TiO2-Assisted Laser Desorption/Ionization Mass Spectrometry for Rapid Profiling of Candidate Metabolite Biomarkers from Antimicrobial-Resistant Bacteria

Heterogeneous MXene Hybrid-Oriented Exosome Isolation and Metabolic Profiling for Early Screening, Subtyping and Follow-up Evaluation of Bladder Cancer

Exosome metabolite-based noninvasive liquid biopsy is an emerging research hotspot that tends to substitute current means in clinics. Nanostructure-based mass spectrometry enables continuous exosome isolation and metabolic profiling with superior analysis speed and high efficiency. Herein, we construct a heterogeneous MXene hybrid that possesses ternary binding sites for exosome capture and outstanding matrix performance for metabolite analysis. Upon optimizing experimental conditions, the average extraction of exosomes and their metabolic patterns from a 60 mL urine sample is completed within 45 s (40 samples per batch for 30 min). According to the exosomal metabolic patterns and the subsequently established biomarker panel, we distinguish early bladder cancer (BCa) from healthy controls with an area under the curve (AUC) value greater than 0.995 in model training and validation sets. As well, we realize subtype classification of BCa in the blind test on metabolic patterns, with an AUC value of 0.867. We also explore the significant biomarkers that are sensitive to follow-up patients, which indeed present reverse change levels compared with pathological progression. This study has the potential to guide the development of the liquid biopsy approach.

Bovine Omasum-Inspired Interfacial Carbon-Based Nanocomposite for Saliva Metabolic Screening of Gastric Cancer

Gastric cancer is one of the most common malignant digestive cancers, and its diagnostic has still faced challenges based on metabolic analysis due to complex sample pretreatment and low metabolite abundance. In this study, inspired by the structure of bovine omasum, we in situ synthesized a novel interfacial carbon-based nanocomposite of graphene supported nickel nanoparticles-encapsulated in the nitrogen-doped carbon nanotube (Ni/N-CNT/rGO), which was served as a novel matrix with enhanced ionization efficiency for the matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) saliva metabolic analysis of gastric cancer. Benefiting from its high sp² graphitic degree, large surface area, strong UV absorption, and rich active sites, Ni/N-CNT/rGO matrix exhibited excellent performances of reproducibility, coverage, salt-tolerance, sensitivity, and adsorption ability in MALDI-TOF MS. The differential scanning calorimetry (DSC) and thermal conversion behaviors explained the highly efficient LDI mechanism. Based on saliva metabolic fingerprints, Ni/N-CNT/rGO assisted LDI MS with cross-validation analysis could successfully distinguish gastric cancer patients from healthy controls through the screening of four potential biomarkers with an accuracy of 92.50%, specificity of 88.03%, and sensitivity of 97.12%. This work provided a fast and sensitive MS sensing platform for the metabolomics characterization of gastric cancer and might have potential value for precision medicine in the future.

MALDI-TOF Mass Spectrometry in Clinical Analysis and Research

In the decade after being awarded the Nobel Prize in Chemistry in 2002, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been widely used as an analytical chemistry tool for the detection of large and small molecules (e.g., polymers, proteins, peptides, nucleic acids, amino acids, lipids, etc.) and for clinical analysis and research (e.g., pathogen identification, genetic disorders screening, cancer diagnosis, etc.). In view of the fast development of MALDI-TOF MS in clinical usage, this review systematically summarizes the most important applications of MALDI-TOF MS in clinical analysis and research by analyzing MALDI TOF MS-related reviews collected in the Web of Science database. On the basis of the analysis of keyword co-occurrence of over 2000 review articles, four themes consisting of "pathogen identification", "disease diagnosis", "nucleic acids analysis", and "small molecules analysis" were found. For each theme, the review further outlined their application implications, analytical methods, and systems as well as limitations that need to be addressed. Overall, the review summarizes and elaborates on the clinical applications of MALDI-TOF MS, providing a comprehensive picture for researchers embarking on MALDI TOF MS-related clinical analysis and research.

