High-resolution Accurate Mass Research Articles

B-146 Unlocking the potential of large-cohort proteomics studies with the Orbitrap Astral mass platform

Abstract Background Large-cohort proteomics analysis using mass spectrometry is a powerful approach to discover and validate new biomarkers. In combination with clinical data and computational analysis, large-cohort proteomics study brings opportunities in improving early diagnosis, refining patient stratification, and predicting/monitoring treatment response. Yet, to achieve meaningful biological insights in large-cohort studies, robust, reproducible, and comprehensive proteome profiling in a high-throughput manner still remains challenging. Here, we use a high-resolution accurate mass (HRAM) Oribtrap Astral platform to enable high-quality and robust protein quantification across thousands of LC-MS/MS analyses. With a throughput of 100 samples/day, we can reproducibly profile ∼9000 proteins from human cell line and ∼800 proteins from undepleted plasma across multiple instruments and more than 10 consecutive days in a 24/7 operation mode. Methods Experiments were performed on multiple Orbitrap Astral mass spectrometers with and without FAIMS Pro interface. Chromatographic separations were performed using a trap/elute method on Vanquish Neo system at a 11-minute gradient and a flow rate of 1ul/min, resulting in a throughput of 100 samples/day. Undepleted plasma digest was analyzed in a 24/7 mode for > 1000 injections on each LC-MS/MS setup. In addition, HeLa digest as quality control (QC) was analyzed every 12hours. The Oribtrap Astral platform was operated in data-independent acquisition (DIA) mode using a full scan with m/z 380-980, and DIA MS/MS scans with an isolation window of 2Th. Resulting DIA raw files were automatically transferred and processed using Chimerys in a beta version of Proteome Discoverer software. Results Multiple LC-MS/MS systems were operated in DIA mode either with or without FAIMS Pro device in a 24/7 operation mode at a throughput of 100SPD. Undepleted plasma digest was analyzed with >1000 injections on each LC-MS/MS setup. To monitor the baseline performance, HeLa digest served as QC were analyzed periodically every 12 hours with 3 technical replicates each time. To effectively manage and analyze these thousands of data files generated, we developed an automated data transfer and analysis pipeline. Automatically, the resulting DIA raw data files were immediately transferred to a server, then processed by state-of-the-art intelligent search algorithm Chimerys. Benefiting from the ultra-high scan speed of up to 200Hz on the Orbitrap Astral mass spectrometer, a much narrower isolation window width of 2Th was applied in the DIA method, comparing to 10-20Th on the classic DIA method. As a result, ∼9000 proteins from HeLa digest and ∼800 proteins from undepleted plasma digest were identified within only a 11-minutes gradient, respectively. More than 80% of the plasma proteins were reproducibly identified and quantified from all the runs on each LC-MS/MS setup, indicating a great reproducibility from run-to-run longitudinally. Stable and robust peptide quantitation was observed by extracting peptides with high, medium, and low abundant across the runs. Importantly, QC showed no performance degradation throughout the entire study, indicating high robustness of the entire LC-MS/MS setup. Conclusions Orbitrap Astral mass platform can comprehensively analyze the proteome of >1000s of sample robustly and reproducibly in a high-throughput manner, addressing the needs in large-cohort studies.

B-150 Chromatographic Separation and Quantitation of Human Insulin and Lispro Analog in Serum Using Liquid Chromatography High-Resolution Mass Spectrometry

