Operational Modes and Speed Considerations of an Acoustic Droplet Dispenser for Mass Spectrometry

Acoustic ejection mass spectrometry: the potential for personalized medicine

INTRODUCTION

The emergence of personalized medicine (PM) has shifted the focus of healthcare from the traditional 'one-size-fits-all' approach to strategies tailored to individual patients, accounting for genetic, environmental, and lifestyle factors. Acoustic ejection mass spectrometry (AEMS) is a novel technology that offers a robust and scalable platform for high-throughput MS readout. AEMS achieves analytical speeds of one sample per second while maintaining high data quality, broad compound coverage, and minimal sample preparation, making it an invaluable tool for PM.

AREAS COVERED

This article explores the potential of AEMS in critical PM applications, including therapeutic drug monitoring (TDM), proteomics, metabolomics, and mass spectrometry imaging. AEMS simplifies conventional workflows by minimizing sample preparation, enhancing automation compatibility, and enabling direct analysis of complex biological matrices.

EXPERT OPINION

Integrating AEMS with orthogonal separation techniques such as differential mobility spectrometry (DMS) further addresses challenges in isomer discrimination, expanding the platform's analytical capabilities. Additionally, the development of high-throughput data processing tools could further enable AEMS to accelerate the development of personalized medicine.

High-throughput hit identification with acoustic ejection mass spectrometry

This mini-review provides an overview of recent developments in AEMS supporting hit identification in drug discovery, emphasizing its potential to enhance the quality and efficiency of label-free HTS. Future advancements that may further expand the role of AEMS in the drug discovery process will also be discussed.

Differential Mobility Spectrometry Acoustic Ejection Mass Spectrometer System for Screening Isomerization-Mediating Enzyme Drug Targets

We report the first implementation of ion mobility mass spectrometry combined with an ultrahigh throughput sample introduction technology for high-throughput screening (HTS). The system integrates differential mobility spectrometry (DMS) with acoustic ejection mass spectrometry (AEMS), termed DAEMS, enabling the simultaneous quantitation of structural isomers that are the substrates and products of isomerase-mediated reactions in intermediary metabolism. We demonstrate this potential by comparing DAEMS to a luminescence assay for the isoform of phosphoglycerate mutase (iPGM) distinctively present in pathogens, offering an opportunity as a drug target for a variety of microbial and parasite borne diseases. The metabolome consists of many structural isomers that require for separation a mobility resolving power of more than 300. Resolving powers measured in collision cross-section space of 1588 and 1948 for 2- and 3-phosphoglycerate and the citrate/isocitrate isomeric pairs, respectively, are shown. These are the highest reported ion mobility resolving powers for molecules from the metabolome reported to date. The potential for DAEMS as a generalized screening tool is demonstrated with the separation of the substrates and products of two additional isomerases that present as potential therapeutic targets, chorismate mutase and triosephosphate isomerase. The separations are achieved at speeds compatible with the sample introduction rates of AEMS providing sufficient data points to integrate the peaks for quantitation without the use of internal standards. DMS hyphenated with acoustic sample ejection MS provides a unique solution to high-throughput mass spectrometry applications where separation of isomers and other types of isobaric overlaps are required.

High-resolution acoustic ejection mass spectrometry for high-throughput library screening

An approach is described for high-throughput quality assessment of drug candidate libraries using high-resolution acoustic ejection mass spectrometry (AEMS). Sample introduction from 1536-well plates is demonstrated for this application using 2.5 nL acoustically dispensed sample droplets into an Open Port Interface (OPI) with pneumatically assisted electrospray ionization at a rate of one second per sample. Both positive and negative ionization are shown to be essential to extend the compound coverage of this protease inhibitor-focused library. Specialized software for efficiently interpreting this data in 1536-well format is presented. A new high-throughput method for quantifying the concentration of the components (HTQuant) is proposed that neither requires adding an internal standard to each well nor further encumbers the high-throughput workflow. This approach for quantitation requires highly reproducible peak areas, which is shown to be consistent within 4.4 % CV for a 1536-well plate analysis. An approach for troubleshooting the workflow based on the background ion current signal is also presented. The AEMS data is compared to the industry standard LC/PDA/ELSD/MS approach and shows similar coverage but at 180-fold greater throughput. Despite the same ionization process, both methods confirmed the presence of a small percentage of compounds in wells that the other did not. The data for this relatively small, focused library is compared to a larger, more chemically diverse library to indicate that this approach can be more generally applied beyond this single case study. This capability is particularly timely considering the growing implementation of artificial intelligence strategies that require the input of large amounts of high-quality data to formulate predictions relevant to the drug discovery process. The molecular structures of the 872-compound library analyzed here are included to begin the process of correlating molecular structures with ionization efficiency and other parameters as an initial step in this direction.

