Liquid Chromatography Coupled With High-resolution Mass Spectrometry Research Articles

Antiviral Activity of Flavonoids from Bauhinia holophylla Leaves against Zika virus

Zika virus (ZIKV) is involved in the etiology of serious nervous system pathologies. Currently, there are no specific and effective vaccines or antiviral drugs to prevent the diseases caused by ZIKV. This study aimed to assess the activity of flavonoids present in crude hydroethanolic extract (CHE) and fractions obtained from B. holophylla leaves against ZIKV. O-glycosylated flavonoids were characterized by high-performance liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS/MS). The cytotoxic concentration and the effective concentration for 50% of the cells (CC50 and EC50, respectively) were determined, and the selectivity index (SI) was calculated. Molecular networks were constructed based on the chemical composition of the samples and global antiviral activity data using the Global Natural Products Social Molecular Networking (GNPS) platform. Protein–ligand docking was performed in the NS2B-NS3 protease, NS3 helicase, and NS5 methyltransferase of the ZIKV. CHE showed greater antiviral activity at a multiplicity of infection (MOI) of 1.0, with an EC50 of 11.93 µg/mL, SI = 13.38, and reduced cytopathic effects. Molecular networks indicated that O-glycosylated flavonoids are responsible for the activity against ZIKV, being quercetin-O-deoxyhexoside more selective and effective. Molecular docking confirmed the inhibitory activity of quercetin-O-deoxyhexoside, which showed an affinity for the tested targets, especially for NS2B-NS3 protease. The results showed that B. holophylla has flavonoids with potential for future therapeutic applications against ZIKV.

The Discovery of a Multidomain Mannanase Containing Dual-Catalytic Domain of the Same Activity: Biochemical Properties and Synergistic Effect.

In recent years, the wide application of mannan has driven the demand for the exploration of mannanase. As one of the main components of hemicellulose, mannan is an important polysaccharide that ruminants need to degrade and utilize, making rumen a rich source of mannanases. In this study, gene mining of mannanases was performed using bioinformatics, and potential dual-catalytic domain mannanases were heterologously expressed to analyze their properties. The hydrolysis pattern and enzymatic products were identified by liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). A dual-catalytic domain mannanase Man26/5 with the same function as the substrate was successfully mined from the genome of cattle rumen microbiota. Compared to the single-catalytic domain, its higher thermal stability (≤50 °C) and catalytic efficiency confirm the synergistic effect between the two catalytic domains. It exhibited a unique "crab-like" structure where the CBM located in the middle is responsible for binding, and the catalytic domains at both ends are responsible for cutting. The exploration of its multidomain structure and synergistic patterns could provide a reference for the artificial construction and molecular modification of enzymes.

Metabolomic changes in adults with status epilepticus: Ahuman case-control study.

Status epilepticus (SE) is a life-threatening prolonged epileptic seizure that affects ~40 per 100 000 people yearly worldwide. The persistence of seizures may lead to excitotoxic processes, neuronal loss, and neuroinflammation, resulting in long-term neurocognitive and functional disabilities. A better understanding of the pathophysiological mechanisms underlying SE consequences is crucial for improving SE management and preventing secondary neuronal injury. We conducted a comprehensive untargeted metabolomic analysis, using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS), on plasma and cerebrospinal fluid (CSF) samples from 78 adult patients with SE and 107 control patients without SE, including 29 with CSF for both groups. The metabolomic fingerprints were compared between patients with SE and controls. Metabolites with differences in relative abundances that could not be attributed to treatment or nutrition provided in the intensive care unit were isolated. Enrichment analysis was performed on these metabolites to identify the most affected pathways. We identified 76 metabolites in the plasma and 37 in the CSF that exhibited differential expression in patients with SE compared to controls. The enrichment analysis revealed that metabolic dysregulations in patients with SE affected primarily amino acid metabolism (including glutamate, alanine, tryptophan, glycine, and serine metabolism), pyrimidine metabolism, and lipid homeostasis. Specifically, patients with SE had elevated levels of pyruvate, quinolinic acid, and keto butyric acid levels, along with lower levels of arginine, N-acetylaspartylglutamate (NAAG), tryptophan, uracil, and uridine. The tryptophan kynurenine pathway was identified as the most significantly altered in SE, resulting in the overproduction of quinolinic acid, an N-methyl-d-aspartate (NMDA) receptor agonist with pro-inflammatory properties. This study has identified several pathways that may play pivotal roles in SE consequences, such as the tryptophan kynurenine pathway. These findings offer novel perspectives for the development of neuroprotective therapeutics.

