Identification of Unique Fragmentation Patterns of Fentanyl Analog Protomers Using Structures for Lossless Ion Manipulations Ion Mobility-Orbitrap Mass Spectrometry

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.

Differential analysis of volatiles in five types of mosquito-repellent products by chemometrics combined with headspace GC-Orbitrap HRMS nontargeted detection

This paper reports a method for the differential analysis of volatile chemical components in five novel types of mosquito-repellent products based on chemometrics combined with headspace gas chromatography-Orbitrap high-resolution mass spectrometry (HS-GC-Orbitrap HRMS) nontargeted screening. A total of 358 unknown substances were detected in 30 samples under specific headspace conditions. Through principal component analysis and orthogonal partial least-squares discriminant analysis, 36 significantly different substances with variable importance in the projection values greater than 1 were further screened, and these substances were accurately identified by GC-Orbitrap HRMS. Most substances were found for the first time in mosquito-repellent products. The clustered heat map, Venn diagram and peak area histogram showed that the mosquito-repellent products had similar volatile composition, and the volatile species and content of different types of mosquito-repellent products significantly varied. Substances, such as eucalyptol, d-limonene, α-pinene, β-pinene, dl-menthol and methyl salicylate, may be the main sources of odour in mosquito-repellent products. This work explored the characteristic volatile components in mosquito-repellent products and comparatively analysed the chemical composition of different types of products. It can be generalised to consumer products as a case study and has positive implications for promoting product quality and safety and improving production processes.

Full Mass Range ΦSDM Orbitrap Mass Spectrometry for DIA Proteome Analysis

Optimizing data-independent acquisition methods for proteomics applications often requires balancing spectral resolution and acquisition speed. Here, we describe a real-time full mass range implementation of the phase-constrained spectrum deconvolution method (ΦSDM) for Orbitrap mass spectrometry that increases mass resolving power without increasing scan time. Comparing its performance to the standard enhanced Fourier transformation signal processing revealed that the increased resolving power of ΦSDM is beneficial in areas of high peptide density and comes with a greater ability to resolve low-abundance signals. In a standard 2 h analysis of a 200 ng HeLa digest, this resulted in an increase of 16% in the number of quantified peptides. As the acquisition speed becomes even more important when using fast chromatographic gradients, we further applied ΦSDM methods to a range of shorter gradient lengths (21, 12, and 5 min). While ΦSDM improved identification rates and spectral quality in all tested gradients, it proved particularly advantageous for the 5 min gradient. Here, the number of identified protein groups and peptides increased by >15% in comparison to enhanced Fourier transformation processing. In conclusion, ΦSDM is an alternative signal processing algorithm for processing Orbitrap data that can improve spectral quality and benefit quantitative accuracy in typical proteomics experiments, especially when using short gradients.

Peptide-Based Mass Spectrometry for the Investigation of Protein Complexes

In the last two decades, biological mass spectrometry has become the gold standard for the identification of proteins in biological samples. The technological advancement of mass spectrometers and the development of methods for ionization, gas phase transfer, peptide fragmentation as well as for acquisition of high-resolution mass spectrometric data marked the success of the technique. This chapter introduces peptide-based mass spectrometry as a tool for the investigation of protein complexes. It provides an overview of the main steps for sample preparation starting from protein fractionation, reduction, alkylation and focus on the final step of protein digestion. The basic concepts of biological mass spectrometry as well as details about instrumental analysis and data acquisition are described. Finally, the most common methods for data analysis and sequence determination are summarized with an emphasis on its application to protein-protein complexes.

A tool for automatic annotation of orbitrap MS2 spectra using networks grade as selection criteria

We introduce OrbiFragsNets, a tool for automatic annotation of MS2 spectra generated by Orbitrap instruments, as well as the concepts of chemical consistency and fragments networks. OrbiFragsNets takes advantage of the specific confidence interval for each peak in every MS2 spectrum, which is an unclear idea across the high-resolution mass spectrometry literature. The spectrum annotations are expressed as fragments networks, a set of networks with the possible combinations of annotations for the fragments. The model behind OrbiFragsNets is briefly described here and explained in detail in the constantly updated manual available in the GitHub repository. This new approach in MS2 spectrum de novo automatic annotation proved to perform as good as well established tools such as RMassBank and SIRIUS.•A new approach on automatic annotation of Orbitrap MS2 spectra is introduced.•Possible spectrum annotation are described as independent consistent networks, with annotations for each fragment as nodes, and annotations for the mass difference between fragments as edges.•Annotation process is described as the selection of the most connected fragments network.

