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Studying the changes in organic matter and characteristic pollutants during the treatment of penicillin-containing pharmaceutical wastewater, which can be reflected by changes in dissolved organic matter (DOM), is crucial for improving the effectiveness of wastewater treatment units and systems. Herein, water quality indicators, spectroscopic methods, and Fourier-transform ion cyclotron resonance mass spectrometry were utilized to characterize the general molecular compositions and specific molecular changes in DOM during the treatment of typical penicillin-containing pharmaceutical wastewater, including in each of the influent, physicochemical treatment, biological treatment, oxidation treatment, and effluent stages. The influent exhibited a high organic matter content (concentration of dissolved organic carbon >10,000 mg·L -1 ), its DOM mainly contained protein- and lignin-like substances composed of CHON and CHONS molecules, and the relative intensity (RI) of penicillin was extremely high (RI = 0.220). Compared with the influent, the abundance of CHON and CHONS molecules detected after physicochemical treatment decreased by 70.3 % and 62.5 %, respectively, and the RI of penicillin decreased by 85.5 %. Biological treatment caused substantial changes in DOM components through oxidation, dealkylation, and denitrification reactions, accounting for 36.8 %, 28.9 %, and 14.8 % of the total identified reactions, respectively. Additionally, lignin-like substances were generated in large quantities, the overall humification level significantly increased, and the RI value increased for the penicillin intermediate, 6-aminopenicillanic acid (6-APA). Oxidation treatment effectively removed phosphorus-containing substances and some lignin-like substances produced by biological treatment; however, it was not effective in removing characteristic pollutants such as 6-APA. Such characteristic substances continued to be present in the effluent, and the DOM mainly contained protein- and humus-like substances, accounting for 30.8 % and 47.3 %, respectively. The study findings reveal the changes in organic matter and characteristic pollutants during the treatment of penicillin-containing wastewater from the perspective of the general molecular composition and specific molecular changes in DOM, providing support for further exploration of wastewater treatment mechanisms and improvements in treatment unit efficiency., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

GNE myopathy, also known as hereditary inclusion body myopathy (HIBM), is a rare genetic muscle disorder marked by a gradual onset of muscle weakness in young adults. GNE myopathy (GNEM) is caused by bi-allelic variants in the UDP- N -acetylglucosamine 2-epimerase (UDP-GlcNAc 2-epimerase)/ N -acetylmannosamine kinase (ManNAc kinase) gene ( GNE ), clinically resulting in the loss of ambulation within 10-20 years from the onset of the initial symptoms. The disease's mechanism is poorly understood and non-invasive biomarkers are lacking, hindering effective therapy development. Based on the available evidence, we employed a lipidomic approach to study the serum lipid profile of GNE patients. The multivariate statistical analysis revealed a downregulation of carnitines, as well as of lysophosphatidylcholines, in sera samples derived from GNEM patients. Furthermore, we identified lower levels of sphingomyelins and, concomitantly, high levels of ceramides in serum samples from GNEM patients when compared to control samples derived from healthy donors. Moreover, the GNEM serum samples showed the upregulation of Krebs cycle intermediates, in addition to a decrease in oxaloacetic acid. The correlated data gathered in this study can offer a promising diagnostic panel of complex lipids and polar metabolites that can be used in clinic for GNEM in terms of a metabolic fingerprint measurable in a minimally invasive manner.

Background: The global incidence of hypertension, a condition of elevated blood pressure, is rising alarmingly. According to the World Health Organization's Qatar Hypertension Profile for 2023, around 33% of adults are affected by hypertension. This is a significant public health concern that can lead to serious health complications if left untreated. Metabolic dysfunction is a primary cause of hypertension. By studying key biomarkers, we can discover new treatments to improve the lives of those with high blood pressure., Aims: This study aims to use explainable artificial intelligence (XAI) to interpret novel metabolite biosignatures linked to hypertension in Qatari Population., Methods: The study utilized liquid chromatography-mass spectrometry (LC/MS) method to profile metabolites from biosamples of Qatari nationals diagnosed with stage 1 hypertension (n = 224) and controls (n = 554). Metabolon platform was used for the annotation of raw metabolite data generated during the process. A comprehensive series of analytical procedures, including data trimming, imputation, undersampling, feature selection, and biomarker discovery through explainable AI (XAI) models, were meticulously executed to ensure the accuracy and reliability of the results., Results: Elevated Vanillylmandelic acid (VMA) levels are markedly associated with stage 1 hypertension compared to controls. Glycerophosphorylcholine (GPC), N-Stearoylsphingosine (d18:1/18:0)*, and glycine are critical metabolites for accurate hypertension prediction. The light gradient boosting model yielded superior results, underscoring the potential of our research in enhancing hypertension diagnosis and treatment. The model's classification metrics: accuracy (78.13%), precision (78.13%), recall (78.13%), F1-score (78.13%), and AUROC (83.88%) affirm its efficacy. SHapley Additive exPlanations (SHAP) further elucidate the metabolite markers, providing a deeper understanding of the disease's pathology., Conclusion: This study identified novel metabolite biomarkers for precise hypertension diagnosis using XAI, enhancing early detection and intervention in the Qatari population., (© 2024. The Author(s).)

Background: Microcystins are an emergent public health problem. These toxins are secondary metabolites of harmful cyanobacterial blooms, with blooms becoming more prevalent with eutrophication of water. Exposure to microcystins can result in sickness, liver damage, and even death. Over 300 microcystins have been identified to date, with differences in toxicity based on the specific amino acid composition. Because of this diversity in microcystins, as well as the likelihood of detecting as yet undiscovered microcystins, it is vital to establish a methodological workflow to identify any microcystin in a complex sample, regardless of the availability of a reference standard. Additionally, ascribing varying levels of confidence to these identifications is critical to effectively communicate discoveries., Methods: A liquid-chromatography-high-resolution mass spectrometry method was utilized to identify microcystins present in cyanobacterial extracts from a strain of Microcystis aeruginosa and an Aphanizomenon sp. First, microcystin congeners with available standards were identified in the cyanobacterial extract. These known-unknown microcystins were considered to have the highest confidence identifications due to availability of accurate masses, retention times, and library spectra for comparison. Utilizing the spectra of these microcystins, relatively high-abundance diagnostic product-ions were identified and employed to screen the data for additional candidate microcystins. Microcystins without a standard that had an exact mass matching a microcystin published in CyanoMetDB were considered semi-known-unknown microcystins. The remaining microcystins were considered unknown-unknown microcystins. The identities of the microcystins determined herein were additionally supported by product-ion analysis, thiol reactivity, esterification reactions, neutral loss analysis, and literature contextualization., Results: In total, utilizing the systematic workflow presented herein, 23 microcystins were identified in the M. aeruginosa culture, including two not published previously: [d-Asp 3 ]MC-LCit and the incompletely identified MC-L(C 7 H 11 NO 3 )., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Colquhounia root tablets (CRT) and Tripterygium hypoglaucum hutch tablets (THHT), two major Tripterygium hypoglaucum hutch (THH) commercial preparations, have been used to treat chronic kidney diseases or rheumatic diseases. However, there have been no reports on the chemical comparison between CRT and THHT, greatly hindering the understanding of their pharmacological difference as well as their rational application in clinical practice. In the present study, ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry combined with automated data analysis by MS-DIAL software and MS-FLO website was employed to systematically screen and characterize the components in CRT and THHT. Multivariate statistical analysis was used to compare the differences between these two preparations. As a result, up to 92 components were tentatively identified, and 17 of them were characterized for the first time in THH preparations. According to the criteria of variable importance in projection (VIP) >1, p < 0.05, and fold change (FC) > 1.2, 46 components could be screened as major differential chemical components. Among them, phenolic acids, organic acids, amino acids, and diterpenoids were higher in CRT, while the sesquiterpene alkaloids were relatively higher in THHT. This study clarified the chemical material basis and the difference between CRT and THHT, providing a valuable reference for quality control and clinical rational use of THH preparations., (© 2024 Wiley‐VCH GmbH.)

