Dilution-free analysis from picoliter droplets by nano-electrospray ionization mass spectrometry

Droplet Microfluidics for High-Throughput Screening and Directed Evolution of Biomolecules

Directed evolution is a powerful technique for creating biomolecules such as proteins and nucleic acids with tailor-made properties for therapeutic and industrial applications by mimicking the natural evolution processes in the laboratory. Droplet microfluidics improved classical directed evolution by enabling time-consuming and laborious steps in this iterative process to be performed within monodispersed droplets in a highly controlled and automated manner. Droplet microfluidic chips can generate, manipulate, and sort individual droplets at kilohertz rates in a user-defined microchannel geometry, allowing new strategies for high-throughput screening and evolution of biomolecules. In this review, we discuss directed evolution studies in which droplet-based microfluidic systems were used to screen and improve the functional properties of biomolecules. We provide a systematic overview of basic on-chip fluidic operations, including reagent mixing by merging continuous fluid streams and droplet pairs, reagent addition by picoinjection, droplet generation, droplet incubation in delay lines, chambers and hydrodynamic traps, and droplet sorting techniques. Various microfluidic strategies for directed evolution using single and multiple emulsions and biomimetic materials (giant lipid vesicles, microgels, and microcapsules) are highlighted. Completely cell-free microfluidic-assisted in vitro compartmentalization methods that eliminate the need to clone DNA into cells after each round of mutagenesis are also presented.

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.

Advances in coupling droplet microfluidics to mass spectrometry

Droplet microfluidics enables development of workflows with low sample consumption and high throughput. Fluorescence-based assays are most used with droplet microfluidics; however, the requirement of a fluorescent reporter restricts applicability of this approach. The coupling of droplets to mass spectrometry (MS) has enabled selective assays on complex mixtures to broaden the analyte scope. Droplet microfluidics has been interfaced to MS via electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI). The works reviewed herein outline the development of this nascent field as well as initial exploration of its application in biotechnology and bioanalysis, including synthetic biology, reaction development, and in vivo sensing.

Technological advances for analyzing the content of organ-on-a-chip by mass spectrometry

Three-dimensional (3D) cell cultures, including organ-on-a-chip (OOC) devices, offer the possibility to mimic human physiology conditions better than 2D models. The organ-on-a-chip devices have a wide range of applications, including mechanical studies, functional validation, and toxicology investigations. Despite many advances in this field, the major challenge with the use of organ-on-a-chips relies on the lack of online analysis methods preventing the real-time observation of cultured cells. Mass spectrometry is a promising analytical technique for real-time analysis of cell excretes from organ-on-a-chip models. This is due to its high sensitivity, selectivity, and ability to tentatively identify a large variety of unknown compounds, ranging from metabolites, lipids, and peptides to proteins. However, the hyphenation of organ-on-a-chip with MS is largely hampered by the nature of the media used, and the presence of nonvolatile buffers. This in turn stalls the straightforward and online connection of organ-on-a-chip outlet to MS. To overcome this challenge, multiple advances have been made to pre-treat samples right after organ-on-a-chip and just before MS. In this review, we summarised these technological advances and exhaustively evaluated their benefits and shortcomings for successful hyphenation of organ-on-a-chip with MS.

Analysis of double-emulsion droplets with ESI mass spectrometry for monitoring lipase-catalyzed ester hydrolysis at nanoliter scale

Microfluidic double-emulsion droplets allow the realization and study of biphasic chemical processes such as chemical reactions or extractions on the nanoliter scale. Double emulsions of the rare type (o₁/w/o₂) are used here to realize a lipase-catalyzed reaction in the non-polar phase. The surrounding aqueous phase induces the transfer of the hydrophilic product from the core oil phase, allowing on-the-fly MS analysis in single double droplets. A microfluidic two-step emulsification process is developed to generate the (o₁/w/o₂) double-emulsion droplets. In this first example of microfluidic double-emulsion MS coupling, we show in proof-of-concept experiments that the chemical composition of the water layer can be read online using ESI–MS. Double-emulsion droplets were further employed as two-phase micro-reactors for the hydrolysis of the lipophilic ester p-nitrophenyl palmitate catalyzed by the Candida antarctica lipase B (CalB). Finally, the formation of the hydrophilic reaction product p-nitrophenol within the double-emulsion droplet micro-reactors is verified by subjecting the double-emulsion droplets to online ESI–MS analysis.

Quantification of Biocatalytic Transformations by Single Microbial Cells Enabled by Tailored Integration of Droplet Microfluidics and Mass Spectrometry

Improving the performance of chemical transformations catalysed by microbial biocatalysts requires a deep understanding of cellular processes. While the cellular heterogeneity of cellular characteristics, such as the concentration of high abundant cellular content, is well studied, little is known about the reactivity of individual cells and its impact on the chemical identity, quantity, and purity of excreted products. Biocatalytic transformations were monitored chemically specific and quantifiable at the single-cell level by integrating droplet microfluidics, cell imaging, and mass spectrometry. Product formation rates for individual Saccharomyces cerevisiae cells were obtained by i) incubating nanolitre-sized droplets for product accumulation in microfluidic devices, ii) an imaging setup to determine the number of cells in the droplets, and iii) electrospray ionisation mass spectrometry for reading the chemical contents of individual droplets. These findings now enable the study of whole-cell biocatalysis at single-cell resolution.