Orbitrap Mass Spectrometry and High-Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) Enable the in-Depth Analysis of Human Serum Proteoforms

Blood serum and plasma are arguably the most commonly analyzed clinical samples, with dozens of proteins serving as validated biomarkers for various human diseases. Top-down proteomics may provide additional insights into disease etiopathogenesis since this approach focuses on protein forms, or proteoforms, originally circulating in blood, potentially providing access to information about relevant post-translational modifications, truncations, single amino acid substitutions, and many other sources of protein variation. However, the vast majority of proteomic studies on serum and plasma are carried out using peptide-centric, bottom-up approaches that cannot recapitulate the original proteoform content of samples. Clinical laboratories have been slow to adopt top-down analysis, also due to higher sample handling requirements. In this study, we describe a straightforward protocol for intact proteoform sample preparation based on the depletion of albumin and immunoglobulins, followed by simplified protein fractionation via polyacrylamide gel electrophoresis. After molecular weight-based fractionation, we supplemented the traditional liquid chromatography-tandem mass spectrometry (LC-MS2) data acquisition with high-field asymmetric waveform ion mobility spectrometry (FAIMS) to further simplify serum proteoform mixtures. This LC-FAIMS-MS2 method led to the identification of over 1000 serum proteoforms < 30 kDa, outperforming traditional LC-MS2 data acquisition and more than doubling the number of proteoforms identified in previous studies.

Nontargeted analysis and comparison strategies for volatile and semivolatile substances in toys made of different materials

A nontargeted broad-spectrum analysis method for unknown volatile and semivolatile substances in toys was established by gas chromatography-Orbitrap high-resolution mass spectrometry. Based on the NIST spectrum library, unknown substances could be accurately identified by comprehensive scoring, retention index, chemical ionization, and fine comparison of ion fragments. For substances not included in the library, the molecular formulas of unknown substances were retrieved through online compound databases. Possible structural formulas were verified by high-resolution spectra and fragmentation mechanisms. Taking teether toys as an example, the substances differences of products made of different materials were compared through the digitization of chemical composition. Specifically, 59 substances were identified in 50 teether toys. The toys made of two different materials each had their own substance distribution, and the types and quantities of substances in thermoplastic polyurethanes samples were more than those in silicone samples. Substances with high risk included phenol, N-methylaniline, cyclohexanone, and 4-tert-amylphenol. This work can serve as a reference for the identification of unknown substances in toys and other products, as well as for the comparison the chemical composition of products made of different materials. Thus, this work has positive significance in promoting the quality and safety of toys and reducing chemical harm to children.

Immunocomplexed Antigen Capture and Identification by Native Top-Down Mass Spectrometry

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.

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

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.

Coupling of the Liquid Sampling-Atmospheric Pressure Glow Discharge to Orbitrap Mass Analyzers for Uranium Isotope Ratio Analysis: Evolution of the Methodology and Implications to the Field

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.

A comparison of four liquid chromatography-mass spectrometry platforms for the analysis of zeranols in urine

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.

