A Direct Infusion Probe for Rapid Metabolomics of Low-Volume Samples

rIDIMS: A novel tool for processing direct-infusion mass spectrometry data

Metabolomics using mass spectrometry-only (MS) analysis either by continuous or intermittent direct infusion (DIMS) and ambient ionization techniques (AMS) has grown in popularity due to their rapid, high-throughput nature and the advantage of performing fast analysis with minimal or no sample pretreatments. But currently, end-users without programming knowledge do not find applications with Graphical User Interface (GUI) specialized in processing DIMS or AMS data. Specifically, there is a lack of standardized workflow for processing data from limited sample sizes and scans from different total ion chronograms (TIC).To address this gap, we present rIDIMS, a browser-based application that offers a straightforward and fast workflow focusing on high-quality scan selection, grouping of isotopologues and adducts, data alignment, binning, and filtering. We also introduce a novel function for selecting TIC scans that is reproducible and statistically reliable, which is a feature particularly useful for studies with limited sample sizes. After processing in rIDIMS, the result is exported in an HTML report document that presents publication-quality figures, statistical data and tables, ready to be customized and exported. We demonstrate rIDIMS functionality in three cases: (i) Classification of coffee bean species through the chemical profile obtained with Mass Spec Pen; (ii) Public repository DIMS data from lipid profiling in monogenic insulin resistance syndromes, and (iii) Lipids for lung cancer classification. We show that our implementation facilitates the processing of AMS and DIMS data through an easy and intuitive interface, contributing to reproducible and reliable metabolomic investigations. Indeed, rIDIMS function asa user-friendly GUI based Shiny web application for intuitive use by end-users (available at https://github.com/BioinovarLab/rIDIMS).

Metabolomics-driven approaches for identifying therapeutic targets in drug discovery

Identification of therapeutic targets can directly elucidate the mechanism and effect of drug therapy, which is a central step in drug development. The disconnect between protein targets and phenotypes under complex mechanisms hampers comprehensive target understanding. Metabolomics, as a systems biology tool that captures phenotypic changes induced by exogenous compounds, has emerged as a valuable approach for target identification. A comprehensive overview was provided in this review to illustrate the principles and advantages of metabolomics, delving into the application of metabolomics in target identification. This review outlines various metabolomics-based methods, such as dose-response metabolomics, stable isotope-resolved metabolomics, and multiomics, which identify key enzymes and metabolic pathways affected by exogenous substances through dose-dependent metabolite-drug interactions. Emerging techniques, including single-cell metabolomics, artificial intelligence, and mass spectrometry imaging, are also explored for their potential to enhance target discovery. The review emphasizes metabolomics' critical role in advancing our understanding of disease mechanisms and accelerating targeted drug development, while acknowledging current challenges in the field.

Online Direct Infusion Mass Spectrometry of Liquid-Liquid Extraction Phases for Metabolite and Lipid Profiling with the Direct Infusion Probe

Background/Objectives: Profiling of metabolites and lipids in biological samples can provide invaluable insights into life-sustaining chemical processes. The ability to detect both metabolites and lipids in the same sample can enhance these understandings and connect cellular dynamics. However, simultaneous detection of metabolites and lipids is generally hampered by chromatographic systems tailored to one molecular type. This void can be filled by direct infusion mass spectrometry (MS), where all ionizable molecules can be detected simultaneously. However, in direct infusion MS, the high chemical complexity of biological samples can introduce limitations in detectability due to matrix effects causing ionization suppression. Methods: Decreased sample complexity and increased detectability and molecular coverage was provided by combining our direct infusion probe (DIP) with liquid-liquid extraction (LLE) and directly sampling the different phases for direct infusion. Three commonly used LLE methods for separating lipids and metabolites were evaluated. Results: The butanol-methanol (BUME) method was found to be preferred since it provides high molecular coverage and have low solvent toxicity. The established BUME DIP-MS method was used as a fast and sensitive analysis tool to study chemical changes in insulin-secreting cells upon glucose stimulation. By analyzing the metabolome at distinct time points, down to 1-min apart, we found high dynamics of the intracellular metabolome. Conclusions: The rapid workflow with LLE DIP-MS enables higher sensitivity of phase separated metabolites and lipids. The application of BUME DIP-MS provides novel information on the dynamics of the intracellular metabolome of INS-1 during the two phases of insulin release for both metabolite and lipid classes.

Recent Analytical Methodologies in Lipid Analysis

Lipids represent a large group of biomolecules that are responsible for various functions in organisms. Diseases such as diabetes, chronic inflammation, neurological disorders, or neurodegenerative and cardiovascular diseases can be caused by lipid imbalance. Due to the different stereochemical properties and composition of fatty acyl groups of molecules in most lipid classes, quantification of lipids and development of lipidomic analytical techniques are problematic. Identification of different lipid species from complex matrices is difficult, and therefore individual analytical steps, which include extraction, separation, and detection of lipids, must be chosen properly. This review critically documents recent strategies for lipid analysis from sample pretreatment to instrumental analysis and data interpretation published in the last five years (2019 to 2023). The advantages and disadvantages of various extraction methods are covered. The instrumental analysis step comprises methods for lipid identification and quantification. Mass spectrometry (MS) is the most used technique in lipid analysis, which can be performed by direct infusion MS approach or in combination with suitable separation techniques such as liquid chromatography or gas chromatography. Special attention is also given to the correct evaluation and interpretation of the data obtained from the lipid analyses. Only accurate, precise, robust and reliable analytical strategies are able to bring complex and useful lipidomic information, which may contribute to clarification of some diseases at the molecular level, and may be used as putative biomarkers and/or therapeutic targets.

The rapid separation and characterization of sulfates of tyrosine and its metabolites in reaction mixtures and human urine using a cyclic ion mobility device and mass spectrometry

Ion mobility (IM) separations, especially when combined with mass spectrometry, offer the opportunity for the rapid analysis and characterization of mixtures. However, the limited resolution afforded by many IM systems means that in practice applications may be limited. Here we have employed an IM separation on a high-resolution cyclic IM device with MS/MS to separate and characterize mixtures of sulfated isomers of tyrosine and associated metabolites containing multiple sulfated isoforms present in reaction mixtures. The cIMS device allowed ions, not resolved using a single pass, to be subjected to multiple passes, enabling the resolution of those with similar collision cross sections (CCS). Predicted single pass CCS values calculated for the isomers likely to be present in these mixtures showed only small differences between them, ranging between of between 0.1 - 0.7 % depending on structure. These small differences highlight the high degree of mobility resolution required for separating the isomers. Experimentally different isoforms of tyrosine sulfate and sulfated tyrosine metabolites could be sufficiently resolved via multipass separations (3-35 passes). This degree of separation provided resolving powers of up to 384 CCS/ΔCCS for sulfated dopamine which enabled good MS/MS spectra to be generated. In human urine the presence of a single sulfated form of tyrosine was detected and identified as the O-sulfate after 3 passes based on the synthetic standard. Of the other tyrosine-related sulfates for which synthetic standards had been prepared only dopamine sulfate was detected in this sample.

Electrochemical platform produced by 3D printing for analysis of small volumes using different electrode materials

Fused deposition modeling (FDM) 3D printing is a promising additive manufacturing technique to produce low-cost disposable electrochemical devices. However, the print of devices like well-known screen-printed electrodes (all electrodes on the same device) is difficult using the available technology (few materials available for production of working electrodes). In this paper we present a procedure to produce disposable and robust electrochemical devices by FDM 3D printing that allows reproducible analysis of small volumes (50-2000 μL). The device consists of just two printed parts that allow easy coupling of different conductive materials for using as disposable or non-disposable working electrodes with reproducible geometric area. Printed counter and pseudo-reference electrodes can also be easily fitted into the microcell. Moreover, conventional counter (platinum wire) and mini reference electrodes can also be used. As a proof of concept, paracetamol, cocaine and uric acid were used as model analytes using different materials as working electrodes. Linear calibration curves (r > 0.99) with similar slopes (0.29 ± 0.01 μA μmol L-1; RSD = 3.4%) were obtained by square wave voltammetry (SWV) using a complete printed system and different volumes of standard solutions of paracetamol (50, 100, and 200 μL). For uric acid, a linear range of 10-125 μmol L-1 (r > 0.99), was obtained using differential pulse voltammetry as the electrochemical technique and a disposable laser-induced graphene base as the working electrode. With the coupling of boron-doped diamond working electrode, screening tests were successfully performed in seized cocaine samples with selective detection of cocaine in the presence of its most common adulterants. The production cost per unit of a complete electrochemical system is around US 5.00. In large-scale production, only the working electrode needs to be replaced while the microcell and counter/pseudo reference electrodes do not need to be discarded.

Global and Spatial Metabolomics of Individual Cells Using a Tapered Pneumatically Assisted nano-DESI Probe

Single-cell metabolomics has the potential to reveal unique insights into intracellular mechanisms and biological processes. However, the detection of metabolites from individual cells is challenging due to their versatile chemical properties and concentrations. Here, we demonstrate a tapered probe for pneumatically assisted nanospray desorption electrospray ionization (PA nano-DESI) mass spectrometry that enables both chemical imaging of larger cells and global metabolomics of smaller 15 μm cells. Additionally, by depositing cells in predefined arrays, we show successful metabolomics from three individual INS-1 cells per minute, which enabled the acquisition of data from 479 individual cells. Several cells were used to optimize analytical conditions, and 93 or 97 cells were used to monitor metabolome alterations in INS-1 cells after exposure to a low or high glucose concentration, respectively. Our analytical approach offers insights into cellular heterogeneity and provides valuable information about cellular processes and responses in individual cells.

Screening autism-associated environmental factors in differentiating human neural progenitors with fractional factorial design-based transcriptomics

Research continues to identify genetic variation, environmental exposures, and their mixtures underlying different diseases and conditions. There is a need for screening methods to understand the molecular outcomes of such factors. Here, we investigate a highly efficient and multiplexable, fractional factorial experimental design (FFED) to study six environmental factors (lead, valproic acid, bisphenol A, ethanol, fluoxetine hydrochloride and zinc deficiency) and four human induced pluripotent stem cell line derived differentiating human neural progenitors. We showcase the FFED coupled with RNA-sequencing to identify the effects of low-grade exposures to these environmental factors and analyse the results in the context of autism spectrum disorder (ASD). We performed this after 5-day exposures on differentiating human neural progenitors accompanied by a layered analytical approach and detected several convergent and divergent, gene and pathway level responses. We revealed significant upregulation of pathways related to synaptic function and lipid metabolism following lead and fluoxetine exposure, respectively. Moreover, fluoxetine exposure elevated several fatty acids when validated using mass spectrometry-based metabolomics. Our study demonstrates that the FFED can be used for multiplexed transcriptomic analyses to detect relevant pathway-level changes in human neural development caused by low-grade environmental risk factors. Future studies will require multiple cell lines with different genetic backgrounds for characterising the effects of environmental exposures in ASD.

Metabolite profiling and identification in living cells by coupling stable isotope tracing and induced electrospray mass spectrometry

Direct observation of metabolites in living cells by mass spectrometry offers a bright future for biological studies but also suffers a severe challenge to untargeted peak assignment to tentative metabolite candidates. In this study, we developed a method combining stable isotope tracing and induced electrospray mass spectrometry for living-cells metabolite measurement and identification. By using 13C6-glucose and ammonium chloride-15N as the sole carbon and nitrogen sources for cell culture, Escherichia coli synthesized metabolites with 15N and 13C elements. Tracing the number of carbon and nitrogen atoms could offer a complementary dimension for candidate peak searching. As a result, the identification confidence of metabolites achieved a universal improvement based on carbon/nitrogen labelling and filtration.