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Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the recognition and response to antigenic threats. The capability to jointly characterize the BCR and antibody repertoire is crucial for understanding human adaptive immunity. From peripheral blood, bulk BCR sequencing (bulkBCR-seq) currently provides the highest sampling depth, single-cell BCR sequencing (scBCR-seq) allows for paired chain characterization, and antibody peptide sequencing by tandem mass spectrometry (Ab-seq) provides information on the composition of secreted antibodies in the serum. Yet, it has not been benchmarked to what extent the datasets generated by these three technologies overlap and complement each other. To address this question, we isolated peripheral blood B cells from healthy human donors and sequenced BCRs at bulk and single-cell levels, in addition to utilizing publicly available sequencing data. Integrated analysis was performed on these datasets, resolved by replicates and across individuals. Simultaneously, serum antibodies were isolated, digested with multiple proteases, and analyzed with Ab-seq. Systems immunology analysis showed high concordance in repertoire features between bulk and scBCR-seq within individuals, especially when replicates were utilized. In addition, Ab-seq identified clonotype-specific peptides using both bulk and scBCR-seq library references, demonstrating the feasibility of combining scBCR-seq and Ab-seq for reconstructing paired-chain Ig sequences from the serum antibody repertoire. Collectively, our work serves as a proof-of-principle for combining bulk sequencing, single-cell sequencing, and mass spectrometry as complementary methods towards capturing humoral immunity in its entirety. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

The multinuclear nonheme iron-dependent oxidases (MNIOs) are a rapidly growing family of enzymes involved in the biosynthesis of ribosomally synthesized, posttranslationally modified peptide natural products (RiPPs). Recently, a secreted virulence factor from nontypeable Haemophilus influenzae (NTHi) was found to be expressed from an operon, which we designate the hvf operon, that also encodes an MNIO. Here, we show by Mössbauer spectroscopy that the MNIO HvfB contains a triiron cofactor. We demonstrate that HvfB works together with HvfC [a RiPP recognition element (RRE)-containing partner protein] to perform six posttranslational modifications of cysteine residues on the virulence factor precursor peptide HvfA. Structural characterization by tandem mass spectrometry and NMR shows that these six cysteine residues are converted to oxazolone and thioamide pairs, similar to those found in the RiPP methanobactin. Like methanobactin, the mature virulence factor, which we name oxazolin, uses these modified residues to coordinate Cu(I) ions. Considering the necessity of oxazolin for host cell invasion by NTHi, these findings point to a key role for copper during NTHi infection. Furthermore, oxazolin and its biosynthetic pathway represent a potential therapeutic target for NTHi. [ABSTRACT FROM AUTHOR]

Introduction Methods Results Discussion Phosphatidylethanol (PEth) is a long‐term marker of alcohol consumption used frequently in clinical scenarios such as liver transplant evaluation. Recent cases have demonstrated that packed red blood cell (pRBC) transfusion creates the potential for artificial elevation or decrease of observed PEth concentrations in recipients. Very little is known about the prevalence or stability of PEth in pRBCs.Apheresis and whole‐blood (WB) donations were tested for PEth using liquid chromatography – tandem mass spectrometry with limit of quantitation 10 ng/mL. Units were stored under routine blood bank conditions to evaluate the stability of PEth and the impact of irradiation.Over 40% of apheresis and WB donors had PEth ≥10 ng/mL (maximum observed 587 ng/mL). As WB units were processed into component pRBCs, PEth concentrations increased and were higher than donor WB levels (EDTA sample) prior to collection (maximum observed 711 ng/mL). Storage for up to 5 weeks post donation resulted in mean 17.3% decrease in PEth‐positive units; in contrast to a prior report, we observed no PEth formation in units with negative (<10 ng/mL) baseline concentrations. Irradiation of pRBCs did not substantially affect PEth concentrations in either PEth‐positive or PEth‐negative units.PEth concentrations in healthy blood donors may potentially confound alcohol use or abstinence assessment in pRBC recipients. Transfusion medicine services and clinical practices such as transplantation and behavioral medicine should recognize this phenomenon and collaborate on testing protocols to appropriately interpret PEth in pRBC recipients. [ABSTRACT FROM AUTHOR]

BACKGROUND RESULTS CONCLUSION To extract anthocyanins with high efficiency, a hypothesis for high‐speed shear homogenization extraction (HSHE) method was established through a combination of solvent and ultrasonic‐assisted extractions. The efficacy of this hypothesis was demonstrated by performing qualitative and quantitative analyses of 16 anthocyanins extracted from five northern vegetables, and five berry fruits using ultra‐high‐performance Q‐Exactive Orbitrap tandem mass spectrometry. Single‐factor experiments were conducted by varying ethanol concentration, temperature, pH and extraction cycles to determine the optimal conditions for this method.Optimal extraction conditions (ethanol 70–80%, 40–50 °C, pH 3–4, performed twice) were determined using an HSHE (5 min, 10 000 rpm, 25 °C) assisted shaker (60 min) and ultrasonication (40 kHz, 160 W cm−2, 30 min, 25 °C) procedure. Compared to the traditional non‐HSHE method, the total anthocyanin content obtained through HSHE extraction showed a significant increase, ranging from 1.0 to 3.9 times higher, with purple cabbage exhibiting the most pronounced enhancement in content. More types of anthocyanins were detected in blueberry (9), black bean (7) and raspberry (5), of which malvidin was the major anthocyanin (0.426 g kg−1) in blueberry, having an amount five times than previously obtained.The established HSHE method has been proven to be a superior technique for anthocyanin extraction, with higher extraction efficiency and concentrations. This technique also provides a new avenue for extracting bioactive compounds from diverse food sources, with potential applications in improving the functional properties of food products. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical. [ABSTRACT FROM AUTHOR]

Coumarin and furocoumarins characterization in cosmetics plays an important role in protecting consumer health. The analytical technique mostly employed for the analysis of these molecules is certainly liquid chromatography coupled to photodiode array or mass spectrometer detectors. The aim of this article was to investigate on the oxygen heterocyclic compounds content in fifty hydro alcoholic fragrances using a fast, sensitive and eco-friendly liquid chromatography coupled to a triple quadrupole mass spectrometer detector analytical method without any sample pre-treatment. To the best of the author’s knowledge, this is the first research article on the quantification of thirty-six oxygen heterocyclic compounds in hydro alcoholic fragrances in less than 4 min and with the use of water/ethanol as mobile phase. Thanks to the good performance of the analytical method used, this can be proposed among the routine methods for the quality control of cosmetics and finished products. [ABSTRACT FROM AUTHOR]

Background: Hypertrophic cardiomyopathy (HCM) is a crucial heart disease in cats. The clinical manifestations of HCM comprise pulmonary edema, dyspnea, syncope, arterial thromboembolism (ATE), and sudden cardiac death. D-dimer and prothrombin time (PT) are powerful biomarkers used to assess coagulation function. Dysregulation in these two biomarkers may be associated with HCM in cats. This study aims to assess D-dimer levels, PT, and proteomic profiling in healthy cats in comparison to cats with symptomatic HCM. Results: Twenty-nine client-owned cats with HCM were enrolled, including 15 healthy control and 14 symptomatic HCM cats. The D-dimer concentration and PT were examined. Proteomic analysis was conducted by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and liquid chromatography-tandem mass spectrometry (LC-MS/MS). In symptomatic cats, D-dimer levels were statistically significantly higher (mean ± SEM: 372.19 ng/ml ± 58.28) than in healthy cats (mean ± SEM: 208.54 ng/ml ± 10.92) with P-value of less than 0.01, while PT was statistically significantly lower in symptomatic cats (mean ± SEM: 9.8 s ± 0.15) compared to healthy cats (mean ± SEM: 11.08 s ± 0.23) with P-value of less than 0.0001. The proteomics analysis revealed upregulation of integrin subunit alpha M (ITGAM), elongin B (ELOB), and fibrillin 2 (FBN2) and downregulation of zinc finger protein 316 (ZNF316) and ectonucleoside triphosphate diphosphohydrolase 8 (ENTPD8) in symptomatic HCM cats. In addition, protein-drug interaction analysis identified the Ras signaling pathway and PI3K-Akt signaling pathway. Conclusions: Cats with symptomatic HCM have higher D-dimer and lower PT than healthy cats. Proteomic profiles may be used as potential biomarkers for the detection and management of HCM in cats. The use of D-dimer as a biomarker for HCM detection and the use of proteomic profiling for a better understanding of disease mechanisms remain to be further studied in cats. [ABSTRACT FROM AUTHOR]