AzidoTMT Enables Direct Enrichment and Highly Multiplexed Quantitation of Proteome-Wide Functional Residues

Recent advances in targeted covalent inhibitors have aroused significant interest for their potential in drug development for difficult therapeutic targets. Proteome-wide profiling of functional residues is an integral step of covalent drug discovery aimed at defining actionable sites and evaluating compound selectivity in cells. A classical workflow for this purpose is called IsoTOP-ABPP, which employs an activity-based probe and two isotopically labeled azide-TEV-biotin tags to mark, enrich, and quantify proteome from two samples. Here we report a novel isobaric 11plex-AzidoTMT reagent and a new workflow, named AT-MAPP, that significantly expands multiplexing power as compared to the original isoTOP-ABPP. We demonstrate its application in identifying cysteine on- and off-targets using a KRAS G12C covalent inhibitor ARS-1620. However, changes in some of these hits can be explained by modulation at the protein and post-translational levels. Thus, it would be crucial to interrogate site-level bona fide changes in concurrence to proteome-level changes for corroboration. In addition, we perform a multiplexed covalent fragment screening using four acrylamide-based compounds as a proof-of-concept. This study identifies a diverse set of liganded cysteine residues in a compound-dependent manner with an average hit rate of 0.07% in intact cell. Lastly, we screened 20 sulfonyl fluoride-based compounds to demonstrate that the AT-MAPP assay is flexible for noncysteine functional residues such as tyrosine and lysine. Overall, we envision that 11plex-AzidoTMT will be a useful addition to the current toolbox for activity-based protein profiling and covalent drug development.

The first balloon-borne sample analysis of atmospheric carbonaceous components reveals new insights into formation processes

Atmospheric aerosol optical, physical, and chemical properties play a fundamental role in the Earth's climate system. A better understanding of the processes involved in their formation, evolution, and interaction with radiation and the water cycle is critical. We report the analysis of atmospheric molecules/particles collected with a new sampling system that flew under regular weather balloons for the first time. The flight took place on January 18, 2022 from Reims (France). The samples were subsequently analyzed by high-resolution mass spectrometry (Orbitrap) to specifically infer hundreds of organic components present in 4 different layers from the troposphere to the stratosphere (up to 20 km). Additional measurements of O₃, CO, and aerosol concentrations a few hours before this flight took place to contextualize the sampling. After separating common species found on each filter that might be common to atmospheric layers or residuals for contaminations, we found that each sample yields significant differences in the number and size of organic species detected that should reflect the unique composition of atmospheric layers. While tropospheric samples yield significantly oxidized and saturated components, with carbon numbers below 30 that might be explained by complex organics chemistry from local and distant source emissions, the upper tropospheric and stratospheric samples were associated with increased carbon numbers (C > 30), with a significantly reduced unsaturation number for the stratosphere, that might be induced by strong UV radiations. The multimodal distributions of carbon numbers in chemical formulas observed between 15 and 20 km suggest that oligomerization and growth of organic molecules may take place in aged air masses of tropical origin that are known to carry organic compounds even several km above the tropopause where their lifetime significantly increases. In addition, the presence of organics may also reflect the extended influence of wildfires smoke injected during the spring and summer in the NH hemisphere before the in situ observations and their long-lifetime in the upper troposphere and stratosphere.

Comprehensive analysis of alkenones by reversed-phase HPLC-MS with unprecedented selectivity, linearity and sensitivity

Alkenones are among the most widely used paleotemperature biomarkers. Traditionally, alkenones are analyzed using gas chromatography-flame ionization detector (GC-FID), or GC-chemical ionization-mass spectrometry (GC-CI-MS). However, these methods encounter considerable challenges for samples that exhibit matrix interference or low concentrations, with GC-FID requiring tedious sample preparations and GC-CI-MS suffering from nonlinear response and a narrow linear dynamic range. Here we demonstrate that reversed-phase high pressure liquid chromatography-mass spectrometry (HPLC-MS) methods provide excellent resolution, selectivity, linearity and sensitivity for alkenones in complex matrices. We systematically compared the advantages and limitations of three mass detectors (quadrupole, Orbitrap, and quadrupole-time of flight) and two ionization modes (electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI)) for alkenone analyses. We demonstrate that ESI performs better than APCI as response factors of various unsaturated alkenones are similar. Among the three mass analyzers tested, orbitrap MS provided the lowest limit of detection (0.4, 3.8 and 8.6 pg injected masses for Orbitrap, qTOF and single quadrupole MS, respectively) and the widest linear dynamic range (600, 20 and 30 folds for Orbitrap, qTOF and single quadrupole MS, respectively). Single quadrupole MS operated in ESI mode provides accurate quantification of proxy measurements over a wide range of injection masses, and with its modest instrument cost, represents an ideal method for routine applications. Analysis of global core-top sediment samples confirmed the efficacy of HPLC-MS methods for the detection and quantification of paleotemperature proxies based on alkenones and their superiority over GC-based methods. The analytical method demonstrated in this study should also allow highly sensitive analyses of diverse aliphatic ketones in complex matrices.