Development of a generic sample preparation method using dispersive liquid-liquid microextraction for the monitoring of leachable compounds in hospital pharmacy-prepared prefilled drug products.

Performant sample preparation is mandatory in any leachable study to clean and preconcentrate analytes within the sample to offer the best possible extraction recovery as well the best precision for any given substance. The aim consists in developing a sample preparation method for hospital pharmacy-prepared drug products such as long-term storage prefilled syringes, vials and IV bags for the screening of leachable compounds. The Quality Control Laboratory of the Pharmacy of the Lausanne University Hospital (Switzerland) has developed a time- and cost-effective, highly sensitive, robust, and fast method using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) for the analysis of 205 plastic additives. An innovative setup, based on postcolumn infusion (PCI) using 2% ammonium hydroxide in methanol was used to boost the signal intensity of the analytes in MS detection. A database for extractable and leachable trace assessment (DELTA) was built to assist in the screening process of 205 plastic packaging-related compounds. The development of the sample preparation was based on 33 plastic additive candidates in different hospital pharmacy compounding solutions, and their extraction recovery rates as well as their relative standard deviation were taken into consideration. In conclusion, the developed DLLME was assigned with ultrasound assistance and triple extraction, which brought about extraction recovery rates between 67% and 92%, a good RSD <10%, and a preconcentration factor of 50×. Therefore, DLLME could be considered suitable for the semiquantitative screening of leachable additives in simple hospital pharmacy-prepared prefilled drug products.

Distinct metabolic profiles in ocular hypertensive individuals responding

Aims/Purpose: To determine the effect of hypoxia on the plasma metabolic signature of patients with normal‐tension glaucoma (NTG) and ocular hypertension (OHT), compared to healthy controls.Methods: Metabolomic profiles of plasma from patients with NTG (n = 10) and OHT (n = 10) were compared to age‐matched controls (n = 10) to investigate the signature of hypoxia. Participants underwent two hours of exposure to normobaric hypoxia, followed by a 30‐min recovery period in normobaric normoxia. Blood samples were collected at baseline, during hypoxia, and recovery. Plasma samples were analysed using a non‐targeted metabolomics approach based on liquid chromatography coupled with high‐resolution mass spectrometry (LC‐HRMS). Multivariate analyses were conducted using principal component analysis (PCA) and orthogonal partial least squares‐discriminant analysis (OPLS‐DA), as well as univariate analysis with Wilcoxon signed‐rank test and false discovery rate (FDR) correction.Results: Overall, controls, OHT, and NTG patients had similar regulatory patterns. Only few metabolites involved in fatty acid biosynthesis, ketone body metabolism and kynurenine pathway were affected in OHT patients exposed to hypoxia, whereas metabolites related to energy production were not modified in NTG and OHT patients. No differences were found when comparing them pairwise at baseline, or during hypoxia and recovery.Conclusions: OHT patients have altered regulation of ketogenesis and kynurenine pathway, that may explain why they do not suffer from degeneration of the optic nerve. The metabolomes of NTG and OHT patients are regulated differently from controls, and omit to regulate metabolites that are important for energy production. This can potentially contribute to neurodegeneration and ultimately cell death in retinal ganglion cells.

Distinct Metabolic Profiles of Ocular Hypertensives in Response to Hypoxia.

Glaucoma is a neurodegenerative disease that affects the retinal ganglion cells (RGCs). The main risk factor is elevated intraocular pressure (IOP), but the actual cause of the disease remains unknown. Emerging evidence indicates that metabolic dysfunction plays a central role. The aim of the current study was to determine and compare the effect of universal hypoxia on the metabolomic signature in plasma samples from healthy controls (n = 10), patients with normal-tension glaucoma (NTG, n = 10), and ocular hypertension (OHT, n = 10). By subjecting humans to universal hypoxia, we aim to mimic a state in which the mitochondria in the body are universally stressed. Participants were exposed to normobaric hypoxia for two hours, followed by a 30 min recovery period in normobaric normoxia. Blood samples were collected at baseline, during hypoxia, and in recovery. Plasma samples were analyzed using a non-targeted metabolomics approach based on liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). Multivariate analyses were conducted using principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA), and univariate analysis using the Wilcoxon signed-rank test and false discovery rate (FDR) correction. Unique metabolites involved in fatty acid biosynthesis and ketone body metabolism were upregulated, while metabolites of the kynurenine pathway were downregulated in OHT patients exposed to universal hypoxia. Differential affection of metabolic pathways may explain why patients with OHT initially do not suffer or are more resilient from optic nerve degeneration. The metabolomes of NTG and OHT patients are regulated differently from control subjects and show dysregulation of metabolites important for energy production. These dysregulated processes may potentially contribute to the elevation of IOP and, ultimately, cell death of the RGCs.