Diagnosing, Typing, and Staging of Renal Cell Carcinoma by Designer Matrix-Based Urinary Metabolic Analysis

Molecular diagnosing, typing, and staging have been considered to be the ideal alternatives of imaging-based detection methods in clinics. Designer matrix-based analytical tools, with high speed, throughout, efficiency and low/noninvasiveness, have attracted much attention recently for in vitro metabolite detection. Herein, we develop an advanced metabolic analysis tool based on highly porous metal oxides derived from available metal-organic frameworks (MOFs), which elaborately inherit the morphology and porosity of MOFs and newly incorporate laser adsorption capacity of metal oxides. Through optimized conditions, direct high-quality fingerprinting spectra in 0.5 μL of urine are acquired. Using these fingerprinting spectra, we can discriminate the renal cell carcinoma (RCC) from healthy controls with higher than 0.99 of area under the curve (AUC) values (R²Y(cum) = 0.744, Q² (cum) = 0.880), as well, from patients with other tumors (R²Y(cum) = 0.748, Q²(cum) = 0.871). We also realize the typing of three RCC subtypes, including clear cell RCC, chromophobe RCC (R²Y(cum) = 0.620, Q²(cum) = 0.656), and the staging of RCC (R²Y(cum) = 0.755, Q²(cum) = 0.857). Moreover, the tumor sizes (threshold value is 3 cm) can be remarkably recognized by this advanced metabolic analysis tool (R²Y(cum) = 0.710, Q²(cum) = 0.787). Our work brings a bright prospect for designer matrix-based analytical tools in disease diagnosis, typing and staging.

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.

Metabolic Molecular Diagnosis of Inflammatory Bowel Disease by Synergistical Promotion of Layered Titania Nanosheets with Graphitized Carbon

Due to inefficient diagnostic methods, inflammatory bowel disease (IBD) normally progresses into severe complications including cancer. Highly efficient extraction and identification of metabolic fingerprints are of significance for disease surveillance. In this work, we synthesized a layered titania nanosheet doped with graphitized carbon (2D-GC-mTNS) through a simple one-step assembly process for assisting laser desorption ionization mass spectrometry (LDI-MS) for metabolite analysis. Based on the synergistic effect of graphitized carbon and mesoporous titania, 2D-GC-mTNS exhibits good extraction ability including high sensitivity (< 1 fmol µL^-1) and great repeatability toward metabolites. A total of 996 fingerprint spectra were collected from hundreds of native urine samples (including IBD patients and healthy controls), each of which contained 1220 m/z metabolite features. Diagnostic model was further established for precise discrimination of patients from healthy controls, with high area under the curve value of 0.972 and 0.981 toward discovery cohort and validation cohort, respectively. The 2D-GC-mTNS promotes LDI-MS to be close to clinical application, with rapid speed, minimum sample consumption and free of sample pretreatment.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-022-00055-0.

Microtoxicology by microfluidic instrumentation: a review

Microtoxicology is concerned with the toxic effects of small amounts of substances. This review paper discusses the application of small amounts of noxious substances for toxicological investigation in small volumes. The vigorous development of miniaturized methods in microfluidics over the last two decades involves chip-based devices, micro droplet-based procedures, and the use of micro-segmented flow for microtoxicological studies. The studies have shown that the microfluidic approach is particularly valuable for highly parallelized and combinatorial dose-response screenings. Accurate dosing and mixing of effector substances in large numbers of microcompartments supplies detailed data of dose-response functions by highly concentration-resolved assays and allows evaluation of stochastic responses in case of small separated cell ensembles and single cell experiments. The investigations demonstrate that very different biological targets can be studied using miniaturized approaches, among them bacteria, eukaryotic microorganisms, cell cultures from tissues of multicellular organisms, stem cells, and early embryonic states. Cultivation and effector exposure tests can be performed in small volumes over weeks and months, confirming that the microfluicial strategy is also applicable for slow-growing organisms. Here, the state of the art of miniaturized toxicology, particularly for studying antibiotic susceptibility, drug toxicity testing in the miniaturized system like organ-on-chip, environmental toxicology, and the characterization of combinatorial effects by two and multi-dimensional screenings, is discussed. Additionally, this review points out the practical limitations of the microtoxicology platform and discusses perspectives on future opportunities and challenges.

Rapid Antibiotic Susceptibility Testing by Deuterium Labeling of Bacterial Lipids in On-Target Microdroplet Cultures

Antimicrobial resistance is a serious challenge facing human and veterinary health. Current methods of detecting resistance are limited in turn-around time or universal detection. In this work, a new antimicrobial susceptibility test is developed and validated, which utilizes deuterium labeling of membrane lipids to track the growth of bacterial cells. We hypothesize that deuterium uptake and subsequent labeling of lipids can be detected using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Additionally, bacteria growth is performed on the MALDI target, minimizing sample preparation materials and time. When two Escherichia coli strains are grown in the presence of deuterium oxide, labeling can be detected in as little as 30 min to 2 h. The labeling efficiency, or the ratio of labeled to unlabeled lipid peaks, provides information about the growth rate of bacteria. This growth ratio can differentiate between resistant and susceptible strains of bacteria as a resistant strain will maintain ∼50% labeling efficiency between untreated and treated cultures. In comparison, a susceptible strain will see a decrease in fractional abundance of deuterium from ∼50% in the untreated to ∼10% in the treated. This approach is applied to measure the minimum inhibitory concentration (MIC) of the resistant and susceptible strains from on-target microdroplet culture in a range of antibiotic concentrations. The first antibiotic concentration with a significant decrease in fractional abundance of deuterium correlates well with a traditionally obtained MIC using broth dilution, indicating the clinical relevance of the results.