Background: Intensive glycemic control is insufficient to reduce the risk of heart failure in patients with diabetes mellitus. While the hyperglycemic memory in the diabetic cardiomyopathy has been well documented, its underlying mechanisms are not fully understood. The present study tried to investigate whether the dysregulated proteins/biological pathways, which persistently altered in diabetic hearts during normoglycemia, participate in the hyperglycemic memory., Methods: Hearts of streptozotocin-induced diabetic mice, with or without intensive glycemic control using slow-release insulin implants, were collected. Proteins from total heart samples and subcellular fractions were assessed by mass spectrometry, Western blotting, and KEGG pathway enrichment analysis. mRNA sequencing was used to determine whether the persistently altered proteins were regulated at the transcriptional or post-transcriptional level., Results: Western blot validation of several proteins with high pathophysiological importance, including MYH7, HMGCS2, PDK4, and BDH1, indicated that mass spectrometry was able to qualitatively, but not quantitatively, reflect the fold changes of certain proteins in diabetes. Pathway analysis revealed that the peroxisome, PPAR pathway, and fatty acid metabolism could be efficiently rescued by glycemic control. However, dysregulation of oxidative phosphorylation and reactive oxygen species persisted even after normalization of hyperglycemia. Notably, mRNA sequencing revealed that dysregulated proteins in the oxidative phosphorylation pathway were not accompanied by coordinated changes in mRNA levels, indicating post-transcriptional regulation. Moreover, literature review and bioinformatics analysis suggested that hyperglycemia-induced persistent alterations of miRNAs targeted genes from the persistently dysregulated oxidative phosphorylation pathway, whereas, oxidative phosphorylation dysfunction-induced ROS regulated miRNA expression, which thereby might sustained the dysregulation of miRNAs., Conclusions: Glycemic control cannot rescue hyperglycemia-induced alterations of subcellular proteins in the diabetic heart, and persistently altered proteins are involved in multiple functional pathways, including oxidative phosphorylation. These findings might provide novel insights into hyperglycemic memory in diabetic cardiomyopathy., (© 2024 The Author(s). Journal of Diabetes published by Ruijin Hospital, Shanghai Jiaotong University School of Medicine and John Wiley & Sons Australia, Ltd.)

Background: Circulating levels of the antiangiogenic protein, vasoinhibin, derived from the proteolytic cleavage of prolactin (PRL), in prolactinoma are unknown, as is the molecular nature of its isoforms. Dimerization of recombinant vasoinhibin has been reported., Methods: Vasoinhibin in a human serum sample was identified by using preparative electrophoresis with subsequent SDS-PAGE and Western blot analysis, as well as mass spectrometry (MS) and ELISA., Results: MS identified a partial vasoinhibin sequence in a 14-kDa protein band from human serum, which eluted in the 28-kDa fraction from the preparative electrophoresis. Measurement of vasoinhibin levels by ELISA identified a concentration of 284 ng/mL at a PRL level of 9,850 ng/mL. Recombinant human vasoinhibin demonstrated dimerization and multimerization when analyzed directly by SDS-PAGE and Western blot analysis under reducing and non-reducing conditions, as well as after immunoprecipitation., Conclusions: The vasoinhibin sequence was identified in a higher molecular weight fraction, corroborating experi-mental evidence showing the dimerization and aggregation of recombinant human vasoinhibin. This report is sig-nificant, regarding the higher risk of cardiovascular disease and mortality in male patients with hyperprolactin-emia as well as emerging reports of linking PRL and vasoinhibin levels in patients with prolactinoma with left ventricular dysfunction and Takotsubo syndrome.

Autonomous laboratories can accelerate discoveries in chemical synthesis, but this requires automated measurements coupled with reliable decision-making 1,2 . Most autonomous laboratories involve bespoke automated equipment 3-6 , and reaction outcomes are often assessed using a single, hard-wired characterization technique 7 . Any decision-making algorithms 8 must then operate using this narrow range of characterization data 9,10 . By contrast, manual experiments tend to draw on a wider range of instruments to characterize reaction products, and decisions are rarely taken based on one measurement alone. Here we show that a synthesis laboratory can be integrated into an autonomous laboratory by using mobile robots 11-13 that operate equipment and make decisions in a human-like way. Our modular workflow combines mobile robots, an automated synthesis platform, a liquid chromatography-mass spectrometer and a benchtop nuclear magnetic resonance spectrometer. This allows robots to share existing laboratory equipment with human researchers without monopolizing it or requiring extensive redesign. A heuristic decision-maker processes the orthogonal measurement data, selecting successful reactions to take forward and automatically checking the reproducibility of any screening hits. We exemplify this approach in the three areas of structural diversification chemistry, supramolecular host-guest chemistry and photochemical synthesis. This strategy is particularly suited to exploratory chemistry that can yield multiple potential products, as for supramolecular assemblies, where we also extend the method to an autonomous function assay by evaluating host-guest binding properties., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

This study has developed a new targeted methodology for the separation, detection, and quantification of metabolites from the wider energy metabolome of industrially important microorganisms such as Saccharomyces cerevisiae in a single analytical sample. This has been achieved using UHPLC-MS technology in HILIC mode. Absolute concentrations of metabolites nicotinamide adenine dinucleotide (NAD), nicotinamide adenine dinucleotide reduced (NADH), nicotinamide adenine dinucleotide phosphate (NADP), nicotinamide adenine dinucleotide phosphate reduced (NADPH), flavin adenine dinucleotide (FAD), adenosine-monophosphate (AMP), adenosine-diphosphate (ADP), and adenosine-triphosphate (ATP) were determined in a single extraction and analytical methodology. This study demonstrated the development of a rapid, statistically robust, and reproducible methodology through regression calibrations of standard samples from 0.1 to 100 µMol providing a correlation value of r 2  = >0.98 for all metabolites. Sample preparation, extraction and analytical methodologies used showed high accuracy, sensitivity, and recovery. With an LOD and LOQ for the targeted analysis of metabolites from the wider energy metabolism in a single sample and analytical run with the lowest LOD of 0.055 nMol (±0.002) and lowest LOQ of 0.167 nMol (±0.006). This method was then applied to Saccharomyces cerevisiae cell culture to evaluate the methodology in industrially used microbial cultures. Results obtained have been statistically determined to be robust and reproducible through recovery analysis using deuterated and isotopically labelled internal standards AMP- 15 N, ADP- 15 N and ATP-d 14 ., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

The preparation of cellular metabolomics samples and how to achieve comprehensive coverage of different polar metabolites in cell samples in the analysis pose a challenge for cellular metabolomics. In this study, we optimized a metabolomics protocol based on ultra-high-performance liquid chromatography high-resolution mass spectrometry (UPLC/HRMS) for the extraction and detection of metabolites in A549 cells and exploration of the intervention effect of Qi-Yu-San-Long decoction (QYSLD) on A549 cells. The results indicate that the lowest level of ATP leakage was observed when A549 cells were quenched under liquid nitrogen. MeOH/chloroform/H 2 O (1:2:1) extraction yielded more chromatographic peaks and excellent reproducibility, and the relative extraction efficiency of most target metabolites was also high. And we optimized the chromatographic separation conditions in both HILIC and RPLC modes, enabling comprehensive detection and analysis of metabolites with varying polarities. Then, we applied the optimized method to UPLC-Q-TOF/MS-based metabolomics of A549 cells to study the mechanism of QYSLD intervention in non-small cell lung cancer (NSCLC). The CCK-8, EdU staining, and cell cycle assay showed that QYSLD inhibited the proliferation of A549 cells by interfering with the cell cycle and blocking them in the G1 phase. A total of 36 differential metabolites associated with the antitumor effects of QYSLD on NSCLC were identified, mainly involving nicotinate and nicotinamide metabolism, sphingolipid metabolism, and glycerophospholipid metabolism. And western blotting confirmed that the change in 1-methylnicotinamide levels after QYSLD intervention was associated with the inhibition of nicotinamide N-methyltransferase expression in A549 cells., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.)

Hurler-Scheie syndrome (MPS IH/S), also known as mucopolysaccharidosis type I-H/S (MPS IH/S), is a lysosomal storage disorder caused by deficiency of the enzyme alpha-L-iduronidase (IDUA) leading to the accumulation of glycosaminoglycans (GAGs) in various tissues, resulting in a wide range of symptoms affecting different organ systems. Postgenomic omics technologies offer the promise to understand the changes in proteome, phosphoproteome, and phosphorylation-based signaling in MPS IH/S. Accordingly, we report here a large dataset and the proteomic and phosphoproteomic analyses of fibroblasts derived from patients with MPS IH/S ( n = 8) and healthy individuals ( n = 8). We found that protein levels of key lysosomal enzymes such as cathepsin D, prosaposin, arylsulfatases (arylsulfatase A and arylsulfatase B), and IDUA were downregulated. We identified 16,693 unique phosphopeptides, corresponding to 4,605 proteins, in patients with MPS IH/S. We found that proteins related to the cell cycle, mitotic spindle assembly, apoptosis, and cytoskeletal organization were differentially phosphorylated in MPS IH/S. We identified 12 kinases that were differentially phosphorylated, including hyperphosphorylation of cyclin-dependent kinases 1 and 2, hypophosphorylation of myosin light chain kinase, and calcium/calmodulin-dependent protein kinases. Taken together, the findings of the present study indicate significant alterations in proteins involved in cytoskeletal changes, cellular dysfunction, and apoptosis. These new observations significantly contribute to the current understanding of the pathophysiology of MPS IH/S specifically, and the molecular mechanisms involved in the storage of GAGs in MPS more generally. Further translational clinical omics studies are called for to pave the way for diagnostics and therapeutics innovation for patients with MPS IH/S.