Targeting antimalarial metabolites from the actinomycetes associated with the Red Sea sponge Callyspongia siphonella using a metabolomic method

Malaria is a persistent illness that is still a public health issue. On the other hand, marine organisms are considered a rich source of anti‑infective drugs and other medically significant compounds. Herein, we reported the isolation of the actinomycete associated with the Red Sea sponge Callyspongia siphonella. Using "one strain many compounds" (OSMAC) approach, a suitable strain was identified and then sub-cultured in three different media (M1, ISP2 and OLIGO). The extracts were evaluated for their in-vitro antimalarial activity against Plasmodium falciparum strain and subsequently analyzed by Liquid chromatography coupled with high-resolution mass spectrometry (LC-HR-MS). In addition, MetaboAnalyst 5.0 was used to statistically analyze the LC-MS data. Finally, Molecular docking was carried out for the dereplicated metabolites against lysyl-tRNA synthetase (PfKRS1). The phylogenetic study of the 16S rRNA sequence of the actinomycete isolate revealed its affiliation to Streptomyces genus. Antimalarial screening revealed that ISP2 media is the most active against Plasmodium falciparum strain. Based on LC-HR-MS based metabolomics and multivariate analyses, the static cultures of the media, ISP2 (ISP2-S) and M1 (M1-S), are the optimal media for metabolites production. OPLS-DA suggested that quinone derivatives are abundant in the extracts with the highest antimalarial activity. Fifteen compounds were identified where eight of these metabolites were correlated to the observed antimalarial activity of the active extracts. According to molecular docking experiments, saframycin Y3 and juglomycin E showed the greatest binding energy scores (-6.2 and -5.13) to lysyl-tRNA synthetase (PfKRS1), respectively. Using metabolomics and molecular docking investigation, the quinones, saframycin Y3 (5) and juglomycin E (1) were identified as promising antimalarial therapeutic candidates. Our approach can be used as a first evaluation stage in natural product drug development, facilitating the separation of chosen metabolites, particularly biologically active ones.

Hunting the missing fluorine in aqueous film-forming foams containing per- and polyfluoroalkyl substances

Since aqueous film-forming foams (AFFFs) are major sources of per- and polyfluoroalkyl substances (PFAS), understanding the quantity and type of PFAS present in AFFFs is crucial for assessing environmental risk and remediation. We characterized 25 foams from Canada and Europe, including two non-AFFFs and two fluorine-free AFFFs. We used liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) to identify novel PFAS, as well as total oxidizable precursor assays (TOP) and total organofluorine (TOF) measurements for comparison. LC-HRMS showed that the two non-AFFF foams and two PFAS-free AFFFs contained little or no PFAS, confirmed by TOF measurement using combustion ion chromatography (CIC). The PFAS-containing AFFFs, however, spanned a wide concentration range of TOF (2200–45,000 mg F/L) and contained 22 new classes of polyfluoroalkyl substances not previously reported. As a result of identifying new compounds, LC-HRMS was fully able to capture the oxidizable precursors determined by TOP assay in all tested fluorotelomer (FT) AFFFs, while unknown compounds still constituted a significant fraction (19–53 mol%) in most electrochemical fluorination (ECF) AFFFs. A fluorine mass balance was achieved by comparing the amounts of compounds identified by LC-HRMS with those detected by CIC, although LC-HRMS overestimated TOF with a recovery of 127 ± 36%.

LC-HRMS analysis of 13 classes of pharmaceutical substances in food supplements

ABSTRACT Food supplements should not contain substances considered unsafe or pose a health risk to consumers. In recent years illegal adulterants have been found in various functional foods without notification of their presence or amount in the labelling. In this study, a validated method was developed and applied as a screening method to detect 124 forbidden substances belonging to 13 classes of compounds in food supplements. Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) and a simple and rapid extraction protocol was applied to 110 food supplements collected from the internet market or during official controls in Italy. The percentage of non-compliant samples was 4.5%, relatively high compared with the official control results for these substances usually obtained on other food matrices. The results suggested the need to strengthen controls in this field to detect food supplement adulteration, which represents a potential health risk for the consumer.

