Proteolysis in microfluidic droplets: an approach to interface protein separation and peptide mass spectrometry

A review on hyphenation of droplet microfluidics to separation techniques: From instrumental conception to analytical applications for limited sample volumes

In this study, we review various strategies to couple sample processing in microfluidic droplets with different separation techniques, including liquid chromatography, mass spectrometry, and capillary electrophoresis. Separation techniques interfaced with droplet microfluidics represent an emerging trend in analytical chemistry, in which micro to femtoliter droplets serve as microreactors, a bridge between analytical modules, as well as carriers of target analytes between sample treatment and separation/detection steps. This allows to overcome the hurdles encountered in separation science, notably the low degree of module integration, working volume incompatibility, and cross contamination between different operational stages. For this droplet-separation interfacing purpose, this review covers different instrumental designs from all works on this topic up to May 2023, together with our viewpoints on respective advantages and considerations. Demonstration and performance of droplet-interfaced separation strategies for limited sample volumes are also discussed.

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.

Ion Mobility-Mass Spectrometry Coupled to Droplet Microfluidics for Rapid Protein Structure Analysis and Drug Discovery

Native mass spectrometry coupled to ion mobility (IM-MS) has become an important tool for the investigation of protein structure and dynamics upon ligand binding. Additionally, collisional activation or collision induced unfolding (CIU) can further probe conformational changes induced by ligand binding; however, larger scale screens have not been implemented due to limitations associated with throughput and sample introduction. In this work we explore the high-throughput capabilities of CIU fingerprinting. Fingerprint collection times were reduced 10-fold over traditional data collections through the use of improved smoothing and interpolation algorithms. Fast-CIU was then coupled to a droplet sample introduction approach using 40 nL droplet sample volumes and 2 s dwell times at each collision voltage. This workflow, which increased throughput by ∼16-fold over conventional nanospray CIU methods, was applied to a 96-compound screen against Sirtuin-5, a protein target of clinical interest. Over 20 novel Sirtuin-5 binders were identified, and it was found that Sirtuin-5 inhibitors will stabilize specific Sirtuin-5 gas-phase conformations. This work demonstrates that droplet-CIU can be implemented as a high-throughput biophysical characterization approach. Future work will focus on improving the throughput of this workflow and on automating data acquisition and analysis.

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-assisted electrospray phase separation using an integrated silicon microfluidic platform

We report a silicon microfluidic platform that enables monolithic integration of transparent micron-scale microfluidic channels, an on-chip segmentation of analyte flows into picoliter-volume droplets, and a nano-electrospray ionization emitter that enables spatial and temporal separation of oil and aqueous phases during electro-spray for subsequent mass spectrometry analysis.

Droplet Microfluidics with MALDI-MS Detection: The Effects of Oil Phases in GABA Analysis

Microfluidic and mass spectrometry (MS) methods are widely used to sample and probe the chemical composition of biological systems to elucidate chemical correlates of their healthy and disease states. Though matrix-assisted laser desorption/ionization-mass spectrometry (MALDI)-MS has been hyphenated to droplet microfluidics for offline analyses, the effects of parameters related to droplet generation, such as the type of oil phase used, have been understudied. To characterize these effects, five different oil phases were tested in droplet microfluidics for producing samples for MALDI-MS analysis. Picoliter to nanoliter aqueous droplets containing 0.1 to 100 mM γ-aminobutyric acid (GABA) and inorganic salts were generated inside a polydimethylsiloxane microfluidic chip and deposited onto a conductive glass slide. Optical microscopy, Raman spectroscopy, and MALDI-mass spectrometry imaging (MSI) of the droplet samples and surrounding areas revealed patterns of solvent and oil evaporation and analyte deposition. Optical microscopy detected the presence of salt crystals in 50-100 μm diameter dried droplets, and Raman and MSI were used to correlate GABA signals to the visible droplet footprints. MALDI-MS analyses revealed that droplets prepared in the presence of octanol oil led to the poorest detectability of GABA, whereas the oil phases containing FC-40 provided the best detectability; GABA signal was localized to the footprint of 65 pL droplets with a limit of detection of 23 amol. The effect of the surfactant perfluorooctanol on analyte detection was also investigated.

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.

How electrospray potentials can disrupt droplet microfluidics and how to prevent this

A pressure-resistant microfluidic glass chip that integrates a packed-bed HPLC column, a droplet generator and a monolithic electrospray emitter is presented. This approach enables a seamless coupling of chip-HPLC and droplet microfluidics with ESI-MS detection. For the electrical contacting of the emitter, an electrode was integrated into the channel, which reaches up to the emitter tip. The incidental finding that under certain circumstances, the electrospray potential can strongly disturb the droplet microfluidics by electrowetting, was investigated in detail. Strategies to avoid this are evaluated and include electrical shielding and/or chip layouts, where the droplet generator is positioned at a long distance from the emitter.