Mass spectrometry imaging (MSI)-based spatially resolved metabolomics addresses the limitations inherent in traditional liquid chromatography-tandem mass spectrometry (LC-MS)-based metabolomics, particularly the loss of spatial context within heterogeneous tissues. MSI not only enhances our understanding of disease aetiology but also aids in the identification of biomarkers and the assessment of drug toxicity and therapeutic efficacy by converting invisible metabolites and biological networks into visually rendered image data. In this comprehensive review, we illuminate the key advancements in MSI-driven spatially resolved metabolomics over the past few years. We first outline recent innovations in preprocessing methodologies and MSI instrumentation that improve the sensitivity and comprehensiveness of metabolite detection. We then delve into the progress made in functional visualization techniques, which enhance the precision of metabolite identification and annotation. Ultimately, we discuss the significant potential applications of spatially resolved metabolomics technology in translational medicine and drug development, offering new perspectives for future research and clinical translation. HIGHLIGHTS: MSI-driven spatial metabolomics preserves metabolite spatial information, enhancing disease analysis and biomarker discovery. Advances in MSI technology improve detection sensitivity and accuracy, expanding bioanalytical applications. Enhanced visualization techniques refine metabolite identification and spatial distribution analysis. Integration of MSI with AI promises to advance precision medicine and accelerate drug development., (© 2024 The Author(s). Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.)

Chronic obstructive pulmonary disease (COPD) is India's second largest cause of death and is largely caused by smoking. Asymptomatic smokers develop COPD due to genetic, environmental, and molecular variables, making early screening crucial. Data-independent acquisition mass spectrometry (DIA-MS) based-proteomics offers an unbiased method to analyze proteomic profiles. This study is the first to use DIA-based proteomics to analyze individual serum samples from three distinct male cohorts: healthy individuals ( n = 10), asymptomatic smokers ( n = 10), and COPD patients ( n = 10). This comprehensive approach identified 667 proteins with a 1% false discovery rate. Differentially expressed proteins included 40 in the normal versus asymptomatic comparison, 88 in the COPD versus normal comparison, and 40 in the COPD versus asymptomatic comparison. Among them, protein-associated genes such as PRDX6 , ELANE , PRKCSH , PRTN3 , and MNDA could help differentiate COPD from asymptomatic smokers, while ELANE , H3-3A , IGHE , SLC4A1 , and SERPINA11 could differentiate COPD from healthy subjects. Pathway enrichment and protein-protein interaction analyses revealed significant alterations in hemostasis, immune system functions, fibrin clot formation, and post-translational protein modifications. Key proteins were validated using a parallel reaction monitoring assay. DIA data are available via ProteomeXchange with identifier PXD055242. Our findings reveal key protein classifiers in COPD patients, asymptomatic smokers, and healthy individuals, helping clinicians understand disease pathobiology and improve disease management and quality of life.

Protein structure, including various post-translational modifications and higher-order structures, regulates diverse biological functions. Native mass spectrometry (native MS) is a powerful analytical technique used to determine the masses of biomolecules, such as proteins and their complexes, while preserving their native folding in solution. This method provides structural information on the composition of monomers or complexes and the stoichiometry of subunits within each complex, significantly contributing to protein structural analysis. Native MS has evolved to incorporate top-down approaches, enabling the characterization of proteoforms and non-covalent interactions between metabolites or proteins and specific targets. This perspective highlights the advancements in native MS for intracellular proteins and protein complexes, and discusses future research directions toward cellular biology., (© 2024 John Wiley & Sons Ltd.)

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. "Molecular networks" (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. This paper introduces "molecular hypernetworks" (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their "clique reconstructions", demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

Integrating cross-linking mass spectrometry (XL-MS) into structural biology workflows provides valuable information about the spatial arrangement of amino acid stretches, which can guide elucidation of protein assembly architecture. Additionally, the combination of XL-MS with peptide quantitation techniques is a powerful approach to delineate protein interface dynamics across diverse conditions. While XL-MS is increasingly effective with isolated proteins or small complexes, its application to whole-cell samples poses technical challenges related to analysis depth and throughput. The use of enrichable cross-linkers has greatly improved the detectability of protein interfaces in a proteome-wide scale, facilitating global protein-protein interaction mapping. Therefore, bringing together enrichable cross-linking and multiplexed peptide quantification is an appealing approach to enable comparative characterization of structural attributes of proteins and protein interactions. Here, we combined phospho-enrichable cross-linking with TMT labeling to develop a streamline workflow (PhoXplex) for the detection of differential structural features across a panel of cell lines in a global scale. We achieved deep coverage with quantification of over 9000 cross-links and long loop-links in total including potentially novel interactions. Overlaying AlphaFold predictions and disorder protein annotations enables exploration of the quantitative cross-linking data set, to reveal possible associations between mutations and protein structures. Lastly, we discuss current shortcomings and perspectives for deep whole-cell profiling of protein interfaces at large-scale.

Summary: Joint analysis of mass spectrometry images (MS images) and microscopy images of hematoxylin and eosin (H&E) stained tissues assists pathologists in characterizing the morphological structure of the tissues, and in performing diagnosis. Unfortunately, the analysis is undermined by substantial differences between these modalities in terms of aspect ratios, spatial resolution, number of channels in each image, as well as by large global or small local elastic spatial deformations of one image with respect to the other. Therefore, accurate coregistration of the images is a critical pre-requisite for their joint interpretation. We introduce MSIreg, an open-source R package for coregistration of MSI and H&E images. MSIreg is designed for high-dimensional MSI experiments where each spatial location is represented by thousands of mass features. Unlike most existing coregistration methods, MSIreg implements a landmark free workflow, and quantitative metrics for performance evaluation. We evaluate the performance of MSIreg on six case studies, including coregistration of contiguous tissues with large deformations, as well as simultaneous coregistration of 29 tissue microarray cores., Availability and Implementation: The R package, installation instructions, and fully reproducible vignettes describing methods and Case Studies are available open-source under the GPL-3.0 license at https://github.com/sslakkimsetty/msireg/., (© The Author(s) 2024. Published by Oxford University Press.)

Glioblastoma multiforme (GBM) is the most prevalent and aggressive brain tumor found in adult humans with a poor prognosis and average survival of 14-15 months. In order to have a comprehensive understanding of proteome and identify novel therapeutic targets, this study focused mainly on the differentially abundant proteins (DAPs) of Ras V12 -induced GBM. Ras V12 is a constitutively active Ras mutant form essential for tumor progression by continuously activating signaling pathways leading to uncontrolled tumor growth. This study used a transgenic Drosophila model with Ras V12 overexpression using the repo-GAL4 driver line, specifically in glial cells, to study GBM. The high-resolution mass spectrometry (HRMS)-based proteomic analysis of the GBM larval central nervous system identified three novel DAPs specific to mitochondria. These DAPs, probable maleylacetoacetate isomerase 2 (Q9VHD2), bifunctional methylene tetrahydrofolate dehydrogenase (Q04448), and glutamine synthetase1 (P20477), identified through HRMS were further validated by qRT-PCR. The protein-protein interaction analysis revealed interactions between Ras V12 and DAPs, with functional links to mitochondrial dynamics regulators such as Drp1, Marf, Parkin, and HtrA2. Notably, altered expressions of Q9VHD2, P20477, and Q04448 were observed during GBM progression, which offers new insights into the involvement of mitochondrial dynamic regulators in Ras V12 -induced GBM pathophysiology.

Liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS)-based methods have become the gold standard methodology for the comprehensive profiling of the human plasma lipidome. However, both the complexity of lipid chemistry and LC-HRMS-associated data pose challenges to the characterization of this biological matrix. In accordance with the current consensus of quality requirements for LC-HRMS lipidomics data, we aimed to characterize the NIST® Standard Reference Material for Human Plasma (SRM 1950) using an LC-ESI(+/-)-MS method compatible with high-throughput lipidome profiling. We generated a highly curated lipid database with increased coverage, quality, and consistency, including additional quality assurance procedures involving adduct formation, within-method m/z evaluation, retention behavior of species within lipid chain isomers, and expert-driven resolution of isomeric and isobaric interferences. As a proof-of-concept, we showed the utility of our in-house LC-MS lipidomic database -consisting of 592 lipid entries- for the fast, comprehensive, and reliable lipidomic profiling of the human plasma from healthy human volunteers. We are confident that the implementation of this robust resource and methodology will have a significant impact by reducing data redundancy and the current delays and bottlenecks in untargeted plasma lipidomic studies., Competing Interests: Conflict of Interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Ginger, which is the rhizome of Zingiber officinale Roscoe, is widely distributed and consumed. The taste and aroma of ginger differ depending on its geographical origin. To distinguish the origin of ginger, ginger extracts from Korea, Peru, and China were analyzed using ultra-performance liquid chromatography (UPLC) coupled to quadrupole time-of-flight mass spectrometry and nuclear magnetic resonance spectroscopy for metabolomics. Korean ginger contained more 10-gingerol, and Peruvian ginger contained more 6-gingerol and 8-gingerol. Several amino acids negatively correlated with gingerols, suggesting that amino acids are related to the biosynthesis of gingerols. Sugars, which are the main energy source, positively correlated with gingerols. Organic acids and gingerols were also positively correlated, indicating that both organic acids and gingerols are used for adaptation to the environment surrounding the root. We confirmed the features of the primary and secondary metabolites by verifying the correlation between metabolites and differences in metabolites according to ginger origin. We additionally optimized a simultaneous UPLC analytical method of marker compounds for the simple and rapid quality control of ginger. This method exhibits excellent linearity, sensitivity, and reproducibility. Using metabolomics, differences in origin were observed, and a low-end equipment analysis method for quality control can be used in the ginger industry., (© 2024 The Author(s). Journal of Food Science published by Wiley Periodicals LLC on behalf of Institute of Food Technologists.)

Bile acid (BA) is one of the main active components of bile and has multiple isomers, the structure or content of its isomers often changes due to diseases and other health problems; thus, the accurate detection of BA isomers is very important. In this study, two groups of BA isomers of glycine-conjugated BAs and taurine-conjugated BAs were simultaneously separated and quantitatively analyzed by ion mobility mass spectrometry (IM-MS). Especially, baseline mobility separation between the isomers was achieved by the formation of binary complexes via simple interaction with spiramycin (SPM), for which a separation resolution (R p-p ) of 1.96 was reached. Moreover, BA isomers were quantitatively analyzed, and the limit of detection (LOD) of absolute quantification for TCDCA/TUDCA and GUDCA/GCDCA/GHDCA was 0.514 and 0.611 ng∙mL -1 , respectively; the LODs for molar ratio ranges of relative quantification for TCDCA/TUDCA, GUDCA/GHDCA, and GCDCA/GHDCA were 1:18-30:1, 1:18-21:1, and 1:19-21:1, respectively. Additionally, BA isomers analyzed in pig bile powder and bear bile powder were measured, which were in good consistency with those labeled, revealing the differences in BA composition and content between the two powders. Finally, BA detection and recovery analyses were performed on serum samples, with a recovery rate of ≥73.69%, RSD of ≤6.8%, and S R (standard deviation of recoveries, the degree of difference between measured values and average recovery) of ≤1.27. Due to the simple, rapid, and lack of need for complex sample preparation and chromatographic separation, the proposed method can be an effective method for BA detection in practical samples., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.)

Bile salt hydrolase (BSH), a pivotal enzyme in cholesterol management, holds significant promise in both human and animal subjects. This study investigated the effect of fermentation dynamics in Heyndrickxia coagulans ATCC 7050 and Lactiplantibacillus plantarum ATCC 10012 to enhance BSH production. Cultivation of cultures in MRS and M17 media revealed that MRS medium enhanced BSH production by 235.98 % in H. coagulans ATCC 7050 and 147.37 % in L. plantarum ATCC 10012, compared to M 17 medium. Additionally, varying oxygen concentration levels indicated that H. coagulans ATCC 7050 exhibited its minimum doubling time of 79.8 ± 0.64 min in anaerobic conditions, whereas L.plantarum ATCC 10012 demonstrated its minimum doubling time of 85.5 ± 1.2 min under microaerophilic conditions. However, their highest BSH activity was observed during the stationary phase under anaerobic conditions, yielding 17.14 ± 0.78 U/mL by H. coagulans ATCC 7050 and 19.04 ± 0.81 U/mL by L.plantarum ATCC 10012. Furthermore, it was observed that both organisms did not retain BSH within their cells. BSH activity was assessed using ninhydrin assay that detected free taurine liberated from sodium taurocholate. However, ninhydrin can yield false-positive results owing to its interaction with other free amino acids. To subjugate this limitation, the study introduced a novel and sensitive HPTLC-MS method capable of accurately detecting taurine. By comprehending fermentation dynamics and selecting appropriate conditions, BSH production increased 2.1-fold in both organisms. These findings illuminate critical insights, offering a pathway for novel strategies to enhance the BSH-producing capabilities of these LAB strains., Competing Interests: Declaration of competing interest The authors state that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in the paper titled “ Fermentation dynamics of bile salt hydrolase production in Heyndrickxia coagulans ATCC 7050 and Lactiplantibacillus plantarum ATCC 10012: Addressing ninhydrin assay limitations with a novel HPTLC-MS method”., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The liquid chromatography-high resolution mass spectrometry (LC-HRMS) technique enables the detection of phytochemicals present in the extracts. LC-HRMS-generated mass list showed abundant compounds of interest, artifacts, and primary metabolites. The identification of a secondary metabolite of interest within the extract is very challenging. We hypothesized that identifying the "new metabolite" in the whole metabolome is more challenging than identifying it within the class of metabolites. The proposed prioritization strategy focused on the elimination of unknown and prioritizing the known class of secondary metabolites to identify new metabolites. The prioritization strategy demonstrated on Murraya paniculata for the identification of new metabolites. LC-HRMS-generated information is used as a filter to target the secondary metabolite and the new metabolites. This strategy successfully annotated the new coumarin and coumarin alkaloids from the mass list of 1448 metabolites. Varanasine ( 3 ), schroffanone ( 4 ), schroffanene ( 5 ), and O -methylmurraol ( 9 ) are new compounds, and coumarin ( 1 , 2 , and 6-8 ) are known. Varanasine ( 3 ) is the first naturally occurring 7-aminocoumarin with additional N -formyl functionality. The isolates were screened for cytotoxicity against the panel of cancer cell lines. Varanasine ( 3 ) and minumicrollin ( 6 ) showed significant cytotoxicity and apoptosis-inducing potential. The immunoblot analysis confirmed inhibition of apoptotic protein PARP-1 and caspase-3 expression by 3 and 6 .

Biological sex is key information for archeological and forensic studies, which can be determined by proteomics. However, the lack of a standardized approach for fast and accurate sex identification currently limits the reach of proteomics applications. Here, we introduce a streamlined mass spectrometry (MS)-based workflow for the determination of biological sex using human dental enamel. Our approach builds on a minimally invasive sampling strategy by acid etching, a rapid online liquid chromatography (LC) gradient coupled to a high-resolution parallel reaction monitoring (PRM) assay allowing for a throughput of 200 samples per day (SPD) with high quantitative performance enabling confident identification of both males and females. Additionally, we developed a streamlined data analysis pipeline and integrated it into a Shiny interface for ease of use. The method was first developed and optimized using modern teeth and then validated in an independent set of deciduous teeth of known sex. Finally, the assay was successfully applied to archeological material, enabling the analysis of over 300 individuals. We demonstrate unprecedented performance and scalability, speeding up MS analysis by 10-fold compared to conventional proteomics-based sex identification methods. This work paves the way for large-scale archeological or forensic studies enabling the investigation of entire populations rather than focusing on individual high-profile specimens. Data are available via ProteomeXchange with the identifier PXD049326.

Background: While REIMS technology has successfully been demonstrated for the histological identification of ex-vivo breast tumor tissues, questions regarding the robustness of the approach and the possibility of tumor molecular diagnostics still remain unanswered. In the current study, we set out to determine whether it is possible to acquire cross-comparable REIMS datasets at multiple sites for the identification of breast tumors and subtypes., Methods: A consortium of four sites with three of them having access to fresh surgical tissue samples performed tissue analysis using identical REIMS setups and protocols. Overall, 21 breast cancer specimens containing pathology-validated tumor and adipose tissues were analyzed and results were compared using uni- and multivariate statistics on normal, WT and PIK3CA mutant ductal carcinomas., Results: Statistical analysis of data from standards showed significant differences between sites and individual users. However, the multivariate classification models created from breast cancer data elicited 97.1% and 98.6% correct classification for leave-one-site-out and leave-one-patient-out cross validation. Molecular subtypes represented by PIK3CA mutation gave consistent results across sites., Conclusions: The results clearly demonstrate the feasibility of creating and using global classification models for a REIMS-based margin assessment tool, supporting the clinical translatability of the approach., (© 2024. Waters Technologies Corporation and The Author(s).)