Improved Teflon lift-off for droplet microarray generation and single-cell separation on digital microfluidic chips

Droplet microarrays (DMAs) leveraging wettability differences are instrumental in digital immunoassays, single-cell analysis, and high-throughput screening. This study introduces an enhanced Teflon lift-off process to fabricate hydrophilic-hydrophobic patterns on a digital microfluidic (DMF) chip, thereby integrating DMAs with DMF technology. By employing DMF for droplet manipulation and utilizing wettability differences, the automated generation of high-throughput DMAs was achieved. The volume of the microdroplets ranged from picoliters to nanoliters. For droplets with a diameter of 150 μm, the array density reached up to 1282 cm-2. We systematically investigated the influence of various DMF parameters on the formation of DMAs and applied this technique to particle distribution, achieving a single-cell isolation rate of approximately 30%. We believe that this method will be a potent tool to enhance the capabilities of DMAs and DMF technology and extend their applicability across more fields.

A Differential Ion Mobility Acoustic Ejection Mass Spectrometer System for Screening Isomerization-Mediating Enzyme Drug Targets

We report the first implementation of ion mobility mass spectrometry combined with an ultra-high throughput sample introduction technology for high throughput screening (HTS). The system integrates differential ion mobility (DMS) with acoustic ejection mass spectrometry (AEMS), termed DAEMS, enabling the simultaneous quantitation of structural isomers that are the sub-strates and products of isomerase mediated reactions in intermediary metabolism. We demonstrate this potential by comparing DAEMS to a luminescence assay for the isoform of phosphoglycerate mutase (iPGM) distinctively present in pathogens offering an opportunity as a drug target for a variety of microbial and parasite borne diseases. The metabolome consists of many structural isomers that require for separation a mobility resolving power of more than 300. Resolving powers measured in collision cross section space of 1588 and 1948 for 2- and 3-phosphoglycerate and the citrate/isocitrate isomeric pairs respectively are shown. These are the highest reported ion mobility resolving powers for molecules from the metabolome reported to date. The potential for DAEMS as a generalized screening tool is demonstrated with the separation of the substrates and products of two additional isomerases that present as potential therapeutic targets, chorismate mutase and triosephosphate isomerase. The separations are achieved at speeds compatible with the sample introduction rates of AEMS providing sufficient data points to integrate the peaks for quantitation without the use of internal standards. DMS hyphenated with acoustic sample ejection MS provides a unique solution to high throughput mass spectrom-etry applications where isomer and other types of separations are required.

Sample-Specific MS/MS Methods in High-Throughput Mass Spectrometry

The drug discovery process increasingly relies on high-throughput sample analysis to accelerate the identification of viable drug candidates. Recently, chromatographic-free high-throughput mass spectrometry (HT-MS) technologies have emerged, significantly increasing sample readout speed and enabling the analysis of large sample sets. These HT-MS platforms continuously acquire data from various samples into a single data file, presenting challenges in applying distinctive data acquisition methods to specific samples. This study introduces a novel approach that integrates real-time sample loading status to activate sample-specific MS/MS data acquisition methods on the high-throughput acoustic ejection mass spectrometry platform. Effective method switching and high signal reproducibility were demonstrated across different data acquisition window durations in multiple reaction monitoring (MRM), high-resolution MRM (MRMHR), and information-dependent acquisition modes. This advancement provides a user-friendly and robust solution to the method-setting challenges of HT-MS, expanding the implementation of HT-MS platforms in drug discovery and other high-throughput analytical applications.

Optimizing the affinity selection mass spectrometry workflow for efficient identification and ranking of potent USP1 inhibitors

An optimized Affinity Selection-Mass Spectrometry (AS-MS) workflow has been developed for the efficient identification of potent USP1 inhibitors. USP1 was immobilized on agarose beads, ensuring low small molecule retention, efficient protein capture, and protein stability. The binding affinity of 49 compounds to USP1 was evaluated using the optimized AS-MS method, calculating binding index (BI) values for each compound. Biochemical inhibition assays validated the AS-MS results, revealing a potential correlation between higher BI values and lower IC50 values. This optimized workflow enables rapid identification of high-quality USP1 inhibitor hits, facilitating structure-activity relationship studies and accelerating the discovery of potential cancer therapeutics.

High-Throughput Covalent Modifier Screening with Acoustic Ejection Mass Spectrometry

Interests in covalent drugs have grown in modern drug discovery as they could tackle challenging targets traditionally considered "undruggable". The identification of covalent binders to target proteins typically involves directly measuring protein covalent modifications using high-resolution mass spectrometry. With a continually expanding library of compounds, conventional mass spectrometry platforms such as LC-MS and SPE-MS have become limiting factors for high-throughput screening. Here, we introduce a prototype high-resolution acoustic ejection mass spectrometry (AEMS) system for the rapid screening of a covalent modifier library comprising ∼10,000 compounds against a 50 kDa-sized target protein─Werner syndrome helicase. The screening samples were arranged in a 1536-well format. The sample buffer containing high-concentration salts was directly analyzed without any cleanup steps, minimizing sample preparation efforts and ensuring protein stability. The entire AEMS analysis process could be completed within a mere 17 h. An automated data analysis tool facilitated batch processing of the sample data and quantitation of the formation of various covalent protein-ligand adducts. The screening results displayed a high degree of fidelity, with a Z' factor of 0.8 and a hit rate of 2.3%. The identified hits underwent orthogonal testing in a biochemical activity assay, revealing that 75% were functional antagonists of the target protein. Notably, a comparative analysis with LC-MS showcased the AEMS platform's low risk of false positives or false negatives. This innovative platform has enabled robust high-throughput covalent modifier screening, featuring a 10-fold increase in library size and a 10- to 100-fold increase in throughput when compared with similar reports in the existing literature.

