Rapid discrimination of bacteria by paper spray mass spectrometry

Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers

Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical.

Paper Spray Mass Spectrometry with On-Paper Electrokinetic Manipulations: Part-Per-Trillion Detection of Per/Polyfluoroalkyl Substances in Water and Opioids in Urine

We developed a simple, paper-based device that enables sensitive detection by mass spectrometry (MS) without solid phase extraction or other sample preparation. Using glass fiber filter papers within a 3D printed holder, the device employs electrokinetic manipulations to stack, separate, and desalt charged molecules on paper prior to spray into the MS. Due to counter-balanced electroosmotic flow and electrophoresis, charged analytes stack on the paper and desalting occurs in minutes. One end of the paper strip was cut into a sharp point and positioned near the inlet of a MS. The stacked analyte bands move toward the paper tip with the EOF where they are ionized by paper spray. The device was applied to analysis of PFAS in tap water with sub part-per-trillion detection limits in less than ten minutes with no sample pretreatment. Analysis of opioids in urine also occurs in minutes. The crucial parameters to enable stacking, separation, and MS ionization of both positively and negatively charged analytes were determined and optimized. Experimental and computational modeling studies confirm the electrokinetic stacking and analyte transport mechanisms. On-paper separations were carried out by stacking analyte bands at different locations depending on their electrophoretic mobility, achieving baseline separation in some cases.

Laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS) demonstrates a direct impact of hypochlorous acid stress on PQS-mediated quorum sensing in Pseudomonas aeruginosa

To establish infections in human hosts, Pseudomonas aeruginosa must overcome innate immune-generated oxidative stress, such as the hypochlorous acid (HOCl) produced by neutrophils. We set out to find specific biomarkers of oxidative stress through the development of a protocol for the metabolic profiling of P. aeruginosa cultures grown in the presence of different oxidants using a novel ionization technique for mass spectrometry, laser desorption rapid evaporative ionization mass spectrometry (LD-REIMS). We demonstrated the ability of LD-REIMS to classify samples as untreated or treated with a specific oxidant with 100% accuracy and identified a panel of 54 metabolites with significantly altered concentrations after exposure to one or more of the oxidants. Key metabolic changes were conserved in P. aeruginosa clinical strains isolated from patients with cystic fibrosis lung infections. These data demonstrated that HOCl stress impacted the Pseudomonas quinolone signal (PQS) quorum sensing system. Ten 2-alkyl-4-quinolones (AHQs) associated with the PQS system were significantly lower in concentration in HOCl-stressed P. aeruginosa cultures, including 2-heptyl-3-hydroxy-4(1H)-quinolone (PQS), the most active signal molecule of the PQS system. The PQS system regulates the production of virulence factors, including pyocyanin and elastase, and their levels were markedly affected by HOCl stress. No pyocyanin was detectable and elastase concentrations were reduced by more than 75% in cultures grown with sub-lethal concentrations of HOCl, suggesting that this neutrophil-derived oxidant may disrupt the ability of P. aeruginosa to establish infections through interference with production of PQS-associated virulence factors.

IMPORTANCE

This work demonstrates that a high-throughput ambient ionization mass spectrometry method can be used successfully to study a bacterial stress response. Its application to the opportunistic pathogen Pseudomonas aeruginosa led to the identification of specific oxidative stress biomarkers, and demonstrated that hypochlorous acid, an oxidant specifically produced by human neutrophils during infection, affects quorum sensing and reduces production of the virulence factors pyocyanin and elastase. No pyocyanin was detectable and elastase levels were reduced by more than 75% in bacteria grown in the presence of hypochlorous acid. This approach has the potential to be widely applicable to the characterization of the stress responses of bacteria.

A high-throughput platform enables in situ screening of fatty acid-producing strains using laser ablation electrospray ionization mass spectrometry and a Python package

Microbial fatty acid-producing strains are commonly engineered to improve their performance for industrial applications. However, it is challenging to efficiently and rapidly screen target strains for engineering. This study reported an in situ analytical platform using laser ablation electrospray ionization mass spectrometry (LAESI-MS) for fast profiling of triacylglycerols in cellular lipid droplets of Aurantiochytrium sp. colonies cultured on agar plates. LAESI-MS approach allowed for the direct acquisition of a colony cell's characteristic fingerprint mass spectrum and MS/MS facilitated the identification of triacylglycerol species containing three fatty acyl groups. The fatty acid contents of colony cells were calculated based on the intensities of triacylglycerols from their characteristic fingerprint mass spectrum. A Python package called TAFA-LEMS (Triacylglycerol to Fatty Acid by LAESI-MS) was also developed to process the high-throughput MS data and extract fatty acid contents in colony cells. The results demonstrated that the LAESI-MS platform is fast, stable, and reproducible, with a data acquisition rate of ≤2 s per sampling point and ≤13.69% RSDs of the relative contents of fatty acids. In addition, LAESI-MS was successfully performed on the analysis of P. tricornutum and Y lipolytica strains. This in situ MS platform has the potential to become a common biotechnology platform for microbial strain engineering.