Uncovering the interference from lipid fragments on the qualification and quantification of serum metabolites in matrix-assisted laser desorption/ionization time-of-flight mass spectrometric analysis

RATIONALE

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has exhibited great advantages in rapid analysis of metabolites. However, the influence of lipid fragments generated by in-source fragmentation (ISD) and/or post-source fragmentation (PSD) on the accurate qualification and quantification of metabolites has not been fully demonstrated.

METHODS

Phospholipid standards and serum extract were analyzed by MALDI MS with both TiO₂ nanoparticle (TiO₂ NP) and 2,5-DHB matrices to illustrate the structures of lipid fragments and their influence on the qualitative and quantitative analysis of metabolites in biological samples. Monophasic and biphasic extraction methods were also compared for their efficiency in removing potential interferents.

RESULTS

The fragment ions derived from the phosphocholine head group of phosphatidylcholines (PC) interfere with peaks of low molecular weight (LMW) metabolites at both the MS and MS² levels. The biphasic extraction system with methanol/chloroform very efficiently removed the interference from PC fragments, and the metabolites choline and carnitine in serum were directly and accurately quantified by MALDI MS by using this biphasic extraction.

CONCLUSIONS

The phospholipids could produce fragment ions through ISD and PSD in MALDI MS with both nanoparticle and organic matrices. The fragments exerted influence on the qualification and qualification of metabolites in serum. By choosing the proper extraction method, the interference from lipid fragments could be efficiently alleviated.

Capture and identification of bacteria from fish muscle based on immunomagnetic beads and MALDI-TOF MS

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A protocol for the bacterial analysis in fish muscle was developed.

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Anti-bacterial antibodies modified magnetic beads (MBs) were used to capture bacteria.

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The bacterial identification accuracy from different complex food matrices was good.

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The presence of 10 CFU/mL E. coli is still detectable.

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It is promising to be applied in bacterial analysis to ensure muscle food safety.

In the present study, E. coli was taken as a model bacterium, anti-E. coli functionalized magnetic beads were constructed and used to capture E. coli from aqueous extracts of fish sarcoplasmic protein (FSP) and fish muscle protein of sablefish. The excellency of the reproducibility of the present protocol was demonstrated by capturing E. coli from sablefish FSP extracts. The presence of 10 CFU/mL E. coli is still detectable. A microbial safety test on the surface of fish muscle was successfully performed. The bacterial identification accuracy from samples with different matrices was found to be excellent with RSD = 3%. High specific detection of target bacteria in complex biological samples was testified by spiking Staphylococcus aureus and Klebsiella pneumoniae in samples as interference. Ten biomarker ions were discovered for E. coli’s recognition. It is promising to apply the present protocol in bacterial analysis in muscle food samples to ensure their safety.

Submicron 3,4-dihydroxybenzoic acid–TiO2 composite particles for enhanced MALDI MS imaging of secondary metabolites in the root of differently aged baical skullcap

This work provides a high-efficient organic-inorganic hybrid matrix for MALDI MSI of secondary metabolites in plant tissues.

SERS and MALDI-TOF MS based plasma exosome profiling for rapid detection of osteosarcoma

Osteosarcoma is the most frequent primary bone cancer, particularly among children and adolescents. The early diagnosis of osteosarcoma is significant for timely clinical treatment to reduce the mortality of patients. Exosomes play a significant role in intercellular communication and serve as promising biomarkers in liquid biopsy for the diagnosis and monitoring of tumors. Herein, we report the utility of surface-enhanced Raman scattering (SERS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for rapid identification of osteosarcoma. We firstly profiled the intrinsic SERS signals and MALDI-TOF mass fingerprints of different subgroups of extracellular vesicles (EVs) and the corresponding cells, demonstrating that the SERS signals and MALDI-TOF mass spectra of exosomes from different types of cells were more discriminative compared to those of large and medium EVs and the cells themselves. Then, we characterized plasma-derived exosomes of 15 osteosarcoma patients and 15 healthy volunteers using SERS and MALDI-TOF MS, revealing distinctive biochemical differences in the spectra. We further utilized a data fusion approach to combine the two types of spectroscopic techniques, differentiating osteosarcoma patients from healthy controls with higher precision than either technique. The results reveal that the non-invasive liquid biopsy method using SERS and MALDI-TOF MS fingerprinting of exosomes has great potential for rapid diagnosis of osteosarcoma.

