being used in analytical applications while their overall size keeps decreasing. Detection sensitivity for these microdevices gains more importance as device sizes and consequently, sample volumes, decrease. This paper reviews optical, electrochemical, electrical, and mass spectrometric detection methods that are applicable to capillary scale and microfluidic devices, with brief introduction to the principles in each case. Much of this is considered in the context of separations. We do consider theoretical aspects of separations by open tubular liquid chromatography, arguably the most potentially fertile area of separations that has been left fallow largely because of lack of scale-appropriate detection methods. We also examine the theoretical basis of zone electrophoretic separations. Optical detection methods discussed include UV/Vis absorbance, fluorescence, chemiluminescence and refractometry. Amperometry is essentially the only electrochemical detection method used in microsystems. Suppressed conductance and especially contactless conductivity (admittance) detection are in wide use for the detection of ionic analytes. Microfluidic devices, integrated to various mass spectrometers, including ESI-MS, APCI-MS, and MALDI-MS are discussed. We consider the advantages and disadvantages of each detection method and compare the best reported limits of detection in as uniform a format as the available information allows. While this review pays more attention to recent developments, our primary focus has been on the novelty and ingenuity of the approach, regardless of when it was first proposed, as long as it can be potentially relevant to miniature platforms.

3D printed microfluidic devices for integrated solid-phase extraction and microchip electrophoresis of preterm birth biomarkers

BACKGROUND

Preterm birth (PTB) is a leading cause of neonatal mortality, such that the need for a rapid and accurate assessment for PTB risk is critical. Here, we developed a 3D printed microfluidic system that integrated solid-phase extraction (SPE) and microchip electrophoresis (μCE) of PTB biomarkers, enabling the combination of biomarker enrichment and labeling with μCE separation and fluorescence detection.

RESULTS

Reversed-phase SPE monoliths were photopolymerized in 3D printed devices. Microvalves in the device directed sample between the SPE monolith and the injection cross-channel in the serpentine μCE channel. Successful on-chip preconcentration, labeling and μCE separation of four PTB-related polypeptides were demonstrated in these integrated microfluidic devices. We further show the ability of these devices to handle complex sample matrices through the successful analysis of labeled PTB biomarkers spiked into maternal blood serum. The detection limit was 7 nM for the PTB biomarker, corticotropin releasing factor, in 3D printed SPE-μCE integrated devices.

SIGNIFICANCE

This work represents the first successful demonstration of integration of SPE and μCE separation of disease-linked biomarkers in 3D printed microfluidic devices. These studies open up promising possibilities for rapid bioanalysis of medically relevant analytes.

Multiplex fluorescence detection of single-cell droplet microfluidics and its application in quantifying protein expression levels

This study presented a platform of multiplex fluorescence detection of single-cell droplet microfluidics with demonstrative applications in quantifying protein expression levels. The platform of multiplex fluorescence detection mainly included optical paths adopted from conventional microscopy enabling the generation of three optical spots from three laser sources for multiple fluorescence excitation and capture of multiple fluorescence signals by four photomultiplier tubes. As to platform characterization, microscopic images of three optical spots were obtained where clear Gaussian distributions of intensities without skewness confirmed the functionality of the scanning lens, while the controllable distances among three optical spots validated the functionality of fiber collimators and the reflector lens. As to demonstration, this platform was used to quantify single-cell protein expression within droplets where four-type protein expression of α-tubulin, Ras, c-Myc, and β-tubulin of CAL 27 (Ncell = 1921) vs WSU-HN6 (Ncell = 1881) were quantitatively estimated, which were (2.85 ± 0.72) × 105 vs (4.83 ± 1.58) × 105, (3.69 ± 1.41) × 104 vs (5.07 ± 2.13) × 104, (5.90 ± 1.45) × 104 vs (9.57 ± 2.85) × 104, and (3.84 ± 1.28) × 105 vs (3.30 ± 1.10) × 105, respectively. Neural pattern recognition was utilized for the classification of cell types, achieving successful rates of 69.0% (α-tubulin), 75.4% (Ras), 89.1% (c-Myc), 65.8% (β-tubulin), and 99.1% in combination, validating the capability of this platform of multiplex fluorescence detection to quantify various types of single-cell proteins, which could provide comprehensive evaluations on cell status.