Background/aim: Tandem mass spectrometry is helpful in diagnosing amino acid metabolism disorders, organic acidemias, and fatty acid oxidation disorders and can provide rapid and accurate diagnosis for inborn errors of metabolism. The aim of this study was to predict inborn errors of metabolism in children with the help of artificial neural networks using tandem mass spectrometry data. Materials and methods: Forty-seven and 13 parameters of tandem mass spectrometry datasets obtained from 2938 different patients were respectively taken into account to train and test the artificial neural networks. Different artificial neural network models were established to obtain better prediction performances. The obtained results were compared with each other for fair comparisons. Results: The best results were obtained by using the rectified linear unit activation function. One, two, and three hidden layers were considered for artificial neural network models established with both 47 and 13 parameters. The sensitivity of model B2 for definitive inherited metabolic disorders was found to be 80%. The accuracy rates of model A3 and model B2 are 99.3% and 99.2%, respectively. The area under the curve value of model A3 was 0.87, while that of model B2 was 0.90. Conclusion: The results showed that the proposed artificial neural networks are capable of predicting inborn errors of metabolism very accurately. Therefore, developing new technologies to identify and predict inborn errors of metabolism will be very useful. [ABSTRACT FROM AUTHOR]

Motivation Tandem mass spectrometry (MS/MS) is a crucial technology for large-scale proteomic analysis. The protein database search or the spectral library search are commonly used for peptide identification from MS/MS spectra, which, however, may face challenges due to experimental variations between replicated spectra and similar fragmentation patterns among distinct peptides. To address this challenge, we present SpecEncoder, a deep metric learning approach to address these challenges by transforming MS/MS spectra into robust and sensitive embedding vectors in a latent space. The SpecEncoder model can also embed predicted MS/MS spectra of peptides, enabling a hybrid search approach that combines spectral library and protein database searches for peptide identification. Results We evaluated SpecEncoder on three large human proteomics datasets, and the results showed a consistent improvement in peptide identification. For spectral library search, SpecEncoder identifies 1%–2% more unique peptides (and PSMs) than SpectraST. For protein database search, it identifies 6%–15% more unique peptides than MSGF+ enhanced by Percolator, Furthermore, SpecEncoder identified 6%–12% additional unique peptides when utilizing a combined library of experimental and predicted spectra. SpecEncoder can also identify more peptides when compared to deep-learning enhanced methods (MSFragger boosted by MSBooster). These results demonstrate SpecEncoder's potential to enhance peptide identification for proteomic data analyses. Availability and Implementation The source code and scripts for SpecEncoder and peptide identification are available on GitHub at https://github.com/lkytal/SpecEncoder. Contact: hatang@iu.edu. [ABSTRACT FROM AUTHOR]

Motivation One of the core problems in the analysis of protein tandem mass spectrometry data is the peptide assignment problem: determining, for each observed spectrum, the peptide sequence that was responsible for generating the spectrum. Two primary classes of methods are used to solve this problem: database search and de novo peptide sequencing. State-of-the-art methods for de novo sequencing use machine learning methods, whereas most database search engines use hand-designed score functions to evaluate the quality of a match between an observed spectrum and a candidate peptide from the database. We hypothesized that machine learning models for de novo sequencing implicitly learn a score function that captures the relationship between peptides and spectra, and thus may be re-purposed as a score function for database search. Because this score function is trained from massive amounts of mass spectrometry data, it could potentially outperform existing, hand-designed database search tools. Results To test this hypothesis, we re-engineered Casanovo, which has been shown to provide state-of-the-art de novo sequencing capabilities, to assign scores to given peptide-spectrum pairs. We then evaluated the statistical power of this Casanovo score function, Casanovo-DB, to detect peptides on a benchmark of three mass spectrometry runs from three different species. In addition, we show that re-scoring with the Percolator post-processor benefits Casanovo-DB more than other score functions, further increasing the number of detected peptides. [ABSTRACT FROM AUTHOR]

In this study, a rapid and sensitive ultra‐high performance liquid chromatography‐tandem mass spectrometry method was established for the simultaneous determination of four Vitexin‐4"‐O‐glucoside (VOG), Vitexin‐2"‐O‐rhamnoside (VOR), vitexin (VIT), and hyperoside (HP) in plasma, which are representative flavonoids constituents of hawthorn leaves. The four components were separated by CORTECS UPLC C18 column (100 × 3.0 mm, 1.6 µm), using acetonitrile‐water containing 0.02% formic acid and 2 mmol/L ammonium formate as the mobile phase, the gradient elution flow rate was 0.30 mL/min. The analyte was quantified using an electrospray ionization triple quadrupole mass spectrometer. The analytes and baicalin internal standard were performed at m/z 593.2/413.2 for VOG, m/z 577.2/413.1 for VOR, m/z 431.1/310.9 for VIT, m/z 463.2/300 for HP and m/z 445.1/269 for internal standard. Among the four flavonoids, the correlation coefficient of the standard curve of each component is between 0.9939 and 0.9987. After oral administration of hawthorn leaf extract, VOG and VOR showed similar pharmacokinetic characteristics; VIT was eliminated in the body more slowly than the other three flavonoids and distributed more in the tissues; HP can be quickly absorbed in the blood. The developed analytical method has high sensitivity, precision, and accuracy with no interference from plasma components and has been successfully used in pharmacokinetic studies. [ABSTRACT FROM AUTHOR]

Amphetamines (AMPHs) and their derivatives are potent central nervous system stimulants, in 2020 an astonishing 34 million regular users were reported worldwide. Consequently, there has been a critical need for the development of methods capable of detecting these compounds in alternative biological matrices. The review article discusses the analysis of amphetamines and their derivatives in alternative biological matrices, such as hair and oral fluid (OF), using liquid chromatography‐mass spectrometry. Compiles data from 28 articles published between 2012 and 2022, focusing on 13 articles on OFs and 15 on hair analysis. The article highlights the advantages of using these alternative matrices, including less invasive collection methods, greater sample stability, and simplified extraction processes. Additionally, prevalent analytical practices such as the use of C18 columns and the incorporation of formic acid and methanol into mobile phases are discussed. Furthermore, it demonstrates that the most used method for collecting OF is the Quantisal device, as well as solid phase extraction is also the most used for the same matrix. The review serves as a guide for researchers interested in analytical methods for identifying AMPHs, offering insights into advances, challenges, and the most used in the area. [ABSTRACT FROM AUTHOR]