Data processing for high-throughput mass spectrometry in drug discovery

INTRODUCTION

High-throughput mass spectrometry that could deliver > 10 times faster sample readout speed than traditional LC-based platforms has emerged as a powerful analytical technique, enabling the rapid analysis of complex biological samples. This increased speed of MS data acquisition has brought a critical demand for automatic data processing capabilities that should match or surpass the speed of data acquisition. Those data processing capabilities should serve the different requirements of drug discovery workflows.

AREAS COVERED

This paper introduced the key steps of the automatic data processing workflows for high-throughput MS technologies. Specific examples and requirements are detailed for different drug discovery applications.

EXPERT OPINION

The demand for automatic data processing in high-throughput mass spectrometry is driven by the need to keep pace with the accelerated speed of data acquisition. The seamless integration of processing capabilities with LIMS, efficient data review mechanisms, and the exploration of future features such as real-time feedback, automatic method optimization, and AI model training is crucial for advancing the drug discovery field. As technology continues to evolve, the synergy between high-throughput mass spectrometry and intelligent data processing will undoubtedly play a pivotal role in shaping the future of high-throughput drug discovery applications.

Acoustic ejection mass spectrometry empowers ultra-fast protein biomarker quantification

The global scientific response to COVID 19 highlighted the urgent need for increased throughput and capacity in bioanalytical laboratories, especially for the precise quantification of proteins that pertain to health and disease. Acoustic ejection mass spectrometry (AEMS) represents a much-needed paradigm shift for ultra-fast biomarker screening. Here, a quantitative AEMS assays is presented, employing peptide immunocapture to enrich (i) 10 acute phase response (APR) protein markers from plasma, and (ii) SARS-CoV-2 NCAP peptides from nasopharyngeal swabs. The APR proteins were quantified in 267 plasma samples, in triplicate in 4.8 h, with %CV from 4.2% to 10.5%. SARS-CoV-2 peptides were quantified in triplicate from 145 viral swabs in 10 min. This assay represents a 15-fold speed improvement over LC-MS, with instrument stability demonstrated across 10,000 peptide measurements. The combination of speed from AEMS and selectivity from peptide immunocapture enables ultra-high throughput, reproducible quantitative biomarker screening in very large cohorts.

High-Throughput Compound Quality Assessment with High-Mass-Resolution Acoustic Ejection Mass Spectrometry: An Automatic Data Processing Toolkit

Pharmacological screening heavily relies on the reliability of compound libraries. To ensure the accuracy of screening results, fast and reliable quality control (QC) of these libraries is essential. While liquid chromatography (LC) with ultraviolet (UV) or mass spectrometry (MS) detection has been employed for molecule QC on small sample sets, the analytical throughput becomes a bottleneck when dealing with large libraries. Acoustic ejection mass spectrometry (AEMS) is a high-throughput analytical platform that covers a broad range of chemical structural space. In this study, we present the utilization of an AEMS system equipped with a high-resolution MS analyzer for high-throughput compound QC. To facilitate efficient data processing, which is a key challenge for such a high-throughput application, we introduce an automatic data processing toolkit that allows for the high-throughput assessment of the sample standards' quantitative and qualitative characteristics, including purity calculation with the background processing option. Moreover, the toolkit includes a module for quantitatively comparing spectral similarity with the reference library. Integrating the described high-resolution AEMS system with the data processing toolkit effectively eliminates the analytical bottleneck, enabling a rapid and reliable compound quality assessment of large-scale compound libraries.

Microarray Platforms Based on 3D Printing

This paper introduces an innovative method for the fabrication and infusion of microwell arrays based on digital light processing (DLP) 3D printing. A low-cost DLP 3D printer is employed to fabricate microstructures rapidly with a broad dynamic range while maintaining high precision and fidelity. We constructed microwell arrays with varying diameters, from 200 to 2000 μm and multiple aspect ratios, in addition to microchannels with widths ranging from 45 to 1000 μm, proving the potential and flexibility of this fabrication method. The superimposition of parallel microchannels onto the microwell array, facilitated by positive or negative pressure, enabled the transfer of liquid to the microwells. Upon removal of the microchannel chip, a dispensed microdroplet array was obtained. This array can be modulated by adjusting the volume of the microwells and the inflow fluid. The filled microwell array allows chip-to-chip dispensing to the microreactor array through binding and centrifugation, facilitating multistep and multireagent assays. The 3D printing approach also enables the fabrication of intricate cavity designs, such as micropyramid arrays, which can be integrated with parallel microchannels to generate spheroid flowcells. This device demonstrated the ability to generate spheroids and manipulate their environment. We have successfully utilized precise modulation of spheroids size and performed parallel drug dose-response assays to evaluate its effectiveness. Furthermore, we managed to execute dynamic drug combinations based on a compact spheroids array, utilizing two orthogonal parallel microchannels. Our findings suggest that both the combination and temporal sequence of drug administration have a significant impact on therapeutic outcomes.