Validation of a non-targeted method devoted to identification and quantitation of toxicologically relevant compounds in plasma with HRMS

The objective of this study was to develop and validate a simple method using liquid chromatography hyphenated to high resolution mass spectrometry (HRMS) allowing both the performance of a non-targeted screening and the simultaneous quantification of 29 compounds of interest in clinical and forensic toxicology. Extraction was done with QuEChERS salts and acetonitrile, after addition of internal standard to 200 μL of human plasma samples. The mass spectrometer was an Orbitrap, with a heated electrospray ionization (HESI) probe. The analyses were carried out in full scan experiment with a nominal resolving power of 60,000 FWHM within the 125-650 m/z mass range, followed by four cycles of data dependent analysis (DDA) with a mass resolution of 16,000 FWHM. The untargeted screening was evaluated using 132 compounds, mean limit of identification (LOI) was 8.8 ng/mL (min = 0.05 ng/mL, max = 500 ng/mL) and mean limit of detection (LOD) was 0.25 ng/mL (min = 0.05 ng/mL, max = 5 ng/mL). The method was linear in the 5 to 500 ng/mL range (0.5 to 50 ng/mL for cannabinoids, 6-acetylmorphine and buprenorphine) with correlation coefficients > 0.99, intra- and inter-day accuracy and precision were < 15% for all compounds. The method was successfully applied to 31 routine samples.

Exploring within-ecodistrict lake organic matter variability and identifying possible environmental contaminant biomarkers using sedimentomics

Sedimentomics methods offer insight into the physiological parameters that influence freshwater sediment organic matter (sedOM). To date, most sedimentomics studies characterized variations across large spatial and environmental gradients; here we examine whether sedimentomics methods capture subtle sedOM variations within a relatively homogeneous study area in southwestern Nova Scotia, Canada. Additionally, we explore the lake sedimentome for candidate biomarkers related to ongoing carnivorous animal farming in the region. Sediment cores were recovered from seven lakes across a trophic (oligo- to eu- trophic) and anthropogenic land use gradient (carnivorous animal farming in catchment, downstream of farming, no farming nearby). Subsamples that dated prior to 1910 (pre-carnivorous animal farming) and later than 2010 (during carnivorous animal farming) were analyzed using UHPLC-HRMS in both negative (ESI-) and positive (ESI+) electrospray ionization modes. Cluster analysis (k-means) showed replicate samples from a given lake clustered distinctly from one another in both ESI modes, indicating sedOM captured subtle variations between lake systems. PCA combined with multiple linear regression indicated carnivorous animal farming and OM source explained most of the observed variation in lake sedOM. Principal component analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA) of ESI- and ESI+ data sets identified 103 unique candidate biomarkers. Ten strong candidate biomarkers were identified using graphical methods; more research is required for biomarker verification and molecular characterization. Our results indicate sedimentomics could be used in environmentally homogeneous areas, offering insight into the controls of sedOM cycling. Additionally, we identified prospective biomarkers related to carnivorous animal farming that could be used to understand relative contributions of farming to ongoing eutrophication issues in southwestern Nova Scotia.

Achieving Sub-Parts-per-Million Mass Measurement Accuracy on an Orbitrap Mass Spectrometry Imaging Platform without Automatic Gain Control

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.