A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening

Mass spectrometry (MS) enables detection of different chemical species with a very high specificity; however, it can be limited by its throughput. Integrating MS with microfluidics has a tremendous potential to improve throughput and accelerate biochemical research. In this work, we introduce Drop-NIMS, a combination of a passive droplet loading microfluidic device and a matrix-free MS laser desorption ionization technique called nanostructure-initiator mass spectrometry (NIMS). This platform combines different droplets at random to generate a combinatorial library of enzymatic reactions that are deposited directly on the NIMS surface without requiring additional sample handling. The enzyme reaction products are then detected with MS. Drop-NIMS was used to rapidly screen enzymatic reactions containing low (on the order of nL) volumes of glycoside reactants and glycoside hydrolase enzymes per reaction. MS "barcodes" (small compounds with unique masses) were added to the droplets to identify different combinations of substrates and enzymes created by the device. We assigned xylanase activities to several putative glycoside hydrolases, making them relevant to food and biofuel industrial applications. Overall, Drop-NIMS is simple to fabricate, assemble, and operate and it has potential to be used with many other small molecule metabolites.

In-depth analysis of biocatalysts by microfluidics: An emerging source of data for machine learning

Nowadays, the vastly increasing demand for novel biotechnological products is supported by the continuous development of biocatalytic applications which provide sustainable green alternatives to chemical processes. The success of a biocatalytic application is critically dependent on how quickly we can identify and characterize enzyme variants fitting the conditions of industrial processes. While miniaturization and parallelization have dramatically increased the throughput of next-generation sequencing systems, the subsequent characterization of the obtained candidates is still a limiting process in identifying the desired biocatalysts. Only a few commercial microfluidic systems for enzyme analysis are currently available, and the transformation of numerous published prototypes into commercial platforms is still to be streamlined. This review presents the state-of-the-art, recent trends, and perspectives in applying microfluidic tools in the functional and structural analysis of biocatalysts. We discuss the advantages and disadvantages of available technologies, their reproducibility and robustness, and readiness for routine laboratory use. We also highlight the unexplored potential of microfluidics to leverage the power of machine learning for biocatalyst development.

Point-of-care diagnostics for sepsis using clinical biomarkers and microfluidic technology

Sepsis is a life-threatening immune response which is caused by a wide variety of sources and is a leading cause of mortality globally. Rapid diagnosis and appropriate antibiotic treatment are critical for successful patient outcomes; however, current molecular diagnostic techniques are time-consuming, costly and require trained personnel. Additionally, there is a lack of rapid point-of-care (POC) devices available for sepsis detection despite the urgent requirements in emergency departments and low-resource areas. Recent advances have been made toward developing a POC test for early sepsis detection that will be more rapid and accurate compared to conventional techniques. Within this context, this review discusses the use of current and novel biomarkers for early sepsis diagnosis using microfluidics devices for POC testing.

Application of Microfluidics for Bacterial Identification

Bacterial infections continue to pose serious public health challenges. Though anti-bacterial therapeutics are effective remedies for treating these infections, the emergence of antibiotic resistance has imposed new challenges to treatment. Often, there is a delay in prescribing antibiotics at initial symptom presentation as it can be challenging to clinically differentiate bacterial infections from other organisms (e.g., viruses) causing infection. Moreover, bacterial infections can arise from food, water, or other sources. These challenges have demonstrated the need for rapid identification of bacteria in liquids, food, clinical spaces, and other environments. Conventional methods of bacterial identification rely on culture-based approaches which require long processing times and higher pathogen concentration thresholds. In the past few years, microfluidic devices paired with various bacterial identification methods have garnered attention for addressing the limitations of conventional methods and demonstrating feasibility for rapid bacterial identification with lower biomass thresholds. However, such culture-free methods often require integration of multiple steps from sample preparation to measurement. Research interest in using microfluidic methods for bacterial identification is growing; therefore, this review article is a summary of current advancements in this field with a focus on comparing the efficacy of polymerase chain reaction (PCR), loop-mediated isothermal amplification (LAMP), and emerging spectroscopic methods.

