Universal, untargeted detection of bacteria in tissues using metabolomics workflows

Fast and reliable identification of bacteria directly in clinical samples is a critical factor in clinical microbiological diagnostics. Current approaches require time-consuming bacterial isolation and enrichment procedures, delaying stratified treatment. Here, we describe a biomarker-based strategy that utilises bacterial small molecular metabolites and lipids for direct detection of bacteria in complex samples using mass spectrometry (MS). A spectral metabolic library of 233 bacterial species is mined for markers showing specificity at different phylogenetic levels. Using a univariate statistical analysis method, we determine 359 so-called taxon-specific markers (TSMs). We apply these TSMs to the in situ detection of bacteria using healthy and cancerous gastrointestinal tissues as well as faecal samples. To demonstrate the MS method-agnostic nature, samples are analysed using spatial metabolomics and traditional bulk-based metabolomics approaches. In this work, TSMs are found in >90% of samples, suggesting the general applicability of this workflow to detect bacterial presence with standard MS-based analytical methods.

Present and future perspectives on mass spectrometry for clinical microbiology

In the last decade, MALDI-TOF Mass Spectrometry (MALDI-TOF MS) has been introduced and broadly accepted by clinical laboratory laboratories throughout the world as a powerful and efficient tool for rapid microbial identification. During the MALDI-TOF MS process, microbes are identified using either intact cells or cell extracts. The process is rapid, sensitive, and economical in terms of both labor and costs involved. Whilst MALDI-TOF MS is currently the gold-standard, it suffers from several shortcomings such as lack of direct information on antibiotic resistance, poor depth of analysis and insufficient discriminatory power for the distinction of closely related bacterial species or for reliably sub-differentiating isolates to the level of clones or strains. Thus, new approaches targeting proteins and allowing a better characterization of bacterial strains are strongly needed, if possible, on a very short time scale after sample collection in the hospital. Bottom-up proteomics (BUP) is a nice alternative to MALDI-TOF MS, offering the possibility for in-depth proteome analysis. Top-down proteomics (TDP) provides the highest molecular precision in proteomics, allowing the characterization of proteins at the proteoform level. A number of studies have already demonstrated the potential of these techniques in clinical microbiology. In this review, we will discuss the current state-of-the-art of MALDI-TOF MS for the rapid microbial identification and detection of resistance to antibiotics and describe emerging approaches, including bottom-up and top-down proteomics as well as ambient MS technologies.

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.

Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms

Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.

Desorption Electrospray Ionization Mass Spectrometry: 20 Years

Mass spectrometry (MS) is one of the most widely used technologies in the chemical sciences. With applications spanning the monitoring of reaction products, the identification of disease biomarkers, and the measurement of thermodynamic parameters and aspects of structural biology, MS is well established as a universal analytical tool applicable to small compounds as well as large molecular complexes. Regardless of the application, the generation of gas-phase ions from neutral compounds is a key step in any MS experiment. However, this ionization step was for many years limited to high-energy approaches that required gas-phase analytes and thus it was restricted to volatile samples. Over the last few decades, new methodologies have been developed to address this limitation and facilitate ionization of biological molecules. Electrospray ionization (ESI) is the most broadly used of these methods, as it facilitates the ionization of intact polar compounds from solution.

Twenty years ago, our group reported a new ionization method that uses a charged solvent spray to impact a surface, generating ions from objects rather than just solutions and doing so directly in the ambient environment with no vacuum requirements and little to no sample preparation. This method was termed desorption electrospray ionization (DESI), and it initiated a new field that would come to be known as ambient mass spectrometry. The simplicity and wide applicability of the DESI technology—and the tens of ambient ionization methods developed subsequently—revolutionized the MS analysis of complex materials for their organic components, especially for in situ applications.