Development of a candidate reference measurement procedure by ID-LC-MS/MS for total tau protein measurement in cerebrospinal fluid (CSF).

In clinical pratice, tau protein measurement generally relies on immunoassays (IAs), whose major drawback is the lack of results comparability due to differences in selectivity and/or calibration. This underlines the importance of establishing a traceability chain for total tau (t-tau) measurements. The objective of this work is to develop a higher order candidate reference measurement procedure (RMP) for the absolute quantification of t-tau in cerebrospinal fluid (CSF). To calibrate the candidate RMP and establish metrological traceability to the SI units, a primary calibrator consisting in a highly purified recombinant protein was sourced. Its purity was evaluated by liquid chromatography coupled with high resolution mass spectrometry (LC-HRMS) and the protein mass fraction in solution was certified by amino acid analysis (AAA). An isotopically-labelled homologue was obtained to develop a candidate RMP by isotope dilution mass spectrometry (IDMS) for t-tau absolute quantification in CSF. Calibration blends and quality control (QC) materials were gravimetrically prepared and subjected to the same preparation workflow as CSF samples, followed by LC-HRMS analysis in Parallel Reaction Monitoring (PRM) mode. A primary calibrator has been developed and an IDMS candidate RMP has been validated for CSF t-tau. The candidate RMP was used to certify t-tau concentration in three pools of CSF (low, medium, high). The candidate RMP will pave the road towards global standardization of CSF t-tau measurements. Together with commutable Certified Reference Materials (CRMs), it will allow evaluating and improving the accuracy and comparability of results provided by IAs.

The Fate of Sulfur Radical Cation of N-Acetyl-Methionine: Deprotonation vs. Decarboxylation

In the present study, we investigated the photooxidation of the biomimetic model of C-terminal methionine, N-Acetyl-Methionine (N-Ac-Met), sensitized by a 3-Carboxybenzophenone (3CB) excited triplet in neutral and basic aqueous solutions. The short-lived transient species that formed in the reaction were identified and quantified by laser flash photolysis and the final stable products were analyzed using liquid chromatography coupled with high-resolution mass spectrometry (LC-MS) and tandem mass spectrometry (MSMS). Based on these complementary methods, it was possible to calculate the quantum yields of both competing reactions, and the deprotonation was found to be favored over decarboxylation (for neutral pH: ϕ-H = 0.23 vs. ϕ-CO2 = 0.09, for basic pH: ϕ-H = 0.23 vs. ϕ-CO2 = 0.05). Findings on such a model system, which can possibly mimic the complex protein environment, are important in understanding complicated biological systems, for example, the studied compound, N-Ac-Met, can, to some extent, mimic the methionine in the C-terminal domain of β-amyloid, which is thought to be connected with the pathogenesis of Alzheimer’s disease.

Development of a kit for urine collection on filter paper as an alternative for Pompe disease screening and monitoring by LC-HRMS.

Pompe disease (PD) is an inborn error of metabolism caused by α-glucosidase acid enzyme deficiency. It significantly impacts patients' health and life quality and may lead to death in the first few years of life. Among the well-established diagnostic methods, urinary glucose tetrasaccharide (Glc4) screening by high performance-liquid chromatography has been helpful in monitoring Glc4 levels in patients on enzyme replacement therapy, demonstrating therapy efficacy. However, the specimen shipping process from a sample collecting location to a specialized laboratory for monitoring the Glc4 is costly and presents preanalytical challenges. In this work, we developed a filter paper based-urine collection kit to facilitate specimen shipment, and liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) analysis to determine Glc4 and creatinine in dried urine on filter paper. The LC-HRMS was based on a combination of targeted and untargeted screening on the same specimen injection and was successfully developed and validated. Bland-Altman statistics revealed a good relationship between dried and liquid urine samples and Glc4 and creatinine. Glc4 and other metabolites in dried urine showed stability for at least 7 days at 4 and 22 °C, and 3 days at 50 °C. The stability of the analytes and the efficiency of the kit were tested simulating real conditions by sending it by post. After two days in transit without refrigeration, the stability of compounds was maintained, showing the reliability of the urine collection kit and analysis method to determine the PD biomarker Glc4.

Glycosylation Profiling of the Neoplastic Biomarker Alpha Fetoprotein through Intact Mass Protein Analysis.