It is of significant importance to public health that reliable monitoring of nitroimidazoles be conducted, while certified reference materials (CRMs) are essential for accurate and reliable detection. A project has been initiated with the objective of developing nitroimidazole purity CRMs to ensure that results from nationwide monitoring laboratories for nitroimidazoles in antibiotic residues can be compared and traced. The candidates were successively characterized in terms of their structure by means of infrared (IR) spectroscopy and mass spectrometry (MS). The mass balance (MB) method and the quantitative nuclear magnetic resonance (qNMR) method were utilized to determine the purity of nitroimidazoles with remarkable accuracy. Furthermore, a methodical investigation was conducted on homogeneity, stability, and uncertainty. Six nitroimidazole purity CRMs, including tinidazole (GBW09252), secnidazole (GBW09286), ronidazole (GBW09288), metronidazole (GBW(E)090755), dimetridazole (GBW(E)090819), and ornidazole (GBW(E)090820), were finally manufactured following authorization from China's State Administration for Market Regulation (SAMR). By using these CRMs, it is possible to improve the traceability, accuracy, and comparability of nitroimidazole measurements in a range of agricultural products, protecting public health., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.)

Xiao-Jian-Zhong-Tang (XJZT) has the effect of warming the middle and tonifying the deficiency, easing the urgency and relieving pain according to the theory of traditional Chinese medicine (TCM), and is able to treat spleen deficiency type chronic atrophic gastritis (CAG). Metabolites of TCM in cecum contents are common metabolites of intestinal bacteria and hosts, which can reflect the metabolic status in disease states. The present work was performed to study the effect of XJZT against CAG coupled with the cecal metabolites analysis and bioinformatics. A total of nine prototypical components and 144 metabolites were firstly identified in the cecum metabolites of XJZT using ultra-high performance liquid chromatography added to the quadrupole-time of flight mass spectrometry (UHPLC-Q-TOF/MS), which underwent the metabolism of oxidation, reduction, methylation, and glucuronic acid reaction Furthermore, different prototypical compounds might metabolize into identical metabolites in the presence of intestinal flora. Bioinformatics was further used to correlate these metabolites with the disease and intestinal flora. Components and targets were screened by Cytoscape, and molecular docking of key targets and core components showed good binding ability. This study provided important information for exploring the mechanism of TCM formulae., (© 2024 John Wiley & Sons Ltd.)

Modern mass spectrometry technology allows for extensive sequencing of the ~ 25 kDa subunits of monoclonal antibodies (mAbs) produced by IdeS proteolysis followed by disulfide bond reduction, an approach known as middle-down mass spectrometry (MD MS). However, the spectral congestion of tandem mass spectra of large polypeptides dramatically complicates fragment ion assignment. Here, we report the development and benchmark of an MD MS strategy based on the combination of different ion fragmentation techniques with proton transfer charge reduction (PTCR) to simplify the gas-phase sequencing of mAb subunits. Applied on the liquid chromatography time scale using an Orbitrap Tribrid mass spectrometer, PTCR produces easy-to-interpret mass spectra with limited ion signal overlap. We demonstrate that the accurate estimation of the number of charges submitted to the Orbitrap mass analyzer after PTCR allows for the detection of charge-reduced product ions over a wide mass-over-charge (m/z) window with low parts per million m/z accuracy. Therefore, PTCR-based MD MS analysis increases not only sequence coverage, number of uniquely identified fragments, and number of assigned complementary ion pairs, but also the general confidence in the assignment of subunit fragments. This data acquisition method can be readily applied to any class of mAbs without an apparent need for optimization, and benefits from the high resolving power of the Orbitrap mass analyzer to return sequence coverage of individual subunits exceeding 80% in a single run, and > 90% when just two experiments are combined., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.)

Affinity-oriented online ligand screening with LC coupled to different detectors is widely popular to capture active compounds from herbal medicines (HMs). However, false-positive extensively occurs because insufficient information is recorded for the existence and stability of ligand-protein complex. Here, efforts were made to advance the hit confidences via configuring post-column infusion-LC-energy-resolved-affinity MS (PCI-LC-ER-AMS) to achieve "four-in-one" monitoring of: 1) response decrement of potential ligands; 2) response decrement of protein; 3) ions relating to ligand-protein complexes; and 4) ligand-protein binding strength. Ligand fishing for Cyt C from HMs was conducted as a proof-of-concept. For utility justification, a mimic sample containing twelve well-defined ligands and two negative controls underwent LC separation and met Cyt C prior to Qtof-MS measurements. Compared to Cyt C- or ligand-free assay, twelve ligands instead of negative controls showed response decrements that were consistent with twelve negative peaks observed at retention times corresponding to the ligands in Cyt C ion current chromatogram. Serial ions correlating to each ligand-Cyt C complex were observed. After recording breakdown graphs, optimal collision energy (OCE) corresponding to the non-covalent bond dissociation was positively correlated with binding strength. Two HMs including Scutellariae Radix (SR) and Aconiti Lateralis Radix Preparata were investigated. Consequently, 24 compounds were merely fished from SR, and particularly, flavonoid glycosides exhibited greater OCEs and also binding strengths over aglycones. Affinity assays and cellular evaluations consolidated the significant interactions between each captured compound and Cyt C. Overall, PCI-LC-ER-AMS is eligible for confidence-enhanced online ligand screening for Cyt C from HMs through "four-in-one" measurement., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Lupins, and other legumes, have attained international interest due to their reported remarkable health benefits. Currently, the seed coats are discarded as waste or animal feed. The research presented here summarizes the potential for incorporating the seed coats into 'whole grain' foods. We aimed to identify metabolites found in the seed coats of nine commercial Australian cultivars of lupin (Lupinus angustifolius and L. albus species), and to evaluate and compare their functional, nutritional, antioxidant, and antidiabetic properties, along with in silico exploration of mechanisms of action for selected identified secondary metabolites. The seed coats were found to contain 79 to 90% dietary fibers and substantial quantity of essential macrometals. LC-QTOF MS-based, untargeted bioactive metabolite profiling explored a total of 673 chemical entities, and identified 63 bioactive secondary metabolites including: biophenols, unsaturated fatty acids, triterpenoids, alkaloids, and dietary prebiotics (insoluble fibers). The seed coats from these nine cultivars show substantial antioxidant activity. The cultivars of L. angustifolius inhibit α-amylase and α-glucosidase significantly in vitro. Moreover, in silico docking and dynamic simulation along with ADME/T analysis suggest that quercetin 3-methyl ether and 8-C-methylquercetin 3-methyl ether as molecules, novel in lupin seed coats, are responsible for the α-amylase and α-glucosidase inhibition. The findings indicated that lupin seed coats might be beneficial food components, rather than be discarded as 'mill waste'., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Cytochrome P450 enzymes (CYPs) represent a diverse family of heme-thiolate proteins involved in the metabolism of a wide range of endogenous compounds and xenobiotics. In recent years, proteomics and metabolomics have been used to obtain a comprehensive insight into the role of CYPs in health and disease aspects. The objective of the present work is to better understand the status of proteomics and metabolomics in CYP research in optimizing therapeutics and patient safety from a personalized medicine approach. The literature used in this narrative review was procured by electronic search of PubMed, Medline, Embase, and Google Scholar databases. The following keywords were used in combination to identify related literature: "proteomics," "metabolomics," "cytochrome P450," "drug metabolism," "disease conditions," "proteome," "liquid chromatography-mass spectrometry," "integration," "metabolites," "pathological conditions." We reviewed studies that utilized proteomics and metabolomics approaches to explore the multifaceted roles of CYPs in identifying disease markers and determining the contribution of CYP enzymes in developing treatment strategies. The applications of various cutting-edge analytical techniques, including liquid chromatography-mass spectrometry, nuclear magnetic resonance, and bioinformatics analyses in CYP proteomics and metabolomics studies, have been highlighted. The identification of CYP enzymes through metabolomics and/or proteomics in various disease conditions provides key information in the diagnostic and therapeutic landscape. Leveraging both proteomics and metabolomics presents a powerful approach for an exhaustive exploration of the multifaceted roles played by CYP enzymes in personalized medicine. Proteomics and metabolomics have enabled researchers to unravel the complex connection between CYP enzymes and metabolic markers associated with specific diseases. As technology and methodologies evolve, an integrated approach promises to further elucidate the role of CYPs in human health and disease, potentially ushering in a new era of personalized medicine., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