The medicinal nature of traditional Chinese medicine (TCM) mainly plays a role in regulating the energy and material metabolism of the body. The energy metabolism of the body is also regulated by the nervous and endocrine systems, and the hormones are an important component of the endocrine system to realize the coordinated action. Therefore, the medicinal nature of TCM is inextricably linked with the metabolism of hormones. Hyperthyroidism, qi-yin deficiency syndrome is regarded as the classic heat syndrome category in Chinese medicine, which can be used as model to reflect the mechanism and difference of qi tonifying of ginseng herbs with different medicinal natures. Steroid hormones are synthesized in the adrenal cortex, mitochondria of placental cells, smooth endoplasmic reticulum, and gonads of the human body by the participation of various metabolic enzymes. Meanwhile, most of the patients with hyperthyroidism have adrenocortical dysfunction in the clinic, and the corresponding clinical symptoms are closely related to the hypothalamic-pituitary-thyroid axis (HPT), the hypothalamic-pituitary-adrenal axis (HPA), and the hypothalamic-pituitary-gonadal axis (HPG). When hyperthyroidism occurs, the production and release of steroid hormones will be affected to a certain extent. To explore the correlation between the level of steroid hormones and hyperthyroidism, and the ameliorative effects of red ginseng and ginseng leaves of different types of the genus Ginseng on hypermetabolism of hyperthyroidism and the changes of related indexes, a method of ultra-high performance liquid chromatography coupled to triple quadrupole tandem mass spectrometry (UPLC-QqQ-MS/MS) was established for rapid identification and quantification of chemical components, including adrenaline, androstenedione, testosterone, dehydroepiandrosterone, estriol, progesterone, 17α-hydroxypregnenolone, corticosterone, and cortisol in rat serum. Then, multivariate analysis method, principal component analysis (PCA), and Spearman test were used to analyze the correlation among adrenaline, steroid hormones, and thyroid function. The results showed that the contents of steroid hormone in the serum of the model group of rats decrease to different degrees, compared with the control group, and increase after the administration of different types of ginsengs. Meanwhile, it was proved that the established method has high sensitivity, good reproducibility, high accuracy, and fast analysis, which can screen a large number of steroid hormones in complex samples in a short time, for accurately investigation of the effects of ginsengs on the content of 9 types of steroid hormones in hyperthyroidism rats. The abnormal levels of steroid hormones are related to thyroid hormones. Corticosterone and adrenaline can serve as key indicators for regulating steroid hormone metabolism of TCMs like ginsengs. Testosterone can be used as the biomarker for regulating steroid hormones of the cold nature herbs. Adrenaline and androstenedione can be used as biomarkers for regulating steroid hormones of the warm nature herbs. This method can conveniently, quickly, accurately, and efficiently complete the analysis of target components in samples. The average recoveries of steroid hormones in rat serum range from 88.75% to 106.94%, and the relative standard deviation is less than 1.99%. This can be used for the determination of steroid hormones in rat serum systematically, rapidly, accurately and efficiently, and provides a methodological reference for the analysis and determination of steroid hormones. [ABSTRACT FROM AUTHOR]

Exposure of firefighting instructors to polycyclic aromatic hydrocarbons (PAHs) such as naphthalene is unavoidable during live fire training. The study aimed to investigate naphthalene uptake by measuring the urinary excretion of the naphthalene metabolite 1,2-dihydroxynaphthalene (DHN), to describe the DHN elimination kinetics and to evaluate the results by comparison to further biomarkers of PAH exposure. N = 6 male non-smoking firefighting instructors completed five training sessions each in a residential fire simulation unit under respiratory protection. All participants provided two urine samples before and another seven samples within an 18-h-interval after each session. DHN was detected by gas chromatography/tandem mass spectrometry (GC–MS/MS) in all samples (n = 237) with median concentrations ranging from 3.3 µg/g crea. (range 0.9–10.2) before exposure to 134.2 µg/g crea. (43.4–380.4) post exposure. Maximum elimination found 3.3 h (median) after onset of exposure decreased with a mean half-life of 6.6 h to 27.1 µg/g crea. (15.7–139.5) 18 h after training. DHN sensitively indicated a presumed dermal naphthalene intake during training, showing similar elimination kinetics like other naphthalene metabolites. Internal exposure of the participants transiently exceeded exposures determined for non-smokers in the general population, but was lower than at other workplaces with PAH exposure. Despite limited uptake, accumulation is possible with daily exposure. [ABSTRACT FROM AUTHOR]

Background: Ketamine is an NMDAR antagonist with aggregating use across many areas of medicine. P450 enzymes heavily metabolise ketamine, where norketamine is a first pass formed metabolite following initial N-demethylation. Serum ketamine monitoring is becoming increasingly important, requiring a sensitive method with a robust lower limit of quantitation. Methods: Samples were prepared using protein precipitation or solid phase extraction. Ion suppression was investigated to optimise sample preparation technique, followed by reverse-phase chromatography coupled with tandem mass spectrometry to analyse extractions using a Waters Xevo TQ-S Micro and associated Acquity chromatography systems. Performance characteristics were analysed to validate the assay. Results: Ketamine and norketamine retention times were 1.28 and 1.23 min, respectively. Ketamine and norketamine precursor ions fragmented into 2 distinguishable product ions (238.14 > 207.18/125.06 and 224.1 > 178.96/124.86). Performance characteristics include an assay recovery of 103.7% (ketamine) and 96.3% (norketamine), lower limit of quantitation 36.2 µg/L (ketamine) and 38.9 µg/L (norketamine), and intra-assay imprecision ≤ 7.04% on average. Conclusions: A robust and reproducible assay with limited sample preparation has been designed and validated. The linearity of the assay covers all ranges of interest reported in the literature. Ion suppression was clearly reduced via use of solid phase extraction. The method will form the basis of ketamine monitoring and providing valuable patient information on tolerance and metabolism. [ABSTRACT FROM AUTHOR]

Amyloidosis is a disease characterized by local and systemic extracellular deposition of amyloid protein fibrils where its excessive accumulation in tissues and resistance to degradation can lead to organ failure. Diagnosis is challenging because of approximately 36 different amyloid protein subtypes. Imaging methods like immunohistochemistry and the use of Congo red staining of amyloid proteins for laser capture microdissection combined with liquid chromatography tandem mass spectrometry (LMD/LC–MS/MS) are two diagnostic methods currently used depending on the expertise of the pathology laboratory. Here, we demonstrate a streamlined in situ amyloid peptide spatial mapping by Matrix Assisted Laser Desorption Ionization–Mass Spectrometry Imaging (MALDI-MSI) combined with Trapped Ion Mobility Spectrometry for potential transthyretin (ATTR) amyloidosis subtyping. While we utilized the standard LMD/LC–MS/MS workflow for amyloid subtyping of 31 specimens from different organs, we also evaluated the potential introduction in the MS workflow variations in data acquisition parameters like dynamic exclusion, or testing Data Dependent Acquisition combined with High-Field Asymmetric Waveform Ion Mobility Spectrometry (DDA FAIMS) versus Data Independent Acquisition (DIA) for enhanced amyloid protein identification at shorter acquisition times. We also demonstrate the use of Mascot's Error Tolerant Search and PEAKS de novo sequencing for the sequence variant analysis of amyloidosis specimens. [ABSTRACT FROM AUTHOR]

Purpose: Staphylococcus aureus is one of the most common pathogens causing bloodstream infection. A rapid characterisation of resistance to methicillin and, occasionally, to aminoglycosides for particular indications, is therefore crucial to quickly adapt the treatment and improve the clinical outcomes of septic patients. Among analytical technologies, targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as a promising tool to detect resistance mechanisms in clinical samples. Methods: A rapid proteomic method was developed to detect and quantify the most clinically relevant antimicrobial resistance effectors in S. aureus in the context of sepsis: PBP2a, PBP2c, APH(3')-III, ANT(4')-I, and AAC(6')-APH(2"), directly from positive blood cultures and in less than 70 min including a 30-min cefoxitin-induction step. The method was tested on spiked blood culture bottles inoculated with 124 S.aureus, accounting for the known genomic diversity of SCCmec types and the genetic background of the strains. Results: This method provided 99% agreement for PBP2a (n = 98/99 strains) detection. Agreement was 100% for PBP2c (n = 5/5), APH(3')-III (n = 16/16), and ANT(4')-I (n = 20/20), and 94% for AAC(6')-APH(2'') (n = 16/17). Across the entire strain collection, 100% negative agreement was reported for each of the 5 resistance proteins. Additionally, relative quantification of ANT(4')-I expression allowed to discriminate kanamycin-susceptible and -resistant strains, in all strains harbouring the ant(4')-Ia gene. Conclusion: The LC-MS/MS method presented herein demonstrates its ability to provide a reliable determination of S. aureus resistance mechanisms, directly from positive blood cultures and in a short turnaround time, as required in clinical laboratories. [ABSTRACT FROM AUTHOR]