High-Throughput Acoustic Ejection Mass Spectrometry with Adjustable Signal Durations

High-throughput mass spectrometry (MS) has witnessed rapid advancements and has found extensive applications across various disciplines. It enables the fast and accurate analysis of large sample sets, delivering a 10-fold or greater enhancement in analytical throughput when compared to conventional LC-MS methods. However, the signal duration in these high-throughput MS technologies is typically confined to a narrow range, presenting challenges for workflows demanding prolonged signal durations. In this study, we introduce a method that enables precise modulation of the signal duration on an acoustic ejection mass spectrometry (AEMS) system while ensuring high signal reproducibility. This flexibility allows for simultaneous and precise analysis of a significantly greater number of MS/MS transitions in high-throughput MS environments. Additionally, it offers a unique approach for parameter optimization and method development with minimal sample volume requirements. This advancement enhances the efficiency of MS-based analyses across diverse applications and facilitates broader utilization of MS technologies in high-throughput settings, including data-dependent acquisition (DDA) and data-independent acquisition (DIA).

High-throughput mass spectrometry analysis using immediate drop-on-demand technology coupled with an open port sampling interface

RATIONALE

The sampling throughput of immediate drop-on-demand technology (I.DOT) coupled with an open port sampling interface (OPSI) is limited by software communication. To enable much-needed high-throughput mass spectrometry (MS) analysis capabilities, a novel software was developed that allows for flexible sample selection from a 96-well plate and for maximized analysis throughput using I.DOT/OPSI-MS coupling.

METHODS

Wells of a 96-well I.DOT plate were filled with propranolol solution and were used to test maximum sampling throughput strategies to minimize analysis time. Demonstration of chemical reaction monitoring was done using acid-catalyzed ring closure of 2,3-diaminonaphthalene (DAN) with nitrite to form 2,3-naphthotriazole (NAT). Analytes were detected in positive electrospray ionization mode using selected reaction monitoring.

RESULTS

A maximum throughput of 1.54 s/sample (7.41 min/96-well plate with three technical replicates) was achieved, and it was limited by the peak width of the MS signal resulting in an occasional slight overlap between the peaks. Relative standard deviation was 10 ± 1% with all tested sampling strategies. Chemical reaction monitoring of DAN to NAT using nitrite was successfully accomplished with 2 s/sample throughout showing almost complete transformation in 10 min with no signal overlap.

CONCLUSIONS

This work illustrates the development of a noncontact, automated I.DOT/OPSI-MS system with improved throughput achieved through an optimized software interface. Its achievable analysis time and precision make it a viable approach for drug discovery and in situ reaction monitoring studies.

A high-throughput quality control method for assessing the serial dilution performance of dose-response plates with acoustic ejection mass spectrometry

This study aimed to develop a streamlined method for evaluating the dilution ratio of drug dose-response plates created by automated liquid handlers in the early stages of drug discovery. The quantitative techniques commonly used for this purpose have restrictions due to their limited linear dynamic range and inaccuracies in assessing serial dilution performance. To address this challenge, we describe a method based on acoustic ejection mass spectrometry (AEMS). The method involves using standard compounds and an internal standard to evaluate each dilution point in quality control (QC) plates. The samples are transferred to a chromatography-free tandem mass spectrometry system through an acoustic source, enabling the analysis of one sample per three seconds from a microtiter plate. This approach provides precise, accurate, label-free, and rapid data acquisition to support high-throughput screening efforts.

Rapid Droplet Sampling Interface for Low-Volume, High-Throughput Mass Spectrometry Analysis

Here, we present a rapid droplet sampling interface (RDSI) electrospray ionization mass spectrometry (ESI-MS) system as a high-throughput, low-volume, noncontact, and minimal-carryover approach for characterization of liquids. Liquid characterization was achieved by combining droplet ejection with an open-face microflow capillary with a 2.5 μL/min continuous flow of carrier solvent. Through this implementation, single 0.3 nL droplets containing the analyte effectively mix with 4-8 nL of carrier solvent and create a combined electrospray plume. The carrier solvent continuously cleaned the system, eliminating carryover. A sampling rate of 5 Hz was achieved for droplets containing 1 μM propranolol or 5 μM leu-enkephalin with each droplet fully baseline-resolved (138 ± 32 ms baseline-to-baseline). Using a SCIEX API4000 mass spectrometer, a lower limit of quantification (LLOQ) of propranolol was 15 nM, corresponding to 1.16 fg of propranolol in the droplet, and was linear across 3 orders of magnitude. Quantitation could be achieved by adding an isotopically labeled internal standard, as done in conventional ESI. Signal transients were faster than the acquisition speed of the mass spectrometer, resulting in artificially high reproducibility of 15-30% RSD droplet-to-droplet. Analyte-solvent mixing ratios could be controlled by adjusting droplet positioning along the open-face capillary with an optimal position about 0.4 mm from the tip end. The range of analyte coverage was exemplified by measures of peptides and drugs in methanol, water, and buffer solutions. In a comparison to the Open Port Sampling Interface (OPSI) implemented on the same system, the RDSI had 78× greater sensitivity, 6× greater throughput and used significantly less carrier solvent.

Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies

High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries. Key features • Mass spectrometry analyzes a range of compounds from E. coli colonies as a proxy for liquid culture testing enzyme mutant libraries. • Colonies are transferred to a MALDI target plate by a simple imprinting method. • The screen compares the ratio among several products or searches for the qualitative presence of specific compounds. • The protocol requires a MALDI mass spectrometer.

Open Port Interface for Coupling Capillary Electrophoresis and Mass Spectrometry: Performance Evaluation for Capillary Isoelectric Focusing

Capillary electrophoresis (CE) combined with mass spectrometry (MS) is a powerful analytical technique that utilizes the resolving power of CE and the mass-detection capabilities of MS. In many cases, CE is coupled to MS via a sheath-flow interface (SFI). This interface has a simple design and can be easily constructed; however, it often suffers from issues such as MS signal suppression, interference of MS and CE electrical circuits, and the inability to set an optical point of detection close to the capillary end due to the specific design of the coupling union. In this paper, we describe a novel coupling of CE and MS based upon the open port interface (OPI). The OPI differs from classical sheath flow interfaces by operating at flow rates at least 1 order of magnitude higher. In addition to the flow rate difference, the OPI provides more efficient mixing of the capillary eluates with the transport fluid and thus minimizes MS signal suppression. In this work, we compared the performance of OPI and SFI in a series of capillary isoelectric focusing (cIEF) experiments with 5 pI markers, carbonic anhydrase II and NIST antibody. The evaluation criteria for the comparison of the OPI and SFI were analytical sensitivity, reproducibility, and pI marker linearity. Given the extent of sample dilution in the OPI, we also compared the peak resolution determined using an upstream UV detector to those determined by the downstream mass spectrometer. The results suggested that the OPI configuration reduced signal suppression, with no adverse effect on peak resolution. In addition, the OPI provided better decoupling of the CE and MS potentials as well as reduced signal dependence upon the sheath liquid composition. While these results are preliminary, they suggest that the OPI is a viable approach for CE-MS coupling.

A Comprehensive Review of Surface Acoustic Wave-Enabled Acoustic Droplet Ejection Technology and Its Applications

This review focuses on the development of surface acoustic wave-enabled acoustic drop ejection (SAW-ADE) technology, which utilizes surface acoustic waves to eject droplets from liquids without touching the sample. The technology offers advantages such as high throughput, high precision, non-contact, and integration with automated systems while saving samples and reagents. The article first provides an overview of the SAW-ADE technology, including its basic theory, simulation verification, and comparison with other types of acoustic drop ejection technology. The influencing factors of SAW-ADE technology are classified into four categories: fluid properties, device configuration, presence of channels or chambers, and driving signals. The influencing factors discussed in detail from various aspects, such as the volume, viscosity, and surface tension of the liquid; the type of substrate material, interdigital transducers, and the driving waveform; sessile droplets and fluid in channels/chambers; and the power, frequency, and modulation of the input signal. The ejection performance of droplets is influenced by various factors, and their optimization can be achieved by taking into account all of the above factors and designing appropriate configurations. Additionally, the article briefly introduces the application scenarios of SAW-ADE technology in bioprinters and chemical analyses and provides prospects for future development. The article contributes to the field of microfluidics and lab-on-a-chip technology and may help researchers to design and optimize SAW-ADE systems for specific applications.

Label-free high-throughput screening via acoustic ejection mass spectrometry put into practice

Acoustic droplet ejection-open port interface-mass spectrometry (ADE-OPI-MS) is a novel label-free analytical technique, promising to become a versatile readout for high-throughput screening (HTS) applications. The recent introduction of ADE-OPI-MS devices to the laboratory equipment market, paired with their compatibility with laboratory automation platforms, should facilitate the adoption of this technology by a broader community. Towards this goal, instrument robustness in the context of HTS campaigns - where up to millions of samples in complex matrices are tested in a short time frame - represents a major challenge, which explains the absence of detailed literature reports on this subject. Here, we present the results of our first fully automated HTS campaign, based on the ADE-OPI-MS technology, aiming to identify inhibitors of a metabolic enzyme in a >1 million compound library. The report encompasses the assay development and validation steps, as well as the adaptation for HTS requirements, where refinement of the capillary cleaning concept was crucial for final success. Altogether, our study unequivocally demonstrates the applicability of the ADE-OPI-MS technology for HTS-based drug discovery.