Machine-Learning Classification of Bacteria Using Two-Dimensional Tandem Mass Spectrometry

Biothreat detection has continued to gain attention. Samples suspected to fall into any of the CDC's biothreat categories require identification by processes that require specialized expertise and facilities. Recent developments in analytical instrumentation and machine learning algorithms offer rapid and accurate classification of Gram-positive and Gram-negative bacterial species. This is achieved by analyzing the negative ions generated from bacterial cell extracts with a modified linear quadrupole ion-trap mass spectrometer fitted with two-dimensional tandem mass spectrometry capabilities (2D MS/MS). The 2D MS/MS data domain of a bacterial cell extract is recorded within five s using a five-scan average after sample preparation by a simple extraction. Bacteria were classified at the species level by their lipid profiles using the random forest, k-nearest neighbor, and multilayer perceptron machine learning models. 2D MS/MS data can also be treated as image data for use with image recognition algorithms such as convolutional neural networks. The classification accuracy of all models tested was greater than 99%. Adding to previously published work on the 2D MS/MS analysis of bacterial growth and the profiling of sporulating bacteria, this study demonstrates the utility and information-rich nature of 2D MS/MS in the identification of bacterial pathogens at the species level when coupled with machine learning.

Collision cross section measurement and prediction methods in omics

Omics studies such as metabolomics, lipidomics, and proteomics have become important for understanding the mechanisms in living organisms. However, the compounds detected are structurally different and contain isomers, with each structure or isomer leading to a different result in terms of the role they play in the cell or tissue in the organism. Therefore, it is important to detect, characterize, and elucidate the structures of these compounds. Liquid chromatography and mass spectrometry have been utilized for decades in the structure elucidation of key compounds. While prediction models of parameters (such as retention time and fragmentation pattern) have also been developed for these separation techniques, they have some limitations. Moreover, ion mobility has become one of the most promising techniques to give a fingerprint to these compounds by determining their collision cross section (CCS) values, which reflect their shape and size. Obtaining accurate CCS enables its use as a filter for potential analyte structures. These CCS values can be measured experimentally using calibrant-independent and calibrant-dependent approaches. Identification of compounds based on experimental CCS values in untargeted analysis typically requires CCS references from standards, which are currently limited and, if available, would require a large amount of time for experimental measurements. Therefore, researchers use theoretical tools to predict CCS values for untargeted and targeted analysis. In this review, an overview of the different methods for the experimental and theoretical estimation of CCS values is given where theoretical prediction tools include computational and machine modeling type approaches. Moreover, the limitations of the current experimental and theoretical approaches and their potential mitigation methods were discussed.

Strain-Level Discrimination of Bacteria by Liquid Chromatography and Paper Spray Ion Mobility Mass Spectrometry

Determining bacterial identity at the strain level is critical for public health to enable proper medical treatments and reduce antibiotic resistance. Herein, we used liquid chromatography, ion mobility, and tandem MS (LC-IM-MS/MS) to distinguish Escherichia coli (E. coli) strains. Numerical multivariate statistics (principal component analysis, followed by linear discriminant analysis) showed the capability of this method to perform strain-level discrimination with prediction rates of 96.1% and 100% utilizing the negative and positive ion information, respectively. The tandem MS and LC separation proved effective in discriminating diagnostic lipid isomers in the negative mode, while IM separation was more effective in resolving lipid conformational biomarkers in the positive ion mode. Because of the clinical importance of early detection for rapid medical intervention, a faster technique, paper spray (PS)-IM-MS/MS, was used to discriminate the E. coli strains. The achieved prediction rates of the analysis of E. coli strains by PS-IM-MS/MS were 62.5% and 73.5% in the negative and positive ion modes, respectively. The strategy of numerical data fusion of negative and positive ion data increased the classification rates of PS-IM-MS/MS to 80.5%. Lipid isomers and conformers were detected, which served as strain-indicating biomarkers. The two complementary multidimensional techniques revealed biochemical differences between the E. coli strains confirming the results obtained from comparative genomic analysis. Moreover, the results suggest that PS-IM-MS/MS is a rapid, highly selective, and sensitive method for discriminating bacterial strains in environmental and food samples.

AIEgen-Based Nanomaterials for Bacterial Imaging and Antimicrobial Applications: Recent Advances and Perspectives

Microbial infections have always been a thorny problem. Multi-drug resistant (MDR) bacterial infections rendered the antibiotics commonly used in clinical treatment helpless. Nanomaterials based on aggregation-induced emission luminogens (AIEgens) recently made great progress in the fight against microbial infections. As a family of photosensitive antimicrobial materials, AIEgens enable the fluorescent tracing of microorganisms and the production of reactive oxygen (ROS) and/or heat upon light irradiation for photodynamic and photothermal treatments targeting microorganisms. The novel nanomaterials constructed by combining polymers, antibiotics, metal complexes, peptides, and other materials retain the excellent antimicrobial properties of AIEgens while giving other materials excellent properties, further enhancing the antimicrobial effect of the material. This paper reviews the research progress of AIEgen-based nanomaterials in the field of antimicrobial activity, focusing on the materials' preparation and their related antimicrobial strategies. Finally, it concludes with an outlook on some of the problems and challenges still facing the field.

