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

The consequences of climate change along with diverse food regulations and agricultural practices worldwide are complexifying the occurrence and management of chemical contaminants in food. In this context, we present an ultra-high-performance liquid chromatography high-resolution mass spectrometry (LC-HRMS) approach for the simultaneous identification and quantitation of over 1100 pesticide residues, mycotoxins, and plant toxins in cereals and fruits and vegetables. Analytical conditions were optimized to maximize the scope of the targeted molecules, the reliability of compound identification, and quantification performance within a single method. The method was further transferred and validated in another laboratory to assess its ruggedness. Validation according to the SANTE 11312/2021v2 guidelines showed that 92% and 98% of the molecules fulfill the quantification criteria at the lowest validated level in the cereals and fruits and vegetables groups, respectively. Analysis of fifteen certified reference materials led to a 96% satisfactory rate of z-scores confirming method's competitiveness. Furthermore, the occurrence of these contaminants was studied in 205 cereals and grains samples collected worldwide. The low µg/kg quantification limits make this LC-HRMS method a valuable tool to ensure compliance toward regulations and to screen for non-regulated substances for which occurrence data are crucial for an appropriate risk evaluation. [ABSTRACT FROM AUTHOR]

Dalbavancin is the second‐generation approved semisynthetic lipoglycopeptide by the United States Food and Drug Administration (USFDA) for the treatment of acute bacterial skin and skin‐structure infections. Unlike other lipoglycopeptides, the stability behavior of Dalbavancin was least explored, which is a prerequisite. The current study endeavors to elucidate the oxidative and hydrolytic stability behavior of Dalbavancin by exposing the drug to oxidative, acidic, and basic stress conditions. A simple liquid chromatography (LC) method was developed, where significant resolution between Dalbavancin, its homologs, and the generated degradation products was achieved. Seven degradation products were identified under acidic, basic, and oxidative stress conditions. Using liquid chromatography and high‐resolution mass spectrometry (LC‐HRMS), MS/MS studies, the generated degradation products were identified and characterized. Formation of isomeric degradation products was identified especially upon exposure to basic stress conditions. The mechanistic fragmentation pathway for the seven degradation products was established, and the chemical structure for the identified degradation products was elucidated. The results strongly suggest that Dalbavancin is highly susceptible to degradation under oxidative and hydrolytic stress conditions. This study provides insights into the hydrolytic and oxidative stability of Dalbavancin, which can be employed during drug development and discovery in synthesizing relatively stable analogs. [ABSTRACT FROM AUTHOR]

Established in recent years as an important approach to unraveling the heterogeneity of intact monoclonal antibodies, native mass spectrometry has been rarely utilized for sequencing these complex biomolecules via tandem mass spectrometry. Typically, top-down mass spectrometry has been performed starting from highly charged precursor ions obtained via electrospray ionization under denaturing conditions (i.e., in the presence of organic solvents and acidic pH). Here we systematically benchmark four distinct ion dissociation methodsnamely, higher-energy collisional dissociation, electron transfer dissociation, electron transfer dissociation/higher-energy collisional dissociation, and 213 nm ultraviolet photodissociationin their capability to characterize a therapeutic monoclonal antibody, trastuzumab, starting from denatured and native-like precursor ions. Interestingly, native top-down mass spectrometry results in higher sequence coverage than the experiments carried out under denaturing conditions, with the exception of ultraviolet photodissociation. Globally, electron transfer dissociation followed by collision-based activation of product ions generates the largest number of backbone cleavages in disulfide protected regions, including the complementarity determining regions, regardless of electrospray ionization conditions. Overall, these findings suggest that native mass spectrometry can certainly be used for the gas-phase sequencing of whole monoclonal antibodies, although the dissociation of denatured precursor ions still returns a few backbone cleavages not identified in native experiments. Finally, a comparison of the fragmentation maps obtained under denaturing and native conditions strongly points toward disulfide bonds as the primary reason behind the largely overlapping dissociation patterns. [ABSTRACT FROM AUTHOR]

The widespread use of per- and polyfluoroalkyl substances (PFASs) with different physico–chemical properties poses a great threat to the environment and human health. Simultaneous detection of different classes of PFASs is a difficult task, especially for rapid analysis of polluted water samples in environmental forensic cases. In this study, a simple sample preparation ultrahigh-performance liquid chromatography coupled with quadrupole Orbitrap high-resolution mass spectrometry was established for the detection of PFASs in a wide range of water matrices. By optimizing the conditions of pretreatment and the parameters of the instrument, the developed method provided good linearity of calibration standards (R2 > 0.99), and demonstrated excellent MLOQ (0.008–1.2 µg/L), with spiked recoveries ranging from 57.7% to 151% for 47 targets in surface water samples, and from 45.7 to 165% for 46 targets in ground and waste water samples, respectively. This method required an injection volume of 3 µL and an analysis time of only 18 min per sample. The validation method was successfully applied to the analysis of 20 environmental water samples, in which 15 target substances with different concentrations were detected, with total concentrations of 0.082 to 262.455 μg/L. The method is simple and exclusive, and can rapidly confirm the occurrence of PFASs in different water samples, providing a convenient and fast high-throughput analysis, which is especially suitable for the application in the environmental forensic investigation of PFASs pollution. [ABSTRACT FROM AUTHOR]

Immature citruses are an important resource for the pharmaceutical industry due to their high levels of metabolites with health benefits. In this study, we used untargeted liquid chromatography–mass spectrometry (LC-MS) metabolomics to investigate the changes associated with fruit size in immature citrus fruits in the first weeks of growth. Three orange cultivars (Citrus sinensis 'Navel', Citrus sinensis 'Valencia', and Citrus sinensis 'Valencia Late') and a mandarin (Citrus reticulata Blanco 'Fremont') were separated into eight fruit sizes, extracted, and analyzed. Statistical analyses revealed a distinct separation between the mandarin and the oranges based on 56 metabolites, with an additional separation between the 'Navel' orange and the 'Valencia' and 'Valencia Late' oranges based on 21 metabolites. Then, metabolites that evolved significantly with fruit size growth were identified, including 40 up-regulated and 31 down-regulated metabolites. This study provides new insights into the metabolite modifications of immature Citrus sinensis and Citrus reticulata in the first weeks of growth and emphasizes the significance of including early sampled fruits in citrus maturation studies. [ABSTRACT FROM AUTHOR]