This Account describes the history of DESI, starting with the development of the technique from early electrosonic spray ionization (ESSI) experimental observations as well as the studies leading to the understanding of its mechanism as a “droplet pick-up” phenomenon involving sequential events (i.e. , thin film formation, solid–liquid extraction, secondary droplet generation, and ESI-like ionization from these droplets). We also overview the developments and applications of the technology that have been demonstrated by our group during the last two decades. In particular, we describe (i) the use of DESI for tissue imaging, one of its more significant applications to date, and its extension to intraoperative clinical diagnosis; (ii) the integration of the technology with portable instrumentation for in situ analysis, especially when coupled with tandem mass spectrometry (MS/MS); (iii) the use of DESI microdroplets as microvessels to accelerate organic reactions by orders of magnitude compared to those in bulk solution; and (iv) the combination of all these capabilities for automated high-throughput experiments aimed at accelerating drug discovery.

Automated high-throughput characterization of microbial metabolites and species using array ballpoint electrospray ionization technique

RATIONALE

Microbial metabolites are widely used in agriculture, food, environment, and medicine. However, there is a lack of high-throughput, nonclogging, and simple methods for the identification of microbial metabolites and their subspecies using ambient mass spectrometry (MS). Here, we proposed a method for analyzing the microbial metabolites and identifying their species using the array ballpoint electrospray ionization (aBPESI) technique.

METHODS

The previously developed BPESI was combined with the array analysis technique to form a high-throughput analysis technique called aBPESI. The bacteria cultured on the plate medium were directly analyzed using MS with aBPESI. Principal component analysis-linear discriminant analysis (PCA-LDA) algorithm was used to analyze the different subspecies groups.

RESULTS

The results showed that aBPESI was capable of completing a sample analysis within 30 s, and the level of metabolite detection was comparable to existing techniques. The accuracy of bacterial subspecies identification was 90% (Pseudomonas aeruginosa) and 100% (Serratia marcescens).

CONCLUSIONS

A new high-throughput and robust MS technique aBPESI was proposed. It does not require sample pretreatment and greatly reduces the sample analysis time. aBPESI shows a strong ability in microbial analysis and is expected to be further applied in other research fields.

Electrochemical monitoring of the Pseudomonas aeruginosa growth and the formation of a biofilm in TSB media

Understanding and sensing microbial biofilm formation onto surfaces remains highly challenging for preventing corrosion and biofouling processes. For that purpose, we have thoroughly investigated biofilm formation onto glassy carbon electrode surfaces by using electrochemical technics. Pseudomonas aeruginosa was studied because of its remarkable ability to form biofilms in many environments. The modification of the electrode-solution interface during biofilm growth was monitored by in-situ measurement of the open-circuit potential and correlated with results obtained by electrochemical impedance spectroscopy, cyclic voltammetry, scanning electron microscopy and bioassays. The sensing of the biofilm formation hence suggests a multi-steps mechanism, which may include pre-formation of an insulating layer onto the surface prior to the bacteria adhesion and biofilm formation.

Advances in Mass Spectrometry-Based Single Cell Analysis

Technological developments and improvements in single-cell isolation and analytical platforms allow for advanced molecular profiling at the single-cell level, which reveals cell-to-cell variation within the admixture cells in complex biological or clinical systems. This helps to understand the cellular heterogeneity of normal or diseased tissues and organs. However, most studies focused on the analysis of nucleic acids (e.g., DNA and RNA) and mass spectrometry (MS)-based analysis for proteins and metabolites of a single cell lagged until recently. Undoubtedly, MS-based single-cell analysis will provide a deeper insight into cellular mechanisms related to health and disease. This review summarizes recent advances in MS-based single-cell analysis methods and their applications in biology and medicine.

Interaction of a natural compound nanoemulsion with Gram negative and Gram positive bacterial membrane; a mechanism based study using a microfluidic chip and DESI technique

The antibacterial activity of a nanoemulsion prepared from Satureja Khusitanica essential oil against a Gram-negative (Escherichia coli) and a Gram-positive (Bacillus atrophaeus) bacteria evaluated using microfluidic and conventional techniques. The effect of different residence time and concentrations on the antibacterial activity of nanoemulsion was studied by measuring the release of protein, nucleic acids, potassium, and also recording the MIC, MBC and time killing assays. Remarkable intensification was observed by employing microfluidic chip regarding a high-contact surface area between nanodroplets and bacterial membrane. The MIC and MBC values for E. coli and B. atrophaeus in conventional method were 400 and 1600 µg mL^-1, respectively, whereas these values reduced to 11 to 50 µg mL^-1 using microfluidic system. B. atrophaeus seemed to be more resistant than E. coli to the nanoemulsion treatment, perhaps due to different cell wall structures. Bacterial cell wall changes were examined using a desorption electrospray ionization (DESI) technique. It was found that the structural changes were more imminent in Gram negative E. coli by detecting a number of released lipids including phosphatidyl glycerol and phosphatidyl ethanolamines. The DESI spectra of B. atrophaeus revealed no M/Z related lipid release. These findings may help providing novel nano based natural antibacterials.