Elevated serum alpha-fetoprotein (AFP) can be observed in liver cirrhosis and hepatocellular carcinoma (HCC). The glycosylation patterns of AFP have been shown to differentiate these conditions, with AFP glycoforms with core fucosylation (AFP-L3) serving as a malignancy risk predictor for HCC. We have developed a method to detect endogenously present AFP proteoforms and to quantify the relative abundance of AFP-L3 glycoforms (AFP-L3%) in serum samples. This method consists of immune enrichment of endogenous AFP, followed by liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) intact protein analysis of AFP. Data are available via ProteomeXchange with identifier PXD038606. Based on the AFP profiles in authentic patient serum samples, we have identified that the frequently observed AFP glycoforms without core fucosylation (AFP-L1) are G2S2 and G2S1, and common AFP-L3 glycoforms are G2FS1 and G2FS2. The intensities of glycoforms in the deconvoluted spectrum are used to quantify AFP-L3% in each sample. The method evaluation included reproducibility, specificity, dilution integrity, and comparison of AFP-L3% with a lectin-binding gel shift electrophoresis (GSE) assay. The AFP-L1 and AFP-L3 proteoforms were reproducibly identified in multiple patient serum samples, resulting in reproducible AFP-L3% quantification. There was considerable agreement between the developed LC-HRMS and commercial GSE methods when quantifying AFP-L3% (Pearson r = 0.63) with a proportional bias.

Extracellular Vesicle-Based Liquid Biopsy Shows Clinical Relevance and Reveals Links with Single-Cell Metabolic Signature in Acute Myeloid Leukemia

Background. Acute myeloid leukemia (AML) is an aggressive disease that shows dysregulated cell metabolism and a high relapse rate. To date, less invasive tools are urgently needed to explore disease dynamics in AML. In this regard, Extracellular Vesicles (EV) from plasma represent a promising tool for liquid biopsy. Also, the material extracted from blood (including circulating leukemic stem cells, LSC) can be used for clinical purposes revealing clinically relevant (metabolic) vulnerabilities. Along with EV profiling in AML patients, we explored the clinically relevant (metabolic) signature carried by CD34+ cells in circulation. Methods. Peripheral blood (PB) was collected from AML patients at diagnosis (n=70) and healthy donors (HD, n=20). EVs were purified from platelet-poor plasma by size exclusion chromatography and ultrafiltration. Quantitative lipidomic profiling was performed by Liquid Chromatography coupled with High-Resolution Mass Spectrometry (LC/HRMS). Single Cell ENergetic metabolism by Profiling Translation inhibition (SCENITH) has been performed in fresh whole blood. Results. We profiled the surface protein of isolated circulating EVs by AML patients at diagnosis. Compared to EV from HD, leukemic EV from newly diagnosed AML patients were mainly enriched in cancer stem cell marker, CD44. Intriguingly, the area under the curve (AUC) confirmed a reliable performance for employing this marker on EVs to discriminate EVs from AML patients. Among other 36 markers explored, CD4 (immune marker), CD105 (mesenchymal stromal cell marker), CD14 (monocyte marker), and CD133-1 (stem cell marker) were highly expressed only in leukemic EVs. In particular, CD11c as the well-known dendritic marker was solely expressed in EVs from some AML patients and totally absent in healthy EVs. By contrast, in circulating leukemic EVs, we observed depletion in markers such as CD62P, CD41b, and CD41a suggesting an impaired function in leukemic megakaryocytes and platelets. From the clinic point of view, according to European LeukemiaNet (ELN) 2017 risk classification, we observed that CD9, CD29, CD31, and CD42a were enriched in the favorable AML group in comparison with adverse/intermediate-risk AML patients. Notably, non-survivor AML patients showed a significant reduction in the expression of EV markers including CD11c, CD69, and ROR-1. Then, to further highlight crucial characteristics in EV composition, we performed an untargeted lipidomic analysis on circulating EVs. Fatty acids (FA) and Diacylglycerols (DG) were significantly overexpressed in leukemic EVs compared to healthy EVs. Leukemic EVs were depleted in Cholesteryl ester (CE) suggesting an increase in membrane stiffness. Interestingly, the lipid CE18:2 was found high in adverse-risk AML patients encouraging further studies on EV lipidomic profiles for better AML stratification. An in-depth investigation of the metabolic dependencies of leukemia (stem) cells from blood might be crucial for detecting novel metabolic vulnerabilities in AML patients. Thus, we applied the innovative SCENITH approach in fresh blood from AML patients at diagnosis. We found that circulating AML CD34+ cells were highly dependent on glucose oxidation and less prone to use fatty acids and amino acids as sources for ATP production when glucose oxidation was inhibited. Also, AML CD34+ cells in circulation reported a higher glycolytic capacity compared to mitochondrial dependence. Towards a clinically relevant implication, SCENITH analysis showed that mitochondrial dependence was solely increased in adverse and intermediate-risk AML patients compared to favorable AML patients. Interestingly, the percentage of mitochondrial dependence in AML CD34+ was positively correlated to the expression of CD24 (cancer stem marker) observed on leukemic EVs suggesting a novel potential link between EV profiling and energy metabolism for leukemia. Conclusion. Overall, these results demonstrate that an abnormal signature characterizes the phenotype of circulating EVs in AML patients. Indeed, the depletion of selected EV markers could be associated with high-risk AML disease and supports their prognostic relevance. This work might reveal novel metabolic vulnerabilities in the AML scenario by exploiting both EV-based liquid biopsy and single-cell metabolic phenotyping.