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.

A piezo-ring-on-chip microfluidic device for simple and low-cost mass spectrometry interfacing

Mass spectrometry (MS) interfacing technology provides the means for incorporating microfluidic processing with post MS analysis.

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.

High-throughput screening of filamentous fungi using nanoliter-range droplet-based microfluidics

Filamentous fungi are an extremely important source of industrial enzymes because of their capacity to secrete large quantities of proteins. Currently, functional screening of fungi is associated with low throughput and high costs, which severely limits the discovery of novel enzymatic activities and better production strains. Here, we describe a nanoliter-range droplet-based microfluidic system specially adapted for the high-throughput sceening (HTS) of large filamentous fungi libraries for secreted enzyme activities. The platform allowed (i) compartmentalization of single spores in ~10 nl droplets, (ii) germination and mycelium growth and (iii) high-throughput sorting of fungi based on enzymatic activity. A 10(4) clone UV-mutated library of Aspergillus niger was screened based on α-amylase activity in just 90 minutes. Active clones were enriched 196-fold after a single round of microfluidic HTS. The platform is a powerful tool for the development of new production strains with low cost, space and time footprint and should bring enormous benefit for improving the viability of biotechnological processes.

Multi-Dimensional Nanostructures for Microfluidic Screening of Biomarkers: From Molecular Separation to Cancer Cell Detection

Rapid screening of biomarkers, with high specificity and accuracy, is critical for many point-of-care diagnostics. Microfluidics, the use of microscale channels to manipulate small liquid samples and carry reactions in parallel, offers tremendous opportunities to address fundamental questions in biology and provide a fast growing set of clinical tools for medicine. Emerging multi-dimensional nanostructures, when coupled with microfluidics, enable effective and efficient screening with high specificity and sensitivity, both of which are important aspects of biological detection systems. In this review, we provide an overview of current research and technologies that utilize nanostructures to facilitate biological separation in microfluidic channels. Various important physical parameters and theoretical equations that characterize and govern flow in nanostructure-integrated microfluidic channels will be introduced and discussed. The application of multi-dimensional nanostructures, including nanoparticles, nanopillars, and nanoporous layers, integrated with microfluidic channels in molecular and cellular separation will also be reviewed. Finally, we will close with insights on the future of nanostructure-integrated microfluidic platforms and their role in biological and biomedical applications.

Advances in coupling microfluidic chips to mass spectrometry

Microfluidic technology has shown advantages of low sample consumption, reduced analysis time, high throughput, and potential for integration and automation. Coupling microfluidic chips to mass spectrometry (Chip-MS) can greatly improve the overall analytical performance of MS-based approaches and expand their potential applications. In this article, we review the advances of Chip-MS in the past decade, covering innovations in microchip fabrication, microchips coupled to electrospray ionization (ESI)-MS and matrix-assisted laser desorption/ionization (MALDI)-MS. Development of integrated microfluidic systems for automated MS analysis will be further documented, as well as recent applications of Chip-MS in proteomics, metabolomics, cell analysis, and clinical diagnosis.

Droplet-based microfluidics platform for ultra-high-throughput bioprospecting of cellulolytic microorganisms

Discovery of microorganisms producing enzymes that can efficiently hydrolyze cellulosic biomass is of great importance for biofuel production. To date, however, only a miniscule fraction of natural biodiversity has been tested because of the relatively low throughput of screening systems and their limitation to screening only culturable microorganisms. Here, we describe an ultra-high-throughput droplet-based microfluidic system that allowed the screening of over 100,000 cells in less than 20 min. Uncultured bacteria from a wheat stubble field were screened directly by compartmentalization of single bacteria in 20 pl droplets containing a fluorogenic cellobiohydrolase substrate. Sorting of droplets based on cellobiohydrolase activity resulted in a bacterial population with 17- and 7-fold higher cellobiohydrolase and endogluconase activity, respectively, and very different taxonomic diversity than when selected for growth on medium containing starch and carboxymethylcellulose as carbon source.

Enzymatic Catalysis Combining the Breath Figures and Layer-by-Layer Techniques: Toward the Design of Microreactors

Herein, we report the fabrication of microstructured porous surfaces with controlled enzymatic activity by combining the breath figures and the layer-by-layer techniques. Two different types of porous surfaces were designed based on fluorinated and carboxylated copolymers in combination with PS, using poly(2,3,4,5,6-pentafluorostyrene)-b-polystyrene (PS5F31-b-PS21) and polystyrene-b-poly(acrylic acid) (PS19-b-PAA10) block copolymers, respectively. For comparative purposes, flat surfaces having similar chemistry were obtained by spin-coating. Poly(sodium 4-styrenesulfonate)/poly(allylamine hydrochloride) (PSS/PAH) multilayers incorporating alkaline phosphatase (ALP) were built on these porous surfaces to localize the enzyme both inside and outside of the pores using PS/PS5F31-b-PS21 surfaces and only inside the pores on PS/PS19-b-PAA10 surfaces. A higher catalytic activity of ALP (about three times) was obtained with porous surfaces compared to the flat ones. The catalysis happens specifically inside the holes of PS/PS19-b-PAA10surfaces, where ALP is located. This opens the route for applications in microreactors.