Material-assisted mass spectrometric analysis of low molecular weight compounds for biomedical applications

Low molecular weight compounds play an important role in encoding the current physiological state of an individual. Laser desorption/ionization mass spectrometry (LDI MS) offers high sensitivity with low cost for molecular detection, but it is not able to cover small molecules due to the drawbacks of the conventional matrix. Advanced materials are better alternatives, showing little background interference and high LDI efficiency. Herein, we first classify the current materials with a summary of compositions and structures. Matrix preparation protocols are then reviewed, to enhance the selectivity and reproducibility of MS data better. Finally, we highlight the biomedical applications of material-assisted LDI MS, at the tissue, bio-fluid, and cellular levels. We foresee that the advanced materials will bring far-reaching implications in LDI MS towards real-case applications, especially in clinical settings.

Quantitative Analysis of Immunosuppressive Drugs Using Tungsten Disulfide Nanosheet-Assisted Laser Desorption Ionization Mass Spectrometry

For organ transplantation patients, the therapeutic drug monitoring (TDM) of immunosuppressive drugs is essential to prevent the toxicity or rejection of the organ. Currently, TDM is done by immunoassays or liquid chromatography-tandem mass spectrometry (LC-MS/MS) methods; however, these methods lack specificity or are expensive, require high levels of skill, and offer limited sample throughput. Although matrix-assisted (MA) laser desorption ionization (LDI) mass spectrometry (MS) can provide enhanced throughput and cost-effectiveness, its application in TDM is limited due to the limitations of the matrixes such as a lack of sensitivity and reproducibility. Here, we present an alternative quantification method for the TDM of the immunosuppressive drugs in the blood of organ transplant patients by utilizing laser desorption ionization mass spectrometry (LDI-MS) based on a tungsten disulfide nanosheet, which is well-known for its excellent physicochemical properties such as a strong UV absorbance and high electron mobility. By adopting a microliquid inkjet printing system, a high-throughput analysis of the blood samples with enhanced sensitivity and reproducibility was achieved. Furthermore, up to 80 cases of patient samples were analyzed and the results were compared with those of LC-MS/MS by using Passing-Bablok regression and Bland-Altman analysis to demonstrate that our LDI-MS platform is suitable to replace current TDM techniques. Our approach will facilitate the rapid and accurate analysis of blood samples from a large number of patients for immunosuppressive drug prescriptions.

Design of Multi-Shelled Hollow Cr2 O3 Spheres for Metabolic Fingerprinting

Schizophrenia (SZ) detection enables effective treatment to improve the clinical outcome, but objective and reliable SZ diagnostics are still limited. An ideal diagnosis of SZ suited for robust clinical screening must address detection throughput, low invasiveness, and diagnosis accuracy. Herein, we built a multi-shelled hollow Cr₂ O₃ spheres (MHCSs) assisted laser desorption/ionization mass spectrometry (LDI MS) platform for the direct metabolic profiling of biofluids towards SZ diagnostics. The MHCSs displayed strong light absorption for enhanced ionization and microscale surface roughness with stability for the effective LDI of metabolites. We profiled urine and serum metabolites (≈1 μL) with the enhanced LDI efficacy in seconds. We discriminated SZ patients (SZs) from healthy controls (HCs) with the highest area under the curve (AUC) value of 1.000 for the blind test. We identified four compounds with optimal diagnostic power as a simplified metabolite panel for SZ and demonstrated the metabolite quantification for clinic use. Our approach accelerates the growth of new platforms toward a precision diagnosis in the near future.

Self-Assembled Au Nanoparticle Arrays for Precise Metabolic Assay of Cerebrospinal Fluid

Precise and rapid monitoring of metabolites in biofluids is a desirable but unmet goal for disease diagnosis and management. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) exhibits advantages in metabolite analysis. However, the low accuracy in quantification of the technique limits its transformation to clinical usage. We report herein the use of Au nanoparticle arrays self-assembled at liquid-liquid interfaces for mass spectrometry (MS)-based quantitative biofluids metabolic profiling. The two-dimensional arrays feature uniformly and closely packed Au nanoparticles with 3 nm interparticle gaps. The experimental study and theoretical simulation show that the arrays exhibit high photothermal conversion and heat confinement effects, which enhance the laser desorption/ionization efficacy. With the nanoscale roughness, the AuNP arrays as laser desorption/ionization substrates can interrupt the coffee-ring effect during droplet evaporation. Therefore, high reproducibility (RSD <5%) is obtained, enabling accurate quantitative analysis of diverse metabolites from 1 μL of biofluids in seconds. By quantifying glucose in the cerebrospinal fluid (CSF), it allows us to identify patients with brain infection and rapidly evaluate the clinical therapy response. Consequently, the method shows potential in advanced metabolite analysis and biomedical diagnostics.

Microfluidic filter device coupled mass spectrometry for rapid bacterial antimicrobial resistance analysis

The problem of antimicrobial resistance (AMR) is becoming increasingly serious. Bacteria producing extended spectrum beta-lactamase (ESBL), which can hydrolyze beta-lactam antibiotics, are among the most important drug resistant bacteria. Rapid AMR analysis methods are essential for identifying antibiotic resistant bacteria, which is of significant positive value to the clinical therapy of infectious disease. We developed a platform which integrates a sandwich microfluidic filter device with electrospray ionization mass spectrometry (ESI-MS). Bacterial cells were loaded in the sandwich microfluidic chip and antibiotic drugs were injected to pass through the blocked bacterial cells. By online ESI-MS analysis of the antibiotic drugs and their hydrolysis products, the AMR of the bacteria can be assessed within 30 minutes. Four Escherichia coli strains, namely two ESBL-positive and two ESBL-negative, were successfully discriminated using ampicillin and the third generation cephalosporin ceftriaxone. Considering the simplicity and high efficiency of the assay, the microfluidic chip integrated online ESI-MS system is promising in the rapid clinical diagnosis of ESBL-producing bacteria.

Surface-enhanced laser desorption/ionization mass spectrometry for rapid analysis of organic environmental pollutants by using polydopamine nanospheres as a substrate

Polydopamine nanospheres (PDA) were designed to serve as a new substrate for surface-enhanced desorption/ionization mass spectrometry (SELDI-MS). Compared with conventional organic matrices, the PDA substrate showed superior LDI performance for analyzing a wide variety of environmental pollutants, including polycyclic aromatic hydrocarbons, bisphenols, benzophenones, sulfonamides, perfluorinated compounds and estrogens. Benzoapyrene was used to evaluate the ability of quantitative analysis and its corresponding limit of detection (LOD) of as low as 0.1 ng was achieved. High sensitivity and good reproducibility of PDA-based SELDI-MS allowed us to determine ultratrace PAHs in airborne particulate matters (PM_2.5), and the corresponding concentration of BaP in different PM_2.5 were 5.32, 8.97 and 9.79 ng m^-3. Significantly, PDA exhibits the characteristics of simple synthesis, low cost, non-toxicity and less matrix interference, which provides the possibility for the sensitive analysis of organic small molecule pollutants at low concentrations in complex environmental samples.

Hybrid CuCoO-GO enables ultrasensitive detection of antibiotics with enhanced laser desorption/ionization at nano-interfaces

The soaring concerns globally on antibiotic overuse have made calls for the development of rapid and sensitive detection methods urgent. Here we report that the hybrid CuCoO-GO matrix allows for sensitive detection of various antibiotics in combination with MALDI TOF MS. The new matrix is composed of few-layered GO nanosheets decorated with CuCoO nanoparticles with an average size of 10 nm, and exhibits excellent aqueous suspensibility. Accurate quantitation of the sulfonamide antibiotics in milk samples have been demonstrated using a CuCoO-GO matrix and a stable isotope (C¹³)-labeled analyte as the internal standard. Our experiments have achieved lower limits of detection (LOD) by several hundred fold for the detection of a panel of representative antibiotics, in comparison with the literature reports. Both intrabacterial and extrabacterial residual antibiotics can be sensitively detected with our method. We have further investigated the molecular mechanism of the enhanced desorption/ionization efficiency by the CuCoO-GO matrix with synchrotron radiation techniques for the first time. This work provides a sensitive matrix enabling MALDI-TOF MS to be applied in small molecular analysis, but also presents a distinct perspective on the mechanism behind the material functions.

Plasmonic Janus hybrids for the detection of small metabolites

Janus hybrids with amphiphilic structures were used for the sensitive detection of small metabolites.