Integration of target, suspect, and nontarget screening with risk modeling for per- and polyfluoroalkyl substances prioritization in surface waters

Though thousands of per- and polyfluoroalkyl substances (PFAS) have been on the global market, most research focused on only a small fraction, potentially resulting in underestimated environmental risks. Here, we used complementary target, suspect, and nontarget screening for quantifying and identifying the target and nontarget PFAS, respectively, and developed a risk model considering their specific properties to prioritize the PFAS in surface waters. Thirty-three PFAS were identified in surface water in the Chaobai river, Beijing. The suspect and nontarget screening by Orbitrap displayed a sensitivity of > 77%, indicating its good performance in identifying the PFAS in samples. We used triple quadrupole (QqQ) under multiple-reaction monitoring for quantifying PFAS with authentic standards due to its potentially high sensitivity. To quantify the nontarget PFAS without authentic standards, we trained a random forest regression model which presented the differences up to only 2.7 times between measured and predicted response factors (RFs). The maximum/minimum RF in each PFAS class was as high as 1.2-10.0 in Orbitrap and 1.7-22.3 in QqQ. A risk-based prioritization approach was developed to rank the identified PFAS, and four PFAS (i.e., perfluorooctanoic acid, hydrogenated perfluorohexanoic acid, bistriflimide, 6:2 fluorotelomer carboxylic acid) were flagged with high priority (risk index > 0.1) for remediation and management. Our study highlighted the importance of a quantification strategy during environmental scrutiny of PFAS, especially for nontarget PFAS without standards.

Molecular behavior and interactions with microbes during anaerobic degradation of bio-derived DOM in waste leachate

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.

Characterization of the Ciguatoxin Profile in Fish Samples from the Eastern Atlantic Ocean using Capillary Liquid Chromatography-High Resolution Mass Spectrometry

Ciguatera Poisoning is an emerging risk in the east Atlantic Ocean. Despite characterization efforts, the complete profile of ciguatoxin chemical species in these waters is still unknown. These efforts have been complicated by a lack of reference materials and scarcity of fish contaminated with high levels of ciguatoxins. Development and application of analytical methods with enhanced selectivity and sensitivity is essential for ciguatoxin characterization. Here, we developed an analytical characterization approach using capillary liquid chromatography coupled to high resolution mass spectrometry applied to reference materials obtained from ciguatoxin contaminated fish. Capillary LC coupled mass spectrometry resulted in increased sensitivity leading to the confirmation of C-CTX1 as the principal ciguatoxin present in these samples. We also detected and structurally characterized minor C-CTXs analogues consisting of C-CTX3/4, hydroxy-, didehydro-, and methoxy- metabolites.

Automated method using direct-immersion solid-phase microextraction and on-fiber derivatization coupled with comprehensive two-dimensional gas chromatography high-resolution mass spectrometry for profiling naphthenic acids in produced water

Naphthenic acids (NAs) are naturally occurring organic acids in petroleum and are found in waste waters generated during oil production (produced water, PW). Profiling this class of compounds is important due to flow assurance during oil exploration. Compositional analysis of PW is also relevant for waste treatment to reduce negative impacts on the environment. Here, comprehensive two-dimensional gas chromatography coupled with high-resolution mass spectrometry (GC×GC-HRMS) was applied as an ideal platform for qualitative analysis of NAs by combining the high peak capacity of the composite system with automated scripts for group-type identification based on accurate mass measurements and fragmentation patterns. To achieve high-throughput profiling of NAs in PW samples, direct-immersion solid phase microextraction (DI-SPME) was selected for extraction, derivatization and preconcentration. A fully automated DI-SPME method was developed to combine extraction, fiber rinsing and drying, and on-fiber derivatization with N-methyl-N‑tert-butyldimethylsilyltrifluoroacetamide (MTBSTFA). Data processing was based on filtering scripts using the Computer Language for Identifying Chemicals (CLIC). The method successfully identified up to 94 NAs comprising carbon numbers between 6 and 18 and hydrogen deficiency values ranging from 0 to -4. The proposed method demonstrated wider extraction coverage compared to traditional liquid-liquid extraction (LLE) - a critical factor for petroleomic investigations. The method developed also enabled quantitative analysis, exhibiting detection limits of 0.5 ng L^-1 and relative standard deviation (RSD) at a concentration of NAs of 30 µg L^-1 ranging from 4.5 to 25.0%.