Advances in Mass Spectrometry-Metabolomics Based Approaches

Highly selective and sensitive analytical techniques are necessary for microbial metabolomics due to the complexity of the microbial sample matrix. Hence, mass spectrometry (MS) has been successfully applied in microbial metabolomics due to its high precision, versatility, sensitivity, and wide dynamic range. The different analytical tools using MS have been employed in microbial metabolomics investigations and can contribute to the discovery or accelerate the search for bioactive substances. The coupling with chromatographic and electrophoretic separation techniques has resulted in more efficient technologies for the analysis of microbial compounds occurring in trace levels. This book chapter describes the current advances in the application of mass spectrometry-based metabolomics in the search for new biologically active agents from microbial sources; the development of new approaches for in silico annotation of natural products; the different technologies employing mass spectrometry imaging to deliver more comprehensive analysis and elucidate the metabolome involved in ecological interactions as they enable visualization of the spatial dispersion of small molecules. We also describe other ambient ionization techniques applied to the fingerprint of microbial natural products and modern techniques such as ion mobility mass spectrometry used to microbial metabolomic analyses and the dereplication of natural microbial products through MS.

Embossed Paper Platform for Whole Blood Collection, Room Temperature Storage, and Direct Analysis by Pinhole Paper Spray Mass Spectrometry

Dry-state microsampling techniques are convenient and advantageous for sample collection in resource-limited settings, including healthcare systems designed for the underserved population. In this work, a microsampling platform based on an embossed hydrophobic paper substrate is introduced together with three-dimensional (3D) printed cartridges that offer opportunities for rapid (<30 min) drying of the collected samples while also preserving sample integrity when the embossed paper chip is shipped at room temperature. More importantly, a new pinhole paper spray ionization method was developed that facilitates direct mass spectrometry (MS) analysis of the dried blood samples without prior sample preparation. We compared the direct pinhole paper spray MS method with a liquid chromatographic (LC) MS approach that relied upon electrospray ionization (ESI) after analytes present in the blood sample were extracted through liquid-liquid extraction. Limits of detection as low as 0.12 and 0.49 ng/mL were calculated for cocaine and its metabolite benzoylecgonine, respectively, when using the direct pinhole paper spray MS method. Analytical merits such as precision and accuracy, recovery, carryover effects, and analyte stability were all quantified for this new paper spray method and compared to the traditional LC-ESI-MS. Although LC-ESI-MS was observed to be 10× more sensitive, the linear dynamic range for both methods was determined to be the same, in the range of 1-500 ng/mL for both cocaine and benzoylecgonine analytes. When fully developed, the current microsampling strategy could offer an easy-to-use kit that can enable a more effective MS analysis of 20 μL dried blood samples delivered by mail. Both sensitivity (10×) and sample stability are found to be more superior for blood prepared in the embossed hydrophobic paper compared to samples prepared in the planar hydrophilic paper.

Systematic Optimization of Ambient Ionization Ion Mobility Mass Spectrometry for Rapid Separation of Isomers

Current methods typically used for metabolite screening and disease diagnosis often require extensive sample preparation, which increases analysis time and associated costs. While ambient ionization techniques enable the analysis of various samples in complex matrices with little or no sample preparation in a short time (typically within a minute), their reduced selectivity, even when coupled with high-resolution mass spectrometers, limits their application in certain fields. In this study, we have optimized the coupling of paper spray (PS) and leaf spray (LS) ambient ionization techniques with a commercially available ion mobility mass spectrometer (IM-MS) and demonstrated the separation of geometric and constitutional isomers. Ambient ionization techniques allow simultaneous introduction and ionization of samples, while background noise and matrix interference from paper and leaf substrates are filtered out by IM separation, resulting in high sensitivity and selectivity of the PS-IM-MS and LS-IM-MS workflows. In addition, we introduced a novel approach to perform single-field collision cross section (CCS) measurements, which resulted in CCS values that differ by 0.15% and 0.25% from traditional stepped-field and single-field methods, respectively. In addition, we used advanced computational tools to confidently identify analyte structures by comparing CCS values from experimental IM measurements and theoretical calculations. These results suggest that the coupling of ambient ionization methods with ion mobility techniques enables rapid, sensitive, and highly selective analysis that can be used in different fields, such as agrochemical screening and disease diagnostics.

AIEgens for Bacterial Imaging and Ablation

Accurate and sensitive diagnosis of pathogenic bacterial infection is a fundamental first step for correct bacteria management, helping to avoid the development of drug-resistant bacteria caused by the inappropriate use and overuse of antibiotics. Fluorescence probes as a promising visual tool can help identify pathogens rapidly and reliably. However, rigidly structured traditional fluorescence probes generally suffer from the drawback of aggregation-caused quenching (ACQ) effect, which greatly undermines their advantages with respect to sensitivity. Luminogens with aggregation-induced emission properties, namely AIEgens, can overcome the ACQ effect and certain AIEgen-based materials are capable of generating reactive oxygen species (ROS) in the aggregate states. Hence, they have become powerful tools for imaging and killing bacteria. This review summarizes the recent advances in AIEgens for the diagnosis and treatment of pathogen infections. Special attention has been paid to the molecular design, the application in bacterial imaging and ablation in vitro and in vivo, and the biocompatibility of AIEgens. Finally, the challenges and prospects are discussed in terms of using AIEgens to advance precision therapies for pathogen infections.

Immediate and sensitive detection of sporulated Bacillus subtilis by microwave release and tandem mass spectrometry of dipicolinic acid

Spore lysis of Bacillus species is achieved by brief (1 min) microwave irradiation while tandem mass spectrometry (MS/MS) allows identification of the characteristic spore marker, dipicolinic acid. This rapid measurement, made on 10⁵-10⁸ spores, has significant implications for biothreat recognition.