Ultrasonic sample introduction combined with flame assisted thermal ionization: Pretreatment-free direct mass spectrometry analysis for fraction collecting tubes of preparative liquid chromatography

Ultrasonic sample introduction combined with flame assisted thermal ionization mass spectrometry (USI-FATI-MS) was developed to monitor the fractions of preparative liquid chromatography. Recently, ultrasound-based sample introduction techniques have achieved great advance in the field of high-throughput analysis. However, it is still a challenge to directly apply these existing techniques to the analysis of macro volume samples (mL level). In this work, ultrasonic sample introduction combined with flame assisted thermal ionization was used for pretreatment-free direct mass spectrometry analysis of micro to macro volume samples (μL-mL level). Utilizing this unique design of ultrasonic sample introduction, liquid sample in the container can be quickly atomized to the gas phase without contact. Then, due to the flame assisted thermal ionization source, desolvation and ionization of the sample droplets will occur immediately. USI-FATI-MS has shown excellent sensitivity, repeatability and great compatibility to solvents and compounds with a wide range of polarity. As a proof of concept, USI-FATI-MS has been applied for rapid monitoring and identification of purified synthetic and natural products in fractions.

Perspective on high-throughput bioanalysis to support in vitro assays in early drug discovery

As the desire for a shortened design/make/test/learn cycle increases in early drug discovery, the pressure to rapidly deliver drug metabolism pharmacokinetic data continues to rise. From a bioanalytical standpoint, in vitro assays are challenging because they are amenable to automation and thus capable of generating a high number of samples for analysis. To keep up with analysis demands, automated method development workflows, rapid sample analysis approaches and efficient data analysis software must be utilized. This work provides an outline of how we implemented those three aspects to provide bioanalytical support for in vitro drug metabolism pharmacokinetic assays, which include developing hundreds of mass spectrometry methods and analyzing thousands of samples per week, while delivering a median bioanalytical turnaround time of 1-2 business days.

3D printer platform and conductance feedback loop for automated imaging of uneven surfaces by liquid microjunction-surface sampling probe mass spectrometry

RATIONALE

Molecular imaging of samples using mass spectrometric techniques, such as matrix-assisted laser desorption ionization or desorption electrospray ionization, requires the sample surface to be even/flat and sliced into thin sections (c. 10 μm). Furthermore, sample preparation steps can alter the analyte composition of the sample. The liquid microjunction-surface sampling probe (LMJ-SSP) is a robust sampling interface that enables surface profiling with minimal sample preparation. In conjunction with a conductance feedback system, the LMJ-SSP can be used to automatically sample uneven specimens.

METHODS

A sampling stage was built with a modified 3D printer where the LMJ-SSP is attached to the printing head. This setup can scan across flat and even surfaces in a predefined pattern ("static sampling mode"). Uneven samples are automatically probed in "conductance sampling mode" where an electric potential is applied and measured at the probe. When the probe contacts the electrically grounded sample, the potential at the probe drops, which is used as a feedback signal to determine the optimal position of the probe for sampling each location.

RESULTS

The applicability of the probe/sensing system was demonstrated by first examining the strawberry tissue using the "static sampling mode." Second, porcine tissue samples were profiled using the "conductance sampling mode." With minimal sample preparation, an area of 11 × 15 mm was profiled in less than 2 h. From the obtained results, adipose areas could be distinguished from non-adipose parts. The versatility of the approach was further demonstrated by directly sampling the bacteria colonies on agar and resected human kidney (intratumoral hemorrhage) specimens with thicknesses ranging from 1 to 4 mm.

CONCLUSION

The LMJ-SSP in conjunction with a conductive feedback system is a powerful tool that allows for fast, reproducible, and automated assessment of uneven surfaces with minimal sample preparation. This setup could be used for perioperative assessment of tissue samples, food screening, and natural product discovery, among others.

Ultrahigh-Throughput Intact Protein Analysis with Acoustic Ejection Mass Spectrometry

The need for high-throughput intact protein analysis has been rising as drug discovery increasingly requires the analysis of large sets of covalent modifiers and protein therapeutics. Liquid chromatography-mass spectrometry (LC-MS) is the primary analytical tool used to date to characterize proteins within the biopharmaceutical industry. However, the speed of LC-MS prevents the analysis of large-scale sample sets (>1000 within a day). Acoustic ejection mass spectrometry (AEMS) has recently been established as an electrospray ionization (ESI)-MS based platform with both fast analytical throughput and high data quality. Since its introduction, this technology has been applied in numerous fields with a primary focus on small-molecule analysis in high-throughput drug discovery and development. Here we explore the application of AEMS to high-throughput intact protein analysis for proteins ranging in molecular weight from 17 to 150 kDa on a prototype high-resolution quadrupole time-of-flight (HR QTOF) based AEMS system. Data quality obtained on this platform is comparable to LC-MS, while the analysis speed is significantly improved to one-second-per-sample. This ultrahigh-throughput intact protein analysis platform has the potential to be used broadly in drug discovery.