Pharmaceuticals released into the aquatic and soil environments can be absorbed by plants and soil organisms, potentially leading to the formation of unknown metabolites that may negatively affect these organisms or contaminate the food chain. The aim of this study was to identify pharmaceutical metabolites through a triplet approach for metabolite structure prediction (software-based predictions, literature review, and known common metabolic pathways), followed by generating in silico mass spectral libraries and applying various mass spectrometry modes for untargeted LC-qTOF analysis. Therefore, Eisenia fetida and Lactuca sativa were exposed to a pharmaceutical mixture (atenolol, enrofloxacin, erythromycin, ketoprofen, sulfametoxazole, tetracycline) under hydroponic and soil conditions at environmentally relevant concentrations. Samples collected at different time points were extracted using QuEChERS and analyzed with LC-qTOF in data-dependent (DDA) and data-independent (DIA) acquisition modes, applying both positive and negative electrospray ionization. The triplet approach for metabolite structure prediction yielded a total of 3762 pharmaceutical metabolites, and an in silico mass spectral library was created based on these predicted metabolites. This approach resulted in the identification of 26 statistically significant metabolites (p < 0.05), with DDA + and DDA - outperforming DIA modes by successfully detecting 56/67 sample type:metabolite combinations. Lettuce roots had the highest metabolite count (26), followed by leaves (6) and earthworms (2). Despite the lower metabolite count, earthworms showed the highest peak intensities, closely followed by roots, with leaves displaying the lowest intensities. Common metabolic reactions observed included hydroxylation, decarboxylation, acetylation, and glucosidation, with ketoprofen-related metabolites being the most prevalent, totaling 12 distinct metabolites. In conclusion, we developed a high-throughput workflow combining open-source software with LC-HRMS for identifying unknown metabolites across various sample types., (© 2024. The Author(s).)

Infectious diseases, driven by a diverse array of pathogens, can swiftly undermine public health systems. Accurate diagnosis and treatment of infectious diseases-centered around the identification of biomarkers and the elucidation of disease mechanisms-are in dire need of more versatile and practical analytical approaches. Mass spectrometry (MS)-based molecular profiling methods can deliver a wealth of information on a range of functional molecules, including nucleic acids, proteins, and metabolites. While MS-driven omics analyses can yield vast datasets, the sheer complexity and multi-dimensionality of MS data can significantly hinder the identification and characterization of functional molecules within specific biological processes and events. Artificial intelligence (AI) emerges as a potent complementary tool that can substantially enhance the processing and interpretation of MS data. AI applications in this context lead to the reduction of spurious signals, the improvement of precision, the creation of standardized analytical frameworks, and the increase of data integration efficiency. This critical review emphasizes the pivotal roles of MS based omics strategies in the discovery of biomarkers and the clarification of infectious diseases. Additionally, the review underscores the transformative ability of AI techniques to enhance the utility of MS-based molecular profiling in the field of infectious diseases by refining the quality and practicality of data produced from omics analyses. In conclusion, we advocate for a forward-looking strategy that integrates AI with MS-based molecular profiling. This integration aims to transform the analytical landscape and the performance of biological molecule characterization, potentially down to the single-cell level. Such advancements are anticipated to propel the development of AI-driven predictive models, thus improving the monitoring of diagnostics and therapeutic discovery for the ongoing challenge related to infectious diseases., Competing Interests: Declaration of competing interest All authors declare that they have no conflicts of interest., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The analysis of steroids for endocrine disorders is in transition from immunoassay of individual steroids to more specific chromatographic and mass spectrometric methods with simultaneous determination of several steroids. Gas chromatography (GC) and liquid chromatography (LC) coupled with mass spectrometry (MS) offer unrivalled analytical capability for steroid analysis. These specialist techniques were often judged to be valuable only in a research laboratory but this is no longer the case. In a urinary steroid profile up to 30 steroids are identified with concentrations and excretion rates reported in a number of ways. The assays must accommodate the wide range in steroid concentrations in biological fluids from micromolar for dehydroepiandrosterone sulphate (DHEAS) to picomolar for oestradiol and aldosterone. For plasma concentrations, panels of 5-20 steroids are reported. The profile results are complex and interpretation is a real challenge in order to inform clinicians of likely implications. Although artificial intelligence and machine learning will in time generate reports from the analysis this is a way off being adopted into clinical practice. This review offers guidance on current interpretation of the data from steroid determinations in clinical practice. Using this approach more laboratories can use the techniques to answer clinical questions and offer broader interpretation of the results so that the clinician can understand the conclusion for the steroid defect, and can be advised to program further tests if necessary and instigate treatment. The biochemistry is part of the patient workup and a clinician led multidisciplinary team discussion of the results will be required for challenging patients. The laboratory will have to consider cost implications, bearing in mind that staff costs are the highest component. GC-MS and LC-MS/MS analysis of steroids are the choices. Steroid profiling has enormous potential to improve diagnosis of adrenal disorders and should be adopted in more laboratories in favour of the cheap, non-specific immunological methods., (Copyright © 2024. Published by Elsevier Inc.)

Background: Acute lung injury (ALI) is a respiratory disease characterized by pulmonary inflammation and increased microvascular permeability, resulting in significant mortality and a lack of effective pharmacological treatment. Huangqin Qingfei Decoction (HQQFD), a Traditional Chinese Medicine (TCM) prescription known for its heat-clearing and detoxifying properties, has shown efficacy in treating ALI. However, the underlying mechanisms of HQQFD to against ALI remain to be elucidated., Purpose: This study aims to discover the mechanisms and the principal bioactive compounds contributing to HQQFD's protective effects in the treatment of ALI., Methods: An ultra-high performance liquid chromatography-Orbitrap high-resolution mass spectrometry (UHPLC-Orbitrap HRMS) method was employed to characterize the chemical profile in HQQFD and xenobiotics (prototypes and metabolites) in rat lung tissue. Based on prototypes identified, a symptom-guided pharmacological networks of ALI were performed. Molecular docking and extensive literature reviews were conducted to validate our findings., Results: A total of 105 compounds were identified in HQQFD, and a total of 194 HQQFD-related xenobiotics (30 prototypes and 163 metabolites) were detected in rat lung tissue. Based on prototypes identified in rat lung, a symptom-guided pharmacological networks of ALI were constructed, AKT1, TNF, EGFR, MMP2, GSK3B, STAT3, MAPK8, IL-6, CDK2 and TP53 were finally identified as key targets. Subsequently, 11 compounds with protective and therapeutic activity were selected by molecular docking analysis, including genipin 1-gentiobioside, chrysin-6-C-α-L-arabinoside-8-C-β-d-glucoside, scutellarin, chrysin-6-C-β-d-glucoside-8-C-α-L-arabinoside, 6''-O-[(E)-p-coumaroyl] genipin-gentiobioside, apigenin 7-O-glucoside, baicalin, dihydrobaicalin, wogonoside, crocin I, crocetin. Bioinformatics and literature analysis suggested that, baicalin, wogonoside, genipin 1-gentiobioside and crocetin may be the primary active compounds of HQQFD, potentially targeting GSK3B, MAPK8, IL-6, AKT1 and TNF for HQQFD in addressing ALI. The therapeutic effects of HQQFD may be mediated through the IL-17 and PI3K-AKT signaling pathways., Conclusion: The predominant components of HQQFD against ALI are baicalein, wogonoside, genipin 1-gentiobiosid and crocetin, with the IL-17 and PI3K-AKT pathways playing crucial roles. This study provides a foundational guide for future research and introduces innovative methods for exploring the mechanisms of other drug combinations or TCM formulas., Competing Interests: Declaration of competing interest The authors declare that there are no conflicts of interest., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

Membranous nephropathy (MN) results from accumulation of antigen-antibody immune complexes along the subepithelial region of the glomerular basement membranes. Over the last years, 13 target antigens have been discovered and include PLA2R, THSD7A, EXT1 and EXT2, NELL1, SEMA3B, NCAM1, CNTN1, HTRA1, FAT1, PCDH7, NTNG1, PCSK6 and NDNF, accounting for 80-90% of MN antigens. MN associated with many of these antigens have distinctive clinicopathologic findings. It is important to accurately identify the antigen in MN. Immunohistochemical (IHC) and/or immunofluorescence (IF) methods are currently used to detect PLA2R, THSD7A, NELL1, SEMA3B and EXT1/EXT2. However, for the remaining antigens, IHC/IF methods do not exist and are not practical for detection. Here, we developed laser microdissection-based mass spectrometry methodology (LMD/MS) as a one-stop clinical test for the detection of MN antigens using paraffin-embedded kidney biopsy tissue. The LMD/MS test was validated in two steps. LMD/MS was used to detect the antigen in 75 cases of MN with known antigens and correctly identified the antigen in all these cases. Next, LMD/MS was used to identify the antigen in 61 MN cases where the antigen was unknown and identified one of the known antigens in 40 of 61 cases including many of the less common antigens. This lower-than-expected detection rate is explained by intentional enrichment of the cohort with PLA2R-negative MN. Overall, PLA2R was identified in 16.4%, one of the other antigens detected in 49.1%, and in the remaining 34.5% of cases, none of the above antigens was detected. Thus, LMD/MS is an extremely useful and reliable method for the detection of known MN antigens and possibly indicating an unknown MN antigen for eventual discovery., (Copyright © 2024 International Society of Nephrology. Published by Elsevier Inc. All rights reserved.)