Nanostructured microfluidic digestion system for rapid high-performance proteolysis

A novel microfluidic protein digestion system with a nanostructured and bioactive inner surface was constructed by an easy biomimetic self-assembly strategy for rapid and effective proteolysis in 2 minutes, which is faster than the conventional overnight digestion methods. It is expected that this work would contribute to rapid online digestion in future high-throughput proteomics.

High-efficiency nano/micro-reactors for protein analysis

This article reviews the recent advances regarding the development of nanomaterial-based nanoreactors and microfluidic droplet reactors and their applications in protein analysis.

Droplet microfluidics in (bio)chemical analysis

Droplet microfluidics may soon change the paradigm of performing chemical analyses and related instrumentation.

Microfluidics-to-mass spectrometry: a review of coupling methods and applications

Microfluidic devices offer great advantages in integrating sample processes, minimizing sample and reagent volumes, and increasing analysis speed, while mass spectrometry detection provides high information content, is sensitive, and can be used in quantitative analyses. The coupling of microfluidic devices to mass spectrometers is becoming more common with the strengths of both systems being combined to analyze precious and complex samples. This review summarizes select achievements published between 2010 and July 2014 in novel coupling between microfluidic devices and mass spectrometers. The review is subdivided by the types of ionization sources employed, and the different microfluidic systems used.

Lab-on-a-Chip hyphenation with mass spectrometry: strategies for bioanalytical applications

The Lab-on-a-Chip concept aims at miniaturizing laboratory processes to enable automation and/or parallelization via microfluidic chips that are capable of handling minute sample volumes. Mass spectrometry is nowadays the detection method of choice, because of its selectivity, sensitivity and wide application range. We review the most interesting examples over the last two-and-a-half years where the two techniques were used for bioanalytical applications. Furthermore, we discuss the merits and limitations of such hyphenated systems. We inventorize the reported applications and approaches. We see an ongoing trend towards chip-based liquid chromatography-mass spectrometry usage and small volume analysis applications, particularly in the field of proteomics where bottom-up approaches profit from chip-based technologies and hyphenation with complex cell cultures.

Capillary liquid chromatography fraction collection and postcolumn reaction using segmented flow microfluidics

A challenge for capillary LC (cLC) is fraction collection and the manipulation of fractions from microscale columns. An emerging approach is the use of segmented flow or droplet technology to perform such tasks. In this work, a fraction collection and postcolumn reaction system based on segmented flow was developed for the gradient cLC of proteins. In the system, column effluent and immiscible oil are pumped into separate arms of a tee resulting in regular fractions of effluent segmented by oil. Fractions were generated at 1 Hz corresponding to 5 nL volumes. The fraction collection rate was high enough to generate over 30 fractions per peak and preserve chromatographic resolution achieved for a five-protein test mixture. The resulting fractions could be stored and subsequently derivatized for fluorescence detection by pumping them into a second tee where naphthalene dicarboxyaldehyde, a fluorogenic reagent, was pumped into a second arm and added to each fraction. Proteins were derivatized within the droplets enabling postcolumn fluorescence detection of the proteins. The experiments demonstrate that fraction collection from cLC by segmented flow can be extended to proteins. Further, they illustrate a potential workflow for protein analysis based on postcolumn derivatization for fluorescence detection.

Recent advances in microfluidics combined with mass spectrometry: technologies and applications

Instrument miniaturization is one of the critical issues to improve sensitivity, speed, throughput, and to reduce the cost of analysis. Microfluidics possesses the ability to handle small sample amounts, with minimal concerns related to sample loss and cross-contamination, problems typical for standard fluidic manipulations. Moreover, the native properties of microfluidics provide the potential for high-density, parallel sample processing, and high-throughput analysis. Recently, the coupling of microfluidic devices to mass spectrometry, especially electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI), has attracted an increasing interest and produced tremendous achievements. The interfaces between microfluidics and mass spectrometry are one of the primary focused problems. In this review, we summarize the latest achievements since 2008 in the field of the technologies and applications in the combining of microfluidics with ESI-MS and MALDI-MS. The integration of several analytical functions on a microfluidic device such as sample pretreatment and separations before sample introduction into the mass spectrometer is also discussed.