In Situ Construction of COF-Based Paper Serving as a Plasmonic Substrate for Enhanced PSI-MS Detection of Polycyclic Aromatic Hydrocarbons

Accurate detection, quantitation, and differentiation of polycyclic aromatic hydrocarbons (PAHs) and their isomers in diverse samples is elusive for paper spray ionization mass spectrometry (PSI-MS). To address these issues, herein, for the first time, we propose to fabricate a novel, flexible, and stable paper substrate based on covalent organic frameworks (COFs) via an in situ method under room temperature in air. After embedding gold nanoparticles (AuNPs), this paper substrate (COFs-paper) could further serve as a multifunctional plasmonic matrix (AuNPs-COFs-paper) for dual-wavelength laser-assisted PSI-MS detection of PAHs and feasible paper surface-enhanced Raman scattering (pSERS)-aided isomer discrimination. Taking advantage of the synergistic effect between the AuNPs and COFs present on the novel AuNP-embedded COFs-paper substrate, a satisfied LOD of 0.50 ng/μL for phenanthrene was realized, which improved almost 300 times compared with the naked-paper matrix, and the regression coefficient R² was up to 0.999. Real sample corn oil-containing PAHs can be efficiently detected and identified using this technique. The established platform has promising potential for on-site chemical analysis with portable PSI-MS and pSERS instruments.

Liquid Extraction Surface Analysis Mass Spectrometry of ESKAPE Pathogens

The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) represent clinically important bacterial species that are responsible for most hospital-acquired drug-resistant infections; hence, the need for rapid identification is of high importance. Previous work has demonstrated the suitability of liquid extraction surface analysis mass spectrometry (LESA MS) for the direct analysis of colonies of two of the ESKAPE pathogens (Staphylococcus aureus and Pseudomonas aeruginosa) growing on agar. Here, we apply LESA MS to the remaining four ESKAPE species (E. faecium E745, K. pneumoniae KP257, A. baumannii AYE, and E. cloacae S11) as well as E. faecalis V583 (a close relative of E. faecium) and a clinical isolate of A. baumannii AC02 using an optimized solvent sampling system. In each case, top-down LESA MS/MS was employed for protein identification. In total, 24 proteins were identified from 37 MS/MS spectra by searching against protein databases for the individual species. The MS/MS spectra for the identified proteins were subsequently searched against multiple databases from multiple species in an automated data analysis workflow with a view to determining the accuracy of identification of unknowns. Out of 24 proteins, 19 were correctly assigned at the protein and species level, corresponding to an identification success rate of 79%.

Extracellular Vesicle Analysis by Paper Spray Ionization Mass Spectrometry

Paper spray ionization mass spectrometry (PSI-MS) is a direct MS analysis technique with several reported bacterial metabolomics applications. As with most MS-based bacterial studies, all currently reported PSI-MS bacterial analyses have focused on the chemical signatures of the cellular unit. One dimension of the bacterial metabolome that is often lost in such analyses is the exometabolome (extracellular metabolome), including secreted metabolites, lipids, and peptides. A key component of the bacterial exometabolome that is gaining increased attention in the microbiology and biomedical communities is extracellular vesicles (EVs). These excreted structures, produced by cells in all domains of life, contain a variety of biomolecules responsible for a wide array of cellular functions, thus representing a core component of the bacterial secreted metabolome. Although previously examined using other MS approaches, no reports currently exist for a PSI-MS analysis of bacterial EVs, nor EVs from any other organism (exosomes, ectosomes, etc.). PSI-MS holds unique analytical strengths over other commonly used MS platforms and could thus provide an advantageous approach to EV metabolomics. To address this, we report a novel application representing, to our knowledge, the first PSI-MS analysis of EVs from any organism (using the human gut resident Oxalobacter formigenes as the experimental model, a bacterium whose EVs were never previously investigated). In this report, we show how we isolated and purified EVs from bacterial culture supernatant by EV-specific affinity chromatography, confirmed and characterized these vesicles by nanoparticle tracking analysis, analyzed the EV isolate by PSI-MS, and identified a panel of EV-derived metabolites, lipids, and peptides. This work serves as a pioneering study in the field of MS-based EV analysis and provides a new, rapid, sensitive, and economical approach to EV metabolomics.

Microdroplet Impact-Induced Spray Ionization Mass Spectrometry (MISI MS) for Online Reaction Monitoring and Bacteria Discrimination

Microdroplet impact-induced spray ionization (MISI) is demonstrated involving the impact of microdroplets produced from a paper and their impact on another, leading to the ionization of analytes deposited on the latter. This cascaded process is more advantageous in comparison to standard spray ionization as it performs reactions and ionization simultaneously in the absence of high voltage directly applied on the sample. In MISI, we apply direct current (DC) potential only to the terminal paper, used as the primary ion source. Charge transfer due to microdroplet/ion deposition on the flowing analyte solution on the second surface generates secondary charged microdroplets from it carrying the analytes, which ionize and get detected by a mass spectrometer. In this way, up to three cascaded spray sources could be assembled in series. We show the detection of small molecules and proteins in such ionization events. MISI provides a method to understand chemical reactions by droplet impact. The C-C bond formation reactions catalyzed by palladium and alkali metal ion encapsulation using crown ether were studied as our model reactions. To demonstrate the application of our ion source in a bioanalytical context, we studied the noninvasive in situ discrimination of bacteria samples under ambient conditions.