Per- and polyfluoroalkyl substances (PFASs) have attracted increasing attention due to their persistence in the environment and potential adverse effects on human and animal health. The detection and quantification of PFASs in livestock could substantially contribute to monitoring their presence within the food chain. We developed a targeted quantification method for 34 PFASs in livestock serum by liquid chromatography-high-resolution mass spectrometry (LC-HRMS). We used protein precipitation for serum sample extraction and accurate mass measurement of targeted PFAS compounds for quantification. We validated the method with various analytical parameters, achieving accuracy of 70-120% and precision of <20%. The method also demonstrated good analytical sensitivity, with a limit of detection of <0.051 ng/mL and a limit of quantification of <0.175 ng/mL. When applying the developed method to actual serum samples from a variety of livestock, we successfully identified and quantified various PFASs in different livestock species. Our method has the potential to be a valuable tool for veterinary laboratory analysis of PFAS contamination in livestock., Competing Interests: Declaration of conflicting interestsThe authors declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Dried blood spot (DBS) technique has become a new popular topic in anti-doping field in recent years due to its advantages of sample stability and easy operation. It can be employed as a supplementary method to routine urine analysis. However, the small volume of DBS samples (usually 10-20 μL) significantly reduces the application value of this technique. Therefore, the development of sensitive detection methods for the analysis of prohibited substances in DBS is particularly important. In this study, based on the characteristics of low molecular mass peptide (LMMP) drugs, systematic optimization strategies were utilized for the first time to establish a sensitive detection method for LMMPs in DBS. Without using DMSO to enhance mass spectrometry ionization efficiency of peptides, the limits of detection (LOD) ranged between 0.05 and 3.74 ng/mL, significantly better than the previously reported method (0.5-20 ng/mL). This method was validated according to the guidelines of the World Anti-Doping Agency (WADA), and corresponding post-administration study was conducted, demonstrating that the method could be applied to routine analysis of LMMP drugs in DBS. Moreover, since DMSO is not involved, this method also has the potential to simultaneously detect both LMMP and small molecular drugs., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.)

A new flow batch (FB) system for chemical vapor generation (CVG) is proposed for mercury (Hg) determination in fish. An inductively coupled plasma mass spectrometer was used as a detector. Low-cost peristaltic mini pumps were used to propel the solutions and different configurations of FB systems (reactor/gas/liquid separator) were studied. The proposed configuration of the FB-CVG system allows good sensitivity, low limit of detection (LOD) and low consumption of reagents and sample solutions. In summary, only 1 mL of reductant, 1 mL of acid and 0.16 mL of sample are needed. The proposed method has good linearity, precision (better than 5 %), LOD of 0.008 μg g -1 and LOQ of 0.012 μg g -1 , and high sample throughput, allowing 90 measurements/h. The accuracy of the method was evaluated through the analysis of a certified reference material (DOLT-4 Dogfish Liver), whose result is in good agreement with certified value (t-test with 95 % confidence level) and the quantification limit meets current legislations, of 1.0 μg g -1 (Brazil) and 0.3 μg g -1  (EU). In addition, analyte recovery test was done, where Hg recovery was better than 95 %, demonstrating the good analytical performance of the method. To demonstrate the applicability of the method, five samples of fish tissue (muscle) were analyzed. The proposed FB-CVG system, in addition to being low cost, is robust and requires only the volume of reagents necessary for Hg vapor generation, producing a very low amount of waste. It can be concluded that the proposed system can be used for routine analysis for Hg determination in fish tissue. It is worth noting that with the appropriate adjustments, the system can be coupled to different Hg detectors., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

New psychoactive substances are produced and marketed to mimic the effects of their illicit counterparts and to attempt to evade drug tests and prosecution. Here, we present the optimisation, validation and application of an analytical method using liquid chromatography-time-of-flight mass spectrometry to detect and quantify 37 new psychoactive substances and illicit substances in wastewater from South Wales, UK, using a targeted analysis method. Sample preparation was performed using solid-phase extraction with Oasis HLB cartridges. The LC separation was performed using a YMC-Triart Phenyl 450 bar column (12 nm, 5 μm, 100 × 3 mm) which provided good separation and resolution for all targeted analytes with a run time of 9 min. The method was validated using the following parameters: sensitivity, selectivity, linearity, accuracy, precision, recovery and matrix effects. The method was then applied to influent wastewater samples collected from two wastewater treatment plants in Wales, UK., (© 2024 The Authors. Drug Testing and Analysis published by John Wiley & Sons Ltd.)

Respiratory health is negatively influenced by the dimensions and constituents of particulate matter (PM). Although mass concentration is widely acknowledged to be key to assessing dust retention by urban trees, the role of plant leaves in filtering PM from the urban atmosphere, particularly regarding the particle dimensions and chemical constituents of retained PM on the leaf, remains elusive. Here we combined single-particle aerosol mass spectrometry and a particle resuspension chamber to investigate how urban tree species capture PM constituents. Results indicate that leaves are efficient in capturing relatively larger particles (1.0-2.0 μm). Compositionally, airborne particles were mostly composed of elemental carbon (EC, 20%), organic carbon (OC, 17%), and secondary reaction products (13%). However, leaf surfaces revealed a preference for retaining crustal species, comprising 55% of captured particulates. Notably, specific tree species demonstrated varied affinities for different PM constituents: Osmanthus fragrans Lour. predominantly captured levoglucosan (LEV), indicative of its efficiency against biomass burning particles, whereas Cinnamomum camphora (L.) J.Presl and Sabina chinensis var. kaizuca W.C.Cheng & W.T.Wang were more effective in capturing heavy metals (HMs). XGBoost modelling identified indicator ions, e.g., CN - , NO 3 - , NO 2 - , PO 3 - , with SHAP values surpassing 0.035, suggesting a preferential adsorption of these ions among different tree species. These findings demonstrate that the particulate capture efficiency of urban tree species varies with species-specific leaf properties, particularly in their ability to selectively adsorb particles containing hazardous constituents such as LEV and HMs. This study provides a scientific basis for the strategic selection of tree species in urban forestry initiatives aimed at improving air quality and public health., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Correlative imaging of cutaneous tumors provides additional information to the standard histopathologic examination. However, the joint progress in the establishment of analytical techniques, such as Laser-Induced Breakdown Spectroscopy (LIBS) and Laser Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS) in clinical practice is still limited. Their combination provides complementary information as it is also shown in our study in terms of major biotic (Ca, Mg, and P) and trace (Cu and Zn) elements. To elucidate changes in the elemental composition in tumors, we have compiled a set of malignant tumors (Squamous Cell Carcinoma, Basal Cell Carcinoma, Malignant Melanoma, and Epithelioid Angiosarcoma), one benign tumor (Pigmented Nevus) and one healthy-skin sample. The data processing was based on a methodological pipeline involving binary image registration and affine transformation. Thus, our paper brings a feasibility study of a practical methodological concept that enables us to compare LIBS and LA-ICP-MS results despite the mutual spatial distortion of original elemental images. Moreover, we also show that LIBS could be a sufficient pre-screening method even for a larger number of samples according to the speed and reproducibility of the analyses. Whereas LA-ICP-MS could serve as a ground truth and reference technique for preselected samples., Competing Interests: Declaration of competing interest All authors hereby declare that they have no conflict of interest with regard to the presented study. Moreover, the ethical issues related to the handling and analysis of clinical samples (biopsies of human cutaneous tumors and healthy skin) were done under the approval of the ethical committee of the Hradec Králové University Hospital (ref. number 201805 S08P) where the patients were treated., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: Taurine (2-aminoethanesulfonic acid) is an essential β-amino acid, which is one of the most abundant intracellular amino acid component in humans. The level of free taurine in human milk is higher than in bovine milk. Since taurine is considered important for the development of a newborn, fortification of infant nutrition with taurine is common. This publication describes a rapid method for the determination of taurine in infant formula and adult/pediatric nutritionals., Objective: This publication demonstrates the suitability and applicability of the method to determine taurine content in infant formula and adult/pediatric nutritionals., Methods: Test portions are deproteinized by acid in an aqueous environment prior to analysis. The level of taurine is analyzed by hydrophilic interaction chromatography (HILIC) coupled with multiple reaction monitoring MS (MRM-MS). Quantitation is accomplished using a stable isotope-labeled internal standard (SILS) for taurine., Results: The accuracy of the method was validated using standard reference materials and spike recovery studies. The average recoveries ranged between 92% and 105%. The relative standard deviation repeatability (RSDr) and relative standard deviation intermediate precision (RSDiR) were in the range of 0.7-4.6% (RSDr) and 1.3-6.7% (RSDiR). The limit of quantitation (LOQ) was below the requirement of 0.5 mg/100 g., Conclusion: The single-laboratory validation (SLV) of the method for determination of taurine content in infant formula and adult/pediatric nutritionals demonstrates that it meets the requirements per AOAC INTERNATIONAL Standard Method Performance Requirements (SMPR) 2014.013., Highlights: A fast method to selectively determine the content of taurine in infant formula and adult/pediatric nutritionals was evaluated and found to be fit for purpose for routine product compliance testing. Based on the results of this SLV, the method was approved by the AOAC Stakeholder Program on Infant Formula and Adult Nutritionals (SPIFAN) Expert Review Panel for SPIFAN Nutrient Methods for First Action Official MethodsSM status., (© The Author(s) 2024. Published by Oxford University Press on behalf of AOAC INTERNATIONAL. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Mass spectrometry (MS) has long been considered a cornerstone technique in analytical chemistry. However, the use of MS in animal health laboratories (AHLs) has been limited, however, largely because of the expense involved in purchasing and maintaining these systems. Nevertheless, since ~2020, the use of MS techniques has increased significantly in AHLs. As expected, developments in new instrumentation have shown significant benefits in veterinary analytical toxicology as well as bacteriology. Creative researchers continue to push the boundaries of MS analysis, and MS now promises to impact disciplines other than toxicology and bacteriology. I include a short discussion of MS instrumentation, more detailed discussions of the MS techniques introduced since ~2020, and a variety of new techniques that promise to bring the benefits of MS to disciplines such as virology and pathology., Competing Interests: Declaration of conflicting interestsThe author declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