Abstract Background Factitious hypoglycemia, a deliberate attempt to induce low blood glucose levels occurring secondary to the surreptitious administration of exogenous insulin, can be difficult to diagnose due to a variety of factors including the increased use of synthetic insulin analogs in clinical practice. Traditional insulin immunoassays demonstrate variable cross-reactivity with commonly prescribed insulin analogues and their metabolites, making it difficult to measure specific analogs. The development of liquid chromatography high resolution accurate mass (LC-HRAM)-mass spectrometry (MS) assays has largely circumvented the limitations of traditional immunoassays for detection and quantitation of insulin analogs. Analytical challenges remain, however, specifically in differentiating lispro, an isomeric human insulin analog formed by the transposition of proline and lysine near the C-terminal end of the B chain, from human insulin in patient samples due to the equivalent mass-to-charge ratios of their precursor ions. Methods Immunoaffinity purification of insulin from calibrators and quality control material prepared by spiking insulin-depleted serum with pharmaceutical insulin preparations, as well as patient samples, was performed using tips coupled with anti-insulin monoclonal antibody. An automated liquid handler was programmed to perform aspiration and dispense cycles. Eluate from the purification protocol was submitted for analysis using a TLX-2 multiplex LC system paired with a Thermo Scientific Q Exactive Plus mass spectrometer. Various HPLC column chemistries were evaluated, a column passivation procedure was established, and column heater temperature was optimized to identify a combination of parameters yielding the best chromatographic separation of human insulin and lispro. Additionally, parallel reaction monitoring (PRM) targeted tandem mass spectrometry (MS/MS) analysis was utilized in combination with the full scan data to increase specificity through the monitoring of fragment ions produced from human insulin and each insulin analog. Results We found that a 1000 Å Diphenyl, 2.7 µm, 2.1 x 100 mm analytical column in a column heater maintained at a temperature of 80°C allowed for human insulin and lispro to be differentiated as two chromatographically separated extracted ion chromatographic peaks (XICs) and quantified down to 2.5 mcIU/mL with near-baseline separation. Before use, the column required passivation with a high protein buffer (0.05% bovine serum albumin in 20% acetonitrile [ACN] + 0.2% acetic acid) followed by increasingly organic buffers (20% ACN + 0.2% acetic acid and 50% ACN + 0.2% acetic acid). MS/MS was used to confirm the presence of analogs detected. Conclusions The LC-HRAM-MS method described here, coupled with optimized column chemistry, column passivation, and proper column temperature control allows for chromatographic separation of human insulin and lispro. Incorporating a PRM scan into the mass spectrometry full scan method provides confirmation of the insulin detected in the XICs. The results obtained from preliminary studies suggest this method is appropriate for use to facilitate the clinical investigation of suspected factitious hypoglycemia with the ability to differentiate isomeric compounds, such as human insulin and lispro.

Identification of chemical constituents and pharmacokinetic characteristics of Xiaoyan Tuire Granule in rats

Xiaoyan Tuire Granule is a type of Chinese patent medicine that has been proven effective in treating respiratory tract infections. However, while it has been successfully introduced into clinical use, more knowledge is still needed regarding its chemical components and pharmacokinetics. This study investigated the chemical profile in the medicine and rat plasma by ultra high-performance liquid chromatography coupled with Q Exactive hybrid quadrupole-orbitrap high-resolution accurate mass spectrometry (UHPLC-Orbitrap-MS/MS). Subsequently, it developed a validated ultra high-performance liquid chromatography coupled with quadrupole mass spectrometry (UHPLC-MS/MS) method for determining five components in rat plasma after oral administration of Xiaoyan Tuire Granule. As a result, a total of 106 constituents were inferred, including 9 terpenoids, 29 flavonoids, 33 organic acids, 12 phenylpropanoids and 23 other compounds. After administration, 86 compounds were inferred in rat plasma, including 73 prototypes and 13 metabolites. The metabolic pathways were primarily hydrogenation, glucuronic acid conjugation, sulfate conjugation, hydrolysis and methylation. The established method determined the contents of esculetin, esculin, isovitexin, caffeic acid and p-coumaric acid had a good separation, and all the legal verification met the requirements. The pharmacokinetic results indicate that the absorption rate of the five compounds in vivo was rapid, with a Tmax of less than 0.25 h, and the elimination rate was also fast, with a half-time (T1/2) ranging from 1.22 h to 2.19 h. It is worth noting that esculin and esculetin have similar half-time in vivo due to their structural similarities. Among these five compounds, the AUC0-∞ and MRT0-∞ of p-coumaric acid and esculetin were relatively higher, indicating higher exposure and longer residence time of both compounds in vivo. In conclusion, this paper researched the chemical constituents and pharmacokinetics of Xiaoyan Tuire Granule, which provided the reference for further study.

Applying UHPLC-HRAM MS/MS Method to Assess Host Cell Protein Clearance during the Purification Process Development of Therapeutic mAbs.