2-Benzylbenzimidazoles, or "nitazenes", are a class of novel synthetic opioids (NSOs) that are increasingly being detected alongside fentanyl analogs and other opioids in drug overdose cases. Nitazenes can be 20× more potent than fentanyl but are not routinely tested for during postmortem or clinical toxicology drug screens; thus, their prevalence in drug overdose cases may be under-reported. Traditional analytical workflows utilizing liquid chromatography-tandem mass spectrometry (LC–MS/MS) often require additional confirmation with authentic reference standards to identify a novel nitazene. However, additional analytical measurements with ion mobility spectrometry (IMS) may provide a path toward reference-free identification, which would greatly accelerate NSO identification rates in toxicology laboratories. Presented here are the first IMS and collision cross section (CCS) measurements on a set of fourteen nitazene analogs using a structures for lossless ion manipulations (SLIM)-orbitrap MS. All nitazenes exhibited two high intensity baseline-separated IMS distributions, which fentanyls and other drug and druglike compounds also exhibit. Incorporating water into the electrospray ionization (ESI) solution caused the intensities of the higher mobility IMS distributions to increase and the intensities of the lower mobility IMS distributions to decrease. Nitazenes lacking a nitro group at the R1 position exhibited the greatest shifts in signal intensities due to water. Furthermore, IMS-MS/MS experiments showed that the higher mobility IMS distributions of all nitazenes possessing a triethylamine group produced fragment ions with m/z 72, 100, and other low intensity fragments while the lower mobility IMS distributions only produced fragment ions with m/z 72 and 100. The IMS, solvent, and fragmentation studies provide experimental evidence that nitazenes potentially exhibit three gas-phase protomers. The cyclic IMS capability of SLIM was also employed to partially resolve four sets of structurally similar nitazene isomers (e.g., protonitazene/isotonitazene, butonitazene/isobutonitazene/secbutonitazene), showcasing the potential of using high-resolution IMS separations in MS-based workflows for reference-free identification of emerging nitazenes and other NSOs. [ABSTRACT FROM AUTHOR]

Mass spectrometry is commonly used in the identification of species present in microbial samples, but the high similarity in the peptide composition between strains of a single species has made analysis at the subspecies level challenging. Prior research in this area has employed methods such as Principal Component Analysis (PCA), the k-Nearest Neighbors' (kNN) algorithm, and Pearson correlation. Previously, 1D cross-correlation of mass spectra has been shown to be useful in the classification of small molecule compounds as well as in the identification of peptide sequences via the SEQUEST algorithm and its variants. While direct application of cross-correlation to mass spectral data has been shown to aid in the identification of many other types of compounds, this type of analysis has not been demonstrated in the literature for the purpose of LC-MS based identification of microbial strains. A method of identifying microbial strains is presented here that applies the principle of 2D cross-correlation to LC-MS data. For a set of N = 30 yeast isolate samples representing 5 yeast strains (K-97, S-33, T-58, US-05, WB-06), high-resolution LC-MS-Orbitrap data were collected. Reference spectra were then generated for each strain from the combined data of each sample of that strain. Sample strains were then predicted by computing the 2D cross-correlation of each sample against the reference spectra, followed by application of correction factors measuring the asymmetry of the 2D correlation functions. [ABSTRACT FROM AUTHOR]

We investigated the pharmacokinetic pathway of berberine and its metabolites in vitro, in Caco-2 cells, and in human participants following the administration of dihydroberberine (DHB) and micellar berberine (LipoMicel®, LMB) formulations. A pilot trial involving nine healthy volunteers was conducted over a 24 h period; blood samples were collected and subjected to Ultra High-Performance Liquid Chromatography–High Resolution Mass Spectrometry (UHPLC-HRMS) analyses to quantify the concentrations of berberine and its metabolites. Pharmacokinetic correlations indicated that berberrubine and thalifendine follow distinct metabolic pathways. Additionally, jatrorrhizine sulfate appeared to undergo metabolism differently compared to the other sulfated metabolites. Moreover, berberrubine glucuronide likely has a unique metabolic pathway distinct from other glucuronides. The human trial revealed significantly higher blood concentrations of berberine metabolites in participants of the DHB treatment group compared to the LMB treatment group—except for berberrubine glucuronide, which was only detected in the LMB treatment group. Similarly, results from in vitro investigations showed significant differences in berberine metabolite profiles between DHB and LMB. Dihydroberberine, dihydroxy-berberrubine/thalifendine and jatrorrhizine sulfate were detected in LMB-treated cells, but not in DHB-treated cells; thalifendine and jatrorrhizine-glucuronide were detected in DHB-treated cells only. While DHB treatment provided higher blood concentrations of berberine and most berberine metabolites, both in vitro (Caco-2 cells) and in vivo human studies showed that treatment with LMB resulted in a higher proportion of unmetabolized berberine compared to DHB. These findings suggest potential clinical implications that merit further investigation in future large-scale trials. [ABSTRACT FROM AUTHOR]

Peptide pools consist of short amino acid sequences and have proven to be versatile tools in various research areas in immunology and clinical applications. They are commercially available in many different compositions and variants. However, unlike other reagents that consist of only one or a few compounds, peptide pools are highly complex products which makes their quality control a major challenge. Quantitative peptide analysis usually requires sophisticated methods, in most cases isotope-labeled standards and reference materials. Usually, this would be prohibitively laborious and expensive. Therefore, an approach is needed to provide a practical and feasible method for quality control of peptide pools. With insufficient quality control, the use of such products could lead to incorrect experimental results, worsening the well-known reproducibility crisis in the biomedical sciences. Here we propose the use of ultra-high performance liquid chromatography (UHPLC) with two detectors, a standard UV detector at 214 nm for quantitative analysis and a high-resolution mass spectrometer (HRMS) for identity confirmation. To be cost-efficient and fast, quantification and identification are performed in one chromatographic run. An optimized protocol is shown, and different peak integration methods are compared and discussed. This work was performed using a peptide pool known as CEF advanced, which consists of 32 peptides derived from cytomegalovirus (CMV), Epstein–Barr virus (EBV) and influenza virus, ranging from 8 to 12 amino acids in length. [ABSTRACT FROM AUTHOR]

The opioid crisis in the United States is being fueled by the rapid emergence of new fentanyl analogs and precursors that can elude traditional library-based screening methods, which require data from known reference compounds. Since reference compounds are unavailable for new fentanyl analogs, we examined if fentanyls (fentanyl + fentanyl analogs) could be identified in a reference-free manner using a combination of electrospray ionization (ESI), high-resolution ion mobility (IM) spectrometry, high-resolution mass spectrometry (MS), and higher-energy collision-induced dissociation (MS/MS). We analyzed a mixture containing nine fentanyls and W-15 (a structurally similar molecule) and found that the protonated forms of all fentanyls exhibited two baseline-separated IM distributions that produced different MS/MS patterns. Upon fragmentation, both IM distributions of all fentanyls produced two high intensity fragments, resulting from amine site cleavages. The higher mobility distributions of all fentanyls also produced several low intensity fragments, but surprisingly, these same fragments exhibited much greater intensities in the lower mobility distributions. This observation demonstrates that many fragments of fentanyls predominantly originate from one of two different gas-phase structures (suggestive of protomers). Furthermore, increasing the water concentration in the ESI solution increased the intensity of the lower mobility distribution relative to the higher mobility distribution, which further supports that fentanyls exist as two gas-phase protomers. Our observations on the IM and MS/MS properties of fentanyls can be exploited to positively differentiate fentanyls from other compounds without requiring reference libraries and will hopefully assist first responders and law enforcement in combating new and emerging fentanyls. [ABSTRACT FROM AUTHOR]