Identification criteria, in-house compound libraries and SWATH: A benchmark implementation of quadrupole time-of-flight mass spectrometry in routine toxicological casework

To establish the identification criteria sufficient for the daily and routine reporting of compounds using Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) in forensic casework. Liquid chromatography coupled with High Resolution Mass Spectrometry (LC-HRMS) provides sensitive full-spectrum MS and MS/MS data for the identification of known and previously unknown compounds. However, the daily and routine implementation of methods that use LC-HRMS techniques in routine analysis can be challenging due to the establishment of identification criteria and confidence in reporting suspected positive detections. With the large amount of data that is collected during SWATH, it is important to have a well-developed and validated identification criterion, that is also high throughput. To identify previously published identification criterion, literature searches were conducted for the keywords Quadrupole Time of Flight, Toxicology, QTOF, Forensic Toxicology, Sequential Window Acquisition, SWATH and Mass Spectrometry. A total of 11 articles were evaluated regarding the use of SWATH in clinical or forensic toxicology. Based off these findings, we performed internal studies to validate identification criteria. Curation of an internal library were conducted using available reference standards. For compound identification and confirmation, criterion acceptability of exact mass ±5 ppm, retention time (RT) ±0.5 min, and library match for MS and MSMS including comparison of isotopic pattern and product ion pattern to the library. A combined weighted score (CWS) for each candidate species was calculated based on these criteria with a reporting score of >75% set. In reviewing the literature of SWATH methods that have already been developed, it has been found that the most common target drug classes are stimulants, benzodiazepines, opiates, NPS’, cannabinoids and anti-depressants. In the acquisition process, the number of SWATH windows ranges from 12-30. Mass error, isotopic ratio difference, retention time error and library scores were used as the identification criteria for all studies. HRMS acquisition is data-rich, voluminous and complicated. We have adopted categories to delineate the identification and reportion of compounds through the QTOF Method: Target Qualitative, Target Quantitative, Target Monitored, Suspect Screening and Unknown Screening. Each category must pass a pre-set identification criterion that resulted from identification criteria studies. The described method uses five levels of identification and confirmation, and three types of mass spectral libraries consisting of a main of an in-house curated library, updated quarterly. New targets are added through a vigorous process including interference studies, as many NPS show similar fragmentation and identical molecular weights. Interference studies may result in the grouping of compounds that have the same exact mass, identical fragmentation, and/or small retention time differences. For HRMS analysis, robust assessment of accurate mass information and reference to in-house libraries are essential in the accurate identification and reporting of drugs in forensic toxicological casework.

Using MetaboAnalyst 5.0 for LC-HRMS spectra processing, multi-omics integration and covariate adjustment of global metabolomics data.

Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has become a workhorse in global metabolomics studies with growing applications across biomedical and environmental sciences. However, outstanding bioinformatics challenges in terms of data processing, statistical analysis and functional interpretation remain critical barriers to the wider adoption of this technology. To help the user community overcome these barriers, we have made major updates to the well-established MetaboAnalyst platform ( www.metaboanalyst.ca ). This protocol extends the previous 2011 Nature Protocol by providing stepwise instructions on how to use MetaboAnalyst 5.0 to: optimize parameters for LC-HRMS spectra processing; obtain functional insights from peak list data; integrate metabolomics data with transcriptomics data or combine multiple metabolomics datasets; conduct exploratory statistical analysis with complex metadata. Parameter optimization may take ~2 h to complete depending on the server load, and the remaining three stages may be executed in ~60 min.