Host cell proteins (HCPs) are one of the process-related impurities that need to be well characterized and controlled throughout biomanufacturing processes to assure the quality, safety, and efficacy of monoclonal antibodies (mAbs) and other protein-based biopharmaceuticals. Although ELISA remains the gold standard method for quantification of total HCPs, it lacks the specificity and coverage to identify and quantify individual HCPs. As a complementary method to ELISA, the LC-MS/MS method has emerged as a powerful tool to identify and profile individual HCPs during the downstream purification process. In this study, we developed a sensitive, robust, and reproducible analytical flow ultra-high-pressure LC (UHPLC)-high-resolution accurate mass (HRAM) data-dependent MS/MS method for HCP identification and monitoring using an Orbitrap Ascend BioPharma Tribrid mass spectrometer. As a case study, the developed method was applied to an in-house trastuzumab product to assess HCP clearance efficiency of the newly introduced POROS™ Caprylate Mixed-Mode Cation Exchange Chromatography resin (POROS Caprylate mixed-mode resin) by monitoring individual HCP changes between the trastuzumab sample collected from the Protein A pool (purified by Protein A chromatography) and polish pool (purified by Protein A first and then further purified by POROS Caprylate mixed-mode resin). The new method successfully identified the total number of individual HCPs in both samples and quantified the abundance changes in the remaining HCPs in the polish purification sample.

High-quality identification of volatile organic compounds (VOCs) originating from breath

IntroductionVolatile organic compounds (VOCs) can arise from underlying metabolism and are detectable in exhaled breath, therefore offer a promising route to non-invasive diagnostics. Robust, precise, and repeatable breath measurement platforms able to identify VOCs in breath distinguishable from background contaminants are needed for the confident discovery of breath-based biomarkers.ObjectivesTo build a reliable breath collection and analysis method that can produce a comprehensive list of known VOCs in the breath of a heterogeneous human population.MethodsThe analysis cohort consisted of 90 pairs of breath and background samples collected from a heterogenous population. Owlstone Medical’s Breath Biopsy® OMNI® platform, consisting of sample collection, TD-GC-MS analysis and feature extraction was utilized. VOCs were determined to be “on-breath” if they met at least one of three pre-defined metrics compared to paired background samples. On-breath VOCs were identified via comparison against purified chemical standards, using retention indexing and high-resolution accurate mass spectral matching.Results1471 VOCs were present in > 80% of samples (breath and background), and 585 were on-breath by at least one metric. Of these, 148 have been identified covering a broad range of chemical classes.ConclusionsA robust breath collection and relative-quantitative analysis method has been developed, producing a list of 148 on-breath VOCs, identified using purified chemical standards in a heterogenous population. Providing confirmed VOC identities that are genuinely breath-borne will facilitate future biomarker discovery and subsequent biomarker validation in clinical studies. Additionally, this list of VOCs can be used to facilitate cross-study data comparisons for improved standardization.

Determination of Anthropogenic Pollutants in Adipose Tissue of the Caspian Seal Pusa caspica Gmelin, 1788 by High-Resolution Accurate Mass Spectrometry.

Tissue contamination with persistent organic pollutants (POPs) in organisms proved possible to comprehensively characterize in a single test by combining gas chromatography and high-resolution accurate mass spectrometry. Adipose tissue samples were collected from two Caspian seals (Pusa caspica Gmelin, 1788) found dead on the Caspian Sea shore in 2020. Organochlorine pesticides, primarily DDT and HCH, and polychlorinated biphenyls (PCBs) were major pollutants found in the Caspian seals. The distribution of metabolites indicated the absence of recent pesticide use. The PCB content was relatively high, but still at the lower limit of the range of values determined previously, as was also the case with pesticides. Chlordanes, polychlorinated naphthalenes, and polybrominated diphenyl ethers were detected in minor quantities and were therefore not considered to be major pollutants of the Caspian seal. The pollutant levels were below a threshold at which a distinct effect on seal health can be expected. High-resolution accurate mass (HRAM) spectrometry was found to provide a convenient tool for both targeted and nontargeted analyses of a wide range of organic pollutants in a single experiment.

Improved multi-food allergen analysis of processed foods using HRAM-LC-MS/MS with an ELISA-validated extraction solution and MS sample prep kit.

Food allergens in processed foods are affected by heating, processing, and the food matrix. To conduct highly reliable tests, extracting allergens into test solutions is necessary for appropriate detection. In addition to the commonly used enzyme-linked immunosorbent assay (ELISA), liquid chromatography-mass spectrometry (LC-MS), which has the advantage of simultaneously detecting multiple allergens in foods, is being increasingly used. When managing food allergens at food manufacturing sites, obtaining the same measured values is desirable, regardless of the analytical method used. Therefore, in this study, we focused on the importance of pretreatment steps for LC-MS when examining food allergens in processed foods, which can be difficult to analyze. The ELISA method uses food extracts optimized for analyzing allergens in processed foods. We developed a high-resolution accurate mass spectrometry (HRAM)-LC-MS/MS method using the same food extract used in the ELISA method and an MS sample preparation kit. Multiple food allergen analysis was performed using 1, 5, 10, and 20ppm of allergen-incurred processed foods. Overall, a strong correlation was observed between the measured values of HRAM-LC-MS/MS and ELISA, demonstrating the applicability of multi-allergen analysis using LC-MS.