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage. [ABSTRACT FROM AUTHOR]

Since it was introduced, the Orbitrap has been proved to be a powerful ion analyzer whose resolution is affected by the fringing field in the electrode structure. Orbitrap is an ultra-high precision instrument. The gap between two outer half electrodes and the design of ion perforation on one side of the outer electrode will produce fringing field effect, resulting in the distortion of the ideal electrostatic field. The distorted field formed in the internal space of Orbitrap will have a serious impact on the resolution. Thermo Fisher Scientific is the only company that has a patent on Orbitrap mass spectrometers and related technologies, however, it has not provided relevant materials to explain the problem in detail and specific solutions, and few researchers have conducted in-depth research. Therefore, it is necessary to study the influence of the distortion field caused by the ion perforation and the outer electrode gap on the resolution, and propose a solution to the fringing field effect. In this work, ion optical simulation software (SIMION) was used to establish ideal, distorted and corrected models, in order to measure the limiting resolution of the orbital trap by measuring the axial vibration period dispersion corresponding to different initial axial amplitudes and different orbital radius. By comparing the experimental and theoretical results of the ideal model, the reliability of the selection of simulation parameters and the calculation method of ion motion were verified. In the distortion model experiment, the ion axial motion period dispersion caused by the fringing field effect arising from the outer electrode gap and ion perforation and its influence on the resolution was investigated. In the correction model experiment, it was proved that the distortion field can be corrected by adjusting the voltage of the two compensating electrodes, so as to overcome the fringing field effect caused by the ion perforation and the outer electrode gap. In addition, it was also found that the axial flight period error caused by radial dispersion in the corrected model is smaller than that in the ideal model, and the difference between the two is small in the axial dispersion. The comprehensive result of the corrected model is better than that of the ideal model. Therefore, the error caused by scratches on the surface of the electrodes can be corrected by adjusting the voltage of the compensating electrodes. The final simulation results showed that the limiting mass resolution for m/z 100 ion can reach to 2 500 000. [ABSTRACT FROM AUTHOR]

This manuscript presents a comprehensive review of high‐resolution mass spectrometry in the field of food analysis and metabolomics. We have followed the historical evolution of metabolomics, its associated techniques and technologies, and its increasing role in food science and research. The review provides a critical comparison and synthesis of tentative identification guidelines proposed for over 15 years, offering a condensed resource for researchers in the field. We have also examined a wide range of recent metabolomics studies, showcasing various methodologies and highlighting key findings as a testimony of the versatility of the field and the possibilities it offers. In doing so, we have also carefully provided a compilation of the software tools that may be employed in this type of studies. The manuscript also explores the prospects of high‐resolution mass spectrometry and metabolomics in food science. By covering the history, guidelines, applications, and tools of metabolomics, this review attempts to become a comprehensive guide for researchers in a rapidly evolving field. [ABSTRACT FROM AUTHOR]

The consequences of climate change along with diverse food regulations and agricultural practices worldwide are complexifying the occurrence and management of chemical contaminants in food. In this context, we present an ultra-high-performance liquid chromatography high-resolution mass spectrometry (LC-HRMS) approach for the simultaneous identification and quantitation of over 1100 pesticide residues, mycotoxins, and plant toxins in cereals and fruits and vegetables. Analytical conditions were optimized to maximize the scope of the targeted molecules, the reliability of compound identification, and quantification performance within a single method. The method was further transferred and validated in another laboratory to assess its ruggedness. Validation according to the SANTE 11312/2021v2 guidelines showed that 92% and 98% of the molecules fulfill the quantification criteria at the lowest validated level in the cereals and fruits and vegetables groups, respectively. Analysis of fifteen certified reference materials led to a 96% satisfactory rate of z-scores confirming method’s competitiveness. Furthermore, the occurrence of these contaminants was studied in 205 cereals and grains samples collected worldwide. The low µg/kg quantification limits make this LC-HRMS method a valuable tool to ensure compliance toward regulations and to screen for non-regulated substances for which occurrence data are crucial for an appropriate risk evaluation.

Contaminants of emerging concern (CECs) and their respective transformation products (TPs) formed following photodegradation pose considerable threats to the environment and our health. The formation of TPs during UV-LED-based degradation of three target pollutants in the EU Watch List of CECs was accessed by LC-MS-Orbitrap, and their reaction pathways were elucidated. The influence of different matrices and treatments of choice on TP formation was investigated. Results showed that matrix changes did not produce different reaction pathways during UV-A photocatalysis, although plots of TP peak areas vs. time were different for each case. A new TP was found for the antidepressant venlafaxine, (1-[2-(dimethylnitroryl)-1-(4-methoxyphenyl)ethyl]cyclohexanol. When comparing UV-A photocatalysis with UV-C photolysis, dissimilar pathways were observed due to the distinct reaction mechanisms of each process, since photocatalysis, unlike photolysis, relies on radical-based reaction routes. Different levels of confidence were obtained for each TP depending on the availability of MS2 data in the literature and of standards for comparison. All the found TPs had similar molecular masses in comparison to their respective parent compounds. Most of the TPs remained in the effluent after 6 hours of photodegradation, which highlights the importance of their control, close-monitoring, and further toxicity assessments. HIGHLIGHTS Detection of transformation products of contaminants of emerging concern in water.; Elucidation of reaction pathways for photolysis and photocatalysis.; A new transformation product found for venlafaxine.; No difference in detected compounds for tap and ultrapure water.;

The widespread use of per- and polyfluoroalkyl substances (PFASs) with different physico–chemical properties poses a great threat to the environment and human health. Simultaneous detection of different classes of PFASs is a difficult task, especially for rapid analysis of polluted water samples in environmental forensic cases. In this study, a simple sample preparation ultrahigh-performance liquid chromatography coupled with quadrupole Orbitrap high-resolution mass spectrometry was established for the detection of PFASs in a wide range of water matrices. By optimizing the conditions of pretreatment and the parameters of the instrument, the developed method provided good linearity of calibration standards (R2 > 0.99), and demonstrated excellent MLOQ (0.008–1.2 µg/L), with spiked recoveries ranging from 57.7% to 151% for 47 targets in surface water samples, and from 45.7 to 165% for 46 targets in ground and waste water samples, respectively. This method required an injection volume of 3 µL and an analysis time of only 18 min per sample. The validation method was successfully applied to the analysis of 20 environmental water samples, in which 15 target substances with different concentrations were detected, with total concentrations of 0.082 to 262.455 μg/L. The method is simple and exclusive, and can rapidly confirm the occurrence of PFASs in different water samples, providing a convenient and fast high-throughput analysis, which is especially suitable for the application in the environmental forensic investigation of PFASs pollution.