Rapid Profiling of Metabolic Perturbations to Antibiotics in Living Bacteria by Induced Electrospray Ionization Mass Spectrometry

Rapid monitoring of real bacterial metabolic perturbations to antibiotics may be helpful to better understand the mechanisms of action and more targeted treatment. In this study, the real metabolic responses to antibiotic treatment in living bacteria were profiled rapidly by induced electrospray ionization mass spectrometry. Significant metabolic perturbations were profiled after antibiotic treatment compared with untreated bacteria. Similar and unique metabolic responses were observed with different antibiotic treatments. Further multivariable analysis was performed to determine significant metabolites as potential biomarkers. Moreover, different metabolic disturbances were detected for serial dilutions of antibiotic treatments. Overall, combined with induced electrospray ionization mass spectrometry, the rapid and real bacterial metabolic status caused by antibiotics was monitored, suggesting the potential application of our method in mechanism exploration and clinical diagnosis.

Accelerating strain phenotyping with desorption electrospray ionization-imaging mass spectrometry and untargeted analysis of intact microbial colonies

Reading and writing DNA were once the rate-limiting step in synthetic biology workflows. This has been replaced by the search for the optimal target sequences to produce systems with desired properties. Directed evolution and screening mutant libraries are proven technologies for isolating strains with enhanced performance whenever specialized assays are available for rapidly detecting a phenotype of interest. Armed with technologies such as CRISPR-Cas9, these experiments are capable of generating libraries of up to 10¹⁰ genetic variants. At a rate of 10² samples per day, standard analytical methods for assessing metabolic phenotypes represent a major bottleneck to modern synthetic biology workflows. To address this issue, we have developed a desorption electrospray ionization-imaging mass spectrometry screening assay that directly samples microorganisms. This technology increases the throughput of metabolic measurements by reducing sample preparation and analyzing organisms in a multiplexed fashion. To further accelerate synthetic biology workflows, we utilized untargeted acquisitions and unsupervised analytics to assess multiple targets for future engineering strategies within a single acquisition. We demonstrate the utility of the developed method using Escherichia coli strains engineered to overproduce free fatty acids. We determined discrete metabolic phenotypes associated with each strain, which include the primary fatty acid product, secondary products, and additional metabolites outside the engineered product pathway. Furthermore, we measured changes in amino acid levels and membrane lipid composition, which affect cell viability. In sum, we present an analytical method to accelerate synthetic biology workflows through rapid, untargeted, and multiplexed metabolomic analyses.

Assessing direct analysis in real-time mass spectrometry for the identification and serotyping of Legionella pneumophila

AIMS

The efficacy of ambient mass spectrometry to identify and serotype Legionella pneumophila was assessed. To this aim, isolated waterborne colonies were submitted to a rapid extraction method and analysed by direct analysis in real-time mass spectrometry (DART-HRMS).

METHODS AND RESULTS

The DART-HRMS profiles, coupled with partial least squares discriminant analysis (PLS-DA), were first evaluated for their ability to differentiate Legionella spp. from other bacteria. The resultant classification model achieved an accuracy of 98.1% on validation. Capitalising on these encouraging results, DART-HRMS profiling was explored as an alternative approach for the identification of L. pneumophila sg. 1, L. pneumophila sg. 2-15 and L. non-pneumophila; therefore, a different PLS-DA classifier was built. When tested on a validation set, this second classifier reached an overall accuracy of 95.93%. It identified the harmful L. pneumophila sg. 1 with an impressive specificity (100%) and slightly lower sensitivity (91.7%), and similar performances were reached in the classification of L. pneumophila sg. 2-15 and L. non-pneumophila.