Paper Spray Ionization Mass Spectrometry as a Potential Tool for Early Diagnosis of Cervical Cancer

Squamous intraepithelial lesion is an abnormal growth of epithelial cells on the surface of the cervix that may lead to cervical cancer. Analytical protocols for the determination of squamous intraepithelial lesions are in high demand, since cervical cancer is the fourth most diagnosed cancer among women in the world. Here, paper spray ionization mass spectrometry (PSI-MS) is used to distinguish between healthy (negative for intraepithelial lesion or malignancy) and diseased (high-grade squamous intraepithelial lesion) blood plasmas. A total of 86 blood samples of different women (49 healthy samples, 37 diseased samples) were collected, and the plasmas were prepared. Then, 10 μL of each plasma sample was deposited onto triangular papers for PSI-MS analysis. No additional step of sample preparation was necessary. The interval-successive projection algorithm linear discriminant analysis (iSPA-LDA) was applied to the PSI mass spectra, showing six ions (mostly phospholipids) that were predictive of healthy and diseased plasmas. Values of 77% accuracy, 86% sensitivity, 80% positive predictive value (PPV), and 75% negative predictive value (NPV) were achieved. This study provides evidence that PSI-MS may potentially be used as a fast and simple analytical technique for the early diagnosis of cervical cancer.

Direct identification of bacterial and human proteins from infected wounds in living 3D skin models

Trauma is one of the leading causes of death in people under the age of 49 and complications due to wound infection are the primary cause of death in the first few days after injury. The ESKAPE pathogens are a group of bacteria that are a leading cause of hospital-acquired infections and a major concern in terms of antibiotic resistance. Here, we demonstrate a novel and highly accurate approach for the rapid identification of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) directly from infected wounds in 3D in vitro skin models. Wounded skin models were inoculated with bacteria and left to incubate. Bacterial proteins were identified within minutes, directly from the wound, by liquid extraction surface analysis mass spectrometry. This approach was able to distinguish closely related strains and, unlike genomic approaches, can be modified to provide dynamic information about pathogen behaviour at the wound site. In addition, since human skin proteins were also identified, this method offers the opportunity to analyse both host and pathogen biomarkers during wound infection in near real-time.

Emerging trends in paper spray mass spectrometry: Microsampling, storage, direct analysis, and applications

Recent advancements in the sensitivity of chemical instrumentation have led to increased interest in the use of microsamples for translational and biomedical research. Paper substrates are by far the most widely used media for biofluid collection, and mass spectrometry is the preferred method of analysis of the resultant dried blood spot (DBS) samples. Although there have been a variety of review papers published on DBS, there has been no attempt to unify the century old DBS methodology with modern applications utilizing modified paper and paper-based microfluidics for sampling, storage, processing, and analysis. This critical review will discuss how mass spectrometry has expanded the utility of paper substrates from sample collection and storage, to direct complex mixture analysis to on-surface reaction monitoring.

Bacterial identification by lipid profiling using liquid atmospheric pressure matrix-assisted laser desorption/ionization mass spectrometry

Background

In recent years, mass spectrometry (MS) has been applied to clinical microbial biotyping, exploiting the speed of matrix-assisted laser desorption/ionization (MALDI) in recording microbe-specific MS profiles. More recently, liquid atmospheric pressure (AP) MALDI has been shown to produce extremely stable ion flux from homogenous samples and ‘electrospray ionization (ESI)-like’ multiply charged ions for larger biomolecules, whilst maintaining the benefits of traditional MALDI including high tolerance to contaminants, low analyte consumption and rapid analysis. These and other advantages of liquid AP-MALDI MS have been explored in this study to investigate its potential in microbial biotyping.

Methods

Genetically diverse bacterial strains were analyzed using liquid AP-MALDI MS, including clinically relevant species such as Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. Bacterial cultures were subjected to a simple and fast extraction protocol using ethanol and formic acid. Extracts were spotted with a liquid support matrix (LSM) and analyzed using a Synapt G2-Si mass spectrometer with an in-house built AP-MALDI source.

Results

Each species produces a unique lipid profile in the m/z range of 400–1100, allowing species discrimination. Traditional (solid) MALDI MS produced spectra containing a high abundance of matrix-related clusters and an absence of lipid peaks. The MS profiles of the bacterial species tested form distinct clusters using principle component analysis (PCA) with a classification accuracy of 98.63% using a PCA-based prediction model.

Conclusions

Liquid AP-MALDI MS profiles can be sufficient to distinguish clinically relevant bacterial pathogens and other bacteria, based on their unique lipid profiles. The analysis of the lipid MS profiles is typically excluded from commercial instruments approved for clinical diagnostics.

Decoding the Metabolome and Lipidome of Child Malnutrition by Mass Spectrometric Techniques: Present Status and Future Perspectives

Child malnutrition (CM) is a global public health problem. It contributes to poor health in one in four children under five years worldwide and causes serious health problems in children, including stunted, wasted, and overweight growth. These serious public health issues lead to a higher chance of living in poverty in adulthood. Malnutrition is related with reduced economic productivity and increases the serious national and international burden. Currently, there is no meaningful therapeutic intervention of CM, and the use of different therapeutic foods has shown poor outcomes among supplemented malnourished children. The role of metabolites and lipids has been extensively recognized as early determinants of child health, but their contribution in CM and its pathobiology are poorly understood. This perspective provides a most recent update on these aspects. After briefly introducing the disciplines of metabolomics and lipidomics, we describe a mass spectrometry-based metabolic workflow for analysis of both metabolites and lipids and summarize several recent applications of metabolomics and lipidomics in CM. Finally, we discuss the future directions of the field toward the development of meaningful interventions for CM through metabolomics and lipidomics advances.

An update on the routine application of MALDI-TOF MS in clinical microbiology

Introduction: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has entered clinical diagnostics and is today a generally accepted and integral part of the workflow for microbial identification. MALDI-TOF MS identification systems received approval from national and international institutions, such as the USA-FDA, and are continuously improved and adopted to other fields like veterinary and industrial microbiology. The question is whether MALDI-TOF MS also has the potential to replace other conventional and molecular techniques operated in routine diagnostic laboratories. Areas covered: We give an overview of new advancements of mass spectral analysis in the context of microbial diagnostics. In particular, the expansion of databases to increase the range of readily identifiable bacteria and fungi, the refined discrimination of species complexes, subspecies, and types, the testing for antibiotic resistance or susceptibility, progress in sample preparation including automation, and applications of other mass spectrometry techniques are discussed. Expert opinion: Although many new approaches of MALDI-TOF MS are still in the stage of proof of principle, it is expectable that MALDI-TOF MS will expand its role in the clinical microbiology laboratory of the future. New databases, instruments and analytical software modules will continue to be developed to further improve diagnostic efficacy.

In situ analysis of unsaturated fatty acids in human serum by negative-ion paper spray mass spectrometry

In situ identification and quantification of unsaturated fatty acid (FA) C=C positional isomers in human serum is herein performed by negative-ion paper spray (PS) mass spectrometry. Typically, by direct application of an alternating current (AC) voltage to the wet paper, the PS ionization could perform stably in the negative-ion mode without severe discharge. We suppose epoxidation reaction between unsaturated C=C bonds and reactive oxidative species might be initiated by a mild electrical discharge, which could be rapidly and controllably produced via a low amplitude AC voltage. Upon collision-induce dissociation (CID), the epoxide was fragmented to generate diagnostic ions indicating the C=C location. The intensity of the characteristic product ions could also be used for absolute quantification of the FA C=C positional isomers. The limits of detection (LODs) and limits of quantification (LOQs) were roughly in the range of 0.0178-0.0506 μM and 0.0218-0.3634 μM for standard FAs. Without the additional sample preparations or reactive chemical reagents, epoxidation of unsaturated FAs and ionization of the epoxide could be achieved in one-step by negative-ion mode PS, which enable a promising methodology for on-site clinical diagnosis.

Strain-Level Differentiation of Bacteria by Paper Spray Ionization Mass Spectrometry

Paper spray ionization mass spectrometry (PSI-MS) is a relatively new analytical technique allowing for rapid mass spectrometric analysis of biological samples with little or no sample preparation. The expeditious nature of the analysis and minimal requirement for sample preparation make PSI-MS a promising avenue for future clinical assays with one potential application in the identification of different types of bacteria. Although past PSI-MS studies have demonstrated the ability to distinguish between bacteria of different species and morphological classes, achieving within-species strain-level differentiation has never been performed. In this report, we demonstrate the first strain-level bacterial differentiation by PSI-MS with the mammalian intestinal bacterium Oxalobacter formigenes ( Oxf). This novel application holds promising clinical significance as it could be used to differentiate between pathogenic bacteria and their harmless, commensal relatives, saving time and money in clinical diagnostics. Both whole cells and cell lysates of  Oxf strains HC1 and OxWR were analyzed using the Prosolia Velox 360TM PSI source coupled to a Thermo Scientific Q Exactive high-resolution mass spectrometer with a rapid 30 s analytical method. Multivariate statistical analysis followed by examination of significant features provided for and confirmed differentiation between Oxf HC1 and OxWR. We report a panel of strain-exclusive metabolites that could serve as potential strain-indicating biomarkers.

On-substrate derivatization for detection of highly volatile G-series chemical warfare agents via paper spray mass spectrometry

RATIONALE

The analysis of chemical warfare agents (CWAs) from ambient atmosphere presents an analytical challenge due to their ease of degradation and volatility. Herein is described a method for derivatizing CWAs directly onto a paper spray substrate prior to analysis. This derivatization allows for much longer times of analysis without sample degradation and with little to no sample preparation.

METHODS

Derivatization was performed using 2-[(dimethylamino)methyl] phenol both in-vial and directly on paper spray cartridges. Solution studies were carried out over time and samples were analyzed via liquid chromatography/tandem mass spectrometry (LC/MS/MS) operated in positive ion mode. Paper spray substrates impregnated with the derivatizing agent prior to CWA vapor capture were also analyzed over time using a mass spectrometer operated in positive ion mode.

RESULTS

Use of 2-[(dimethylamino)methyl] phenol as a paper spray substrate dopant enables derivatization of G-series compounds into lower volatility complexes. The reaction occurs in solution and in the vapor phase. This new technique effectively traps and captures G-series agents for analysis while extending the time for which the compound remains absorbed. The complex is highly suitable for direct analysis via paper spray mass spectrometry.

CONCLUSIONS

Derivatization of paper spray substrates was shown to greatly increase the time for analysis of CWAs. This technique, combined with the vapor phase capture stage outlined previously, allows for rapid, quantitative CWA detection by paper spray ionization with little or no sample preparation.

On-substrate Enzymatic Reaction to Determine Acetylcholinesterase Activity in Whole Blood by Paper Spray Mass Spectrometry

Currently, all assays measuring acetylcholinesterase (AChE) activity following a suspected nerve agent exposure leverage methodologies that fail to identify the agent. This limits the overall effectiveness and ability to administer proper countermeasures. As such, there is an urgent need to identify novel, rapid, and more comprehensive approaches to establish AChE activity, including identification of the toxicant. Paper spray mass spectrometry was used to monitor the activity of acetylcholinesterase, both in-solution and on modified hydrophobic paper surface. Hydrophobic paper surfaces were prepared using vaporized trichloro(3,3,3-trifluoropropyl)silane. In both approaches, mixtures of diluted human whole blood with and without VX were mixed with a non-endogenous AChE specific substrate, 1,1-dimethyl-4-acetylthiomethylpiperidinium (MATP+). Formation of the cleaved MATP+ product was monitored over time and compared to MATP+ to determine relative AChE activity. This on-substrate assay was effective at determining AChE activity and identifying the toxicant; however, determination of AChE activity in-solution proceeded at a slower rate. The on-substrate assay serves as a pioneering example of an enzymatic reaction occurring on the surface of a paper spray ionization ticket. This work broadens the range of applications relating to paper spray ionization-based clinical diagnostic assays. Graphical Abstract ᅟ.

Paper spray ionization mass spectrometry: recent advances and clinical applications

INTRODUCTION

Paper spray mass spectrometry has provided a rapid, quantitative ambient ionization method for xenobiotic and biomolecule analysis. As an alternative to traditional sample preparation and chromatography, paper spray demonstrates the sampling ionization of a wide range of molecules and significant sensitivity from complex biofluids. The amenability of paper spray with dried blood spots and other sampling types shows strong potential for rapid, point-of-care (POC) analysis without time-consuming separation procedures. Areas covered: This special report summarizes the current state and advances in paper spray mass spectrometry that relate to its applicability for clinical analysis. It also provides our perspectives on the future development of paper spray mass spectrometry and its potential roles in clinical settings. Expert commentary: Paper spray has provided the fundamental aspects of ambient ionization needed for implementation at the POC. With further clinical management and standardization, paper spray has the potential to replace traditional complex analysis procedure for rapid quantitative detection of illicit drugs, therapeutic drugs and metabolites. Surface and substrate modifications also offer significant improvement in desorption and ionization efficiencies, resulting in enhanced sensitivity. Comprehensive analysis of metabolites and lipids will further extend the implementation of paper spray ionization mass spectrometry into clinical applications.

Instantaneous Response of Bacteria to External Stimuli Monitored by Syringe Spray Mass Spectrometry

Microbial adaptation to environmental stress involves complex adaptations of bacteria. Many such responses are transient and dynamic. However, monitoring the dynamic responses of live bacteria to stimulations at the molecular level remain a challenge. This work describes the development of syringe spray mass spectrometry (MS) method that allows direct analyses of molecules released by the bacteria in responses to external stimuli with second level time resolution. We report the application of this technique to visualize the dynamic release of small molecules from Escherichia coli ( E. coli) under ethanol and isopropanol treatments. With the unique time-resolved capability, detailed destruction process of alcohol on bacteria cell wall could be observed. Compared to other ethanol concentrations, 75% ethanol showed stronger damages to lipopolysaccharide (LPS) and peptidoglycan located on E. coli cell wall. Furthermore, isopropanol showed stronger liposolubility and permeability, and an equilibrium could be achieved in a much shorter time.

Characterization of microbial mixtures by mass spectrometry

MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.

Metal-Organic Framework Modified Glass Substrate for Analysis of Highly Volatile Chemical Warfare Agents by Paper Spray Mass Spectrometry

Paper spray mass spectrometry has been shown to successfully analyze chemical warfare agent (CWA) simulants. However, due to the volatility differences between the simulants and real G-series (i.e., sarin, soman) CWAs, analysis from an untreated paper substrate proved difficult. To extend the analytical lifetime of these G-agents, metal-organic frameworks (MOFs) were successfully integrated onto the paper spray substrates to increase adsorption and desorption. In this study, several MOFs and nanoparticles were tested to extend the analytical lifetimes of sarin, soman, and cyclosarin on paper spray substrates. It was found that the addition of either UiO-66 or HKUST-1 to the paper substrate increased the analytical lifetime of the G-agents from less than 5 min detectability to at least 50 min.

Novel Selectivity-Based Forensic Toxicological Validation of a Paper Spray Mass Spectrometry Method for the Quantitative Determination of Eight Amphetamines in Whole Blood

Paper spray tandem mass spectrometry is used to identify and quantify eight individual amphetamines in whole blood in 1.3 min. The method has been optimized and fully validated according to forensic toxicology guidelines, for the quantification of amphetamine, methamphetamine, 3,4-methylenedioxyamphetamine (MDA), 3,4-methylenedioxy-N-methylamphetamine (MDMA), 3,4-methylenedioxy-N-ethylamphetamine (MDEA), para-methoxyamphetamine (PMA), para-methoxymethamphetamine (PMMA), and 4-fluoroamphetamine (4-FA). Additionally, a new concept of intrinsic and application-based selectivity is discussed, featuring increased confidence in the power to discriminate the amphetamines from other chemically similar compounds when applying an ambient mass spectrometric method without chromatographic separation. Accuracy was within ±15% and average precision was better than 15%, and better than 20% at the LLOQ. Detection limits between 15 and 50 ng/mL were obtained using only 12 μL of whole blood. Graphical abstract ᅟ.

Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria

We have previously shown that liquid extraction surface analysis (LESA) mass spectrometry (MS) is a technique suitable for the top-down analysis of proteins directly from intact colonies of the Gram-negative bacterium Escherichia coli K-12. Here we extend the application of LESA MS to Gram-negative Pseudomonas aeruginosa PS1054 and Gram-positive Staphylococcus aureus MSSA476, as well as two strains of E. coli (K-12 and BL21 mCherry) and an unknown species of Staphylococcus. Moreover, we demonstrate the discrimination between three species of Gram-positive Streptococcus (Streptococcus pneumoniae D39, and the viridans group Streptococcus oralis ATCC 35037 and Streptococcus gordonii ATCC35105), a recognized challenge for matrix-assisted laser desorption ionization time-of-flight MS. A range of the proteins detected were selected for top-down LESA MS/MS. Thirty-nine proteins were identified by top-down LESA MS/MS, including 16 proteins that have not previously been observed by any other technique. The potential of LESA MS for classification and characterization of novel species is illustrated by the de novo sequencing of a new protein from the unknown species of Staphylococcus. Graphical Abstract ᅟ.

Paper Spray Mass Spectrometry for the Forensic Analysis of Black Ballpoint Pen Inks

This article describes the use of paper spray mass spectrometry (PS-MS) for the direct analysis of black ink writings made with ballpoint pens. The novel approach was developed in a forensic context by first performing the classification of commercially available ballpoint pens according to their brands. Six of the most commonly worldwide utilized brands (Bic, Paper Mate, Faber Castell, Pentel, Compactor, and Pilot) were differentiated according to their characteristic chemical patterns obtained by PS-MS. MS on the negative ion mode at a mass range of m/z 100-1000 allowed prompt discrimination just by visual inspection. On the other hand, the concept of relative ion intensity (RII) and the analysis at other mass ranges were necessary for the differentiation using the positive ion mode. PS-MS combined with partial least squares (PLS) was utilized to monitor changes on the ink chemical composition after light exposure (artificial aging studies). The PLS model was optimized by variable selection, which allowed the identification of the most influencing ions on the degradation process. The feasibility of the method on forensic investigations was also demonstrated in three different applications: (1) analysis of overlapped fresh ink lines, (2) analysis of old inks from archived documents, and (3) detection of alterations (simulated forgeries) performed on archived documents. Graphical Abstract ᅟ.

Electrospray Modifications for Advancing Mass Spectrometric Analysis

Generation of analyte ions in gas phase is a primary requirement for mass spectrometric analysis. One of the ionization techniques that can be used to generate gas phase ions is electrospray ionization (ESI). ESI is a soft ionization method that can be used to analyze analytes ranging from small organics to large biomolecules. Numerous ionization techniques derived from ESI have been reported in the past two decades. These ion sources are aimed to achieve simplicity and ease of operation. Many of these ionization methods allow the flexibility for elimination or minimization of sample preparation steps prior to mass spectrometric analysis. Such ion sources have opened up new possibilities for taking scientific challenges, which might be limited by the conventional ESI technique. Thus, the number of ESI variants continues to increase. This review provides an overview of ionization techniques based on the use of electrospray reported in recent years. Also, a brief discussion on the instrumentation, underlying processes, and selected applications is also presented.

Development and Application of a Brush-Spray Derived from a Calligraphy-Brush-Style Synthetic Hair Pen for Use in ESI/MS

The development of a novel type of a sampling/ionization kit for use in electrospray ionization/mass spectrometry is reported. Using a small calligraphy-brush-style synthetic hair pen (nylon-brush), and analogous to paper-spray mass spectrometry, the analytes can be collected, elution/desorption and then ionized from the surface of the nylon-brush. The body of the kit was produced by means of a commercial 3D-printer, in which ABS (acrylonitrile butadiene styrene) was used as the starting material. Meanwhile, a small nylon-brush was embedded inside a 3D-printed plastic cell, in which a solvent was supplied to rinse the brush by means of capillary action. The size and weight of the kit were 1 g and 4 cm, respectively. The kit is disposable and it has various functions, including non-invasive sampling, sample-evaporation and ionization. As a result, when a type of pesticide was selected as the test sample (dimethoate; C5H12NO3PS2), the limit of detection was determined to be 0.1 μg/mL. Collecting the pesticide from a leaf-surface (lettuce) was also successful. The process for fabricating the nylon-brush kit and the optimized experimental conditions are reported herein.