Where have all the ions gone, long time passing? Tandem quadrupole mass spectrometers with atmospheric pressure ionization sensitivity gains since the mid-1970s. A perspective

The gains in sensitivity since 1975 for quadrupole mass spectrometers equipped with atmospheric pressure ionization (API), and in particular triple quadrupole mass spectrometers (QqQs) since 1981, have been driven by the needs of the environmental, biomedical, agricultural, and other scientific research, industrial, regulatory, legal, and sporting communities to continually achieve lower limits of quantitation and identification. QqQs have realized a one-million-fold improvement in sensitivity attempting to address these needs over the past two score years. It is the purpose of this article to describe how that came about, not through an exhaustive review of the literature, but rather by describing what general approaches were used across the industry to improve sensitivity and provide some examples to illustrate its evolution. The majority of the gains came from the ion source and its interface to the vacuum system. "Sampling efficiency" is a measurement of the losses in this area so will be a focus of this review. The discovery of the phenomenon of collisional focusing was key to improving sampling efficiency because it enabled designs that increased the ion-containing gas loads from the ion source, using staged differential pumping backed by increasingly larger pumps, and prevented the scattering losses of ions in the resulting gas expansion inside vacuum. Likewise, systems with smaller pumps and lower ion-containing gas loads could be designed with size and cost reduction in mind while maintaining reasonable sampling efficiencies. As a consequence, advancements in the designs of both larger and smaller turbomolecular vacuum pumps were accelerated by pump manufacturers to accommodate the explosive growth in the use of API-QqQ and API-ion trap mass spectrometers that occurred in the 1990s and continued into the new millennium. Sampling efficiency was further improved by increasing the ion yield from electrospray by increasing the rate of droplet desolvation. An estimate of the practical limit to further sensitivity improvements beyond what has been achieved to date is provided to shed light on what to expect in the future. Lastly, the implications and unforeseen consequences of the sensitivity gains are considered with a particular focus on how they have enabled a dramatic increase in daily sample throughput on triple quadrupole and other types of mass spectrometers.

A Full Scan Data Review Tool to Match the Speed of Acoustic Ejection Mass Spectrometry

Acoustic ejection mass spectrometry (AEMS) has recently emerged as the premier ultrahigh-throughput mass spectrometric methodology for drug discovery and related fields. The ultrahigh analytical speed (~1 s/sample) of AEMS has significantly enhanced the efficiency of many high throughput applications. As a result, a data processing and reviewing tool with a matching speed is in high demand for the large amount of data generated, especially for applications such as quality control (QC) of compound collections and high throughput chemistry, where full-scan MS data required convoluted subsequent peak extraction and evaluation. In this study, we demonstrated the feasibility of a tool developed specifically for this purpose. The process using the tool involved automated splitting of the full scan data to correlate well positions with each signal peak, extraction of expected mass traces, and subsequent peak integration. Data evaluation based on verification rules, such as detected mass accuracy, isotopic pattern, and signal-to-noise ratio (S/N), enabled a comprehensive assessment of sample quality that was complemented by visualization in the form of a plate heat map generated from the selected rules. The tool demonstrated fast and straightforward data review and reporting and, more importantly, at a matching speed of sample analysis by acoustic ejection mass spectrometry. The choice of data processing and storage over the cloud further facilitated results sharing among data users.

Rapid Mass Spectrometric Calibration and Standard Addition Using Hydrophobic/Hydrophilic Patterned Surfaces and Discontinuous Dewetting

The rapid calibration chip (RCC) is a device that uses the fast and reproducible wetting behavior of hydrophilic/hydrophobic patterned surfaces to confine a series of differently sized droplets on a substrate to obtain a calibration curve. Multiple series of droplets can be formed within seconds by dipping an RCC into a calibration solution. No pipetting, sequential droplet deposition, or advanced equipment is required. The performance and reproducibility of RCCs were evaluated with an electrospray ionization triple-quadrupole mass spectrometer equipped with a liquid microjunction-surface sampling probe (LMJ-SSP) that allows for fast sampling of surfaces. Using circular hydrophilic areas with diameters ranging from 0.25 to 2.00 mm, liquid volumes of 4.6-70.6 nL could be deposited. Furthermore, the use of a second hydrophobic/hydrophilic patterned transfer chip can be used to add internal standard solutions to each calibration spot of the RCC, allowing to transfer a liquid volume of 22.5 nL.

An Open Port Sampling Interface for the Chemical Characterization of Levitated Microparticles

Several studies have reported ionization methods to classify the chemical composition of levitated particles held in an electrodynamic balance using mass spectrometry (MS). These methods include electrospray-based paper spray (PS) ionization, plasma discharge ionization, and direct analysis in real-time (DART) ionization, with each showing advantages and disadvantages. Our recent work demonstrated that PS ionization could yield accurate data for the chemical evolution of mixed component particles undergoing evaporation. However, measurements were performed using an internal standard to account for and correct the inherent variability in the PS ionization source. Here, we explore a new electrospray-based method coupled to particle levitation-the Open Port Sampling Interface (OPSI), which provides many advantages over the PS method, with few disadvantages. In this application note we report experiments in which micron-sized particles, containing analytes such as citric acid, maleic acid, and tetraethylene glycol, were levitated and optically probed to determine their size and mass. Subsequent transfer of individual levitated particles into the OPSI allowed for the ionization and mass spectrometry analysis of these particles. We discuss the stability and reproducibility of MS measurements, demonstrate effective quantitation in both positive and negative mode, and determine the sensitivity of the OPSI to a range of analyte mass present in levitated particles. Importantly, we show stability of the OPSI over >6 h without the need for normalizing signal variations with an internal standard in the sample, demonstrating robust application of the OPSI to measurements over extended periods of time.