On-the-Fly Mass Spectrometry in Digital Microfluidics Enabled by a Microspray Hole: Toward Multidimensional Reaction Monitoring in Automated Synthesis Platforms

We report an approach for the online coupling of digital microfluidics (DMF) with mass spectrometry (MS) using a chip-integrated microspray hole (μSH). The technique uses an adapted electrostatic spray ionization (ESTASI) method to spray a portion of a sample droplet through a microhole in the cover plate, allowing its chemical content to be analyzed by MS. This eliminates the need for chip disassembly or the introduction of capillary emitters for MS analysis, as required by state-of-the-art. For the first time, this allows the essential advantage of a DMF device─free droplet movement─to be retained during MS analysis. The broad applicability of the developed seamless coupling of DMF and mass spectrometry was successfully applied to the study of various on-chip organic syntheses as well as protein and peptide analysis. In the case of a Hantzsch synthesis, we were able to show that the method is very well suited for monitoring even rapid chemical reactions that are completed in a few seconds. In addition, the strength of the low resource consumption in such on-chip microsyntheses was demonstrated by the example of enzymatic brominations, for which only a minute amount of a special haloperoxidase is required in the droplet. The unique selling point of this approach is that the analyzed droplet remains completely movable after the MS measurement and is available for subsequent on-DMF chip processes. This is illustrated here for the example of MS analysis of the starting materials in the corresponding droplets before they are combined to investigate the reaction progress by DMF-MS further. This technology enables the ongoing and almost unlimited tracking of multistep chemical processes in a DMF chip and offers exciting prospects for transforming digital microfluidics into automated synthesis platforms.

Interfacing microfluidics with information-rich detection systems for cells, bioparticles, and molecules

The development of elegant and numerous microfluidic manipulations has enabled significant advances in the processing of small volume samples and the detection of minute amounts of biomaterials. Effective isolation of single cells in a defined volume as well as manipulations of complex bioparticle or biomolecule mixtures allows for the utilization of information-rich detection methods including mass spectrometry, electron microscopy imaging, and amplification/sequencing. The art and science of translating biosamples from microfluidic platforms to highly advanced, information-rich detection system is the focus of this review, where we term the translation between the microfluidics elements to the external world “off-chipping.” When presented with the challenge of presenting sub-nanoliter volumes of manipulated sample to a detection scheme, several delivery techniques have been developed for effective analysis. These techniques include spraying (electrospray, nano-electrospray, pneumatic), meniscus-defined volumes (droplets, plugs), constrained volumes (narrow channels, containers), and phase changes (deposition, freezing). Each technique has been proven effective in delivering highly defined samples from microfluidic systems to the detection elements. This review organizes and presents selective publications that illustrate the advancements of these delivery techniques with respect to the type of sample analyzed, while introducing each strategy and providing historical perspective. The publications highlighted in this review were chosen due to their significance and relevance in the development of their respective off-chip technique.

Droplet Microfluidics and Directed Evolution of Enzymes: An Intertwined Journey

Evolution is essential to the generation of complexity and ultimately life. It relies on the propagation of the properties, traits, and characteristics that allow an organism to survive in a challenging environment. It is evolution that shaped our world over about four billion years by slow and iterative adaptation. While natural evolution based on selection is slow and gradual, directed evolution allows the fast and streamlined optimization of a phenotype under selective conditions. The potential of directed evolution for the discovery and optimization of enzymes is mostly limited by the throughput of the tools and methods available for screening. Over the past twenty years, versatile tools based on droplet microfluidics have been developed to address the need for higher throughput. In this Review, we provide a chronological overview of the intertwined development of microfluidics droplet-based compartmentalization methods and in vivo directed evolution of enzymes.

Coupling Droplet Microfluidics with Ion Mobility Spectrometry for Monitoring Chemical Conversions at Nanoliter Scale

We introduce the coupling of droplet microfluidics and ion mobility spectrometry (IMS) to address the challenges of label-free and chemical-specific detection of compounds in individual droplets. In analogy to the established use of mass spectrometry, droplet-IMS coupling can be also achieved via electrospray ionization but with significantly less instrumental effort. Because IMS instruments do not require high-vacuum systems, they are very compact, cost-effective, and robust, making them an ideal candidate as a chemical-specific end-of-line detector for segmented flow experiments. Herein, we demonstrate the successful coupling of droplet microfluidics with a custom-built high-resolution drift tube IMS system for monitoring chemical reactions in nL-sized droplets in an oil phase. The analytes contained in each droplet were assigned according to their characteristic ion mobility with limit of detections down to 200 nM to 1 μM and droplet frequencies ranging from 0.1 to 0.5 Hz. Using a custom sheath flow electrospray interface, we have further achieved the chemical-specific monitoring of a biochemical transformation catalyzed by a few hundred yeast cells, at single droplet level.