Cooking food in microwavable plastic containers: in situ formation of a new chemical substance and increased migration of polypropylene polymers

Microwavable plastic food containers can be a source of toxic substances. Plastic materials such as polypropylene polymers are typically employed as safe materials in food packaging, but recent research demonstrates the migration of plastic substances or their by-products to food simulants, to foodstuff, and, more recently, to the human body through food consumption. However, a thorough evaluation of foodstuff in food contact materials under cooking conditions has not yet been undertaken. Here we show for the first time that plastic migrants present in food contact materials can react with natural food components resulting in a compound that combines a UV-photoinitiator (2-hydroxy-2-methyl-1-phenylpropan-1-one) with maltose from potato starch; this has been identified after cooking potatoes in microwavable plastic food containers. Additionally, polypropylene glycol substances have been found to transfer into food through microwave cooking. Identifying these substances formed in situ requires state-of-the-art high-resolution mass spectrometry instrumentation and metabolomics-based strategies.

Quantification of 25-hydroxyvitamin D2 and D3 in Mitra® devices with volumetric absorptive microsampling technology (VAMS®) by UHPLC-HRMS for regular vitamin D status monitoring

The numbers of vitamin D inadequacies has reportedly increased in the general population, especially in the Northern hemisphere. However, routine measurement of 25(OH) vitamin D is usually associated with a substantial effort due to the requirement of a venous blood sample taken by medical professionals. Thus, the objective of this work is to develop and validate an easy and minimal-invasive method, using a microsampling technique for autonomous blood collections by medically untrained individuals. The assay enables a simplified monitoring of the vitamin D-status in both, risk group and normal population throughout the year. For this purpose, a simple methanol extraction without derivatization combined with a UHPLC-HRMS method was developed to quantify 25(OH)D2 and 25(OH)D3 in capillary blood. For sample collection, a 20 μl Mitra® device with VAMS® technology is used. By employing the six-fold deuterium-labelled 25(OH)D3 as internal standard, the validated assay provides accurate (<10%) and precise (<11%) results. With a LOQ of 5 ng/ml, the approach also proved sensitive enough to adequately identify potential vitamin D deficiencies (< 12 ng/ml), and proof-of-concept analyses of authentic VAMS® samples (n = 20) yielded test results in the expected blood concentration range. Implementing VAMS® sampling for vitamin D-status monitoring enables a higher frequency due to a simplified, straightforward, and time-effective sample collection. VAMS® assures accurate sample volumes because of its absorptive capacities and, thus, area bias and homogeneity issues associated with conventional DBS are avoided. Regular monitoring of 25(OH)D status throughout the year supports people in high-risk groups for vitamin D-deficiency by early identifying inadequacies and, thus, preventing adverse health consequences.

Advances in Ultra-High-Resolution Mass Spectrometry for Pharmaceutical Analysis

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.

Chemophenetic Approach to Selected Senecioneae Species, Combining Morphometric and UHPLC-HRMS Analyses

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.

Development and Validation of a Non-Targeted Screening Method for Most Psychoactive, Analgesic, Anaesthetic, Anti-Diabetic, Anti-Coagulant and Anti-Hypertensive Drugs in Human Whole Blood and Plasma Using High-Resolution Mass Spectrometry

(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.

Retinyl Ester Analysis by Orbitrap Mass Spectrometry

Retinoids are light-sensitive molecules that are normally detected by UV absorption techniques. Here we describe the identification and quantification of retinyl ester species by high-resolution mass spectrometry. Retinyl esters are extracted by the method of Bligh and Dyer and subsequently separated by HPLC in runs of 40 min. The retinyl esters are identified and quantified by mass spectrometry analysis. This procedure enables the highly sensitive detection and characterization of retinyl esters in biological samples such as hepatic stellate cells.