High-Throughput Analysis from Complex Matrices: Acoustic Ejection Mass Spectrometry from Phase-Separated Fluid Samples

Acoustic ejection mass spectrometry is a novel high-throughput analytical technology that delivers high reproducibility without carryover observed. It eliminates the chromatography step used to separate analytes from matrix components. Fully-automated liquid–liquid extraction is widely used for sample cleanup, especially in high-throughput applications. We introduce a workflow for direct AEMS analysis from phase-separated liquid samples and explore high-throughput analysis from complex matrices. We demonstrate the quantitative determination of fentanyl from urine using this two-phase AEMS approach, with a LOD lower than 1 ng/mL, quantitation precision of 15%, and accuracy better than ±10% over the range of evaluation (1–100 ng/mL). This workflow offers simplified sample preparation and higher analytical throughput for some bioanalytical applications, in comparison to an LC-MS based approach.

The liquid micro junction-surface sampling probe (LMJ-SSP); a versatile ambient mass spectrometry interface

Ambient ionization methods have become important tools in mass spectrometry. The LMJ-SSP can significantly simplify/reduce lengthy sample preparation requirements associated with mass spectrometry analysis. Samples may be introduced through direct contact, insertion and droplet injection, enabling applications from drug discovery and surface analysis to tissue profiling and metabolic mapping. This review examines the underlying principles associated with the LMJ-SSP interface and highlights modifications of the original design that have extended its capability. We summarize different application areas that have exploited the method and describe potential future directions for the adaptable ambient ionization source.

Acoustic Ejection Mass Spectrometry for High-Throughput Analysis

We describe a mass spectrometry (MS) analytical platform resulting from the novel integration of acoustic droplet ejection (ADE) technology, an open-port interface (OPI), and electrospray ionization (ESI)-MS that creates a transformative system enabling high-speed sampling and label-free analysis. The ADE technology delivers nanoliter droplets in a touchless manner with high speed, precision, and accuracy. Subsequent sample dilution within the OPI, in concert with the capabilities of modern ESI-MS, eliminates the laborious sample preparation and method development required in current approaches. This platform is applied to a variety of experiments, including high-throughput (HT) pharmacology screening, label-free in situ enzyme kinetics, in vitro absorption, distribution, metabolism, elimination, pharmacokinetic and biomarker analysis, and HT parallel medicinal chemistry.

Acoustic Ejection Mass Spectrometry: A Fully Automatable Technology for High-Throughput Screening in Drug Discovery

Acoustic droplet ejection (ADE)-open port interface (OPI)-mass spectrometry (MS) has recently been introduced as a versatile analytical method that combines fast and contactless acoustic sampling with sensitive and accurate electrospray ionization (ESI)-MS-based analyte detection. The potential of the technology to provide label-free measurements in subsecond analytical cycle times makes it an attractive option for high-throughput screening (HTS). Here, we report the first implementation of ADE-OPI-MS in a fully automated HTS environment, based on the example of a biochemical assay aiming at the identification of small-molecule inhibitors of the cyclic guanosine monophosphate-adenosine monophosphate (GMP-AMP) synthase (cGAS). First, we describe the optimization of the method to enable sensitive and accurate determination of enzyme activity and inhibition in miniaturized 1536-well microtiter plate format. Then we show both results from a validation single-concentration screen using a test set of 5500 compounds, and the subsequent concentration-response testing of selected hits in direct comparison with a previously established matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) readout. Finally, we present the development of an in-line OPI cleaning procedure aiming to match the instrument robustness required for large-scale HTS campaigns. Overall, this work points to critical method development parameters and provides guidance for the establishment of integrated ADE-OPI-MS as HTS-compatible technology for early drug discovery.

An ultrafast and flexible liquid chromatography/tandem mass spectrometry system paves the way for machine learning driven in vivo sample processing in early drug discovery

RATIONALE

The low speed and low flexibility of most liquid chromatography/tandem mass spectrometry (LC/MS/MS) approaches in early drug discovery delay sample analysis from routine in vivo studies within the same day. A high-throughput platform for the rapid quantification of drug compounds in various in vivo assays was developed and established in routine bioanalysis.

METHODS

Automated selection of an efficient and adequate LC method was realized by autonomous sample qualification for ultrafast batch gradients (9 s/sample) or for fast linear gradients (45 s/sample) if samples required chromatography. The hardware and software components of our Rapid and Integrated Analysis System (RIAS) were streamlined for increased analytical throughput via state-of-the-art automation while maintaining high analytical quality.

RESULTS

Online decision-making was based on a quick assay suitability test (AST), based on a small and dedicated sample set evaluated by two different strategies. 84% of the acquired data points were within ±30% accuracy and 93% of the deviations between the lower limit of quantitation (LLOQ) values were ≤2-fold compared with standard LC/MS/MS systems. Speed, flexibility and overall automation significantly improved.

CONCLUSIONS

The developed platform provided an analysis time of only 10 min (batch-mode) and 47 min (gradient-mode) per standard pharmacokinetic (PK) study (62 injections). Automation, data evaluation and results handling were optimized to pave the way for machine learning based on decision-making regarding the evaluation strategy of the AST.