A data processing pipeline for petroleomics based on liquid chromatography-high resolution mass spectrometry

Online liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) has attracted much attention in the molecular characterization of crude oil. Neither open access nor commercially available petroleomics tools were developed specifically to process LC-HRMS data. Here, a novel data processing pipeline was specifically designed for LC-HRMS-based petroleomics data. A customizable formula database was established deriving from the detected sample, which could avoid the interference caused by a large number of redundant molecules in a conventionally theoretical molecular database. Molecular formula candidates were assigned by the formula database using a low noise threshold, and false-positive assignments were eliminated by the chromatographic retention behaviors. Multi-dimensional information was obtained, including heteroatom class, double bond equivalent (DBE), carbon number, retention time, and MS/MS spectra. The developed method was compared with a popular petroleomics software, similar relative abundance class distribution was obtained, and much more formulas of low abundant components were uniquely extracted by the developed method. Finally, it was applied to reveal variation between feed and product oils in hydrodenitrogenation. Significantly compositional and structural differences were revealed. The developed method provides a useful pipeline for molecular data mining of petroleum samples.

Comparison of Illicit Drug Seizures Products of Natural Origin Using a Molecular Networking Approach.

Drug powder composition analysis is of particular interest in forensic investigations to identify illicit substance content, cutting agents and impurities. Powder profiling is difficult to implement due to multiple analytical methods requirement and remains a challenge for forensic toxicology laboratories. Furthermore, visualization tools allowing seizure products identification appear to be under-used to date. The aim of this study is to present the utility of molecular networking for the composition establishment of natural origin drugs. A powder suspected to contain heroin and three powders suspected to contain cocaine obtained from law enforcement agency seizures were analyzed using untargeted screening by liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS/MS). Molecular networking and metabolite annotation applied to suspected heroin sample allowed rapid confirmation of its illicit content (heroin), the identification of structurally related major impurities (6-monoacetylmorphine, 6-monoacetylcodeine, noscapine, and papaverine), as well as cutting agents (acetaminophen and caffeine). The cocaine powder profiling allowed the comparison of its constituents in a semi-quantitative manner (cocaine, benzoylecgonine, trans/cis-cinnamoylcocaine, trimethoxycocaine, hexanoylecgonine methylester, caffeine, hydroxyzine, levamisole, and phenacetin), bringing additional information for their identification, including geographically sourcing of natural product and their putative place in the supply chain. Although this approach does not replace the profiling techniques used by forensic laboratories, the use of molecular networks provides a visual overview of structurally related constituents which aids the comparison and investigation of seizure powders. Molecular networks offers here an ideal way to depict structurally related and unrelated compounds in these often complex mixtures of chemicals.

CPExtract, a Software Tool for the Automated Tracer-Based Pathway Specific Screening of Secondary Metabolites in LC-HRMS Data.

The use of stable isotopically labeled tracers is a long-proven way of specifically detecting and tracking derived metabolites through a metabolic network of interest. While the recently developed stable isotope-assisted methods and associated, supporting data analysis tools have greatly improved untargeted metabolomics approaches, no software tool is currently available that allows us to automatically and flexibly search liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) chromatograms for user-definable isotopolog patterns expected for the metabolism of labeled tracer substances. Here, we present Custom Pattern Extract (CPExtract), a versatile software tool that allows for the first time the high-throughput search for user-defined isotopolog patterns in LC-HRMS data. The patterns can be specified via a set of rules including the presence or absence of certain isotopologs, their relative intensity ratios as well as chromatographic coelution. Each isotopolog pattern satisfying the respective rules is verified on an MS scan level and also in the chromatographic domain. The CPExtract algorithm allows the use of both labeled tracer compounds in nonlabeled biological samples as well as a reversed tracer approach, employing nonlabeled tracer compounds along with globally labeled biological samples. In a proof-of-concept study, we searched for metabolites specifically arising from the malonate pathway of the filamentous fungi Fusarium graminearum and Trichoderma reesei. 1,2,3-13C3-malonic acid diethyl ester and native malonic acid monomethyl ester were used as tracers. We were able to reliably detect expected fatty acids and known polyketides. In addition, up to 46 and 270 further, unknown metabolites presumably including novel polyketides were detected in the F. graminearum and T. reesei culture samples, respectively, all of which exhibited the user-predicted isotopolog patterns originating from the malonate tracer incorporation. The software can be used for every conceivable tracer approach. Furthermore, the rule sets can be easily adapted or extended if necessary. CPExtract is available free of charge for noncommercial use at https://metabolomics-ifa.boku.ac.at/CPExtract.