Degradation of Isotianil in Water and Soil: Kinetics, Degradation Pathways, Mechanisms, and Ecotoxicity Assessments.

Pesticides are transported and transformed in soil and can enter surface water through various pathways. They undergo hydrolysis, oxidation, and photoconversion in surface water. Isotianil is a new fungicide that effectively controls rice blast. However, there are limited reports on its degradation. Herein, the hydrolysis and photolysis of isotianil in water and its degradation in soil samples from five provinces of China were investigated. The degradation products of isotianil were identified using ultrahigh-performance liquid chromatography-Q exactive hybrid quadrupole-orbitrap high-resolution accurate mass spectrometry, and four compounds were discovered for the first time. The degradation pathways of isotianil were inferred, and the reaction active site and degradation mechanism of isotianil were clarified based on density functional theory calculations. The ecotoxicity of the degradation product M118 (aminobenzonitrile) was found to be moderate toward Daphnia magna, which was predicted and confirmed by Ecological Structure Activity Relationships and the experiment, respectively. The results of this study will contribute to a better understanding of the fate of isotianil in the environment.

Effect of biological sex and short-term high-fat diet on cellular proliferation, ribosomal biogenesis, and targeted protein abundance in murine articular cartilage

ObjectiveTo identify factors contributing to sex-differences in OA risk by evaluating the short-term effect of high-fat (HF) diet on sex-specific changes in cartilage cell proliferation, ribosomal biogenesis, and targeted extra-cellular and cellular protein abundance. Materials and methodsKnee cartilage was harvested to the subchondral bone from 20-week-old female and male C57BL/6J mice fed a low-fat or HF diet for 4 weeks and labeled with deuterium oxide for 1, 3, 5, 7, 15, or 21 days. Deuterium enrichment was quantified in isolated DNA and RNA to measure cell proliferation and ribosomal biogenesis, respectively. Protein concentration was measured using targeted high resolution accurate mass spectrometry. ResultsHF diet increased the maximal deuterium incorporation into DNA from approximately 40 to 50%, albeit at a slower rate. These findings, which were magnified in female versus male mice, indicate a greater number of proliferating cells with longer half-lives under HF diet conditions. HF diet caused distinct sex-dependent effects on deuterium incorporation into RNA, increasing the fraction of ribosomes undergoing biogenesis in male mice and doubling the rate of ribosome biogenesis in female mice. HF diet altered cartilage protein abundance similarly in both sexes, except for matrilin-3, which was more abundant in HF versus LF conditions in female mice only. Overall, HF diet treatment had a stronger effect than sex on cartilage protein abundance, with most changes involving extracellular matrix and matrix-associated proteins. ConclusionsShort-term HF diet broadly altered cartilage matrix protein abundance, while sex-dependent effects primarily involved differences in cell proliferation and ribosomal biogenesis.

Discovery of Free Glycated Amines and Glycated Urea in Diabetic Plasma: Potential Implications in Diabetes.

The role of protein glycation in the pathogenesis of diabetes has been well established. Akin to proteins, free amino acids and other small-molecule amines are also susceptible to glycation in hyperglycemic conditions and may have a role in the pathogenesis of the disease. However, information about glycation of free amino acids and other small-molecule amines is relatively obscure. In the quest to discover small-molecule glycated amines in the plasma, we have synthesized glycated amino acids, glycated creatine, and glycated urea, and by using a high-resolution accurate mass spectrometer, a mass spectral library was developed comprising the precursor and predominant fragment masses of glycated amines. Using this information, we report the discovery of the glycation of free lysine, arginine, and leucine/isoleucine from the plasma of diabetic patients. This has great physiological significance as glycation of these amino acids may create their deficiency and affect vital physiological processes such as protein synthesis, cell signaling, and insulin secretion. Also, these glycated amino acids could serve as potential markers of diabetes and its complications. While other amines, such as creatinine and urea, accumulate in the plasma and act as biomarkers of diabetic nephropathy. For the first time, we report the detection of glycated urea in diabetic plasma, which is confirmed by matching the precursor and fragment masses with the in vitro synthesized glycated urea by using 12C6 and 13C6-glucose. Further, we quantified glycated urea detected in two forms, monoglycated urea (MGU) and diglycated urea (DGU), by a targeted mass spectrometric approach in the plasma of healthy, diabetic, and diabetic nephropathy subjects. Both MGU and DGU showed a positive correlation with clinical parameters, such as blood glucose and HbA1c. Given that urea gets converted to glycated urea in hyperglycemic conditions, it is crucial to quantify MGU and DGU along with the urea for the diagnosis of diabetic nephropathy and study their physiological role in diabetes.