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

High-throughput screening technologies are widely used for elucidating biological activities. These typically require trade-offs in assay specificity and sensitivity to achieve higher throughput. Microfluidic approaches enable rapid manipulation of small volumes and have found a wide range of applications in biotechnology providing improved control of reaction conditions, faster assays, and reduced reagent consumption. The integration of mass spectrometry with microfluidics has the potential to create high-throughput, sensitivity, and specificity assays. This review introduces the widely-used mass spectrometry ionization techniques that have been successfully integrated with microfluidics approaches such as continuous-flow system, microchip electrophoresis, droplet microfluidics, digital microfluidics, centrifugal microfluidics, and paper microfluidics. In addition, we discuss recent applications of microfluidics integrated with mass spectrometry in single-cell analysis, compound screening, and the study of microorganisms. Lastly, we provide future outlooks towards online coupling, improving the sensitivity and integration of multi-omics into a single platform.

Integration of segmented microflow chemistry and online HPLC/MS analysis on a microfluidic chip system enabling enantioselective analyses at the nanoliter scale

In this work, we introduce an approach to merge droplet microfluidics with an HPLC/MS functionality on a single chip to analyze the contents of individual droplets. This is achieved by a mechanical rotor-stator interface that precisely positions a microstructured PEEK rotor on a microfluidic chip in a pressure-tight manner. The developed full-body fused silica chip, manufactured by selective laser-induced etching, contained a segmented microflow compartment followed by a packed HPLC channel, which were interconnected by the microfluidic PEEK rotor on the fused silica lid with hair-thin through-holes. This enabled the targeted and leakage-free transfer of 10 nL fractions of droplets as small as 25 nL from the segmented microflow channel into the HPLC compartment that operated at pressures of up to 60 bar. In a proof of concept study, this approach was successfully applied to monitor reactions at the nanoliter scale and to distinguish the formed enantiomers.

Non-aqueous electrophoresis integrated with electrospray ionization mass spectrometry on a thiol-ene polymer-based microchip device

Non-aqueous capillary electrophoresis (NACE) on microfluidic chips is still a comparatively little explored area, despite the inherent advantages of this technique and its application potential for, in particular, lipophilic compounds. A main reason is probably the fact that implementation of NACE on microchips largely precluded the use of polymeric substrate materials. Here, we report non-aqueous electrophoresis on a thiol-ene-based microfluidic chip coupled to mass spectrometry via an on-chip ESI interface. Microchips with an integrated ESI emitter were fabricated using a double-molding approach. The durability of thiol-ene, when exposed to different organic solvents, was investigated with respect to swelling and decomposition of the polymer. Thiol-ene exhibited good stability against organic solvents such as methanol, ethanol, N-methylformamide, and formamide, which allows for a wide range of background electrolyte compositions. The integrated ESI emitter provided a stable spray with RSD% of the ESI signal ≤8%. Separation efficiency of the developed microchip electrophoresis system in different non-aqueous buffer solutions was tested with a mixture of several drugs of abuse. Ethanol- and methanol-based buffers provided comparable high theoretical plate numbers (≈ 6.6 × 10⁴-1.6 × 10⁵ m^-1) with ethanol exhibiting the best separation efficiency. Direct coupling of non-aqueous electrophoresis to mass spectrometry allowed for fast analysis of hydrophobic compounds in the range of 0.1-5 μg mL^-1 and 0.2-10 μg mL^-1 and very good sensitivities (LOD ≈ 0.06-0.28 μg mL^-1; LOQ ≈ 0.20-0.90 μg mL^-1). The novel combination of non-aqueous CE on a microfluidic thiol-ene device and ESI-MS provides a mass-producible and highly versatile system for the analysis of, in particular, lipophilic compounds in a wide range of organic solvents. This offers promising potential for future applications in forensic, clinical, and environmental analysis. Graphical abstract.

Coupling Droplet Microfluidics with Mass Spectrometry for Ultrahigh-Throughput Analysis of Complex Mixtures up to and above 30 Hz

High- and ultrahigh-throughput label-free sample analysis is required by many applications, extending from environmental monitoring to drug discovery and industrial biotechnology. HTS methods predominantly are based on a targeted workflow, which can limit their scope. Mass spectrometry readily provides chemical identity and abundance for complex mixtures, and here, we use microdroplet generation microfluidics to supply picoliter aliquots for analysis at rates up to and including 33 Hz. This is demonstrated for small molecules, peptides, and proteins up to 66 kDa on three commercially available mass spectrometers from salty solutions to mimic cellular environments. Designs for chip-based interfaces that permit this coupling are presented, and the merits and challenges of these interfaces are discussed. On an Orbitrap platform droplet infusion rates of 6 Hz are used for analysis of cytochrome c, on a DTIMS Q-TOF similar rates were obtained, and on a TWIMS Q-TOF utilizing IM-MS software rates up to 33 Hz are demonstrated. The potential of this approach is demonstrated with proof of concept experiments on crude mixtures including egg white, unpurified recombinant protein, and a biotransformation supernatant.