Nitazoxanide (NTZ) is an effective antiparasitic drug with potent antiviral and antimicrobial activity. This randomized, open‐label, 2‐sequence, 2‐period crossover trial was designed to evaluate the bioequivalence (BE) of the NTZ dry suspension in healthy subjects and investigated the effect of food intake on the pharmacokinetic (PK) properties of tizoxanide (an active metabolite of NTZ, TIZ). Sixty healthy Chinese subjects were enrolled and received a single dose of 500 mg/25 mL of preparations on days 1 and 4 under overnight fasting or fed conditions, respectively. The plasma concentration of TIZ was determined using high‐performance liquid chromatography/tandem mass spectrometry. PK parameters were calculated using WinNonlin 8.2 and BE was evaluated using SAS 9.4. The 90% confidence intervals for the geometric mean ratio (test/reference) of maximum concentration (Cmax), the area under the curve from time 0 to the time of the last quantifiable concentration (AUC0‐t), and the area under the curve from time 0 to extrapolation to infinity (AUC0‐∞) were all within the equivalent interval of 80%‐125%, compliant with BE requirements. In comparison with fasting, on taking the reference and test preparations of the NTZ dry suspension after a meal, the AUC0‐t increased by 48.9% and 47.3%, respectively, the AUC0‐∞ increased by 48.4% and 48.3%, respectively, and the post‐meal Tmax was prolonged by 1.8‐2 hours. Our results demonstrate that the test and reference preparations were bioequivalent. High‐fat meals significantly improve the degree of drug absorption and delay the rate of drug absorption. [ABSTRACT FROM AUTHOR]

Objectives We compared tacrolimus concentrations obtained by the more recently US Food and Drug Administration–approved tacrolimus assay (CMIA) on the Alinity i analyzer (Abbott Laboratories) with a liquid chromatography/tandem mass spectrometry (LC-MS/MS)–based method from 2 reference laboratories. We also investigated the correlation between the CMIA tacrolimus and Elecsys tacrolimus assays. Methods Tacrolimus concentrations were measured in EDTA whole blood by the chemiluminescent microparticle immunoassay (CMIA) using the Alinity i analyzer, and then 2 aliquots were sent to 2 reference laboratories, both using ascomycin as the internal standard for the LC-MS/MS method. Results The total precision of the CMIA tacrolimus assay was excellent. When tacrolimus concentrations obtained by the LC-MS/MS method from reference laboratory A were plotted on the x-axis and corresponding CMIA values were plotted on the y-axis, the following regression equation was observed: y = 0.9721x + 1.005 (r = 0.95), indicating no significant bias with the CMIA. However, when tacrolimus values obtained from reference laboratory B were used for comparison, the regression equation was y = 0.7664x + 1.775 (r = 0.93), indicating significant negative bias with the CMIA. When we compared tacrolimus concentrations obtained by reference laboratories A and B, we observed positive bias with tacrolimus concentrations obtained by reference laboratory B. However, tacrolimus concentrations obtained by both CMIA and Elecsys immunoassays were comparable. Conclusions Because of good correlation of tacrolimus concentrations using the CMIA and LC-MS/MS from reference laboratory A, our long-term reference laboratory for drug analysis, we concluded that the CMIA on the Alinity i can be used for therapeutic drug monitoring of tacrolimus. [ABSTRACT FROM AUTHOR]

Megalencephaly–polymicrogyria–polydactyly–hydrocephalus syndrome (MPPH), a type of overgrowth syndrome, is characterized by progressive megalencephaly, cortical brain malformations, and distal limb anomalies. Previous studies have revealed that the overactivity of the phosphatidylinositol 3-kinase-Protein kinase B pathway and the increased cyclin D2 (CCND2) expression were the main factors contributing to this disease. Here, we present the case of a patient who exhibited megalencephaly, polymicrogyria, abnormal neuronal migration, and developmental delay. Serum tandem mass spectrometry and chromosome examination did not detect any metabolic abnormalities or copy number variants. However, whole-exome sequencing and Sanger sequencing revealed a de novo nonsense mutation (NM_001759.3: c.829C>T; p.Gln277X) in the CCND2 gene of the patient. Bioinformatics analysis predicted that this mutation may disrupt the structure and surface charge of the CCND2 protein. This disruption could potentially prevent polyubiquitination of CCND2, leading to its resistance against degradation. Consequently, this could drive cell division and growth by altering the activity of key cell cycle regulatory nodes, ultimately contributing to the development of MPPH. This study not only presents a new case of MPPH and expands the mutation spectrum of CCND2 but also enhances our understanding of the mechanisms connecting CCND2 with overgrowth syndromes. [ABSTRACT FROM AUTHOR]

Vitex negundo has strong antioxidant activity, but its primary antioxidant components are not clear. In this study, the antioxidant components were screened by offline two-dimensional liquid chromatography coupled with electrochemical detection (2D-LC-ECD) and subsequently assessed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) identification, radical scavenging capacity, and molecular docking. Various fractions were isolated from Vitex negundo leaves, and 39 antioxidant components were screened and identified. All of the fractions containing the antioxidant components exhibited certain antioxidant activity. Correlation analysis revealed a strong correlation between the response of LC-ECD and the in vitro antioxidant activity of the fractions. Molecular docking demonstrated that components with high response to LC-ECD exhibited robust interaction with antioxidant-related target proteins. The main antioxidant components of Vitex negundo leaves were isoorientin, chlorogenic acid, agnuside, cynaroside, and scutellarin. The 2D-LCE-CD combined with LC-MS/MS was rapid and effective in screening the antioxidant components in Vitex negundo leaves and could also provide technical support for the discovery of antioxidant components with different polarities and contents in other medicinal and edible plants. [ABSTRACT FROM AUTHOR]

In this study, we performed a quantitative analysis of 12 compounds derived from Piper sarmentosum extract (PSE) and guava leaf extract (GE). In addition, we investigated the effects of mixed extract (ME) of PSE and GE (1:1) on piglets' gut microbiome and metabolome. A total of 200 piglets (Duroc × Landrace × Large Yorkshire, 21‐day‐old) were randomly assigned into two groups with five replicates of 20 piglets/pen having the same initial body weight. Piglets were fed a basal diet supplemented with ME at 0 (T0) or 200 mg/kg (T1) for 3 weeks. The quantitation results by ultraperformance liquid chromatography linked to triple‐quadrupole tandem mass spectrometry showed that vitexin 2‐O‐rhamnoside and pellitorine were the greatest abundant among six compounds detected in the PSE. In addition, quercetin, isoquercitrin and avicularin were found to be the richest of all detected compounds in the GE. Findings on experimental animals indicated that three differential metabolites, comprising L‐alanine, sarcosine and dihydrofolic acid, in T1 compared with T0 groups, have exactly opposite levels trends in serum and faeces. Moreover, two metabolic pathways (i.e., urea cycle and glutamate metabolism) differed significantly in the serum and faeces of piglets between T0 and T1 (p < 0.05). At the same time, T1 had significantly higher relative abundances of Agathobacter and Alloprevotella than T0 at genus level (p < 0.05). Correlation analysis revealed that the genus Agathobacter correlated positively with carbamoyl phosphate (p < 0.01) and oxoglutaric acid (p < 0.05), and negatively with succinic acid (p < 0.01) and ornithine (p < 0.05). These four differential metabolites were also involved in the urea cycle and/or glutamate metabolism pathways. The results here indicated that the tested plant extract mixture represents a worthy feed additive with obvious antioxidative properties. [ABSTRACT FROM AUTHOR]

Following isotonitazene scheduling in 2019, the availability of alternative 2-benzylbenzimidazole opioids (nitazenes) on the global drug market increased, resulting in many fatalities worldwide. Nitazenes are potent µ-opioid receptor agonists with strong narcotic/analgesic effects, and their concentrations in biological matrices are low, making the detection of metabolite biomarkers of consumption crucial to document use in clinical and forensic settings. However, there is little to no data on the metabolism of the most recently available nitazenes, especially desnitro-analogues. The aim of the research was to assess isotonitazene, metonitazene, etodesnitazene, and metodesnitazene human metabolism and identify specific metabolite biomarkers of consumption. The four analogues were incubated with 10-donor-pooled human hepatocytes, and the incubates were analyzed by liquid chromatography-high-resolution tandem mass spectrometry and data mining with Compound Discoverer (Thermo Scientific); the analysis was supported by in silico metabolite predictions with GLORYx open-access software. Metabolites were identified in postmortem blood and/or urine samples from two metonitazene-positive and three etodesnitazene-positive cases following the same workflow, with and without glucuronide hydrolysis in urine, to confirm in vitro results. Twelve, nine, twenty-two, and ten metabolites were identified for isotonitazene, metonitazene, etodesnitazene, and metodesnitazene, respectively. The main transformations were N-deethylation at the N,N-diethylethanamine side chain, O-dealkylation, and further O-glucuronidation. In vitro and autopsy results were consistent, demonstrating the efficacy of the 10-donor-pooled human hepatocyte model to predict human metabolism. We suggest the parent and the corresponding O-dealkyl- and N-deethyl-O-dealkyl metabolites as biomarkers of exposure in urine after glucuronide hydrolysis, and the corresponding N-deethyl metabolite as additional biomarker in blood. [ABSTRACT FROM AUTHOR]