Mass Spectrometry-Based Method to Measure Aflatoxin B1 DNA Adducts in Formalin-Fixed Paraffin-Embedded Tissues.

Aflatoxin B1 (AFB1) is a potent human liver carcinogen produced by certain molds, particularly Aspergillus flavus and Aspergillus parasiticus, which contaminate peanuts, corn, rice, cottonseed, and ground and tree nuts, principally in warm and humid climates. AFB1 undergoes bioactivation in the liver to produce AFB1-exo-8,9-epoxide, which forms the covalently bound cationic AFB1-N7-guanine (AFB1-N7-Gua) DNA adduct. This adduct is unstable and undergoes base-catalyzed opening of the guanine imidazolium ring to form two ring-opened diastereomeric 8,9-dihydro-8-(2,6-diamino-4-oxo-3,4-dihydropyrimid-5-yl-formamido)-9-hydroxy-aflatoxin B1 (AFB1-FapyGua) adducts. The AFB1 formamidopyrimidine (Fapy) adducts induce G → T transversion mutations and are likely responsible for the carcinogenic effects of AFB1. Quantitative liquid chromatography-mass spectrometry (LC-MS) methods have shown that AFB1-N7-Gua is eliminated in rodent and human urine, whereas ring-opened AFB1-FapyGua adducts persist in rodent liver. However, fresh frozen biopsy tissues are seldom available for biomonitoring AFB1 DNA adducts in humans, impeding research advances in this potent liver carcinogen. In contrast, formalin-fixed paraffin-embedded (FFPE) specimens used for histopathological analysis are often accessible for molecular studies. However, ensuring nucleic acid quality presents a challenge due to incomplete reversal of formalin-mediated DNA cross-links, which can preclude accurate quantitative measurements of DNA adducts. In this study, employing ion trap or high-resolution accurate Orbitrap mass spectrometry, we demonstrate that ring-opened AFB1-FapyGua adducts formed in AFB1-exposed newborn mice are stable to the formalin fixation and DNA de-cross-linking retrieval processes. The AFB1-FapyGua adducts can be detected at levels comparable to those in a match of fresh frozen liver. Orbitrap MS2 measurements can detect AFB1-FapyGua at a quantification limit of 4.0 adducts per 108 bases when only 0.8 μg of DNA is assayed on the column. Thus, our breakthrough DNA retrieval technology can be adapted to screen for AFB1 DNA adducts in FFPE human liver specimens from cohorts at risk of this potent liver carcinogen.

If speed is of the essence: rapid analysis of ambergris by APCI compact mass spectrometry

The use of atmospheric pressure chemical ionisation (APCI) compact mass spectrometry (CMS) was investigated for the analysis of jetsam and museum-archived ambergris and of ambergris components in perfumes. The data were compared with those from existing methods. Authentic samples of some individual ambergris constituents (ambrein, coprostanol, epicoprostanol and coprostanone), were also examined. Rapid APCI CMS was achieved using either a solids probe or a probe with solutions held in capillary melting point tubes. Interpretation is made of the spectra of the principal natural product components, the relative ion responses were measured and the elemental composition of key ions in the spectra confirmed using high resolution accurate mass APCI MS. Rapid analysis of ambergris by APCI CMS may prove to be a further convenient method of identifying ambrein, of measuring the relative ratios of ambrein and steroids in ambergris and even of quantifying the latter, with minimal sample preparation.