An automated Teflon microfluidic peptide synthesizer

We present a microfluidic synthesizer made entirely of Teflon material for solid phase peptide synthesis (SPPS). Solvent-resistant perfluoroalkoxy (PFA) was used to construct chip-sized devices featuring multiple tri-layer pneumatic microvalves. Using these devices, model peptides were automatically synthesized and cleaved in situ in a continuous-flow manner. The total coupling and cleavage time was significantly reduced compared to conventional bulk reactors. The synthesis of a decapeptide, for instance, took less than 6 h using our device while it usually takes more than three days using conventional reactors.

A multifunctional microfluidic droplet-array chip for analysis by electrospray ionization mass spectrometry

This paper describes a multifunctional semi-closed droplet-array chip coupled with electrospray ionization mass spectrometry (ESI-MS) detection for multiple sample pretreatment and analysis. A novel interfacing method for coupling droplet system with ESI-MS was proposed using a sampling probe-two-dimensional (2D) droplet-array strategy. The 2D droplet-array system was composed of an 8 × 8 microwell array chip for droplet storage and a layer of oil covering the droplets served as a "virtual wall" to avoid droplet evaporation or cross-contamination. An L-shaped capillary was adopted as the interface of the droplet array and ESI-MS, using its inlet end as a sampling probe for droplets and its outlet with a tip size of ~20 μm as an electrospray emitter, without the need for any droplet extraction device. The droplet analysis was performed by moving the droplet-array chip to allow the capillary sampling probe to sequentially enter into the droplets through the oil and introduce the sample solution into the capillary emitter for MS detection. The MS analysis time for each droplet sample was 40 s with a sample consumption of ca. 13 nL. A good repeatability of 5.7% (RSD, n = 9) was obtained for 10(-6) M reserpine droplet analysis. The uses of the semi-closed 2D droplet array and off-line interfacing mode provide the system with the substantial flexibility and controllability in droplet indexing, multi-step manipulating, and on-demand sampling for MS analysis. We applied the present system in multi-step pretreatment and identification of small amounts of proteomic samples of myoglobin and cytochrome C, including in-droplet protein reduction, alkylation, digestion, and purification based on solid-phase extraction, matrix modification, sample droplet introduction under flow injection mode, and ESI-MS detection.

The potential impact of droplet microfluidics in biology

Droplet microfluidics, which involves micrometer-sized emulsion droplets on a microfabricated platform, is an active research endeavor that evolved out of the larger field of microfluidics. Recently, this subfield of microfluidics has started to attract greater interest because researchers have been able to demonstrate applications of droplets as miniaturized laboratories for biological measurements. This perspective explores the recent developments and the potential future biological applications of droplet microfluidics.

Generation of picoliter droplets of liquid for electrospray ionization with piezoelectric inkjet

We report the association of inkjet and electrospray ionization MS to detect picoliter droplet, where the liquid volume and its position onto the tip can be precisely controlled to form ultrafine droplets for successive ionization of the analyte. Single rectangle pulse was applied to piezoelectric device on inkjet microchip for the ejection of each picoliter droplet, and it was controlled by a computer. The voltage and width of driving pulse for the inkjet were optimized to make reproducible ejection of the solvent with low viscosity. The volume of each droplet was about 600 pl, and a trigger of 10 droplets was selected as the best inlet mode taking relative standard derivation of the droplets into consideration. The target substrate used with high voltage to form ionization was graphite, after several attempts with some materials. High-speed camera was used to capture the breaking-up process of a droplet. The distance between the inkjet nozzle and the tip was set at 2 cm to avoid short circuit. The influences on the mass intensity of the diameter of the tip, the volume and the concentration of the sample were examined. The tip with a small diameter performed greater intensity, and the limit of detection decreased, whereas the small volume of liquid played high ionization efficiency. Linear regression in the range between 1 and 200 ppm for caffeine was conducted, where internal standard theobromine was used. Some real samples were also detected with the instrument.

Microfluidic devices for high-throughput proteome analyses

Over the last decades, microfabricated bioanalytical platforms have gained enormous interest due to their potential to revolutionize biological analytics. Their popularity is based on several key properties, such as high flexibility of design, low sample consumption, rapid analysis time, and minimization of manual handling steps, which are of interest for proteomics analyses. An ideal totally integrated chip-based microfluidic device could allow rapid automated workflows starting from cell cultivation and ending with MS-based proteome analysis. By reducing or eliminating sample handling and transfer steps and increasing the throughput of analyses these workflows would dramatically improve the reliability, reproducibility, and throughput of proteomic investigations. While these complete devices do not exist for routine use yet, many improvements have been made in the translation of proteomic sample handling and separation steps into microfluidic formats. In this review, we will focus on recent developments and strategies to enable and integrate proteomic workflows into microfluidic devices.