Diabetes Retinopathy: New Ways to Detect and Treat

Recent clinical trials demonstrated strong association between lipid abnormalities and progression of diabetic retinopathy (DR); however, whether circulating lipid levels or retinal lipid metabolism, or both, contributes to the pathogenesis of DR is not well understood. Limited amounts of retinal tissue available from animal models, such as mouse models of DR, have proved. Limited amount of retinal tissue was especially challenging for cholesterol and oxysterol detection as it precluded identification of individual isomers of each nonesterified sterol class. To measure cholesterol and oxysterols from limited retinal tissue samples, we developed extremely sensitive electrospray ionization liquid chromatography high-resolution/accurate mass measurements on an LTQ Orbitrap Velos mass spectrometer that are able to resolve sterols and oxysterols separated by reverse-phase HPLC using a gradient of 85-100% methanol containing 0.1% formic acid, with subsequent detection in positive ionization mode. This methodology will aid in our understanding of diabetes-induced changes in retinal cholesterol and oxysterol metabolism.

Characterization of different parts of litchi fruit using UHPLC-QExactive Orbitrap

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.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13197-022-05577-z.

Suspect screening of pharmaceuticals, illicit drugs, pesticides, and other emerging contaminants in Argentinean Piaractus mesopotamicus, a fish species used for local consumption and export

The widespread distribution of contaminants of emerging concern (CECs) is a major concern due to their potential effects on human health and the environment. The insufficient sewage treatment plant infrastructures is a global problem most accentuated in less developed countries and results in the discharge of CECs to water bodies. Pacu (Piaractus mesopotamicus) is a ray-finned freshwater fish species native to the Paraná basin. It is also the most produced aquaculture fish species in Argentina since 2012. Though uninvestigated to date, the occurrence of CECs in pacu may be of high relevance due to production volumes and relevance to human exposure through fish consumption. In this study, we applied a high-resolution mass spectrometry screening method to qualitatively analyze over 100 CECs in pacu. Four extraction/cleanup methods were tested on pooled pacu fillet, including solid-phase extraction and QuEChERS. The method that produced the highest number of detections was selected for further analysis of pacu purchased in supermarkets and fish markets in Argentina between 2017 and 2020. Residues of pesticides, antibiotics, pharmaceuticals, personal care products, plasticizers, sweeteners, drug metabolites, stimulants, and illegal drugs were detected in the samples. A total of 38 CECs were detected, ranging between 24 and 35 CECs per individual sample. 100% of the samples had positive detections of caffeine, 1,7-dimethylxanthine, xanthine, benzoylecgonine, methylparaben, ethylparaben, bis(2-ethylhexyl) phthalate (DEHP), metolachlor, carbendazim, salicylic acid, 2,4-D, saccharin, cyclamate, and dodecanedioic acid. Mappings generated with correspondence analysis were used to explore similarities/dissimilarities among the detected compounds. To our knowledge this is the first report of saccharin, cyclamate, 2,4 - D, carbendazim, metolachlor, ethylparaben, propylparben, bisphenol A, DEHP, and benzotriazole in fish from Argentina, and the first report on the presence of lisinopril, metropolol acid and dodecanedioic acid in fish worldwide.

Screening of pesticides and emerging contaminants in eighteen Greek lakes by using target and non-target HRMS approaches: Occurrence and ecological risk assessment

Lakes, albeit ecosystems of vital importance, are insufficiently investigated with respect to the degradation of water quality due to the organic micropollutants load. As regards Greece, screening of lake waters is scarce and concerns a limited number of contaminants. However, understanding the occurrence of contaminants of emerging concern (CECs) and other micropollutants in lakes is essential to appraise their potential ecotoxicological effects. The aim of this study was to deploy a multiresidue screening approach based on liquid chromatography-high-resolution mass spectrometry (HRMS) to get a first snapshot for >470 target CECs, including pesticides, pharmaceuticals, personal care products (PPCPs), per- and polyfluoroalkyl substances (PFASs), as well as organophosphate flame retardants (OPFRs) in eighteen Greek lakes in Central, Northern and West Northern Greece. The omnipresent compounds were DEET (N,N-diethyl-meta-toluamide), caffeine and TCPP (tris (1-chloro-2-propyl) phosphate). Maximum concentrations varied among the different classes. DEET was detected at a maximum average concentration of >1000 ng/L in Lake Orestiada, while its mean concentration was estimated at 233 ng/L. The maximum total concentrations for pesticides, PPCPs, PFASs, and OPFRs were 5807, 2669, 33.1, and 1214 ng/L, respectively, indicating that Greek lakes are still threatened by the intense agricultural activity. Besides, HRMS enabled a non-target screening by exploiting the rich content of the full-scan raw data, allowing the 'discovery' of tentative candidates, such as surfactants, pharmaceuticals, and preservatives among others, without reference standards. The potential ecotoxicity was assessed by both the risk quotient method and ECOSAR (Ecological Structure Activity Relationships) revealing low risk for most of the compounds.