Decoction regulating phytochemicals’ micromorphology changes and anti-inflammation activity enhancements originated from herb medicine supermolecules

BackgroundMahuang Fuzi decoction (MGF) is composed of three herb medicines that has been clinically used to treat inflammatory diseases for a long history. At present, more and more active phytochemicals’ aggregations have been found during the thermodynamic process of herb medicine decoction, and revealing the clinical efficacy of herb medicine through supramolecular strategies is the focus of current research. However, it is not clear whether decoction induced supermolecules’ morphological changes to modify activity.MethodsDynamic light scattering (DLS) and field emission scanning electron microscopy (FESEM) were used to analyze the micromorphology of MGF, MGF SA (MGF supermolecules), and MIX (physical mixture of MGF single decoction). The interaction and thermodynamic parameters of single herbs in a decoction were investigated by Isothermal titration calorimetry (ITC). The phytochemicals were systematically analyzed by ultra high performance liquid chromatography-Q Exactive hybrid quadrupole-orbitrap high-resolution accurate mass spectrometry (UHPLC-Q-Orbitrap HRMS). Under the safe dose on RAW264.7 cells, NO, IL-6 and TNF-α were determined by Enzyme-Linked ImmunoSorbent Assay (ELISA) method. NF-κB p65 translocation from the cytoplasm into the nucleus was examined using the immunofluorescence assay and the western blot, respectively. Furthermore, Metabolomics was used to discover potential biomarkers and the associated metabolic pathways of MGF SA treatment.ResultsThere were nanoscale aggregations in MGF, and the micromorphology of the extracted MGF SA consisted of uniform particles; while the MIX micromorphology had no uniformity. ITC showed that the interaction MH-GC and FZ-GC were a spontaneous exothermic reaction, indicating that their phytochemicals had the property of self-assembly. Though the micromorphology between MGF, MGF SA, and MIX was obviously different, UHPLC-Q-Orbitrap HRMS results displayed that the main phytochemicals of MGF and MIX had nearly the same components. Interestingly, MGF and MGF SA could significantly inhibit the production of NO, and had better inhibition effect on the expression of nuclear protein NF-κB p65 than MIX, among which MGF SA had the best effect. Further investigation indicated that the perturbance of metabolic profiling in RAW264.7 inflammatory cells was obviously reversed by MGF SA.ConclusionsThe decoction enriched the key active phytochemicals and regulated the formation of homogeneous nanoparticles in MGF SA. The supermolecules in MGF SA significantly enhanced its anti-inflammatory activity, primarily affecting the NF-κB signaling pathway and the biosynthesis and metabolism of arginine in RAW264.7 inflammatory cells. Current study displayed that co-decocting herbal medicine were beneficial to the treatment of diseases than the mixture of the single herbs’ extraction.Graphical

Method Development and Validation for Simultaneous Detection of Corticosteroids, Small Peptides, SARMs and Quaternary Ammonium Drugs in Camel Urine for Doping Control Applications

Background: Detection and identification of a wide range of drugs, including small peptides, corticosteroids, selective androgen receptor modulators (SARMs), and quaternary ammonium drugs (QADs), are imperative across several domains, particularly in anti-doping analysis, given the potential misuse of these substances in animal sports, there is an urgent demand for an allencompassing screening method to effectively identify these compounds. Objective: To develop a robust and sensitive high-resolution method for simultaneous screening of small peptides, corticosteroids, SARMs, and QADs using liquid chromatography accurate mass spectrometry in post-race urine samples. This method integrates a streamlined single-stage extraction approach, significantly enhancing efficiency and adaptability for screening drugs across various classes. Methods: The method development and validation involved a comprehensive solid-phase extraction protocol, which included a sequential elution for corticosteroids, small peptides, SARMs, and QADs. Chromatographic separation was achieved using a reverse-phase C18 column, and the analysis was performed using liquid chromatography - high-resolution accurate mass spectrometry. Results: The developed method was validated using a selection of drugs representing each class. The method exhibited robustness and sensitivity, enabling the simultaneous screening of the specified drug classes. The flexibility inherent in the proposed extraction and analysis method allows for seamless integration of new drug candidates eliminating the need for method redevelopment. Conclusion: A versatile and effective screening method was successfully developed and validated for the simultaneous detection of small peptides, corticosteroids, SARMs, and QADs. The method's ability for retrospective analysis of emerging drugs using full scan HRMS enhances its utility. This method holds great promise across various fields where accurate and comprehensive drug screening is imperative.

Anti-filarial efficacy of Centratherum anthelminticum: unravelling the underlying mechanisms through biochemical, HRAMS proteomics and MD simulation approaches.