2-Phenoxyethanol (PhE) is widely used as a preservative in consumer products such as cosmetics as well as at the workplace as a component of metal-working fluids and hydraulic fluids. Therefore, both industry workers and consumers may potentially be exposed to PhE. An analytical method for the quantification of PhE and three selected metabolites, namely phenoxyacetic acid (PhAA), 4-hydroxyphenoxyacetic acid (4-OH-PhAA), and 4-hydroxyphenoxyethanol (4-OH-PhE), in human urine and blood was developed and validated. The sample preparation includes enzymatic hydrolysis of urine samples or protein precipitation of blood samples, followed by liquid – liquid extraction and silylation of the target analytes. Analyses of the extracts were carried out by gas chromatography with tandem mass spectrometry (GC – MS-MS). 3,4-Hydroxyphenoxyethanol, a probably minor PhE metabolite, could not be reliably analyzed due to its instability. The limits of quantification (LOQ) of the analytes ranged between 0.5 and 6.1 μg/L and 2.0 and 3.9 μg/L in urine and blood, respectively. The method was successfully applied to spot urine samples of 50 individuals without occupational exposure to PhE and additionally to blood samples from seven volunteers. In urine, PhAA and 4-OH-PhAA could be quantified in all analyzed samples, whereas 4-OH-PhE and unchanged PhE were found in 36% and 32% of the samples, respectively. In blood, PhAA was also found in every sample in levels above the LOQ, whereas PhE itself was detected in three of seven samples only. Neither 4-OH-PhAA nor 4-OH-PhE was found in any of the analyzed blood samples. The developed method promises to be a valuable tool for PhE monitoring of urine and blood samples and may also enable an advanced investigation of PhE biotransformation pathways in humans. [ABSTRACT FROM AUTHOR]

Mycotoxins, natural toxins produced by fungi, contaminate nearly 80% of global food crops. Alternaria mycotoxins, including alternariol (AOH), alternariol monomethylether (AME), and tenuazonic acid (TeA), present a health concern due to their prevalence in various plants and fruits. Exposure to these toxins exceeds the threshold of toxicological concern in some European populations, especially infants and toddlers. Despite this, regulatory standards for Alternaria toxins remain absent. The lack of toxicokinetic parameters, reference levels, and sensitive detection methods complicates risk assessment and highlights the necessity for advanced biomonitoring (HBM) techniques. This study addresses these challenges by developing and validating ultra-high performance liquid chromatography method coupled with tandem mass spectrometry to quantify AOH, AME, TeA, and their conjugates in multiple biological matrices. The validated method demonstrates robust linearity, precision, recovery (94–111%), and sensitivity across urine (LOD < 0.053 ng/mL), capillary blood (LOD < 0.029 ng/mL), and feces (LOD < 0.424 ng/g), with significantly lower LOD for TeA compared to existing methodologies. The application of minimally invasive microsampling techniques for the blood collection enhances the potential for large-scale HBM studies. These advancements represent a step toward comprehensive HBM and exposure risk assessments for Alternaria toxins, facilitating the generation of data for regulatory authorities. [ABSTRACT FROM AUTHOR]

Recombinant α1-microglobulin (A1M) is proposed as a protector during 177Lu-octreotate treatment of neuroendocrine tumors, which is currently limited by bone marrow and renal toxicity. Co-administration of 177Lu-octreotate and A1M could result in a more effective treatment by protecting healthy tissue, but the radioprotective action of A1M is not fully understood. The aim of this study was to examine the proteomic response of kidneys and bone marrow early after 177Lu-octreotate and/or A1M administration. Mice were injected with 177Lu-octreotate and/or A1M, while control mice received saline or A1M vehicle solution. Bone marrow, kidney medulla, and kidney cortex were sampled after 24 h or 7 d. The differential protein expression was analyzed with tandem mass spectrometry. The dosimetric estimation was based on 177Lu activity in the kidney. PHLDA3 was the most prominent radiation-responsive protein in kidney tissue. In general, no statistically significant difference in the expression of radiation-related proteins was observed between the irradiated groups. Most canonical pathways were identified in bone marrow from the 177Lu-octreotate+A1M group. Altogether, a tissue-dependent proteomic response followed exposure to 177Lu-octreotate alone or together with A1M. Combining 177Lu-octreotate with A1M did not inhibit the radiation-induced protein expression early after exposure, and late effects should be further studied. [ABSTRACT FROM AUTHOR]

One of the most significant diseases in the swine business, porcine reproductive and respiratory syndrome virus (PRRSV) causes respiratory problems in piglets and reproductive failure in sows. The PRRSV nucleocapsid (N) protein is essential for the virus' assembly, replication, and immune evasion. Stages in the viral replication cycle can be impacted by interactions between the PRRSV nucleocapsid protein and the host protein components. Therefore, it is of great significance to explore the interaction between the PRRSV nucleocapsid protein and the host. Nevertheless, no information has been published on the network of interactions between the nucleocapsid protein and the host proteins in primary porcine alveolar macrophages (PAMs). In this study, 349 host proteins interacting with nucleocapsid protein were screened in the PRRSV-infected PAMs through a liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics approach. Bioinformatics analysis, which included gene ontology annotation, Kyoto Encyclopedia of Genes and Genomes database enrichment, and a protein–protein interaction (PPI) network, revealed that the host proteins interacting with PRRSV-N may be involved in protein binding, DNA transcription, metabolism, and innate immune responses. This study confirmed the interaction between the nucleocapsid protein and the natural immune-related proteins. Ultimately, our findings suggest that the nucleocapsid protein plays a pivotal role in facilitating immune evasion during a PRRSV infection. This study contributes to enhancing our understanding of the role played by the nucleocapsid protein in viral pathogenesis and virus–host interaction, thereby offering novel insights for the prevention and control of PRRS as well as the development of vaccines. [ABSTRACT FROM AUTHOR]

A method for determining human epidermal growth factor (hEGF) in cosmetics was developed using solid-phase extraction with high-performance liquid chromatography – tandem mass spectrometry. The sample was extracted and purified by a mixed anionic solid-phase extraction column (MAX), and the eluent was passed through a nylon filter membrane into a polypropylene vial. The matrix-matched external standard method was used to quantify the analyte in multi-reaction monitoring mode. The analyte had an excellent peak shape within 11 min with a linear range from 5 to 80 ng/mL and a linear correlation coefficient (r) of 0.9995. The limit of detection and limit of quantification were 0.75 and 2.5 μg/kg, respectively. The recovery of the target was from 81.5% to 88.8%, and the relative standard deviation was between 1.16% and 5.07%. The results met the International Organization for Standardization 12787 standard. The established method was successfully applied to 30 cosmetic samples. The proposed method is sensitive, accurate, reliable, and suitable for the quantitative confirmation of hEGF and monitoring its illegal addition to cosmetics. [ABSTRACT FROM AUTHOR]

Neurocysticercosis (NCC), a major cause of global acquired epilepsy, results from Taenia solium larval brain infection. T. solium adult worms release large numbers of infective eggs into the environment contributing to high levels of exposure in endemic areas. This study identifies T. solium proteins in the sera of individuals with and without NCC using mass spectrometry to examine exposure in endemic regions. Forty‐seven patients (18–51 years), 24 parenchymal NCC (pNCC), 8 epilepsy of unknown aetiology, 7 glioma, 8 brain tuberculoma, and 7 healthy volunteers were studied. Trypsin digested sera were subject to liquid chromatography–tandem mass spectrometry and spectra of 375–1700 m/z matched against T. solium WormBase ParaSite database with MaxQuant software to identify T. solium proteins. Three hundred and nineteen T. solium proteins were identified in 87.5% of pNCC and 56.6% of non‐NCC subjects. Three hundred and four proteins were exclusive to pNCC sera, seven to non‐NCC sera and eight in both. Ten percent, exhibiting immune‐modulatory properties, originated from the oncosphere and cyst vesicular fluid. In conclusion, in endemic regions, T. solium proteins are detected in sera of individuals with and without pNCC. The immunomodulatory nature of these proteins may influence susceptibility and course of infection. [ABSTRACT FROM AUTHOR]