Antibody–antigen interactions are central to the immune response. Variation of protein antigens such as isoforms and post-translational modifications can alter their antibody binding sites. To directly connect the recognition of protein antigens with their molecular composition, we probed antibody–antigen complexes by using native tandem mass spectrometry. Specifically, we characterized the prominent peanut allergen Ara h 2 and a convergent IgE variable region discovered in patients who are allergic to peanuts. In addition to measuring the antigen-induced dimerization of IgE antibodies, we demonstrated how immunocomplexes can be isolated in the gas phase and activated to eject, identify, and characterize proteoforms of their bound antigens. Using tandem experiments, we isolated the ejected antigens and then fragmented them to identify their chemical composition. These results establish native top-down mass spectrometry as a viable platform for precise and thorough characterization of immunocomplexes to relate structure to function and enable the discovery of antigen proteoforms and their binding sites. [ABSTRACT FROM AUTHOR]

Purslane (Portulaca oleracea L., Portulacaceae) is a widespread edible plant with significant ethnobotanical and ethnopharmacological importance. The plant is characteristic for the presence of a class of indoline amide glucoside alkaloids, called cyclo-dopa amides, or oleraceins. Additionally, a new, structurally similar to oleraceins, class of indole amides have been discovered recently, called oleraindoles. These compounds have been evaluated to possess antiinflammatory and anticholinesterase activities. Herein, utilizing UHPLC-Orbitrap-MS with MS² filtering by diagnostic ion filtering (DIF), and diagnostic difference filtering (DDF) using different data analysis tools, eight compounds with oleraindole structure were tentatively identified. [ABSTRACT FROM AUTHOR]

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

Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.

Targeted biomonitoring studies quantifying the concentration of zeranols in biological matrices have focused on liquid chromatography interfaced to mass spectrometry (LC–MS). The MS platform for measurement, quadrupole, time-of-flight (ToF), ion trap, etc., is often chosen based on either sensitivity or selectivity. An instrument performance comparison of the benefits and limitations using matrix-matched standards containing 6 zeranols on 4 MS instruments, 2 low-resolution (linear ion traps), and 2 high-resolution (Orbitrap and ToF) was undertaken to identify the best measurement platform for multiple biomonitoring projects characterizing the endocrine disruptive properties of zeranols. Analytical figures of merit were calculated for each analyte to compare instrument performance across platforms. The calibration curves had correlation coefficients r = 0.989 ± 0.012 for all analytes and LODs and LOQs were ranked for sensitivity: Orbitrap > LTQ > LTQXL > G1 (V mode) > G1 (W mode). The Orbitrap had the smallest measured variation (lowest %CV), while the G1 had the highest. Instrumental selectivity was calculated using full width at half maximum (FWHM) and as expected, the low-resolution instruments had the broadest spectrometric peaks, concealing coeluting peaks under the same mass window as the analyte. Multiple peaks from concomitant ions, unresolved at low resolution (within a unit mass window), were present but did not match the exact mass predicted for the analyte. For example, the high-resolution platforms were able to differentiate between a concomitant peak at 319.1915 from the analyte at 319.1551, included in low-resolution quantitative analyses demonstrating the need to consider coeluting interfering ions in biomonitoring studies. Finally, a validated method using the Orbitrap was applied to human urine samples from a pilot cohort study. [ABSTRACT FROM AUTHOR]

The vast pool of structurally and functionally distinct secondary metabolites (i.e., natural products (NPs)) is constantly being expanded, a process also driven by the rapid progress in the development of analytical techniques. Such NPs often show potent biological activities and are therefore prime candidates for drug development and medical applications. The ethyl acetate extract of the tuber of Citrullus naudinianus (C. naudinianus), an African melon with edible fruits and seeds, shows in vitro immunomodulatory activity presumably elicited by cucurbitacins that are known major constituents of this plant. Further potentially immunomodulatory cucurbitacins or cucurbitacin derivatives were assumed to be in the tuber. Given the typically high content of cucurbitacins with similar physicochemical features but often distinct bioactivities, an efficient and reliable separation process is a prerequisite for their detailed characterization and assessment in terms of bioactivity. We therefore developed a detection method to screen and differentiate cucurbitacins via high-performance liquid chromatography/quadrupole-time-of-flight tandem mass spectrometry (HPLC-QTOF-MS/MS). In order to confirm the identification, the fragmentation patterns of two cucurbitacins and one 23,24-dihydrocucurbitacin were also investigated. Six characteristic fragments were identified and three of them were employed for the identification of cucurbitacins and 23,24-dihydrocucurbitacins in the extract. As a result, in addition to eight previously reported cucurbitacins from this plant four distinct 23,24-dihydrocucurbitacins (B, D, E, and I) were putatively identified and newly found in the ethyl acetate extract of the tuber of C. naudinianus. The established methodology enables rapid and efficient LC-MS-based analysis and identification of cucurbitacins and 23,24-dihydrocucurbitacins in plant extracts. [ABSTRACT FROM AUTHOR]

Just over a decade ago, a truly outside-of-the-box approach to isotope ratio mass spectrometry (IRMS) was undertaken between research groups at Clemson University and the Pacific Northwest National Laboratory. The original motivation dealt with projections as to whether or not microplasmas could be developed into practical elemental ionization sources, perhaps for transportable analysis applications. In particular, the use of the liquid sampling–atmospheric pressure glow discharge (LS-APGD) was pursued. Its interfacing to an ultra-high resolution Orbitrap platform, proved not only facile, but opened up a wealth of potential applications. Here, we lay out a historical, tutorial description of the interfacing and the evolution of the methodology regarding IRMS of uranium. Practical challenges and opportunities are described, which hopefully provide guidance to further applications in high resolution IRMS. It is hoped that, while detailed and lengthy, the didactic nature of the presentation provides experimental insights and tips, and also serves as an homage to our very good friend, Professor Gary M. Hieftje, whose scientific inspiration and comradery have been immeasurably important in our own careers. Graphical Abstract This is a visual representation of the abstract. [ABSTRACT FROM AUTHOR]