Traditionally, Centratherum anthelminticum (CA) has been reported to be a potent anti-filarial, however no reports are available detailing its mechanism of action against filarial parasites. In this study, we have evaluated the anti-filarial activity of CA against lymphatic filarial parasites Setaria cervi using ex vivo biochemical, proteomics and in silico approaches. The motility and viability of the parasites decreased significantly after treatment with CA concentrations of ≥125 μg mL-1. An increase in lipid peroxidation (51.92%), protein carbonylation (48.99%), NADPH oxidase (88.88%) activity and decrease in the glutathione (GSH) (-39.23%), glutathione reductase (GR) (-60.17%), and glutathione S-transferase (GST) (-50.48%) activity was also observed after CA treatment. The proteomics analysis was performed by two-dimensional gel electrophoresis and high-resolution accurate mass spectrometry (HRAMS). In total, 185 proteins were differentially expressed (DEPs) following CA treatment. The major DEPs were mostly involved in tRNA processing, biosynthetic processes, metabolic activities, protein transport, the tricarboxylic acid cycle, protein translation, and stress response. The UPLC-ESI-MS/MS analysis of CA extract revealed the presence of 40 bioactive compounds. Further the docking analysis showed 10 CA bioactive compounds to have high binding affinity towards antioxidant proteins of filarial parasites. Additionally, MD simulation studies showed stable interactions (RMSF ≤ 10 Å) of 3-O-methylquercitin, quinic acid, gentisic acid, and vanillin with filarial antioxidant enzymes/proteins. To our knowledge, this is the first report detailing the molecular mechanism of anti-filarial activity of CA, which can be further evaluated for the development of new anti-filarial formulations.

Evaluation of the Mechanisms Involved in the Development of Bladder Toxicity following Exposure to Occupational Bladder Cancer Causative Chemicals Using DNA Adductome Analysis.

Occupational exposure to aromatic amines (AAs) is an important risk factor for urinary bladder cancer. This study aimed to evaluate the toxicity of AAs and analyze the carcinogenic mechanisms in rat bladder by comprehensive analysis of DNA adducts (DNA adductome). DNA was extracted from the bladder epithelia of rats treated with AAs, including acetoacet-o-toluidine (AAOT) and o-toluidine (OTD), and adductome analysis was performed. Principal component analysis-discriminant analysis revealed that OTD and AAOT observed in urinary bladder hyperplasia could be clearly separated from the controls and other AAs. After confirming the intensity of each adduct, four adducts were screened as having characteristics of the OTD/AAOT treatment. Comparing with the in-house DNA adduct database, three of four candidates were identified as oxidative DNA adducts, including 8-OH-dG, based on mass fragmentation together with high-resolution accurate mass (HRAM) spectrometry data. Therefore, findings suggested that oxidative stress may be involved in the toxicity of rat bladder epithelium exposed to AAs. Consequently, the administration of apocynin, an inhibitor of nicotinamide adenine dinucleotide phosphate oxidase, in six-week-old rats fed with 0.6% OTD in their diet resulted in simple hyperplastic lesions in the bladder that were suppressed by apocynin. The labeling indices of Ki67, γ-H2AX, and 8-OHdG were significantly decreased in an apocynin concentration-dependent manner. These findings indicate that oxidative stress may have contributed to the development of urinary cancer induced by OTD.

Multi-Dimensional Liquid Chromatography of Pulse Triacylglycerols with Triple Parallel Mass Spectrometry

We analyzed ten pulses (the dried seeds of legumes), i.e., baby lima beans, black beans, black-eyed peas, butter beans, cranberry beans, garbanzo beans, green split peas, lentils, navy beans, and pinto beans, using three-dimensional liquid chromatography (3D-LC) with parallel second dimensions, LC × (LC + LC). We combined non-aqueous reversed-phase (NARP) chromatography as the first dimension separation, 1D, with argentation UHPLC for separation based on degree and location of unsaturation in the first second dimension, 2D(1), and multi-cycle NARP-UHPLC in the second second dimension, 2D(2). Pulses contained 1.9% to 2.7% lipids, except garbanzo beans, which contained 6.2% lipids. High-resolution, accurate-mass (HRAM) orbitrap mass spectrometry (MS) was used to perform lipidomic analysis of the 2D(2) and percent relative quantification, showing that the most abundant average triacylglycerol (TAG) molecular species across all pulses were PLL at 10.67% and PLLn at 10.45%. Common beans (Phaseolus vulgaris) were clustered together using principal component analysis (PCA), showing the highest levels of linolenic acid, C18:3, in molecular species such as PLnLn, LLnLn, and OLLn, with palmitic (P), C16:0, linoleic (L), 18:2, linolenic (Ln), 18:3, and oleic (O), 18:1, FAs. Calibration curves derived from interweaved sets of regioisomer standards allowed the absolute quantification of 1,2- and 1,3-regioisomers for a subset of TAGs.