High-throughput screening by droplet microfluidics: perspective into key challenges and future prospects

In two decades of development, impressive strides have been made for automating basic laboratory operations in droplet-based microfluidics, allowing the emergence of a new form of high-throughput screening and experimentation in nanoliter to femtoliter volumes. Despite advancements in droplet storage, manipulation, and analysis, the field has not yet been widely adapted for many high-throughput screening (HTS) applications. Broad adoption and commercial development of these techniques require robust implementation of strategies for the stable storage, chemical containment, generation of libraries, sample tracking, and chemical analysis of these small samples. We discuss these challenges for implementing droplet HTS and highlight key strategies that have begun to address these concerns. Recent advances in the field leave us optimistic about the future prospects of this rapidly developing technology.

Advances in ultrahigh-throughput screening for directed enzyme evolution

Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.

Direct Mass Spectrometry Analysis of Complex Mixtures by Nanoelectrospray with Simultaneous Atmospheric Pressure Chemical Ionization and Electrophoretic Separation Capabilities

Accurate and rapid analysis of complex microsamples are challenging tasks in translational research. Nanoelectrospray ionization (nESI) is the method of choice for analyzing small sample volumes by mass spectrometry (MS), but this technique works well only for polar analytes. Herein, we describe a versatile dual noncontact nESI/nAPCI (nanoatmospheric pressure chemical ionization) source that allows simultaneous detection of both polar and nonpolar analytes in microliter quantities of samples under ambient conditions and without pretreatment. The same device can be activated to enable electrophoretic separation. The noncontact nESI/nAPCI MS platform was applied to analyze different samples, including high sensitive direct analysis of biofluids and the efficient detection of proteins in buffers with high concentration of nonvolatile salts. Excellent linearity, accuracy and limits of detection were achieved for compounds with different chemical properties in different matrices. The high sensitivity, universality, simplicity, and ease of operation make this MS technique promising for use in clinical and forensic applications.

Learning from droplet flows in microfluidic channels using deep neural networks

A non-intrusive method is presented for measuring different fluidic properties in a microfluidic chip by optically monitoring the flow of droplets. A neural network is used to extract the desired information from the images of the droplets. We demonstrate the method in two applications: measurement of the concentration of each component of a water/alcohol mixture, and measurement of the flow rate of the same mixture. A large number of droplet images are recorded and used to train deep neural networks (DNN) to predict the flow rate or the concentration. It is shown that this method can be used to quantify the concentrations of each component with a 0.5% accuracy and the flow rate with a resolution of 0.05 ml/h. The proposed method can in principle be used to measure other properties of the fluid such as surface tension and viscosity.

Direct coupling of solid phase microextraction with electrospray ionization mass spectrometry: A Case study for detection of ketamine in urine

Electrospray ionization mass spectrometry (ESI-MS) is a commonly used technique for analysis of various samples. Solid phase microextraction (SPME) is a simple and efficient technique that combines both sampling and sample preparation into one consolidated step, preconcentrating extracted analytes for ultra-sensitive analysis. Historically, SPME has been coupled with chromatography-based techniques for sample separation prior to analysis, however more recently, the chromatographic step has been omitted, with the SPME device directly coupled with the mass spectrometer. In this study, direct coupling of SPME with ESI-MS was developed, and extensively validated to quantitate ketamine from human urine, employing a practical experimental workflow and no extensive hardware modification to the equipment. Among the different fibers evaluated, SPME device coated with C₁₈/benzenesulfonic acid particles was selected for the analysis due to its good selectivity and signal response. Different approaches, including desorption spray, dripping, desorption ESI and nano-ESI were attempted for elution and ionization of the analytes extracted using the SPME fibers. The results showed that the desorption spray and nano-ESI methods offered better signal response and signal duration than the others that were evaluated. The analytical performance of the SPME-nano-ESI-MS setup was excellent, including limit of detection (LOD) of 0.027 ng/mL, limit of quantitation (LOQ) of 0.1 ng/mL, linear range of 0.1-500.0 ng/mL (R² = 0.9995) and recoveries of 90.8-109.4% with RSD 3.4-10.6% for three validation points at 4.0, 40.0 and 400.0 ng/mL, far better than the performance of conventional methods. The results herein presented, demonstrated that the direct coupling of SPME fibers with ESI-MS-based systems allowed for the simple and ultra-sensitive determination of analytes from raw samples such as human urine.