Synovial fluid (SF) from human knee joints with osteoarthritis (OA) has elevated levels of lysophosphatidylcholine (LPC) species, but their functional role is not well understood. This in vitro study was designed to test the hypothesis that various LPCs found elevated in OA SF and their metabolites, lysophosphatidic acids (LPAs), modulate the abundance of proteins and phospholipids (PLs) in human fibroblast-like synoviocytes (FLSs), with even minute chemical variations in lysophospholipids determining the extent of regulation. Cultured FLSs (n = 5–7) were treated with one of the LPC species, LPA species, IL-1β, or a vehicle. Tandem mass tag peptide labeling coupled with LC-MS/MS/MS was performed to quantify proteins. The expression of mRNA from regulated proteins was analyzed using RT-PCR. PL synthesis was determined via ESI-MS/MS, and the release of radiolabeled PLs was determined by means of liquid scintillation counting. In total, 3960 proteins were quantified using multiplexed MS, of which 119, 8, and 3 were significantly and reproducibly regulated by IL-1β, LPC 16:0, and LPC 18:0, respectively. LPC 16:0 significantly inhibited the release of PLs and the synthesis of phosphatidylcholine, LPC, and sphingomyelin. Neither LPC metabolite—LPA 16:0 nor LPA 18:0—had any reproducible effect on the levels of each protein. In conclusion, small chemical variations in LPC species can result in the significantly altered expression and secretion of proteins and PLs from FLSs. IL-1β influenced all proteins that were reproducibly regulated by LPC 16:0. LPC species are likely to modulate FLS protein expression only in more advanced OA stages with low IL-1β levels. None of the eight proteins being significantly regulated by LPC 16:0 have been previously reported in OA. However, our in vitro findings show that the CD81 antigen, calumenin, and B4E2C1 are promising candidates for further study, focusing in particular on their potential ability to modulate inflammatory and catabolic mechanisms. [ABSTRACT FROM AUTHOR]

The collection of profile data is standard practice within the field of mass spectrometry (MS). However, profile data collection often results in large data files that require extensive processing times, especially in mass spectrometry imaging (MSI) studies where thousands of high-resolution scans are recorded. Natively collecting centroid MS data is an alternative that effectively reduces both the resulting file size and the data processing time. Herein, high-resolution accurate mass (HRAM) Orbitrap MSI data on mouse liver tissue sections without automatic gain control (AGC) were natively collected in both profile and centroid modes and compared based on the file size and processing time. Additionally, centroid data were evaluated against the profile data with regard to the spectra integrity, mass measurement accuracy (MMA), and the number of lipid annotations to ensure that centroid data did not compromise the data quality. For both native and postacquisition centroided data, the variation in mass measurement accuracy decreased relative to the profile data collection. Furthermore, centroid data collection increased the number of METASPACE database annotations indicating higher sensitivity and greater accuracy for lipid annotation compared to native profile data collection. Profile MSI data was shown to have a higher likelihood of false positive identifications due to an increased number of data points on either side of the peaks, whereas the same trend was not observed in data collected in native centroid data collection. This publication explores and explains the importance in properly centroiding MSI data, either natively or by adequate centroiding methods, to obtain the most accurate information and come to the best conclusions. These data support that natively collecting centroid data significantly improves MMA to sub-ppm levels without AGC and reduces false positive annotations. [ABSTRACT FROM AUTHOR]

Summary: Mepiquat (MQ) and chlormequat (CQ) are two main food contaminants that could be naturally present in various animal and plant foods due to heat treatments. Cocoa and its derivative products seem to be a matrix inclined, for both chemical characteristics and production technologies, to the formation of MQ and CQ. In this study, exploiting the selectivity and sensitivity of IC‐HRMS, a new reliable analytical method was developed and validated for MQ and CQ quantification. The LOD of the method was set at 1.9 μg kg−1 for both CQ and MQ, and the linearity was defined from 6.25 to 625 μg kg−1. Average recoveries, at 2 μg L−1, were 96.5% and 97.5% for CQ and MQ, respectively, while precision as repeatability (RSDr%) was 2.3% and 5.1% respectively. Subsequently, a laboratory‐scale experiment was conducted to assess, for the first time, the actual risk of MQ and CQ formation, confirming in cocoa products the presence of MQ at detectable concentration after 55 min at 180 °C, approximately 8 μg kg−1 for cocoa and 7 μg kg−1 for chips. However, the investigation of a wide variety of commercial cocoa and nuts products has fortunately ruled out the presence of such contaminants at detectable concentrations. [ABSTRACT FROM AUTHOR]

A new laboratory OrbitrapTM cell-based mass spectrometer, OLYMPIA (Orbitrap anaLYseur MultiPle IonisAtion), without a C-trap module, has been developed and constructed. The first operation of the OrbitrapTM cell-based device with the continuous ion source and without the C-trap module is reported. OLYMPIA is being developed and used as a workbench platform to test and develop technologies for the next generation of spaceborne mass spectrometers and as a laboratory instrument to perform high-resolution studies of space-relevant chemical processes. This instrument has been used to measure the quantitative composition of CO/N2/C2H4 mixtures of the same nominal mass using an electron ionization ion source. The relative abundance of ions has been measured using a short acquisition time (up to 250 ms) with a precision of better than 10% (for most abundant ions) and a mass resolution of 30,000–50,000 (full width at half maximum) over the mass range of m/z 28–86. The achieved mass accuracy of measurements is better than 20 ppm. This performance level is sufficient to resolve and identify the CO/N2/C2H4 components of the mixtures. The dynamic range and relative ion abundance measurements have been evaluated using a reference normal isotopic distribution of krypton gas. The measurement accuracy is about 10% for the 4 most abundant isotopes; 6 isotopes are detectable. [ABSTRACT FROM AUTHOR]

Endothelial cells (ECs) comprise the lumenal lining of all blood vessels and are critical for the functioning of the cardiovascular system. Their phenotypes can be modulated by alternative splicing of RNA to produce distinct protein isoforms. To characterize the RNA and protein isoform landscape within ECs, we applied a long read proteogenomics approach to analyse human umbilical vein endothelial cells (HUVECs). Transcripts delineated from PacBio sequencing serve as the basis for a sample-specific protein database used for downstream mass-spectrometry (MS) analysis to infer protein isoform expression. We detected 53,863 transcript isoforms from 10,426 genes, with 22,195 of those transcripts being novel. Furthermore, the predominant isoform in HUVECs does not correspond with the accepted “reference isoform” 25% of the time, with vascular pathway-related genes among this group. We found 2,597 protein isoforms supported through unique peptides, with an additional 2,280 isoforms nominated upon incorporation of long-read transcript evidence. We characterized a novel alternative acceptor for endothelial-related gene CDH5, suggesting potential changes in its associated signalling pathways. Finally, we identified novel protein isoforms arising from a diversity of RNA splicing mechanisms supported by uniquely mapped novel peptides. Our results represent a high-resolution atlas of known and novel isoforms of potential relevance to endothelial phenotypes and function.