Post mortem blood bromazolam concentrations and co-findings in 96 coronial cases within England and Wales

Bromazolam is a newly emerging benzodiazepine drug which is not licensed for medicinal use. It may be sourced as a New Psychoactive Substance (NPS) for its desired effects or be consumed unknowingly via counterfeit Xanax® or Valium® preparations. As part of our Coronial workload, we observed an increase in the detection of bromazolam from September 2021 to November 2022. We report a series of 96 cases in which bromazolam was quantitated by high resolution accurate mass - mass spectrometry (HRAM - MS) in post-mortem blood. The mean (SD) post-mortem blood bromazolam concentration from our case series was 64.6 ( ± 79.4) µg/L (range <1–425 µg/L). Routine toxicological screening results have also been reported; the most commonly encountered drugs taken in combination with bromazolam were cocaine, gabapentinoids and diazepam. In 48% of cases at least one further designer benzodiazepine drug was also present (etizolam, flualprazolam, flubromazolam, flubromazepam). It is essential that laboratories providing toxicological investigations are aware of the limitations of their assays; and inclusion of bromazolam within targeted screening panels using LC-MS/MS is encouraged. Bromazolam has not been associated with death in isolation from resulting toxic concentrations; however, it is likely to enhance adverse clinical effects when taken in combination with stimulant and/or centrally-acting depressant drugs (poly-drug deaths). Bromazolam, similar to other benzodiazepines, may also impair cognition and decision making skills.

Multi-Attribute Method (MAM) Analytical Workflow for Biotherapeutic Protein Characterization from Process Development to QC.

The multi-attribute method (MAM) has emerged significantly in recent years to support biotherapeutic protein characterization from process development to the QC environment. MAM is a liquid chromatography mass spectrometry (LC-MS) based peptide mapping approach, which combines the benefits from liquid chromatography coupled to high resolution accurate mass mass spectrometry (LC-HRAM MS), enabling direct assessment of protein sequence and product quality attributes with site specificity. These product quality attributes may impact efficacy, safety, stability, and process robustness. MAM is intended to replace conventional analytical approaches as it offers a more streamlined strategy for parallel monitoring of multiple attributes in a single analysis with high sensitivity and confidence, and ultimately supports more robust Quality by Design (QbD) approaches and faster decision cycles for biotherapeutic development. MAM consists of three main stages. The first stage is sample digestion, which typically entails proteolytic digestion of the protein. The second stage is reversed-phase chromatographic separation of the generated peptides and detection by HRAM MS in two phases. During MAM Phase I (discovery phase), data-dependent acquisition (DDA) MS/MS is performed to enable confident identification of peaks and development of a peptide workbook. During MAM Phase II (monitoring phase), full MS acquisition is only carried out for the monitoring of predefined product quality attributes (PQAs). The third stage is data processing, which entails analysis and reporting for each of the two phases including evaluation of sequence coverage, assessment of PQAs and peptide workbook creation during phase I, and targeted monitoring of predefined product attributes and new peak detection (NPD) during phase II. The latter is a comparative analysis that uses a base peak alignment algorithm to determine any non-monitored differences between the LC-MS chromatograms of a test sample and a reference standard. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: In-solution sample digestion Alternate Protocol: Automated sample digestion Basic Protocol 2: Reversed-phase chromatographic separation and detection by HRAM-MS (RPLC-HRAM MS) Basic Protocol 3: Data processing and reporting.

Parallelized Acquisition of Orbitrap and Astral Analyzers Enables High-Throughput Quantitative Analysis.

The growing trend toward high-throughput proteomics demands rapid liquid chromatography-mass spectrometry (LC-MS) cycles that limit the available time to gather the large numbers of MS/MS fragmentation spectra required for identification. Orbitrap analyzers scale performance with acquisition time and necessarily sacrifice sensitivity and resolving power to deliver higher acquisition rates. We developed a new mass spectrometer that combines a mass-resolving quadrupole, the Orbitrap, and the novel Asymmetric Track Lossless (Astral) analyzer. The new hybrid instrument enables faster acquisition of high-resolution accurate mass (HRAM) MS/MS spectra compared with state-of-the-art mass spectrometers. Accordingly, new proteomics methods were developed that leverage the strengths of each HRAM analyzer, whereby the Orbitrap analyzer performs full scans with a high dynamic range and resolution, synchronized with the Astral analyzer's acquisition of fast and sensitive HRAM MS/MS scans. Substantial improvements are demonstrated over previous methods using current state-of-the-art mass spectrometers.