Circulating Extracellular Vesicles from Acute Myeloid Leukemia Patients Drive Distinct Metabolic Profile of Leukemic Cells and Reveal Crucial Lipidomic Biomarkers

Background. Extracellular vesicles (EVs) are submicron vesicles released from various cell types including blood cells with pleiotropic effects on cell signalling and metabolism. EV cargos are enriched in nucleic acids, proteins, and lipids that can be delivered to target cells to influence surrounding microenvironment. Thus, EVs represent a powerful tool for liquid biopsy in hematological malignancies including acute myeloid leukemia (AML).AML is an aggressive disease with high relapse rate and less invasive tools are urgently needed to investigate disease (metabolic) dynamics. Accumulating evidence has reported a key role for EVs in shaping the AML bone marrow niche. However, at present, the metabolic function and the lipidomic signature driven by circulating EVs have yet to fully emerge.Methods. Peripheral blood (PB) and bone marrow (BM) were collected from AML patients at diagnosis (n=40) and PB from age/sex-matched healthy donors (HD, n=20). EVs were purified from platelet-poor plasma by size exclusion chromatography and quantified using the NanoSight technology. Immunomagnetically isolated CD34+ cells from umbilical cord blood (CB) or AML patients were characterized by analyzing the hematopoietic stem/progenitor cell (HSPC)-specific cluster of differentiation marker expression, redox metabolic profiling (using CellROX, glutathione detection reagent and MitoTracker) after 24 hours co-culture with EVs. Quantitative lipidomic profiling of circulating EVs was performed by Liquid Chromatography coupled with High-Resolution Mass Spectrometry (LC/HRMS). Seahorse extracellular flux analyses were performed in leukemia cell lines (including KG-1, KASUMI-1, MOLM-13, THP-1 and OCI-AML3). To functionally define the metabolic reprogramming of leukemic cellular components within their microenvironment, leukemic stem cell subsets were assessed by flow cytometry-based SCENITH (Single Cell ENergetic metabolism by profilIng Translation inHibition) method in both whole blood and BM samples (n=4).Results. In our work, plasma-derived EVs from AML patients showed a significant increase in the size and protein amounts compared to HD counterparts. To explore the metabolic perturbation triggered by EVs, we developed a co-culture system with circulating EVs from either HD or AML patients with CB or AML CD34+. We found a reduction in the frequency of AML CD34+ with high ROS levels in the presence of AML EVs without affecting the ROS levels in normal CB CD34+. In parallel, AML EVs increased the frequency of AML CD34+ with both high mitochondrial activity and glutathione, a key antioxidant molecule involved in many metabolic pathways. Similar metabolic profiles were also confirmed in human leukemic cell lines tested. Specifically, Seahorse flux analysis revealed that EVs induced a cell energy phenotype consistent with quiescent and chemoresistant state in human leukemic cell lines, showing a more glycolytic state in MOLM-13. Interestingly, both CD34+ and CD34+/CD38- leukemic fractions from whole blood and BM of the same AML patients were analyzed by SCENITH after co-cultures with HD/AML EVs. Remarkably, PB CD34+/CD38- leukemic fractions were more dependent on mitochondrial activity in the presence of AML EVs, suggesting a metabolic shift triggered by leukemic EV that apparently occur in the leukemic fractions out of the BM niche.In addition, to give insights into lipidomic signatures of EVs as disease biomarkers, we detected a total of 25 (out of 200) independent lipid species significantly different between AML-derived EVs and HD (n=20, respectively). We reported the abundance of both glycerolipid and fatty acids species in AML EVs. Also, through a multivariate statistical analysis of EV lipidomic profile, we revealed that AML EVs were depleted in sphingomyelin classes, a class of lipids that are interconnected to HSC metabolism. Finally, according to the 2017 ELN risk stratification system, we observed the depletion in important modulators of EV release and formation as ether-linked phosphatidylethanolamine and phosphatidylethanolamine species in adverse-risk AML patients.Conclusion. Overall, our study provides the basis for further investigations on the metabolic alterations trigger by EVs within the BM microenvironment and suggests prognostic biomarkers for leukemic patients that might reveal novel metabolic vulnerabilities in AML scenario. DisclosuresCavo: Sanofi: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; AbbVie: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria; Amgen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Janssen: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: TRAVEL, ACCOMMODATIONS, EXPENSES, Speakers Bureau; Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Other: Travel Accommodations, Speakers Bureau; Takeda: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Adaptive Biotechnologies: Consultancy, Honoraria; GlaxoSmithKline: Consultancy, Honoraria; Bristol-Myers Squib: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Curti: Jazz Pharma: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Novartis: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees.