Direct mass spectrometric screening of antibiotics from bacterial surfaces using liquid extraction surface analysis

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.

Liquid extraction surface analysis-mass spectrometry: An advanced and environment-friendly analytical tool in modern analysis

The Liquid Extraction Surface Analysis technique is a new high-throughput instrument for ambient mass spectrometry. The benefits of the Liquid Extraction Surface Analysis-Mass Spectrometry approach are the high throughput screening of samples and the absence of sample preparation. Liquid Extraction Surface Analysis-Mass Spectrometry also consumes less solvent for extraction, making it more environmentally friendly and there is no substrate restriction. It utilizes advanced instrumentation like the use of robotic pipettes, nanoelectrospray systems, electronspray ionization chips which makes it highly efficient. In recent years, Liquid Extraction Surface Analysis-Mass Spectrometry has seen widespread use in a variety of analytical fields including drug metabolite analysis, mapping drug distribution in tissues, protein and lipid characterization etc. In this review, we have summarized the basic working principles of the Liquid Extraction Surface Analysis-Mass Spectrometry approach in detail along with a detailed description of the recently reported applications in the analysis of proteins, lipids, drugs and foods. The investigated analytes along with detection methodologies and significant outcomes of various research reports have been presented with the help of tables. This tool has also been utilized in clinical investigations of biological fluids, fingerprint analysis and authentication of agarwood. This article is protected by copyright. All rights reserved.

Thiazole-amino acids: influence of thiazole ring on conformational properties of amino acid residues

Post-translational modified thiazole-amino acid (Xaa-Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria. Conformational study of the series of model compounds containing this structural motif with alanine, dehydroalanine, dehydrobutyrine and dehydrophenylalanine were performed using DFT method in various environments. The solid-state crystal structure conformations of thiazole-amino acid residues retrieved from the Cambridge Structural Database were also analysed. The studied structural units tend to adopt the unique semi-extended β2 conformation; which is stabilised mainly by N-H⋯NTzl hydrogen bond, and for dehydroamino acids also by π-electron conjugation. The conformational preferences of amino acids with a thiazole ring were compared with oxazole analogues and the role of the sulfur atom in stabilising the conformations of studied peptides was discussed.

Rapid, Selective, and Sensitive Method for Semitargeted Discovery of Congeneric Natural Products by Liquid Chromatography Tandem Mass Spectrometry

Natural product congeners serve a useful role in the understanding of natural product biosynthesis and structure-activity relationships. A minor congener with superior activity, selectivity, and modifiable functional groups could serve as a more effective lead structure and replace even the original lead molecule that was used for medicinal chemistry modifications. Currently, no effective method exists to discover targeted congeners rapidly, specifically, and selectively from producing sources. Herein, a new method based on liquid-chromatography tandem-mass spectrometry combination is evaluated for targeted discovery of congeners of platensimycin and platencin from the extracts of Streptomyces platensis. By utilizing a precursor-ion searching protocol, tandem mass spectrometry not only confirmed the presence of known congeners but also provided unambiguous detection of many previously unknown congeners of platensimycin and platencin. This high-throughput and quantitative method can be rapidly and broadly applied for dereplication and congener discovery from a variety of producing sources, even when the targeted compounds are obscured by the presence of unrelated natural products.

Probing the Fundamentals of Native Liquid Extraction Surface Analysis Mass Spectrometry of Proteins: Can Proteins Refold during Extraction?

Native ambient mass spectrometry has the potential for simultaneous analysis of native protein structure and spatial distribution within thin tissue sections. Notwithstanding sensitivity, this information can, in principle, be obtained for any protein present with no requirement for a priori knowledge of protein identity. To date, native ambient mass spectrometry has primarily made use of the liquid extraction surface analysis (LESA) sampling technique. Here, we address a fundamental question: Are the protein structures observed following native liquid extraction surface analysis representative of the protein structures within the substrate, or does the extraction process facilitate refolding (or unfolding)? Specifically, our aim was to determine whether protein-ligand complexes observed following LESA are indicative of complexes present in the substrate, or an artifact of the sampling process. The systems investigated were myoglobin and its noncovalently bound heme cofactor, and the Zn-binding protein carbonic anhydrase and its binding with ethoxzolamide. Charge state distributions, drift time profiles, and collision cross sections were determined by liquid extraction surface analysis ion mobility mass spectrometry of native and denatured proteins and compared with those obtained by direct infusion electrospray. The results show that it was not possible to refold denatured proteins with concomitant ligand binding (neither heme, zinc, nor ethoxzolamide) simply by use of native-like LESA solvents. That is, protein-ligand complexes were only observed by LESA MS when present in the substrate.

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

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

Ambient ionisation mass spectrometry for in situ analysis of intact proteins

Ambient surface mass spectrometry is an emerging field which shows great promise for the analysis of biomolecules directly from their biological substrate. In this article, we describe ambient ionisation mass spectrometry techniques for the in situ analysis of intact proteins. As a broad approach, the analysis of intact proteins offers unique advantages for the determination of primary sequence variations and posttranslational modifications, as well as interrogation of tertiary and quaternary structure and protein-protein/ligand interactions. In situ analysis of intact proteins offers the potential to couple these advantages with information relating to their biological environment, for example, their spatial distributions within healthy and diseased tissues. Here, we describe the techniques most commonly applied to in situ protein analysis (liquid extraction surface analysis, continuous flow liquid microjunction surface sampling, nano desorption electrospray ionisation, and desorption electrospray ionisation), their advantages, and limitations and describe their applications to date. We also discuss the incorporation of ion mobility spectrometry techniques (high field asymmetric waveform ion mobility spectrometry and travelling wave ion mobility spectrometry) into ambient workflows. Finally, future directions for the field are discussed.

Dereplicating and Spatial Mapping of Secondary Metabolites from Fungal Cultures in Situ

Ambient ionization mass spectrometry techniques have recently become prevalent in natural product research due to their ability to examine secondary metabolites in situ. These techniques retain invaluable spatial and temporal details that are lost through traditional extraction processes. However, most ambient ionization techniques do not collect mutually supportive data, such as chromatographic retention times and/or UV/vis spectra, and this can limit the ability to identify certain metabolites, such as differentiating isomers. To overcome this, the droplet-liquid microjunction-surface sampling probe (droplet-LMJ-SSP) was coupled with UPLC-PDA-HRMS-MS/MS, thus providing separation, retention times, MS data, and UV/vis data used in traditional dereplication protocols. By capturing these mutually supportive data, the identity of secondary metabolites can be confidently and rapidly assigned in situ. Using the droplet-LMJ-SSP, a protocol was constructed to analyze the secondary metabolite profile of fungal cultures without any sample preparation. The results demonstrate that fungal cultures can be dereplicated from the Petri dish, thus identifying secondary metabolites, including isomers, and confirming them against reference standards. Furthermore, heat maps, similar to mass spectrometry imaging, can be used to ascertain the location and relative concentration of secondary metabolites directly on the surface and/or surroundings of a fungal culture.

Mass spectrometry tools and workflows for revealing microbial chemistry

Since the time Van Leeuwenhoek was able to observe microbes through a microscope, an innovation that led to the birth of the field of microbiology, we have aimed to understand how microorganisms function, interact and communicate. The exciting progress in the development of analytical technologies and workflows has demonstrated that mass spectrometry is a very powerful technique for the interrogation of microbiology at the molecular level. In this review, we aim to highlight the available and emerging tools in mass spectrometry for microbial analysis by overviewing the methods and workflow advances for taxonomic identification, microbial interaction, dereplication and drug discovery. We emphasize their potential for future development and point out unsolved problems and future directions that would aid in the analysis of the chemistry produced by microbes.

Monitoring metabolites from Schizophyllum commune interacting with Hypholoma fasciculare combining LESA-HR mass spectrometry and Raman microscopy

Microbial competition for territory and resources is inevitable in habitats with overlap between niches of different species or strains. In fungi, competition is brought about by antagonistic mycelial interactions which alter mycelial morphology, metabolic processes, secondary metabolite release, and extracellular enzyme patterns. Until now, we were not able study in vivo chemical interactions of different colonies growing on the same plate. In this report, we developed a fast and least invasive approach to identify, quantify, and visualize co culture-induced metabolites and their location of release within Schizophyllum commune. The pigments indigo, indirubin, and isatin were used as examples to show secondary metabolite production in the interaction zone with Hypholoma fasciculare. Using a combinatory approach of Raman spectroscopy imaging, liquid extraction surface analysis (LESA), and high-resolution mass spectrometry, we identified, quantified, and visualized the presence of indigo and indirubin in the interaction zone. This approach allows the investigation of metabolite patterns between wood degrading species in competition to gain insight in community interactions, but could also be applied to other microorganisms. This method advances analysis of living, still developing colonies and are in part not destructive as Raman spectroscopy imaging is implemented.

Liquid Extraction Surface Analysis Mass Spectrometry (LESA MS): Combining Liquid Extraction, Surface Profiling and Ambient Ionization Mass Spectrometry in One Novel Analysis Technique

In this chapter we give an overview of liquid extraction surface analysis mass spectrometry (LESA-MS), a novel analysis technique that combines liquid extraction from a surface of interest and ambient nanoelectrospray ionization combined with mass spectrometry to analyze compounds of interest. LESA MS was first described by van Berkel and Kertesz in 2009 and subsequently made commercially available by Advion Inc. by way of its TriVersa-NanoMate™ robotic nanoelectrospray ionization source. LESA was initially intended as a complementary analysis technique to MALDI imaging in pharmaceutical drug distribution and development; however, soon after the commercial availability of this technique, a broader use became apparent with applications ranging from biofilms on contact lenses, antibiotics expressed by bacteria cultured in agar, dried blood spot analysis, surface properties of aged plastics and aerosols from compactor material – to mention only a few. In this chapter, we will discuss selected applications and provide an outlook of LESA developments as they currently unfold, knowing full well that such a new technology will develop unexpectedly and in application areas not previously envisioned.

Direct analysis of intact proteins from Escherichia coli colonies by liquid extraction surface analysis mass spectrometry

Top-down identification of proteins by liquid extraction surface analysis (LESA) mass spectrometry has previously been reported for tissue sections and dried blood spot samples. Here, we present a modified "contact" LESA method for top-down analysis of proteins directly from living bacterial colonies grown in Petri dishes, without any sample pretreatment. It was possible to identify a number of proteins by use of collision-induced dissociation tandem mass spectrometry followed by searches of the data against an E. coli protein database. The proteins identified suggest that the method may provide insight into the bacterial response to environmental conditions. Moreover, the results show that the "contact" LESA approach results in a smaller sampling area than typical LESA, which may have implications for spatial profiling.

Fully automated laser ablation liquid capture surface analysis using nanoelectrospray ionization mass spectrometry

RATIONALE

Laser ablation provides for the possibility of sampling a large variety of surfaces with high spatial resolution. This type of sampling when employed in conjunction with liquid capture followed by nanoelectrospray ionization provides the opportunity for sensitive and prolonged interrogation of samples by mass spectrometry as well as the ability to analyze surfaces not amenable to direct liquid extraction.

METHODS

A fully automated, reflection geometry, laser ablation liquid capture spot sampling system was achieved by incorporating appropriate laser fiber optics and a focusing lens into a commercially available, liquid extraction surface analysis (LESA(®))-ready Advion TriVersa NanoMate system.