• Bio-derived DOM were confirmed to be degraded under anaerobic condition. • Occurrence frequency analysis and Venn diagram can show the molecular behavior. • Reactivity continuum existed in the biological degradation processes. • Network based on molecular and microbial information identified active microbes. It is the key to control bio-derived dissolved organic matters (DOM) in order to reduce the effluent concentration of wastewater treatment, especially for waste leachate with high organic contaminants. In the present study, the anaerobic degradation of aerobically stabilized DOM was investigated with DOM substrate isolated through electrodialysis. The degradation of bio-derived DOM was confirmed by reduction of 15% of total organic carbon in 100 days. We characterized the molecular behavior of bio-derived DOM by coupling molecular and biological information analysis. Venn based Sankey diagram of mass features showed the transformation of bio-derived DOM mass features. Occurrence frequency analysis divided mass features into six categories so as to distinguish the fates of intermediate metabolites and persistent compounds. Reactivity continuum model and machine learning technologies realized the semi-quantitative determination on the kinetics of DOM mass features in the form of pseudo-first order, and confirmed the reduction of inert mass features. Furthermore, network analysis statistically establish relationship between DOM mass features and microbes to identify the active microbes that are able to utilize bio-derived DOM. This work confirmed the biological technology is still effective in controlling recalcitrant bio-derived DOM during wastewater treatment. [Display omitted] [ABSTRACT FROM AUTHOR]

Pharmaceutical analysis refers to an area of analytical chemistry that deals with active compounds either by themselves (drug substance) or when formulated with excipients (drug product). In a less simplistic way, it can be defined as a complex science involving various disciplines, e.g., drug development, pharmacokinetics, drug metabolism, tissue distribution studies, and environmental contamination analyses. As such, the pharmaceutical analysis covers drug development to its impact on health and the environment. Moreover, due to the need for safe and effective medications, the pharmaceutical industry is one of the most heavily regulated sectors of the global economy. For this reason, powerful analytical instrumentation and efficient methods are required. In the last decades, mass spectrometry has been increasingly used in pharmaceutical analysis both for research aims and routine quality controls. Among different instrumental setups, ultra-high-resolution mass spectrometry with Fourier transform instruments, i.e., Fourier transform ion cyclotron resonance (FTICR) and Orbitrap, gives access to valuable molecular information for pharmaceutical analysis. In fact, thanks to their high resolving power, mass accuracy, and dynamic range, reliable molecular formula assignments or trace analysis in complex mixtures can be obtained. This review summarizes the principles of the two main types of Fourier transform mass spectrometers, and it highlights applications, developments, and future perspectives in pharmaceutical analysis. [ABSTRACT FROM AUTHOR]

Herein, a chemophenetic significance, based on the phenolic metabolite profiling of three Senecio (S. hercynicus, S. ovatus, and S. rupestris) and two Jacobaea species (J. pancicii and J. maritima), coupled to morphometric data, is presented. A set of twelve morphometric characters were recorded from each plant species and used as predictor variables in a linear discriminant analysis (LDA) model. From a total 75 observations (15 from each of the five species), the model correctly assumed their species' membership, except for 2 observations. Among the studied species, S. hercynicus and S. ovatus presented the greatest morphological similarity. A phytochemical profiling of phenolic specialized metabolites by UHPLC-Orbitrap-MS revealed 46 hydroxybenzoic, hydroxycinnamic, and acylquinic acids and their derivatives, 1 coumarin and 21 flavonoids. Hierarchical and PCA clustering applied to the phytochemical data corroborated the similarity of S. hercynicus and S. ovatus, observed in the morphometric analysis. This study contributes to the phylogenetic relationships between the tribe Senecioneae taxa and highlights the chemophenetic similarity/dissimilarity of the studied species belonging to Senecio and Jacobaea genera. [ABSTRACT FROM AUTHOR]

(1) Background: In toxicological laboratories, various screening methods can be used to identify compounds involved in intoxication. High-resolution mass spectrometry has been increasingly used in this context for the last years, because of its sensitivity and reliability. Here, we present the development and validation of a screening method that uses liquid chromatography coupled with a high-resolution mass spectrometer. (2) Methods: This method required only 100 µL of whole blood or plasma sample. Pretreatment consisted of a rapid and simple deproteinisation with methanol/acetonitrile and zinc sulphate. This new assay was validated according to international guidelines. (3) Results: To perform the method validation, 53 compounds were selected. The selection criteria were as follows: various chemical structures and therapeutic families (>15), large m/z distribution, positive or negative ionisation mode, and various elution times. The assays showed high selectivity and specificity, with optimal process efficiency. The identification limits, determined using predefined criteria, were established at sub-therapeutic or therapeutic concentrations. Applicability was evaluated using spiked plasma controls and external quality controls. (4) Conclusions: The new method was then successfully applied to routine clinical and forensic samples. [ABSTRACT FROM AUTHOR]

Modern mass spectrometry is the most demanded method of analysis of biopolymers, first of all, proteins and peptides. The novel methods of ionization of biomolecules developed at the end of the 20th century allowed increasing the efficiency of mass spectrometry in life sciences, first of all, proteomics. The methods of qualitative and quantitative analysis of these compounds are permanently improving. They become faster, more reliable, informative, sensitive, and selective. Significant role plays automation based on the original algorithms of the machine data processing and usage of spectral databases. One of the challenging questions of mass spectrometry involves analysis of polypeptides of various living organisms, whose genomes remain unknown so far. Amphibians represent a typical example of that species. In these cases, de novo sequencing of novel peptides is required. Development of an automated method of the de novo sequencing exclusively by mass spectrometry is of high scientific priority. It deals with top-down analysis, when an array of tandem mass spectrometry tools allows establishing amino acid sequence of each peptide using their polyprotonated molecules as precursor ions and eliminating assembling based on the hydrolysates of these compounds. A number of nuances still require time-consuming manual spectral elucidation. The present review throws light upon certain problems of mass spectrometry for the de novo sequencing of natural peptides of ranid and hylid frogs as typical representatives of amphibians. It tackles the questions related to post translational modifications, differentiation of isobaric and isomeric amino acid residues, cyclization of short peptides, and application of complementary methods of tandem mass spectrometry to trigger fragmentation. The benefits of mass spectrometry in taxonomy studies, e.g., for the reliable differentiation of closely related ranid and hylid frog species and even populations, are also discussed. [ABSTRACT FROM AUTHOR]

The present study aimed to assess the effects of epileptic treatment of the aerial part of Bupleurum chinense DC. in kainic acid (KA)-induced epilepsy rats and LPS-induced BV2 cells, as well as to identify the active chemical constituents. The in vivo and vitro results showed that 20% ethanol elution fractions of the aerial part of B. chinense DC. (BCE-20) and 70% ethanol elution fractions of the aerial part of B. chinense DC. (BCE-70) could improve the epileptic state of the rats and status epilepticus (SE%). Moreover, ultra-high-performance liquid chromatography (UPLC)-Orbitrap- mass spectrometry (MS) analysis identified BCE-20 and 70 as flavonoids and phenylpropanoids, respectively. The mechanistic analysis also showed that BCE-20 and 70 could regulate neurotransmitter abnormalities and suppresses the expression and secretion of pro-inflammatory cytokines. Notably, BCE-20 and 70 could regulate the Triggering receptor expressed on myeloid cells 2 (TREM2)/nuclear factor-k-gene binding (NF-κB)/inhibitor of NF-κB α (IκBα) pathway to inhibit the neuroinflammation. Our findings support the ethnopharmacological use of the constituent polyphenols and flavonoids from the aerial part of B. chinense DC., as the strong anti-epileptic agents. [ABSTRACT FROM AUTHOR]