Jiawei Huoxiang Zhengqi Pill (JHZP) is a commonly used Chinese patent medicine for the clinical treatment of headache, dizziness, chest tightness as well as abdominal distension, and pain caused by wind‐cold flu. In this study, a comprehensive strategy combining ultra‐high performance liquid chromatography with diode array detector (UHPLC‐DAD) fingerprinting and multi‐component quantitative analysis was established and validated for quality evaluation of JHZP. A total of 49 characteristic common peaks were selected in a chromatographic fingerprinting study to assess the similarity of 15 batches of JHZP. Furthermore, 109 compounds were identified or preliminarily identified from JHZP by coupling with an advanced hybrid linear ion trap‐Orbitrap mass spectrometer. For quantification, the optimized ultra‐performance liquid chromatography with tandem mass spectrometry (UPLC‐MS/MS) method was employed for the simultaneous determination of 13 target compounds within 12 min. The sensitivity, precision, reproducibility, and accuracy of the method were satisfactory. This validated UPLC‐MS/MS method was successfully applied to analyzing 15 batches of JHZP. The proposed comprehensive strategy combining UHPLC‐DAD fingerprinting and multi‐component UPLC‐MS/MS analysis proved to be highly efficient, accurate, and reliable for the quality evaluation of JHZP, which can be considered as a reference for the overall quality evaluation of other Chinese herbal formulations. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) is a neurodegenerative disorder associated with behavioral and cognitive impairments. Unfortunately, the drugs the Food and Drug Administration currently approved for AD have shown low effectiveness in delaying the progression of the disease. The focus has shifted to non‐pharmacological interventions (NPIs) because of the challenges associated with pharmacological treatments for AD. One such intervention is environmental enrichment (EE), which has been reported to restore cognitive decline associated with AD effectively. However, the therapeutic mechanisms by which EE improves symptoms associated with AD remain unclear. Therefore, this study aimed to reveal the mechanisms underlying the alleviating effects of EE on AD symptoms using histological, proteomic, and neurotransmitter‐related analyses. Wild‐type (WT) and 5XFAD mice were maintained in standard housing or EE conditions for 4 weeks. First, we confirmed the mitigating effects of EE on cognitive impairment in an AD animal model. Then, histological analysis revealed that EE reduced Aβ accumulation, neuroinflammation, neuronal death, and synaptic loss in the AD brain. Moreover, proteomic analysis by liquid chromatography–tandem mass spectrometry showed that EE enhanced synapse‐ and neurotransmitter‐related networks and upregulated synapse‐ and neurotransmitter‐related proteins in the AD brain. Furthermore, neurotransmitter‐related analyses showed an increase in acetylcholine and serotonin concentrations as well as a decrease in polyamine concentration in the frontal cortex and hippocampus of 5XFAD mice raised under EE conditions. Our findings demonstrate that EE restores cognitive impairment by alleviating AD pathology and regulating synapse‐related proteins and neurotransmitters. Our study provided neurological evidence for the application of NPIs in treating AD. [ABSTRACT FROM AUTHOR]

Coriolopsis trogii is a basidiomycete fungus which utilizes a large array of lignin-modifying enzymes to colonize and decompose dead wood. Its extracellular enzymatic arsenal includes laccases, i.e., polyphenol oxidases of relevant interest for different industrial applications thanks to their ability to oxidize a diverse range of natural and synthetic compounds. In this work, the production of laccases in C. trogii MUT3379 was explored and improved. From an initial production of ca. 10,000 U L−1, the fermentation process was gradually optimized, reaching a final yield of ca. 200,000 U L−1. An SDS-PAGE analysis of the secretome highlighted the presence of a main protein of ca. 60 kDa showing laccase activity, which was designated as Lac3379-1 once its primary sequence was established by tandem mass spectrometry. The characterization of Lac3379-1 revealed a remarkable enzymatic stability in the presence of surfactants and solvents and a diversified activity on a broad range of substrates, positioning it as an interesting tool for diverse biotechnological applications. The high-yield and robust production process indicates C. trogii MUT3379 as a promising cell factory for laccases, offering new perspectives for industrial applications of lignin-modifying enzymes. [ABSTRACT FROM AUTHOR]

This study explores the biotransformation of phenolic compounds in Rosa rugosa through Lactobacillus plantarum fermentation, enhancing their bioaccessibility and antioxidant capacity. We developed a sensitive and reproducible analytical method using ultra-high performance liquid chromatography coupled with triple quadrupole tandem mass spectrometry (UHPLC-QqQ-MS/MS), enabling the analysis of 17 phenolic compounds from Rosa (R) and fermented Rosa (FR). Additionally, we conducted a density functional theory (DFT) study to correlate the structure of key phenolic compounds from R and FR with their antioxidant activity. Our findings revealed that both R and FR mitigate oxidative stress in tert-butyl-hydrogen peroxide (TBHP)-induced Caco-2 and HT-29 cells by elevating the activities of crucial antioxidative enzymes, including superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px), and glutathione reductase (GR). Furthermore, fermented Rosa significantly upregulated Nrf2, γ-GCS, HO-1, and NOQ-1 mRNA expression in TBHP-induced cells with Quantitative and real-time PCR technology, emphasizing its protective function primarily through the Nrf2 signaling pathway. This study is the first to demonstrate the link between the enhanced antioxidant potential in fermented Rosa and the biotransformation of its phenolic compounds. It paves the way for augmenting the antioxidant capacity of plant foods through Lactobacillus plantarum fermentation, offering a novel approach to reinforce their health benefits. [ABSTRACT FROM AUTHOR]

Because of their performance‐enhancing effect, anabolic androgenic steroids (AAS) are often misused in sports. Nearly half of the adverse analytical findings (AAF) in 2022 doping controls are correlated to AAS misuse. Metabolites play a crucial role in the bioanalysis of endogenous and exogenous steroids. Therefore, one important field in antidoping research is the investigation on drug metabolizing and steroidogenic enzymes. The introduction of a hydroxy group is the most common reaction, which is catalyzed by cytochrome P450 (CYP) enzymes in phase‐I metabolism. Analysis of AAS metabolites is commonly performed using gas chromatography mass spectrometry (GC‐MS) systems. Laborious sample preparation and extended run times compared to liquid chromatography (tandem) mass spectrometry (LC‐MS/MS) methods are usually correlated with this type of analysis. On the other hand, liquid chromatography (tandem) mass spectrometry (LC‐MS[/MS]) methods have a lower separation efficiency than GC‐MS methods. Both techniques lack selectivity for hydroxylated 17α‐methyltestosterone metabolites. Therefore, as an orthogonal analytical approach, a supercritical fluid chromatography tandem mass spectrometry method was developed to separate four hydroxy metabolites of 17α‐methyltestosterone (2α‐/2β‐/4‐/6β‐hydroxy‐17α‐methyltestosterone). This project aimed to get a more in‐depth look at the metabolization and analysis of 17α‐methyltestosterone and its hydroxylated metabolites. The developed method revealed lower limits of quantitation between 0.6 and 6 ng/ml at an accuracy of 85–115% using a matrix matched calibration. An in vitro study with human liver microsomes shows 6β‐hydroxy‐17α‐methyltestosterone as main metabolite (15.9%) as well as the metabolite 2β‐hydroxy‐17α‐methyltestosterone (0.5%). The results show that the developed method is sensitive and robust. In addition, the method allows a previously missing discrimination of the hydroxylated metabolites in a short analysis time without prior, complex derivatizations. [ABSTRACT FROM AUTHOR]