Multifunctional microfluidic chips for the single particle inductively coupled plasma mass spectrometry analysis of inorganic nanoparticles

This study aimed at exploiting the so far unexploited potential of carrying out on-line sample pretreatment steps on microfluidic chips for single particle inductively coupled plasma mass spectrometry (spICP-MS) measurements, and demonstrating their ability to practically facilitate most of the simpler tasks involved in the spICP-MS analysis of nanoparticles. For this purpose, polydimethylsiloxane microfluidic chips, capable of high-range dilution and sample injection were made by casting, using high-precision, 3D-printed molds. Optimization of their geometry and functions was done by running several hydrodynamic simulations and by gravimetric, fluorescence enhanced microscope imaging and solution-based ICP-MS experiments. On the optimized microfluidic chips, several experiments were done, demonstrating the benefits of the approach and these devices, such as the determination of nanoparticle concentration using only a few tens of microliters of sample, elimination of solute interferences by dilution, solution-based size calibration and characterisation of binary nanoparticles. Due to the unique design of the chips, they can be linked together to extend the dilution range of the system by more than a magnitude per chip. This feature was also demonstrated in applications requiring multiple-magnitude dilution rates, when two chips were sequentially coupled.

On-Demand Nanoliter Sampling Probe for the Collection of Brain Fluid

Continuous fluidic sampling systems allow collection of brain biomarkers in vivo. Here, we propose a new sequential and intermittent sampling paradigm using droplets, called Droplet on Demand (DoD). It is implemented in a microfabricated neural probe and alternates phases of analyte removal from the tissue and phases of equilibration of the concentration in the tissue. It allows sampling droplets loaded with molecules from the brain extracellular fluid punctually, without the long transient equilibration periods typical of continuous methods. It uses an accurately defined fluidic sequence with controlled timings, volumes, and flow rates, and correct operation is verified by the embedded electrodes and a flow sensor. As a proof of concept, we demonstrated the application of this novel approach in vitro and in vivo, to collect glucose in the brain of mice, with a temporal resolution of 1-2 min and without transient regime. Absolute quantification of the glucose level in the samples was performed by direct infusion nanoelectrospray ionization Fourier transform mass spectrometry (nanoESI-FTMS). By adjusting the diffusion time and the perfusion volume of DoD, the fraction of molecules recovered in the samples can be tuned to mirror the tissue concentration at accurate points in time. Moreover, this makes quantification of biomarkers in the brain possible within acute experiments of only 20-120 min. DoD provides a complementary tool to continuous microdialysis and push-pull sampling probes. Thus, the advances allowed by DoD will benefit quantitative molecular studies in the brain, i.e., for molecules involved in volume transmission or for protein aggregates that form in neurodegenerative diseases over long periods.

A Review of Optical Imaging Technologies for Microfluidics

Microfluidics can precisely control and manipulate micro-scale fluids, and are also known as lab-on-a-chip or micro total analysis systems. Microfluidics have huge application potential in biology, chemistry, and medicine, among other fields. Coupled with a suitable detection system, the detection and analysis of small-volume and low-concentration samples can be completed. This paper reviews an optical imaging system combined with microfluidics, including bright-field microscopy, chemiluminescence imaging, spectrum-based microscopy imaging, and fluorescence-based microscopy imaging. At the end of the article, we summarize the advantages and disadvantages of each imaging technology.