The water-based extract of broad bean hulls contains several bioactive molecules, including polyphenols well-known to exert antioxidant activity, which could justify its use in nutraceutical formulations. Hence, the current investigation aimed to establish the polyphenolic profile of water-based extracts from broad bean hulls through UHPLC–Q-Orbitrap HRMS analysis. The findings highlighted that p-coumaric acid, chlorogenic acid, and epicatechin were the most common compounds found in the tested extracts, being quantified at a mean concentration of 42.1, 32.6, and 31.2 mg/100 g, respectively. Moreover, broad bean hull extracts were encapsulated into a nutraceutical formulation, after which the antioxidant properties and the bioaccessibility of phenolic compounds during the simulated gastrointestinal (GI) process were investigated and compared with the digested non-encapsulated extract. The data highlighted that following the GI process, the capsules were able to preserve active compounds from the adverse effects of digestion, resulting in a greater antioxidant capacity and polyphenol bioaccessibility in the duodenal and colonic phases, compared with the non-encapsulated extract. Our results showed that the water extract from broad bean hulls may be considered a valuable source of natural polyphenolic compounds; in addition, the use of a gastric-resistant capsule could be a suitable alternative to transport these bioactive compounds to the target tissues. [ABSTRACT FROM AUTHOR]

Litchi fruit is consumed across the globe for its high nutritional value and taste. The qualitative profiling of litchi fruit has been carried out by using ultra-high-performance liquid chromatography with QExactive high-resolution accurate mass spectrometry. Acidified water: methanol: acetonitrile (1:1:1) extracts from individual parts (skin, pulp, and seed) of matured litchi, were subjected to LC–MS analysis with electrospray ionization in full MS-ddMS2 mode as a non-target approach. The data was processed through compound discoverer software by the use of mzCloud and ChemSpider databases, for compound identification. We identified 77 compounds with protonated or deprotonated forms based on the polarity and their characteristic fragments are within ± 4 ppm mass error and retention time ± 0.1 min for parent and fragments. Hypoglycin B is the first time reported in litchi fruit along with hypoglycin A. Further, we verified the distribution of the identified components and differentiation of three different parts of litchi through principal component analysis. [ABSTRACT FROM AUTHOR]

The removal of contaminants of emerging concern (CECs) occurring in wastewater effluents, such as pharmaceutically active substances (PhACs) and personal care products, pose a big research challenge since they can be a major source of pollution for water bodies and a danger to public health. The objective of this work was to perform a comprehensive monitoring of a broad set of PhACs (>130) in a wastewater treatment plant (WWTP) close to Thessaloniki (Greece), as well as to evaluate the potential of heterogeneous catalytic ozonation for the removal of CECs from wastewater through a continuous flow system. The high-resolution mass spectrometry analysis revealed the highest average concentrations for irbesartan (1817 ng/L). Antihypertensives along with antibiotics, psychiatrics, and β-blockers were found to aggravate the effluents. Removal efficiency after conventional treatment was >30%. The results from catalytic ozonation unit operation indicate that the introduction of a proper solid material that acts as catalyst can enhance the removal of CECs. A preliminary risk assessment using the risk quotient (RQ) revealed that irbesartan and telmisartan entail high acute risk. The overall results underline the urgent need to incessantly monitor PhACs and expand the toxicological studies to establish the sublethal and chronic effects on aquatic organisms.

• Simple derivatization and isolation of thiols from wine. • Highly selective and sensitive detection of thiols as the form of derivatives by UHPLC–Orbitrap HRMS. • Parallel rection monitoring (PRM) suitable for quantitation of ultratrace thiols. • First quantitative datasets reported for several recently identified thiols in wine. Polyfunctional thiols are key contributors to wine aroma due to their extremely low odor thresholds, and their quantitative analysis remains challenging as a result of their ultratrace concentrations and high reactivity. This work presents the first method based on ultra-high-performance liquid chromatography (UHPLC) coupled to quadrupole Orbitrap high-resolution mass spectrometry (HRMS) in parallel reaction monitoring (PRM) mode for quantifying thiols at nanograms per liter (ng/L) levels in wine. Thiols in wine were derivatized using 4,4′-dithiodipyridine and isolated by liquid-liquid extraction. This protocol allowed rapid sample preparation with minimum labor input and low consumable expenses. Instrumental analysis was conducted using UHPLC–quadrupole Orbitrap HRMS in PRM mode. Twenty thiol analytes, including literature-known, recently identified, and novel thiols were selected and validated by the optimized method in three wine matrices. The overall analytical performances demonstrated by this method were equivalent, and in most cases, greater than many previously developed GC–MS or LC–MS methods. The validated method was applied to analyze a selection of wines in which 12 thiols were quantified. [ABSTRACT FROM AUTHOR]

Given that the determination of biocides in food and feed is currently not routinely done, more information on these compounds is useful for consumer's safety. This work describes a sensitive and reliable method for quantitative analysis of a wide range of biocides in dairy products and slurry feed. The method comprises acetate-buffered QuEChERS extraction without clean-up. Analyses were performed by LC-Q-Orbitrap™-MS and a full-scan acquisition event without fragmentation was followed by five fragmentation events (data-independent acquisition–DIA). The quantitative validation was performed according to SANTE/11312/2021 at 10, 50 and 200 ng g−1 spiking levels, and the results showed that the vast majority of the compounds met the criteria for trueness and precision. The LOQ was 10 ng g−1 for the majority of biocides depending on the matrix. The method was successfully applied to quantify biocides in dairy products and feed. • Multi-residue method for biocides in dairy products and feed • Validated for quantitative analysis in 10–200 ng g−1 range • Biocide found in ice cream samples • LC-Q-Orbitrap-based method, facilitates additional qualitative screening [ABSTRACT FROM AUTHOR]