This study aims to provide the first report on the soluble and polyphenolic profiles of "Farmacista Honorati" (FH) persimmons, which is a marketed cultivar with no existing data on its nutraceutical value. Total soluble tannins (TSTs) and major soluble (poly)phenols in FH fruits before and after post-harvest commercial treatments with carbon dioxide and ethylene were analyzed. Fruits at commercial harvest had a TST content of 1022 ± 286 mg GAL/100 g d.w. Whereas, after deastringency treatments, an 85% and 83% reduction were observed for carbon dioxide- and ethylene-treated fruits, respectively. Carbon dioxide treatment resulted in the insolubilization of tannins around comparable values in most fruit cultivars, despite the variable soluble tannin content in untreated fruit. By targeted metabolomic profiling, nineteen (poly)phenolic substances were quantified in the investigated untreated and treated fruits. Gallic acid (99 mg/100 g d.w.), (+)-catechin (1.8 mg/100 g d.w.), ellagic acid (1.2 mg/100 g d.w.), and (−)-epicatechin (1.1 mg/100 g d.w.) were the predominant compounds in the untreated FH samples. After the application of post-harvest treatments, a non-nutraceutical relevant decrease of 8-19% in the targeted (poly)phenolic content was generally observed. Ethylene induced the most significant reduction in the individual (poly)phenolic compounds in the FH fruits. [ABSTRACT FROM AUTHOR]

This letter, published in the American Journal of Respiratory Cell & Molecular Biology, discusses the need for early diagnosis and intervention to reduce the negative effects of ventilator-induced lung injury (VILI). The authors conducted a time-course proteomic study using a unique experimental ICU model and observed significant alterations in the proteomic profiles of bronchoalveolar lavage fluid (BALF) from Day 5 to Day 8 of mechanical ventilation (MV), indicating VILI. They identified potential biomarkers for VILI, such as MMP9 and intracellular proteins originating from lung and bronchial epithelial cells. The study highlights the importance of biomarkers for early detection of VILI to improve patient outcomes. [Extracted from the article]

Since the early days of time of flight secondary ion mass spectrometry (ToF-SIMS), increasing the ion signal has been crucial. It is even more crucial when performing tandem mass spectrometry experiments. To achieve this goal, many developments have been made over the years, which are divided into two categories: instrumental development and sample modification. The latter involves sample metallization, matrix deposition, or changing the temperature of the measurement. In this study, the possibility of using matrices to enhance the signals of organic light emitting device (OLED) molecules was explored. Seven molecules commonly used in OLEDs were separately deposited on Si wafers: Alq3, 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane, 1,4,5,8,9,11-hexaazatriphenylenehexacarbonitrile, Ir(mppy)3, N,N′-bis(naphthalene-1-yl)-N,N′-bis(phenyl)benzidine, 2,2′,7,7′-tetra(N,N-ditolyl)-amino-spiro-bifluor (STTB), and tris(4-carbazoyl-9-ylphenyl)amine. Using the same solvent, three different matrices with different thicknesses, common in matrix assisted light desorption ionization time of flight mass spectrometry, α-cyano-4-hydroxycinnamic acid, 2,5-dihydrobenzoic acid (DHB), and dihydrochloride N-(1-Naphthyl)ethylenediamine, were sprayed on these surfaces. Spectra were acquired for all compounds and spraying conditions in static ToF-SIMS experiments for Alq3 chemical imaging and depth profiling were performed. This allowed the investigation of the fragmentation pattern of the chosen matrices in ToF-SIMS and, thus, obtained a reference for these molecules. The results show that matrices can enhance the signal of fragments of the studied molecules, for example, the signal of STTB is increased with DHB spraying. Samples sprayed only with the solvent were also prepared to verify the impact of the matrices on the signal. Spraying with the solvent alone can enhance the signal even more than the matrices up to four times in the case of Alq3. This result opens new possibilities in the field of matrix-enhanced ToF-SIMS in terms of applications and matrix choices. [ABSTRACT FROM AUTHOR]

Grapes (Vitis vinifera L.) are known for their deliciousness and health benefits. In the present study, the variations of physicochemical profiles and antioxidant activities of 25 grape varieties were evaluated. Among the varieties tested, glucose and fructose were the main sugars, and tartaric and malic acids were the main organic acids in all grapes. Shine Muscat was characterized as suitable for fresh eating due to its high sugar contents and low acid contents. While JintianMeigui had high sugar and anthocyanins contents, making it suitable for cultivation. Results showed that all grape fractions are sources of phenolic compounds and varied among cultivars. In general, regardless of cultivars, seed extracts showed the highest content of total phenolics and total proanthocyanidins contents, consistent with the observed higher antioxidant activities. Combining high-performance liquid chromatography (HPLC) and high-resolution tandem mass spectrometry (HRMS) technologies, a total of 28 phenolic components were preliminarily identified. The most abundant anthocyanins in skins were petunidin-3-glucoside and malvidin-3-glucoside, as well as catechin and epicatechin were the principal proanthocyanidins in seeds. Pearson correlation coefficient analysis showed the significant linear correlations between proanthocyanidins (catechin, epicatechin, proanthocyanidin A1, proanthocyanidin B1, proanthocyanidin B2, proanthocyanidin C1 and epicatechin-3-O-gallate) and antioxidant activities. However, further studies are needed to demonstrate and elucidate the health benefits of grapes for human nutrition as antioxidants. Overall, our results provided theoretical guidance for the further development and utilization of grapes. [ABSTRACT FROM AUTHOR]

A sensitive and reliable LC–MS/MS method was developed and validated for the quantification of oxycodone and metabolites in human plasma. The method has a runtime of 6 min and a sensitivity of 0.1 μg/L for all analytes. Sample preparation consisted of protein precipitation. Separation was performed on a Kinetix biphenyl column (2.1 × 100 mm, 1.7 μm), using ammonium formate 5 mm in 0.1% aqueous formic acid and methanol LC–MS grade 100% in gradient elution at a flow rate of 0.4 ml/min. Detection was performed in multiple reaction monitoring mode using positive electrospray ionization. The method was linear over the calibration range of 0.1–25.0 μg/L for oxycodone, noroxycodone and noroxymorphone and 0.1–5.0 μg/L for oxymorphone. The method demonstrated good performance in terms of intra‐ and interday accuracy (86.5–110.3%) and precision (CV 1.7–9.3%). The criteria for the matrix effect were met (CV < 15%) except for noroxymorphone, for which an additional method was applied to compensate for the matrix effect. Whole blood samples were stable for 4 h at room temperature. Plasma samples were stable for 24 h at room temperature and 3 months at −20°C. Furthermore, the method was successfully applied in a pharmacokinetic drug interaction study of oxycodone and enzalutamide in patients with prostate cancer. [ABSTRACT FROM AUTHOR]

Over the course of an approximately 11-month period, an outdoor, freshwater, mixed species, recirculating, display system at a public aquarium experienced intermittent mortalities of channel catfish (Ictalurus punctatus) and blue catfish (I. furcatus). Catfish acutely presented for abnormal buoyancy, coelomic distention, and protein-rich coelomic effusion. Gross lesions typically involved massive coelomic distension with protein-rich effusion, generalized edema, and gastric hemorrhage and edema. Microscopically, primary lesions included renal tubular necrosis, gastric edema with mucosal hemorrhages, and generalized edema. Aerobic culture and virus isolation could not recover a consistent infectious agent. Intracoelomic injection of coelomic effusion and aspirated retrobulbar fluid from a catfish into naïve zebrafish (bioassay) produced peracute mortality in 3 of 4 fish and nervous signs in the fourth compared with 2 saline-injected control zebrafish that had - no mortality or clinical signs. Kidney tissue and coelomic effusion were submitted for gas chromatography tandem mass spectrometry by multiple reaction monitoring against laboratory standards, which detected the presence of multiple pyrethroid toxins, including bioallethrin, bifenthrin, trans-permethrin, phenothrin, and deltamethrin. Detection of multiple pyrethroids presumably reflects multiple exposures with several products. As such, the contributions of each pyrethroid toward clinical presentation, lesion development, and disease pathogenesis cannot be determined, but they are suspected to have collectively resulted in disrupted osmoregulation and fluid overload due to renal injury. Pesticide-induced toxicoses involving aquarium fish are rarely reported with this being the first description of pyrethroid-induced lesions and mortality in public aquarium-held fish. [ABSTRACT FROM AUTHOR]

Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of MS/MS spectra originating from published untargeted metabolomics experiments. Entries in this library, or suspects, were derived from unannotated spectra that could be linked in a molecular network to an annotated spectrum. Annotations were propagated to unknowns based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimers brain phenotype. The nearest neighbor suspect spectral library is openly available for download or for data analysis through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.