RESULTS

Under optimized conditions about 10% of laser-ablated material could be captured in a droplet positioned vertically over the ablation region using the NanoMate robot-controlled pipette. The sampling spot size area with this laser ablation liquid capture surface analysis (LA/LCSA) mode of operation (typically about 120 µm × 160 µm) was approximately 50 times smaller than that achievable by direct liquid extraction using LESA(®) (ca 1 mm diameter liquid extraction spot). The setup was successfully applied for the analysis of ink on glass and paper as well as the endogenous components in Alstroemeria Yellow King flower petals. In a second mode of operation with a comparable sampling spot size, termed laser ablation/LESA(®), the laser system was used to drill through, penetrate, or otherwise expose material beneath a solvent resistant surface. Once drilled, LESA(®) was effective in sampling soluble material exposed at that location on the surface.

CONCLUSIONS

Incorporating the capability for different laser ablation liquid capture spot sampling modes of operation into a LESA(®)-ready Advion TriVersa NanoMate enhanced the spot sampling spatial resolution of this device and broadened the surface types amenable to analysis to include absorbent and solvent-resistant materials.

Dereplication of microbial extracts and related analytical technologies

Natural products still continue to have an important role as a resource of various biologically active substances. Dereplication is a key process in natural product screening that analyzes the extracts of microbial fermentation broths or plant samples. In this review article, we describe and discuss the analytical techniques of dereplication and related technologies in the following sections: 1. Direct detection from microbial colonies. 2. Ultra high performance liquid chromatography (UHPLC)-MS profiling for library construction. 3. Micro-fractionation to identify active peaks. 4. Quantification of small-amount compounds. 5. Structure identification from small amounts. Using these techniques, the desired compound in the mixture library can be rapidly identified.

Conformational properties of oxazole-amino acids: effect of the intramolecular N-H···N hydrogen bond

Oxazole ring occurs in numerous natural peptides, but conformational properties of the amino acid residue containing the oxazole ring in place of the C-terminal amide bond are poorly recognized. A series of model compounds constituted by the oxazole-amino acids occurring in nature, that is, oxazole-alanine (L-Ala-Ozl), oxazole-dehydroalanine (ΔAla-Ozl), and oxazole-dehydrobutyrine ((Z)-ΔAbu-Ozl), was investigated using theoretical calculations supported by FTIR and NMR spectra and single-crystal X-ray diffraction. It was found that the main feature of the studied oxazole-amino acids is the stable conformation β2 with the torsion angles φ and ψ of -150°, -10° for L-Ala-Ozl, -180°, 0° for ΔAla-Ozl, and -120°, 0° for (Z)-ΔAbu-Ozl, respectively. The conformation β2 is stabilized by the intramolecular N-H···N hydrogen bond and predominates in the low polar environment. In the case of the oxazole-dehydroamino acids, the π-electron conjugation that is spread on the oxazole ring and C(α)═C(β) double bond is an additional stabilizing interaction. The tendency to adopt the conformation β2 clearly decreases with increasing the polarity of environment, but still the oxazole-dehydroamino acids are considered to be more rigid and resistant to conformational changes.

Ion sources for mass spectrometric identification and imaging of molecular species

Covering: 2013 The ability to transfer molecular species to the gas phase and ionize them is central to the study of natural products and other molecular species by mass spectrometry (MS). MS-based strategies in natural products have focused on a few established ion sources, such as electron impact and electrospray ionization. However, a variety of other ion sources are either currently in use to evaluate natural products or show significant future promise. This review discusses these various ion sources in the context of other articles in this special issue, but is also applicable to other fields of analysis, including materials science. Ion sources are grouped based on the current understanding of their predominant ion formation mechanisms. This broad overview groups ion sources into the following categories: electron ionization and single photon ionization; chemical ionization-like and plasma-based; electrospray ionization; and, laser desorption-based. Laser desorption-based methods are emphasized with specific examples given for laser desorption postionization sources and their use in the analysis of intact microbial biofilms. Brief consideration is given to the choice of ion source for various sample types and analyses, including MS imaging.