CONCLUSIONS

The results of this study show the DART-HMRS method has good accuracy, and it is an effective method for Legionella serogroup profiling.

SIGNIFICANCE AND IMPACT OF THE STUDY

These preliminary findings could open a new avenue for the rapid identification and quick epidemiologic tracing of L. pneumophila, with a consequent improvement to risk assessment.

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.

Addition of Serine Enhances Protein Analysis by DESI-MS

Previous studies have suggested that the loss in sensitivity of DESI-MS for large molecules such as proteins is due to the poor dissolution during the short time scale of desorption and ionization. An investigation into the effect of serine as a solvent additive leads to the interesting observation that there is a concentration-dependent improvement in protein signal intensity when micromolar to low millimolar concentrations of serine is combined with a suitable co-additive in DESI spray. This effect, however, was not observed during similar ESI-MS experiments, where the same solvents and proteins were sprayed directly into the MS inlet. This suggests that the mechanism of signal improvement in DESI is associated with the desorption step of proteins, possibly by facilitating dissolution or improving solubility of proteins on the surface in the solvent micro-layer formed during DESI. Other than poor dissolution, cation adduction such as by sodium ions is also a major contributing factor to the mass-dependent loss in sensitivity in both ESI and DESI, leading to an increase in limits of detection for larger proteins. The adduction becomes a more pressing issue in native-state studies of proteins, as lower charge states are more susceptible to adduction. Previous studies have shown that addition of amino acids to the working spray solution during ESI-MS reduces sodium adduction and can help in stabilization of native-state proteins. Similar to the observed reduction in sodium adducts during native-state ESI-MS, when serine is added to the desorbing spray in DESI-MS, the removal of up to 10 mM NaCl is shown. A selection of proteins with high and low pI and molecular weights was analyzed to investigate the effects of serine on signal intensity by improvements in protein solubility and adduct removal. Graphical Abstract.

Nanospray desorption electrospray ionization mass spectrometry of untreated and treated probiotic Lactobacillus reuteri cells

Mass spectrometry has proven to be a useful technique for rapid identification of bacterial cells. Among various ionization techniques in mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) has been commonly used for the identification of bacterial cells. Recently, MALDI mass spectrometry has also been utilized to distinguish cellular responses. Ambient ionization techniques do support whole bacterial cell analysis, which include desorption electrospray ionization (DESI). Nanospray DESI (nDESI) is a new variant of DESI, and its application to whole-cell mass spectrometry is limited. In this project, the use of nDESI mass spectrometry to measure probiotic Lactobacillus reuteri (LR) cells is explored. A unique and reproducible mass spectral pattern of untreated LR cells was obtained by using 50% methanol/water as nDESI solvent. The use of nDESI mass spectrometry is further extended to distinguish untreated LR cells from treated LR cells that have been exposed to low pH. These findings demonstrate the feasibility of using nDESI in whole-cell mass spectrometry. Graphical abstract ᅟ.

Application of biosurfactant from Bacillus subtilis C9 for controlling cladoceran grazers in algal cultivation systems

Open algal cultivation platforms often suffer crop losses to herbivorous grazers that have potential to devastate biomass production within a few days. While a number of studies suggest synthetic chemicals as control agents for voracious algal grazers, environmental and safety concerns associated with the use of these chemicals encourage the exploration of alternative biological control agents. We hereby propose the application of a biosurfactant produced by Bacillus subtilis C9 (referred to as C9-biosurfactant) for controlling cladoceran grazers commonly found in algal cultivation systems. The results indicated that C9-biosurfactant completely eradicated Daphnia pulex and Moina macrocopa within 24 hours when concentrations were equal to or exceeded 6 mg/L. Moreover, supplying C9-biosurfactant into the cultures of selected algal species with and without cladoceran grazers indicated no adverse effect of C9-biosurfactant on the growth and lipid productivity of algal crops, while cladocerans were selectively controlled by C9-biosurfactant even under the presence of their prey. These results thus indicate that C9-biosurfactant could be an effective biocontrol agent for cladoceran grazers at industrial algal cultivation.