Organic peroxides are key intermediates in the atmosphere but are challenging to detect, especially in the particle phase, due to their instability, which has led to substantial gaps in the understanding of their environmental effects. We demonstrate that matrix-assisted ionization in vacuum (MAIV) mass spectrometry (MS), which does not require an ionization source, enables in situ characterization of peroxides and other products in the surface layers of organic particles. Hydroxyl radical oxidation of glutaric acid particles yields hydroperoxides and organic peroxides, which were detected with signals of the same order of magnitude as the major, more stable products. Product identification is supported by MS/MS analysis, peroxide standards, and offline high-resolution MS. The peroxide signals relative to the stable carbonyl and alcohol products are significantly larger using MAIV compared to those in the offline bulk analysis. This is also the case for analysis using fast, online easy ambient sonic-spray ionization mass spectrometry. These studies demonstrate the advantage of MAIV for the real-time characterization of labile peroxides in the surface layers of solid particles. The presence of peroxides on the surface may be important for surface oxidation processes as well as for the toxicity of inhaled particles.

Four alpine goats developed diarrhea soon after the owner placed plant clippings believed to be yellow oleander (Thevetia peruviana) into their pen on a suburban property near Palm Desert, CA, USA. A 1-y-old female goat died suddenly ~1 h after eating the plant clippings and was submitted to the San Bernardino Branch of the California Animal Health and Food Safety Laboratory System for postmortem examination. The main autopsy and histopathologic findings were myocardial hemorrhage and necrosis, consistent with cardiac glycoside intoxication. Rumen contents were analyzed by LC-MS/MS; peruvoside, a cardiac glycoside, was detected, but oleandrin, the cardiac glycoside of common oleander (Nerium oleander), was not. An LC-high-resolution MS (LC-HRMS) analysis revealed the presence of peruvoside and neriifolin in the rumen contents and in a tested plant fragment, indicating that the plant was a member of the Thevetia genus. A clipping from the plant fed to the goats and submitted by the owner was identified as yellow oleander, Thevetia peruviana (also known as Cascabela thevetia).

Camponotus floridanus ants show altered behaviors followed by a fatal summiting phenotype when infected with manipulating Ophiocordyceps camponoti-floridani fungi. Host summiting as a strategy to increase transmission is also observed with parasite taxa beyond fungi, including aquatic and terrestrial helminths and baculoviruses. The drastic phenotypic changes can sometimes reflect significant molecular changes in gene expression and metabolite concentrations measured in manipulated hosts. Nevertheless, the underlying mechanisms still need to be fully characterized. To investigate the small molecules producing summiting behavior, we infected C. floridanus ants with O. camponoti-floridani and sampled their heads for LC-MS/MS when we observed the characteristic summiting phenotype. We link this metabolomic data with our previous genomic and transcriptomic data to propose mechanisms that underlie manipulated summiting behavior in "zombie ants." This "multiomic" evidence points toward the dysregulation of neurotransmitter levels and neuronal signaling. We propose that these processes are altered during infection and manipulation based on (1) differential expression of neurotransmitter synthesis and receptor genes, (2) altered abundance of metabolites and neurotransmitters (or their precursors) with known behavioral effects in ants and other insects, and (3) possible suppression of a connected immunity pathway. We additionally report signals for metabolic activity during manipulation related to primary metabolism, detoxification, and anti-stress protectants. Taken together, these findings suggest that host manipulation is likely a multi-faceted phenomenon, with key processes changing at multiple levels of molecular organization.

Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) is a neurodegenerative disorder associated with the FMR1 premutation. Currently, it is not possible to determine when and if individual premutation carriers will develop FXTAS. Thus, with the aim to identify biomarkers for early diagnosis, development, and progression of FXTAS, along with associated dysregulated pathways, we performed blood proteomic profiling of premutation carriers (PM) who, as part of an ongoing longitudinal study, emerged into two distinct groups: those who developed symptoms of FXTAS (converters, CON) over time (at subsequent visits) and those who did not (non-converters, NCON). We compared these groups to age-matched healthy controls (HC). We assessed CGG repeat allele size by Southern blot and PCR analysis. The proteomic profile was obtained by liquid chromatography mass spectrometry (LC-MS/MS). We identified several significantly differentiated proteins between HC and the PM groups at Visit 1 (V1), Visit 2 (V2), and between the visits. We further reported the dysregulated protein pathways, including sphingolipid and amino acid metabolism. Our findings are in agreement with previous studies showing that pathways involved in mitochondrial bioenergetics, as observed in other neurodegenerative disorders, are significantly altered and appear to contribute to the development of FXTAS. Lastly, we compared the blood proteome of the PM who developed FXTAS over time with the CSF proteome of the FXTAS patients recently reported and found eight significantly differentially expressed proteins in common. To our knowledge, this is the first report of longitudinal proteomic profiling and the identification of unique biomarkers and dysregulated protein pathways in FXTAS.

Non-targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely used tool for metabolomics analysis, enabling the detection and annotation of small molecules in complex environmental samples. Data-dependent acquisition (DDA) of product ion spectra is thereby currently one of the most frequently applied data acquisition strategies. The optimization of DDA parameters is central to ensuring high spectral quality, coverage, and number of compound annotations. Here, we evaluated the influence of 10 central DDA settings of the Q Exactive mass spectrometer on natural organic matter samples from ocean, river, and soil environments. After data analysis with classical and feature-based molecular networking using MZmine and GNPS, we compared the total number of network nodes, multivariate clustering, and spectrum quality-related metrics such as annotation and singleton rates, MS/MS placement, and coverage. Our results show that automatic gain control, microscans, mass resolving power, and dynamic exclusion are the most critical parameters, whereas collision energy, TopN, and isolation width had moderate and apex trigger, monoisotopic selection, and isotopic exclusion minor effects. The insights into the data acquisition ergonomics of the Q Exactive platform presented here can guide new users and provide them with initial method parameters, some of which may also be transferable to other sample types and MS platforms.

Osteogenesis is modulated by multiple regulatory networks. Recent studies showed that RNA modifications and their reader, writer, and eraser (RWE) proteins are involved in regulating various biological processes. Few studies, however, were conducted to investigate the functions of RNA modifications and their RWE proteins in osteogenesis. By using LC-MS/MS in parallel-reaction monitoring (PRM) mode, we performed a comprehensive quantitative assessment of 154 epitranscriptomic RWE proteins throughout the entire time course of osteogenic differentiation in H9 human embryonic stem cells (ESCs). We found that approximately half of the 127 detected RWE proteins were down-regulated during osteogenic differentiation, and they included mainly proteins involved in RNA methylation and pseudouridylation. Protein-protein interaction (PPI) network analysis unveiled significant associations between the down-regulated epitranscriptomic RWE proteins and osteogenesis-related proteins. Gene set enrichment analysis (GSEA) of publicly available RNA-seq data obtained from osteogenesis imperfecta patients suggested a potential role of METTL1 in osteogenesis through the cytokine network. Together, this is the first targeted profiling of epitranscriptomic RWE proteins during osteogenic differentiation of human ESCs, and our work unveiled potential regulatory roles of these proteins in osteogenesis. LC-MS/MS data were deposited on ProteomeXchange (PXD039249).

Distinct CD4+ T cell epitopes have been associated with spontaneous control of HIV-1 replication, but analysis of antigen-dependent factors that influence epitope selection is lacking. To examine these factors, we used a cell-free antigen processing system that incorporates soluble HLA-DR (DR1), HLA-DM (DM), cathepsins, and full-length protein antigens for epitope identification by LC-MS/MS. HIV-1 Gag, Pol, Env, Vif, Tat, Rev, and Nef were examined using this system. We identified 35 novel epitopes, including glycopeptides. Epitopes from smaller HIV-1 proteins mapped to regions of low protein stability and higher solvent accessibility. HIV-1 antigens associated with limited CD4+ T cell responses were processed efficiently, while some protective epitopes were inefficiently processed. 55% of epitopes obtained from cell-free processing induced memory CD4+ T cell responses in HIV-1+ donors, including eight of 19 novel epitopes tested. Thus, an in vitro processing system utilizing the components of Class II processing reveals factors influencing epitope selection of HIV-1 and represents an approach to understanding epitope selection from non-HIV-1 antigens.