In this study, a boronic acid incorporated metal organic frameworks (inBA-MIL-100) were prepared via metal-ligand-fragment co-assembly strategy. The prepared frameworks can be served either as enrichment sorbent or SALDI-MS matrix for cis-diol containing molecules. Thus, a dual-modal analysis of cis-diols in traditional Chinese medicine has been established. Several significant advantages of the proposed strategy have been experimentally demonstrated, including high selectivity, high binding capacity (70 mg/g), good generality (5-250 μg/mL for HPLC based sample preparation, 10-500 ng/mL for SALDI-MS), high sensitivity (LOD: 180 ng/mL for HPLC based sample preparation, 5 ng/mL for SALDI-MS) and reliable quantification (RSD<3 % for HPLC based sample preparation, RSD<12 % for SALDI-MS) performance. Finally, the successful analysis of various cis-diols (active component and mycotoxin) in various Chinese traditional medicine was also achieved., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Ambient ionisation mass spectrometry (AIMS) is a form of mass spectrometry whereby analyte ionisation occurs outside of a vacuum source under ambient conditions. This enables the direct analysis of samples in their native state, with little or no sample preparation and without chromatographic separation. The removal of these steps facilitates a much faster analytical process, enabling the direct analysis of samples within minutes if not seconds. Consequently, AIMS has gained rapid popularity across a diverse range of applications, in particular the analysis of drugs and toxins. Numerous fields rely upon mass spectrometry for the detection and identification of drugs, including clinical diagnostics, forensic chemistry, and food safety. However, all of these fields are hindered by the time-consuming and laboratory-confined nature of traditional techniques. As such, the potential for AIMS to resolve these challenges has resulted in a growing interest in ambient ionisation for drug and toxin analysis. Since the early 2000s, forensic science, diagnostic testing, anti-doping, pharmaceuticals, environmental analysis and food safety have all seen a marked increase in AIMS applications, foreshadowing a new future for drug testing. In this review, some of the most promising AIMS techniques for drug analysis will be discussed, alongside different applications of AIMS published over a 5-year period, to provide a summary of the recent research activity for ambient ionisation for drug and toxin analysis., (© 2024 The Authors. Drug Testing and Analysis published by John Wiley & Sons Ltd.)

The antioxidant activity of Ginkgo biloba leaf (GBL) extract is closely related to its efficacy against various diseases; however, the antioxidant activities of the specific constituents of GBL remain unclear. In this study, 194 GBL constituents were identified using ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry, including 97 flavonoids, 37 terpenoids, 29 lignans, 19 carboxylic acids, 5 alkylphenolic acids, 5 alkylphenols, and 2 other compounds. The cleavage rules of the main constituents of GBL were dissected in detail. The 36 GBL constituents with high antioxidant activity were subsequently discovered using the oxygen radical absorbance capacity assay, including 30 flavonoids and six carboxylic acids. Finally, an HPLC analysis method was established to determine the content of the nine major antioxidants in the three batches of GBL. Among them, kaempferol 3-O-β-D-(6″-p-coumaroyl) glucopyranosyl-(1-2)-α-L-rhamnopyranoside, kaempferol-3-O-rutinoside, and rutin exhibited high antioxidant activity and were found in significant amounts in GBL, with concentrations greater than 0.7 mg/g. These results provide an important reference for the development of pharmaceuticals and health products containing GBL., (© 2024 John Wiley & Sons Ltd.)

Radix gentianae (RG) is a traditional Chinese medicine used for the treatment of acute and chronic hepatitis in clinic. However, the chemical profile of RG is still unconfirmed, which hindered the progress of pharmacological study and clinical application. In this study, ultra-high performance liquid chromatography together with quadrupole time-of-flight mass spectrometry techniques were employed to separate and characterize the chemical constituents in RG. Under the optimized conditions, a total of 60 compounds were rapidly identified or tentatively characterized. Results indicated that iridoid glucosides, flavonoids, organic acids, amino acids, saccharides and nucleosides were major constituents in RG. It is concluded the established method can help to clarify the substance basis and provide useful information for ascertaining the bioactive constituents and action mechanism of RG., (© The Author(s) 2023. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

A fast and non-separative screening strategy is presented for the analysis of five urinary metabolites of polycyclic aromatic hydrocarbons (PAHs), namely 2-naphthol, 1-acenaphthenol, 2-hydroxyfluorene, 9-phenanthrol and 1-hydroxypyrene. These hydroxylated derivatives (OH-PAHs) were subjected to enzymatic hydrolysis and were extracted from urine using a liquid-liquid extraction (LLE). The profile signals were obtained by direct injection of the sample into a programmed temperature vaporizer coupled to a quadrupole mass spectrometer via a deactivated fused silica tubing (PTV-qMS). Semi-quantitative determination was carried out by means of partial least squares regression (PLS1) using urine samples free of the analytes and spiked at several uncorrelated concentration levels. The multivariate calibration models worked satisfactorily, with errors ranging between 30 and 33 % for all the analytes except for 1-acenaphthenol that provided an error of 39 % when external validation set was considered. The repeatability and reproducibility, expressed as relative standard deviation (RSD), were ranged between 8-16 % and 11-18 %, respectively. The proposed method could be a useful tool for semi-quantification purposes of five OH-PAHs in urine samples, identifying positive samples for subsequent further chromatographic separation (confirmation), thus saving time and costs., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Functional dyspepsia (FD) is a common digestive disease. Jianwei Xiaoshi (JWXS) tablet is composed of Radix Pseudostellariae (TZS), Pericarpium Citri Reticulatae (CP), Rhizoma Dioscoreae (SY), fired Hordei Fructus Germinatus (CMY) and Crataegi Fructus (SZ). It is a commonly used drug in the treatment of FD in China and has good therapeutic effects. However, there is very little research about the substance basis and action mechanism of JWXS tablet. In this research, ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS) and network pharmacology were used to explore the substance basis and action mechanism of the JWXS tablet. Finally, 19, 79, 22, 22 and 39 constituents were identified in the extracts of TZS, CP, SY, CMY and SZ, respectively. Based on these findings, a total of 104 ingredients were identified in JWXS tablet and 29 potentially absorbed ingredients were detected in rat plasma. The results of network pharmacology indicated that the inhibition of gastric acid secretion, the regulation of gastrointestinal motility, inflammation and immune response were the key approaches for treating FD with JWXS tablet. The material basis and potential action mechanism of JWXS tablet in treating FD were comprehensively clarified for the first time. This study will improve our understanding of JWXS tablet., (© 2024 John Wiley & Sons Ltd.)