Early Detection of Biofouling on Water Purification Membranes by Ambient Ionization Mass Spectrometry Imaging

By direct analysis of water purification membranes using ambient ionization mass spectrometry, an attempt has been made to understand the molecular signatures of bacterial fouling. Membrane based purification methods are used extensively in water treatment, and a major challenge for them is biofouling. The buildup of microbes and their extracellular polymeric matrix clog the purification membranes and reduce their efficiency. To understand the early stages of bacterial fouling on water purification membranes, we have used desorption electrospray ionization mass spectrometry (DESI MS), where ion formation occurs in ambient conditions and the ionization event is surface sensitive. Biosurfactants at the air-water interface generated by microorganisms as a result of quorum sensing, influence the water-membrane interface and are important for the bacterial attachment. We show that these biosurfactants produced by bacteria can be indicator molecular species signifying initiation of biofilms on membrane surfaces, demonstrated by specific DESI MS signatures. In Pseudomonas aeruginosa, one of the best studied models for biofilm formation, this process is mediated by rhamnolipids forewarning bacterial fouling. Species dependent variation of such molecules can be used for the precise identification of the microorganisms, as revealed by studies on P. aeroginosa (ATCC 25619). The production of biosurfactants is tightly regulated at the transcriptional level by the quorum-sensing (QS) response. Thus, secretion of these extracellular molecules across the membrane surface allows rapid screening of the biofilm community. We show that, the ambient ionization mass spectrometry can detect certain toxic heavy metals present in water, using surfactant-metal complexes as analytes. We believe that such studies conducted on membranes in various input water streams will help design suitable membrane processes specific to the input streams.

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.

Profiling of Microbial Colonies for High-Throughput Engineering of Multistep Enzymatic Reactions via Optically Guided Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) mass spectrometry (MS) imaging has been used for rapid phenotyping of enzymatic activities, but is mainly limited to single-step conversions. Herein we report a label-free method for high-throughput engineering of multistep biochemical reactions based on optically guided MALDI-ToF MS analysis of bacterial colonies. The bacterial cells provide containment of multiple enzymes and access to substrates and cofactors via metabolism. Automated MALDI-ToF MS acquisition from randomly distributed colonies simplifies procedures to prepare strain libraries without liquid handling. MALDI-ToF MS profiling was utilized to screen both substrate and enzyme libraries for natural product biosynthesis. Computational algorithms were developed to process and visualize the resulting mass spectral data sets. For analogues of the peptidic antibiotic plantazolicin, multivariate analyses by t-distributed stochastic neighbor embedding were used to group similar spectra for rapid identification of nonisobaric variants. After MALDI-ToF MS screening, follow-up analyses using high-resolution MS and tandem MS were readily performed on the same sample target. Separately, relative ion intensities of rhamnolipid congeners with various lipid moieties were evaluated to engineer enzymatic specificity. The glycolipid profiles of each colony were overlaid with optical images to facilitate the recovery of desirable mutants. For both the antibiotic and rhamnolipid cases, large populations of colonies were rapidly surveyed at the molecular level, providing information-rich insights not easily obtained with traditional screening assays. Utilizing standard microbiological techniques with routine microscopy and MALDI-ToF MS instruments, this simple yet effective workflow is applicable for a wide range of screening campaigns targeting multistep enzymatic reactions.

Ammonium Bicarbonate Addition Improves the Detection of Proteins by Desorption Electrospray Ionization Mass Spectrometry

The analysis of protein by desorption electrospray ionization mass spectrometry (DESI-MS) is considered impractical due to a mass-dependent loss in sensitivity with increase in protein molecular weights. With the addition of ammonium bicarbonate to the DESI-MS analysis the sensitivity towards proteins by DESI was improved. The signal to noise ratio (S/N) improvement for a variety of proteins increased between 2- to 3-fold relative to solvent systems containing formic acid and more than seven times relative to aqueous methanol spray solvents. Three methods for ammonium bicarbonate addition during DESI-MS were investigated. The additive delivered improvements in S/N whether it was mixed with the analyte prior to sample deposition, applied over pre-prepared samples, or simply added to the desorption spray solvent. The improvement correlated well with protein pI but not with protein size. Other ammonium or bicarbonate salts did not produce similar improvements in S/N, nor was this improvement in S/N observed for ESI of the same samples. As was previously described for ESI, DESI also caused extensive protein unfolding upon the addition of ammonium bicarbonate. Graphical Abstract ᅟ.

Constant-Distance Mode Nanospray Desorption Electrospray Ionization Mass Spectrometry Imaging of Biological Samples with Complex Topography

A new approach for constant-distance mode mass spectrometry imaging (MSI) of biological samples using nanospray desorption electrospray ionization (nano-DESI) was developed by integrating a shear-force probe with the nano-DESI probe. The technical concept and basic instrumental setup, as well as the general operation of the system are described. Mechanical dampening of resonant oscillations due to the presence of shear forces between the probe and the sample surface enabled the constant-distance imaging mode via a computer-controlled closed-feedback loop. The capability of simultaneous chemical and topographic imaging of complex biological samples is demonstrated using living Bacillus subtilis ATCC 49760 colonies on agar plates. The constant-distance mode nano-DESI MSI enabled imaging of many metabolites, including nonribosomal peptides (surfactin, plipastatin, and iturin) on the surface of living bacterial colonies, ranging in diameter from 10 to 13 mm, with height variations up to 0.8 mm above the agar plate. Co-registration of ion images to topographic images provided higher-contrast images. Based on this effort, constant-mode nano-DESI MSI proved to be ideally suited for imaging biological samples of complex topography in their native states.

Imprint Desorption Electrospray Ionization Mass Spectrometry Imaging for Monitoring Secondary Metabolites Production during Antagonistic Interaction of Fungi

Direct analysis of microbial cocultures grown on agar media by desorption electrospray ionization mass spectrometry (DESI-MS) is quite challenging. Due to the high gas pressure upon impact with the surface, the desorption mechanism does not allow direct imaging of soft or irregular surfaces. The divots in the agar, created by the high-pressure gas and spray, dramatically change the geometry of the system decreasing the intensity of the signal. In order to overcome this limitation, an imprinting step, in which the chemicals are initially transferred to flat hard surfaces, was coupled to DESI-MS and applied for the first time to fungal cocultures. Note that fungal cocultures are often disadvantageous in direct imaging mass spectrometry. Agar plates of fungi present a complex topography due to the simultaneous presence of dynamic mycelia and spores. One of the most devastating diseases of cocoa trees is caused by fungal phytopathogen Moniliophthora roreri. Strategies for pest management include the application of endophytic fungi, such as Trichoderma harzianum, that act as biocontrol agents by antagonizing M. roreri. However, the complex chemical communication underlying the basis for this phytopathogen-dependent biocontrol is still unknown. In this study, we investigated the metabolic exchange that takes place during the antagonistic interaction between M. roreri and T. harzianum. Using imprint-DESI-MS imaging we annotated the secondary metabolites released when T. harzianum and M. roreri were cultured in isolation and compared these to those produced after 3 weeks of coculture. We identified and localized four phytopathogen-dependent secondary metabolites, including T39 butenolide, harzianolide, and sorbicillinol. In order to verify the reliability of the imprint-DESI-MS imaging data and evaluate the capability of tape imprints to extract fungal metabolites while maintaining their localization, six representative plugs along the entire M. roreri/T. harzianum coculture plate were removed, weighed, extracted, and analyzed by liquid chromatography-high-resolution mass spectrometry (LC-HRMS). Our results not only provide a better understanding of M. roreri-dependent metabolic induction in T. harzianum, but may seed novel directions for the advancement of phytopathogen-dependent biocontrol, including the generation of optimized Trichoderma strains against M. roreri, new biopesticides, and biofertilizers.

Direct Protocol for Ambient Mass Spectrometry Imaging on Agar Culture

Herein we describe a new protocol that allows direct mass spectrometry imaging (IMS) of agar cultures. A simple sample dehydration leads to a thin solid agar, which enables the direct use of spray-based ambient mass spectrometry techniques. To demonstrate its applicability, metal scavengers siderophores were imaged directly from agar culture of S. wadayamensis, and well resolved and intense images were obtained using both desorption electrospray ionization (DESI) and easy ambient sonic-spray ionization (EASI) with well-defined selective spatial distributions for the free and the metal-bound molecules, providing clues for their roles in cellular metabolism.

Evaluation of imprint DESI-MS substrates for the analysis of fungal metabolites

Optimized in situ screening, characterization and imaging of fungal metabolites by imprint DESI-MS.

Direct sequencing of a disulfide-linked peptide with electrospray ionization tandem mass spectrometry

Enhanced corona discharge was employed for in-spray dissociation of disulfide bonds, facilitating disulfide-containing peptide sequencing with ESI-MS/MS.

Rapid discrimination of bacteria by paper spray mass spectrometry

Paper spray mass spectrometry ambient ionization is utilized for rapid discrimination of bacteria without sample preparation. Bacterial colonies were smeared onto filter paper precut to a sharp point, then wetted with solvent and held at a high potential. Charged droplets released by field emission were sucked into the mass spectrometer inlet and mass spectra were recorded. Sixteen different species representing eight different genera from Gram-positive and Gram-negative bacteria were investigated. Phospholipids were the predominant species observed in the mass spectra in both the negative and positive ion modes. Multivariate data analysis based on principal component analysis, followed by linear discriminant analysis, allowed bacterial discrimination. The lipid information in the negative ion mass spectra proved useful for species level differentiation of the investigated Gram-positive bacteria. Gram-negative bacteria were differentiated at the species level by using a numerical data fusion strategy of positive and negative ion mass spectra.

Emerging capabilities of mass spectrometry for natural products

Covering up to the end of 2013 A brief history of mass spectrometry in natural products research serves to identify themes which have driven progress in this area of application and in mass spectrometry itself. This account covers six decades of ionization methods, starting with traditional electron ionization and progressing through today's ambient ionization methods. Corresponding developments in mass analyzers are indicated, ranging from sector magnetic fields, through hybrid quadrupole mass filters to miniature ion traps. Current capabilities of mass spectrometry in natural products studies include direct in situ analysis, mass spectrometry imaging, and the study of biosynthetic pathways using metabolomic information. The survey concludes with a discussion of new experiments and capabilities including ion soft landing, preparative mass spectrometry, and accelerated ionic reactions in confined volumes.

Metabolic profiling directly from the Petri dish using nanospray desorption electrospray ionization imaging mass spectrometry

Understanding molecular interaction pathways in complex biological systems constitutes a treasure trove of knowledge that might facilitate the specific, chemical manipulation of the countless microbiological systems that occur throughout our world. However, there is a lack of methodologies that allow the direct investigation of chemical gradients and interactions in living biological systems, in real time. Here, we report the use of nanospray desorption electrospray ionization (nanoDESI) imaging mass spectrometry for in vivo metabolic profiling of living bacterial colonies directly from the Petri dish with absolutely no sample preparation needed. Using this technique, we investigated single colonies of Shewanella oneidensis MR-1, Bacillus subtilis 3610, and Streptomyces coelicolor A3(2) as well as a mixed biofilm of S. oneidensis MR-1 and B. subtilis 3610. Data from B. subtilis 3610 and S. coelicolor A3(2) provided a means of validation for the method while data from S. oneidensis MR-1 and the mixed biofilm showed a wide range of compounds that this bacterium uses for the dissimilatory reduction of extracellular metal oxides, including riboflavin, iron-bound heme and heme biosynthetic intermediates, and the siderophore putrebactin.

Real-time metabolomics on living microorganisms using ambient electrospray ionization flow-probe

Microorganisms such as bacteria and fungi produce a variety of specialized metabolites that are invaluable for agriculture, biological research, and drug discovery. However, the screening of microbial metabolic output is usually a time-intensive task. Here, we utilize a liquid microjunction surface sampling probe for electrospray ionization-mass spectrometry to extract and ionize metabolite mixtures directly from living microbial colonies grown on soft nutrient agar in Petri-dishes without any sample pretreatment. To demonstrate the robustness of the method, this technique was applied to observe the metabolic output of more than 30 microorganisms, including yeast, filamentous fungi, pathogens, and marine-derived bacteria, that were collected worldwide. Diverse natural products produced from different microbes, including Streptomyces coelicolor , Bacillus subtilis , and Pseudomonas aeruginosa are further characterized.

Spatially resolved analysis of glycolipids and metabolites in living Synechococcus sp. PCC 7002 using nanospray desorption electrospray ionization

Microorganisms release a diversity of organic compounds that couple interspecies metabolism, enable communication, or provide benefits to other microbes. Increased knowledge of microbial metabolite production will contribute to understanding of the dynamic microbial world and can potentially lead to new developments in drug discovery, biofuel production, and clinical research. Nanospray desorption electrospray ionization (nano-DESI) is an ambient ionization technique that enables detailed chemical characterization of molecules from a specific location on a surface without special sample pretreatment. Due to its ambient nature, living bacterial colonies growing on agar plates can be rapidly analyzed without affecting the viability of the colony. In this study we demonstrate for the first time the utility of nano-DESI for spatial profiling of chemical gradients generated by microbial communities on agar plates. We found that despite the high salt content of the agar used in this study (~350 mM), nano-DESI analysis enables detailed characterization of metabolites produced by the Synechococcus sp. PCC 7002 colonies. High resolution mass spectrometry and MS/MS analysis of the living Synechococcus sp. PCC 7002 colonies allowed us to detect metabolites and lipids on the colony and on the surrounding agar, and confirm their identities. High sensitivity of nano-DESI enabled identification of several glycolipids that have not been previously reported by extracting the cells using conventional methods. Spatial profiling demonstrated that a majority of lipids and metabolites were localized on the colony while sucrose and glucosylglycerol, an osmoprotective compound produced by cyanobacteria, were secreted onto agar. Furthermore, we demonstrated that the chemical gradients of sucrose and glucosylglycerol on agar depend on the age of the colony. The methodology presented in this study will facilitate future studies focused on molecular-level characterization of interactions between bacterial colonies.

Advances in mass spectrometry for the identification of pathogens

Mass spectrometry (MS) has become an important technique to identify microbial biomarkers. The rapid and accurate MS identification of microorganisms without any extensive pretreatment of samples is now possible. This review summarizes MS methods that are currently utilized in microbial analyses. Affinity methods are effective to clean, enrich, and investigate microorganisms from complex matrices. Functionalized magnetic nanoparticles might concentrate traces of target microorganisms from sample solutions. Therefore, nanoparticle-based techniques have a favorable detection limit. MS coupled with various chromatographic techniques, such as liquid chromatography and capillary electrophoresis, reduces the complexity of microbial biomarkers and yields reliable results. The direct analysis of whole pathogenic microbial cells with matrix-assisted laser desorption/ionization MS without sample separation reveals specific biomarkers for taxonomy, and has the advantages of simplicity, rapidity, and high-throughput measurements. The MS detection of polymerase chain reaction (PCR)-amplified microbial nucleic acids provides an alternative to biomarker analysis. This review will conclude with some current applications of MS in the identification of pathogens.

Sinapine detection in radish taproot using surface desorption atmospheric pressure chemical ionization mass spectrometry

Plant research and natural product detection are of sustainable interests. Benefited by direct detection with no sample preparation, sinapine, a bioactive chemical usually found in various seeds of Brassica plants, has been unambiguously detected in radish taproot (Raphanus sativus) tissue using a liquid-assisted surface desorption atmospheric pressure chemical ionization mass spectrometry (DAPCI-MS). A methanol aqueous solution (1:1) was nebulized by a nitrogen sheath gas toward the corona discharge, resulting in charged ambient small droplets, which affected the radish tissue for desorption/ionization of analytes on the tissue surface. Thus, sinapine was directly detected and identified by tandem DAPCI-MS experiments without sample pretreatment. The typical relative standard deviation (RSD) of this method for sinapine detection was 5-8% for six measurements (S/N=3). The dynamic response range was 10(-12)-10(-7) g/cm2 for sinapine on the radish skin surface. The discovery of sinapine in radish taproot was validated by using HPLC-UV methods. The data demonstrated that DAPCI assisted by solvent enhanced the overall efficiency of the desorption/ionization process, enabling sensitive detection of bioactive compounds in plant tissue.