High-Throughput Nanoelectrospray Ionization-Mass Spectrometry Analysis of Microfluidic Droplet Samples

Droplet microfluidics enables high-throughput manipulation of fL-μL volume samples. Methods implemented for the chemical analysis of microfluidic droplets have been limited in scope, leaving some applications of droplet microfluidics difficult to perform or out of reach entirely. Nanoelectrospray ionization-mass spectrometry (nESI-MS) is an attractive approach for droplet analysis, because it allows rapid, label-free, information-rich analysis with high mass sensitivity and resistance to matrix effects. Previous proof-of-concept systems for the nESI-MS analysis of droplets have been limited by the microfluidics used so that stable, long-term operation needed for high-throughput applications has not been demonstrated. We describe a platform for the stable analysis of microfluidic droplet samples by nESI-MS. Continuous infusion of droplets to an nESI emitter was demonstrated for as long as 2.5 h, corresponding to analysis of over 20 000 samples. Stable signal was observed for droplets as small as 65 pL and for throughputs as high as 10 droplets/s. A linear-concentration-based response and sample-to-sample carryover of <3% were also shown. The system is demonstrated for measuring products of in-droplet enzymatic reactions.

Microfluidic Platform for Multimodal Analysis of Enzyme Secretion in Nanoliter Droplet Arrays

High-throughput screening of cell-secreted proteins is essential for various biotechnological applications. In this article, we show a microfluidic approach to perform the analysis of cell-secreted proteins in nanoliter droplet arrays by two complementary methods, fluorescence microscopy and mass spectrometry. We analyzed the secretion of the enzyme phytase, a phosphatase used as an animal feed additive, from a low number of yeast cells. Yeast cells were encapsulated in nanoliter volumes by droplet microfluidics and deposited on spatially defined spots on the surface of a glass slide mounted on the motorized stage of an inverted fluorescence microscope. During the following incubation for several hours to produce phytase, the droplets can be monitored by optical microscopy. After addition of a fluorogenic substrate at a defined time, the relative concentration of phytase was determined in every droplet. Moreover, we demonstrate the use of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) to monitor the multistep conversion of the native substrate phytic acid by phytase secreted in 7 nL droplets containing 50-100 cells. Our method can be adapted to various other protocols. As the droplets are easily accessible, compounds such as assay reagents or matrix molecules can be added to all or to selected droplets only, or part of the droplet volume could be removed. Hence, this platform is a versatile tool for questions related to cell secretome analysis.

High throughput screening of complex biological samples with mass spectrometry – from bulk measurements to single cell analysis

We review the state of the art in HTS using mass spectrometry with minimal sample preparation from complex biological matrices. We focus on industrial and biotechnological applications.

An integrated chip-mass spectrometry and epifluorescence approach for online monitoring of bioactive metabolites from incubated Actinobacteria in picoliter droplets

We present a lab-on-a-chip approach for the analysis of secondary metabolites produced in microfluidic droplets by simultaneous epifluorescence microscopy and electrospray ionization mass spectrometry (ESI-MS). The approach includes encapsulation and long-term off-chip incubation of microbes in surfactant-stabilized droplets followed by a transfer of droplets into a microfluidic chip for subsequent analysis. Before the reinjected droplets are spaced and electrosprayed from an integrated emitter into a mass spectrometer, the presence of fluorescent marker molecules is monitored nearly simultaneously with a custom-made portable epifluorescence microscope. This combined fluorescence and MS-detection setup allows the analysis of metabolites and fluorescent labels in a complex biological matrix at a single droplet level. Using hyphae of Streptomyces griseus, encapsulated in microfluidic droplets of ~ 200 picoliter as a model system, we show the detection of in situ produced streptomycin by ESI-MS and the feasibility of detecting fluorophores inside droplets shortly before they are electrosprayed. The presented method expands the analytical toolbox for the discovery of bioactive metabolites such as novel antibiotics, produced by microorganisms.

Nanowell-mediated two-dimensional liquid chromatography enables deep proteome profiling of <1000 mammalian cells

Multidimensional peptide separations can greatly increase the depth of coverage in proteome profiling. However, a major challenge for multidimensional separations is the requirement of large biological samples, often containing milligram amounts of protein. We have developed nanowell-mediated two-dimensional (2D) reversed-phase nanoflow liquid chromatography (LC) separations for in-depth proteome profiling of low-nanogram samples. Peptides are first separated using high-pH LC and the effluent is concatenated into 4 or 12 nanowells. The contents of each nanowell are reconstituted in LC buffer and collected for subsequent separation and analysis by low-pH nanoLC-MS/MS. The nanowell platform minimizes peptide losses to surfaces in offline 2D LC fractionation, enabling >5800 proteins to be confidently identified from just 50 ng of HeLa digest. Furthermore, in combination with a recently developed nanowell-based sample preparation workflow, we demonstrated deep proteome profiling of >6000 protein groups from small populations of cells, including ∼650 HeLa cells and 10 single human pancreatic islet thin sections (∼1000 cells) from a pre-symptomatic type 1 diabetic donor.

Label-Free Sensing in Microdroplet-Based Microfluidic Systems

Droplet microfluidic systems have evolved as fluidic platforms that use much less sample volume and provide high throughput for biochemical analysis compared to conventional microfluidic devices. The variety of droplet fluidic applications triggered several detection techniques to be applied for analysis of droplets. In this review, we focus on label-free droplet detection techniques that were adapted to various droplet microfluidic platforms. We provide a classification of most commonly used droplet platform technologies. Then we discuss the examples of various label-free droplet detection schemes implemented for these platforms. While providing the research landscape for label-free droplet detection methods, we aim to highlight the strengths and shortcomings of each droplet platform so that a more targeted approach can be taken by researchers when selecting a droplet platform and a detection scheme for any given application.

Direct Surface and Droplet Microsampling for Electrospray Ionization Mass Spectrometry Analysis with an Integrated Dual-Probe Microfluidic Chip

Ambient mass spectrometry (MS) has revolutionized the way of MS analysis and broadened its application in various fields. This paper describes the use of microfluidic techniques to simplify the setup and improve the functions of ambient MS by integrating the sampling probe, electrospray emitter probe, and online mixer on a single glass microchip. Two types of sampling probes, including a parallel-channel probe and a U-shaped channel probe, were designed for dry-spot and liquid-phase droplet samples, respectively. We demonstrated that the microfabrication techniques not only enhanced the capability of ambient MS methods in analysis of dry-spot samples on various surfaces, but also enabled new applications in the analysis of nanoliter-scale chemical reactions in an array of droplets. The versatility of the microchip-based ambient MS method was demonstrated in multiple different applications including evaluation of residual pesticide on fruit surfaces, sensitive analysis of low-ionizable analytes using postsampling derivatization, and high-throughput screening of Ugi-type multicomponent reactions.

Chemical and Biological Dynamics Using Droplet-Based Microfluidics

Recent years have witnessed an increased use of droplet-based microfluidic techniques in a wide variety of chemical and biological assays. Nevertheless, obtaining dynamic data from these platforms has remained challenging, as this often requires reading the same droplets (possibly thousands of them) multiple times over a wide range of intervals (from milliseconds to hours). In this review, we introduce the elemental techniques for the formation and manipulation of microfluidic droplets, together with the most recent developments in these areas. We then discuss a wide range of analytical methods that have been successfully adapted for analyte detection in droplets. Finally, we highlight a diversity of studies where droplet-based microfluidic strategies have enabled the characterization of dynamic systems that would otherwise have remained unexplorable.

A droplet-chip/mass spectrometry approach to study organic synthesis at nanoliter scale

A droplet-based microfluidic device with seamless hyphenation to electrospray mass spectrometry was developed to rapidly investigate organic reactions in segmented flow providing a versatile tool for drug development. A chip-MS interface with an integrated counterelectrode allowed for a flexible positioning of the chip-emitter in front of the MS orifice as well as an independent adjustment of the electrospray potentials. This was necessary to avoid contamination of the mass spectrometer as well as sample overloading due to the high analyte concentrations. The device was exemplarily applied to study the scope of an amino-catalyzed domino reaction with low picomole amount of catalyst in individual nanoliter sized droplets.

Emerging Droplet Microfluidics

Droplet microfluidics generates and manipulates discrete droplets through immiscible multiphase flows inside microchannels. Due to its remarkable advantages, droplet microfluidics bears significant value in an extremely wide range of area. In this review, we provide a comprehensive and in-depth insight into droplet microfluidics, covering fundamental research from microfluidic chip fabrication and droplet generation to the applications of droplets in bio(chemical) analysis and materials generation. The purpose of this review is to convey the fundamentals of droplet microfluidics, a critical analysis on its current status and challenges, and opinions on its future development. We believe this review will promote communications among biology, chemistry, physics, and materials science.

Segmented flow sampling with push-pull theta pipettes

We report development of a mobile and easy-to-fabricate theta pipette microfluidic device for segmented flow sampling. The theta pipettes were also used as electrospray emitters for analysis of sub-nanoliter segments, which resulted in delivery of analyte to the vacuum inlet of the mass spectrometer without multiple transfer steps. Theta pipette probes enable sample collection with high spatial resolution due to micron or smaller sized probe inlets and can be used to manipulate aqueous segments in the range of 200 pL to tens of nanoliters. Optimized conditions can enable sampling with high spatial and temporal resolution, suitable for chemical monitoring in biological samples and studies of sample heterogeneity. Intercellular heterogeneity among Allium cepa cells was studied by collecting cytoplasm from multiple cells using a single probe. Extracted cytoplasm was analyzed in a fast and high throughput manner by direct electrospray mass spectrometry of segmented sample from the probe tip.

Integrated Electrodes and Electrospray Emitter for Polymer Microfluidic Nanospray-MS Interface

Interfacing of microfluidic devices to mass spectrometry has challenges including dilution from sheath liquid junctions, fragile electrodes, and excessive dead volumes which prevent optimum performance and common use. The goal of this work is to develop a stable nanospray chip-MS interface that contains easily integrated electrodes and an embedded capillary emitter to mitigate current chip-MS problems. This system uses a hybrid polystyrene-poly(dimethylsiloxane) (PS-PDMS) microfluidic platform with an embedded electrode and integrated capillary emitter used as the nanospray interface. Two chip designs were used to evaluate the performance, illustrate on-chip reaction capabilities. By direct infusion, this system showed good performance with LODs of GSH and caffeine of 9 nM and 1 nM, R² of 0.996 and 0.992 and sensitivity of 12 counts/nM and 332 counts/nM over a linear dynamic range of 40 nM to 50 μM and 1 to 50 μM respectively. A reaction was performed on the chip with syringe pumps showing the oxidation of glutathione (GSH) to oxidized glutathione (GSSG) using H₂O₂. The on-chip reaction of GSH oxidation to GSSG, with online-MS detection, successfully demonstrate the stability and robustness of the nanospray interface.

A Label-free Sirtuin 1 Assay based on Droplet-Electrospray Ionization Mass Spectrometry

Sirtuin 1(SIRT1) is a NAD⁺-dependent deacetylase which has been implicated in age-related diseases such as cancer, Alzheimer's disease, type 2 diabetes, and vascular diseases. SIRT1 modulators are of interest for their potential therapeutic use and potential as chemical probes to study the role of SIRT1. Fluorescence-based assays used to identify SIRT1 activators have been shown to have artifacts related to the fluorophore substrates used in the assays. Such problems highlight the potential utility of a label-free high throughput screening (HTS) strategy. In this work, we describe a label-free SIRT1 assay suitable for HTS based on segmented flow-electrospray ionization-mass spectrometry (ESI-MS). In the assay, 0.5 μM SIRT1 was incubated with 20 μM acetylated 21-amino acid peptide, which acts as substrate for the protein. A stable-isotope labeled product peptide was added to the assay mixture as an internal standard after reaction quenching. The resulting samples are formatted into 100 nL droplets segmented by perfluorodecalin and then infused at 0.8 samples/s into an ESI-MS. To enable direct ESI-MS analysis, 11 μM SIRT1 was dialyzed into a 200 μM ammonium formate (pH 8.0) buffer prior to use in the assay. This buffer was demonstrated to minimally affect enzyme kinetics and yet be compatible with ESI-MS. The assay conditions were optimized through enzyme kinetic study, and tested by screening an 80-compound library. The assay Z-factor was 0.7. Four inhibitors and no activators were detected from the library.

Mass spectrometry-based monitoring of millisecond protein-ligand binding dynamics using an automated microfluidic platform

Characterizing protein-ligand binding dynamics is crucial for understanding protein function and for developing new therapeutic agents. We present a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and an integrated electrospray ionization source for mass spectrometry-based monitoring of protein-ligand binding dynamics. This platform offers many advantages, including solution-based binding, label-free detection, automated operation, rapid mixing, and low sample consumption.

Analytics for Metabolic Engineering

Realizing the promise of metabolic engineering has been slowed by challenges related to moving beyond proof-of-concept examples to robust and economically viable systems. Key to advancing metabolic engineering beyond trial-and-error research is access to parts with well-defined performance metrics that can be readily applied in vastly different contexts with predictable effects. As the field now stands, research depends greatly on analytical tools that assay target molecules, transcripts, proteins, and metabolites across different hosts and pathways. Screening technologies yield specific information for many thousands of strain variants, while deep omics analysis provides a systems-level view of the cell factory. Efforts focused on a combination of these analyses yield quantitative information of dynamic processes between parts and the host chassis that drive the next engineering steps. Overall, the data generated from these types of assays aid better decision-making at the design and strain construction stages to speed progress in metabolic engineering research.

Analysis of metabolites in single cells-what is the best micro-platform?

This review covers new innovations and developments in the field of single-cell level analysis of metabolites, involving the role of microfluidic and microarray platforms to manipulate and handle the cells prior their detection. Microfluidic and microarray platforms have shown great promise. The latest developments demonstrate their potential to identify a particular cell or even an ensemble of cells (sharing a common property or phenotype) that co-exist in a much larger cell population. The reason for this is the capability of these platforms to perform several complex analytical processes, such as: cleanup, sorting, derivatization, separation, and detection, with great robustness, speed, and reduced sample/reagent consumption. Here, we present several examples that illustrate the rapid strides that have been made for the routine analysis of metabolites by coupling different microfluidics and microarrays devices to a wide range of analytical detectors (e.g. fluorescent microscopy, electrochemical, and mass spectrometry). Herein, we also present selected examples detailing the use of microfluidics and microarrays in the visualization of the natural occurring cell-to-cell heterogeneity in isogenic populations, in particular during the response to external cues. The possibility to accurate monitor the cell-to-cell heterogeneity based on different levels of key metabolites is of clinical relevance, since cell-to-cell heterogeneity can influence, for example, the outcome of a drug treatment.

Development of a simple droplet-based microfluidic capillary viscometer for low-viscosity Newtonian fluids

Viscosity is an easily measured macroscopic property that provides molecular information and is widely used across the sciences and engineering. Here we report a microfluidic capillary viscometer that forms droplets from aqueous samples in an immiscible carrier phase and encodes information about sample viscosity in the droplet spacing. The device shows exceptional calibration stability, with only a 0.6% drift in calibration factor from run to run, the ability to handle aqueous and nonaqueous samples, and the ability to operate with sample volumes as low as 38 nL. Operating range for aqueous sample viscosity was characterized, and was found to be 0.96-52 cP. Operating range for aqueous shear rate was found to depend on aqueous viscosity and varied from 1.9 × 10(1)-4.4 × 10(2) s(-1) for high viscosity samples to 4.1 × 10(2)-6.0 × 10(3) s(-1) for low viscosity samples. Accuracy was tested by comparing measured viscosities of several samples including crème de menthe peppermint liquor, human urine, and baby oil to viscosities of the same samples obtained with a U-tube viscometer. The device was found to be very accurate, with differences between methods as low as 0.1%. The viscometer presented requires only a basic T junction and can utilize off-chip fluorescence to measure viscosity, which could allow for easy addition of viscometric measurement capabilities to existing droplet platforms. Furthermore, the device is capable of performing measurements on Newtonian fluids without precise control over pressures or flow rates, which significantly simplifies device operation.

A microfluidic chip for ICPMS sample introduction

This protocol discusses the fabrication and usage of a disposable low cost microfluidic chip as sample introduction system for inductively coupled plasma mass spectrometry (ICPMS). The chip produces monodisperse aqueous sample droplets in perfluorohexane (PFH). Size and frequency of the aqueous droplets can be varied in the range of 40 to 60 µm and from 90 to 7,000 Hz, respectively. The droplets are ejected from the chip with a second flow of PFH and remain intact during the ejection. A custom-built desolvation system removes the PFH and transports the droplets into the ICPMS. Here, very stable signals with a narrow intensity distribution can be measured, showing the monodispersity of the droplets. We show that the introduction system can be used to quantitatively determine iron in single bovine red blood cells. In the future, the capabilities of the introduction device can easily be extended by the integration of additional microfluidic modules.

Droplet electrospray ionization mass spectrometry for high throughput screening for enzyme inhibitors

High throughput screening (HTS) is important for identifying molecules with desired properties. Mass spectrometry (MS) is potentially powerful for label-free HTS due to its high sensitivity, speed, and resolution. Segmented flow, where samples are manipulated as droplets separated by an immiscible fluid, is an intriguing format for high throughput MS because it can be used to reliably and precisely manipulate nanoliter volumes and can be directly coupled to electrospray ionization (ESI) MS for rapid analysis. In this study, we describe a "MS Plate Reader" that couples standard multiwell plate HTS workflow to droplet ESI-MS. The MS plate reader can reformat 3072 samples from eight 384-well plates into nanoliter droplets segmented by an immiscible oil at 4.5 samples/s and sequentially analyze them by MS at 2 samples/s. Using the system, a label-free screen for cathepsin B modulators against 1280 chemicals was completed in 45 min with a high Z-factor (>0.72) and no false positives (24 of 24 hits confirmed). The assay revealed 11 structures not previously linked to cathepsin inhibition. For even larger scale screening, reformatting and analysis could be conducted simultaneously, which would enable more than 145,000 samples to be analyzed in 1 day.

A new microfluidics-based droplet dispenser for ICPMS

In this work, a novel droplet microfluidic sample introduction system for inductively coupled plasma mass spectrometry (ICPMS) is proposed and characterized. The cheap and disposable microfluidic chip generates droplets of an aqueous sample in a stream of perfluorohexane (PFH), which is also used to eject them as a liquid jet. The aqueous droplets remain intact during the ejection and can be transported into the ICP with >50% efficiency. The transport is realized via a custom-built system, which includes a membrane desolvator necessary for the PFH vapor removal. The introduction system presented here can generate highly monodisperse droplets in the size range of 40–60 μm at frequencies from 90 to 300 Hz. These droplets produced very stable signals with a relative standard deviation (RSD) comparable to the one achieved with a commercial droplet dispenser. Using the current system, samples with a total volume of <1 μL can be analyzed. Moreover, the capabilities of the setup for introduction and quantitative elemental analysis of single cells were described using a test system of bovine red blood cells. In the future, other modules of the modern microfludics can be integrated in the chip, such as on-chip sample pretreatment or parallel introduction of different samples.

Nanoliter segmented-flow sampling mass spectrometry with online compartmentalization

We report a microfluidic device, using segmented flow in a two-phase system of immiscible liquids, which delivers aqueous droplets into a modified commercial mass spectrometer. The interface coupling the microfluidics to the mass spectrometer achieves up to 96% sample transfer efficiency to the vacuum chamber. Sample ionization is assisted by multipass infrared laser beam in the interface. The system achieves low femtomole detection limits of several analytes ranging from drugs to proteins. Sample ionization in this segmented-flow sampling was found to be remarkably insensitive to the presence of buffer salts and other matrices.