Environmental monitoring is crucial for assessing the overall state of the ecosystems in terms of contaminant impact and chemical landscape. The use of honey bee (Apis mellifera) colonies considerably eases the sampling activities, as honey bees are exposed to a wide range of substances that are transported and accumulated within the beehives. In this work, combining low-resolution and high-resolution mass spectrometry, the APIStrip passive sampler has been employed to evaluate the presence of pesticide residues and the overall characterization of beehive environments. A total of 180 APIStrips have been deployed in 10 Danish apiaries, located in different landscapes, during a five-month sampling period. The targeted methodology for pesticide analysis was based on gas and liquid chromatography coupled with triple quadrupole mass spectrometry, covering 430 pesticide residues. A total of 29 pesticide residues were identified (fluopyram and azoxystrobin being the most frequently detected), with remarkable differences in the pesticide load between apiaries. For its part, the use of non-targeted approaches through liquid chromatography coupled with an Orbitrap mass spectrometer allowed the detection of unknown compounds that were specific of certain environments. Natural products such as eupatilin and gnaphaliin, which are derived from plant sources, were present exclusively in one of the apiaries. Additionally, the detection of drimane sesquiterpenoids, including compounds potentially originating from the Aspergillus genus , suggests the capability of APIStrips to early detect fungal contamination within beehives. This dual approach of low- and high-resolution mass spectrometry maximizes the analytical potential of APIStrips as a tool capable of detecting a wide range of substances with implications for both agricultural practices and ecological health. [Display omitted] • Dual HRMS and LRMS approach to obtain holistic information about chemical landscape. • APIStrips allow the univocal, chemical characterization of beehives. • Landscape type influences but does not solely determines the pesticide load. • APIStrips effective in differentiating high and low pesticide pressure areas. • Detection of fungi-related natural products and floral volatiles. [ABSTRACT FROM AUTHOR]

Group A Streptococcus (GAS) remains one of the top 10 deadliest human pathogens worldwide despite its sensitivity to penicillin. Although the most common GAS infection is pharyngitis (strep throat), it also causes life-threatening systemic infections. A series of complex networks between host and pathogen drive invasive infections, which have not been comprehensively mapped. Attempting to map these interactions, we examined organ-level protein dynamics using a mouse model of systemic GAS infection. We quantified over 11,000 proteins, defining organ-specific markers for all analyzed tissues. From this analysis, an atlas of dynamically regulated proteins and pathways was constructed. Through statistical methods, we narrowed organ-specific markers of infection to 34 from the defined atlas. We show these markers are trackable in blood of infected mice, and a subset has been observed in plasma samples from GAS-infected clinical patients. This proteomics-based strategy provides insight into host defense responses, establishes potentially useful targets for therapeutic intervention, and presents biomarkers for determining affected organs during bacterial infection.

Cultivated soybean (Glycine max (L.)), the world's most important legume crop, has high-to-moderate salt sensitivity. Being the frontier for sensing and controlling solute transport, membrane proteins could be involved in cell signaling, osmoregulation, and stress-sensing mechanisms, but their roles in abiotic stresses are still largely unknown. By analyzing salt-induced membrane proteomic changes in the roots and leaves of salt-sensitive soybean cultivar (C08) seedlings germinated under NaCl, we detected 972 membrane proteins, with those present in both leaves and roots annotated as receptor kinases, calcium-sensing proteins, abscisic acid receptors, cation and anion channel proteins, proton pumps, amide and peptide transporters, and vesicle transport-related proteins etc. Endocytosis, linoleic acid metabolism, and fatty acid biosynthesis pathway-related proteins were enriched in roots whereas phagosome, spliceosome and soluble NSF attachment protein receptor (SNARE) interaction-related proteins were enriched in leaves. Using label-free quantitation, 129 differentially expressed membrane proteins were found in both tissues upon NaCl treatment. Additionally, the 140 NaCl-induced proteins identified in roots and 57 in leaves are vesicle-, mitochondrial-, and chloroplast-associated membrane proteins and those with functions related to ion transport, protein transport, ATP hydrolysis, protein folding, and receptor kinases, etc. Our proteomic results were verified against corresponding gene expression patterns from published C08 RNA-seq data, demonstrating the importance of solute transport and sensing in salt stress responses. [ABSTRACT FROM AUTHOR]

OBJECTIVE: To probe into the metabolic mechanism of Danbei Yifei decoction on idiopathic pulmonary fibrosis rats based on lipidomic technology. METHODS: The rat model of idiopathic pulmonary fibrosis was established by intratracheal injection of bleomycin. Serum lipid changes were detected by ultra-high performance liquid chromatographyperformance liquid chromatography-quadrupole electrostatic field orbital well mass spectrometry, and differential ions were identified to search for potential biomarkers. RESULTS: Lipidomics and pathway enrichment analysis showed that the abnormal metabolism of the rats with idiopathic pulmonary fibrosis mainly involved linoleic acid metabolism, α-linolenic acid metabolism, arachidonic acid metabolism, triglyceride metabolism and glycerophospholipid metabolism. ROC curves showed that 11 lipid components were clearly correlated with idiopathic pulmonary fibrosis, with the tendency of different degrees of regression after the intervention of Danbei Yilong decoction. CONCLUSIONS: Danbei Yiku decoction may achieve the treatment of idiopathic pulmonary fibrosis by regulating biomarkers and related pathways, providing a reliable basis for lipid metabolism in idiopathic pulmonary fibrosis. [ABSTRACT FROM AUTHOR]

Gas-phase sequencing of large intact proteins (>30 kDa) via tandem mass spectrometry is an inherently challenging process that is further complicated by the extensive overlap of multiply charged product ion peaks, often characterized by a low signal-to-noise ratio. Disulfide bonds exacerbate this issue because of the need to cleave both the S-S and backbone bonds to liberate sequence informative fragments. Although electron-based ion activation techniques such as electron transfer dissociation (ETD) have been proven to rupture disulfide bonds in whole protein ions, they still struggle to produce extensive sequencing when multiple, concatenated S-S bonds are present on the same large polypeptide chain. Here, we evaluate the increase in sequence coverage obtained by combining activated-ion ETD (AI-ETD) and proton transfer charge reduction (PTCR) in the analysis of 66 kDa human serum albumin, which holds 17 disulfide bridges. We also describe the combination of AI-ETD with supplemental postactivation of the ETD reaction products via higher-energy collisional dissociation─a hybrid fragmentation method termed AI-EThcD. AI-EThcD leads to a further improvement compared to AI-ETD in both the global number of cleaved backbone bonds and the number of ruptured backbone bonds from disulfide-protected regions. Our results also demonstrate that the full potential of AI-ETD and AI-EThcD is unveiled only when combined with PTCR: reduction in overlap of ion signals leads to a sequence coverage as high as 39% in a single experiment, highlighting the relevance of spectral simplification in top-down mass spectrometry of large proteins.

Mass spectrometry (MS) has become a pivotal analytical tool across various scientific disciplines due to its ability to provide detailed molecular information with high sensitivity and specificity. MS plays a crucial role in various fields, including drug discovery and development, proteomics, metabolomics, environmental analysis, and clinical diagnostics and Forensic science. In this article we are discussing the application of MS across the diverse scientific disciplines by focusing on some classical examples from each field of application. As the technology continues to evolve, it promises to unlock new possibilities in scientific research and practical applications, cementing its position as an essential tool in modern analytical science., Competing Interests: Declaration of conflicting interestsThe author declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.