Orbitrap MS

Chemical isotope labeling (CIL) LC-MS is a powerful tool for metabolome analysis with markedly improved metabolomic coverage and quantification accuracy over the conventional LC-MS technique. In addition, with differential isotope labeling, each labeled metabolite is detected as a peak pair in the mass spectra, offering the possibility of differentiating true metabolite peaks from the singlet noise or background peaks. In this study, we examined the effects of instrument type on the detectability of true metabolites with a focus on the comparison of quadrupole time-of-flight (QTOF) and Orbitrap mass spectrometers. Using the same ultra-high-performance liquid chromatography setup and optimized running conditions for QTOF and Orbitrap, we compared the total number of peak pairs detected and identified from the two instruments using human urine and serum as the test samples. Many common peak pairs were detected from the two instruments; however, there were a significant number of unique peak pairs detected in each type of instrument. By combining the datasets obtained using QTOF and Orbitrap, the total number of peak pairs detected could be significantly increased. We also examined the effect of mass resolving power on peak pair detection in Orbitrap (60,000 vs. 120,000 resolution). The observed differences in peak pair detectability were much less than those of QTOF vs. Orbitrap. However, the type of peak pairs detected using different resolutions could be somewhat different, offering the possibility of increasing the overall number of peak pairs by combining the two datasets obtained at two different resolutions. The results from this study clearly indicate that instrument type can have a profound effect on metabolite detection in CIL LC-MS. Therefore, comparison of metabolome data generated using different instruments needs to be carefully done. Moreover, future research (e.g., hardware modifications) is warranted to minimize the differences in order to generate more reproducible metabolome data from different types of instruments.

Deep Single-Shot NanoLC-MS Proteome Profiling with a 1500 Bar UHPLC System, Long Fully Porous Columns, and HRAM MS

This study demonstrates how the latest ultrahigh-performance liquid chromatography (UHPLC) technology can be combined with high-resolution accurate-mass (HRAM) mass spectrometry (MS) and long columns packed with fully porous particles to improve bottom-up proteomics analysis with nanoflow liquid chromatography–mass spectrometry (nanoLC-MS) methods. The increased back pressures from the UHPLC system enabled the use of 75 μm I.D. × 75 cm columns packed with 2 μm particles at a typical 300 nL/min flow rate as well as elevated and reduced flow rates. The constant pressure pump operation at 1500 bar reduced sample loading and column washing/equilibration stages and overall overhead time, which maximizes MS utilization time. The versatility of flow rate optimization to balance the sensitivity, throughput with sample loading amount, and capability of using longer gradients contributes to a greater number of peptide and protein identifications for single-shot bottom-up proteomics experiments. The routine proteome profiling and precise quantification of >7000 proteins with single-shot nanoLC-MS analysis open possibilities for large-scale discovery studies with a deep dive into the protein level alterations. Data are available via ProteomeXchange with identifier PXD035665.

Non targeted screening of nitrogen containing disinfection by-products in formation potential tests of river water and subsequent monitoring in tap water samples

The generation of disinfection by-products during water chlorination is a major concern in water treatment, given the potential health risks that these substances may pose. In particular, nitrogen-containing DBPs are believed to have greater toxicological significance than carbon-based DBPs. Hence, high performance liquid chromatography coupled to high-resolution mass spectrometry (HPLC-HRMS) in positive mode was employed to identify new non-volatile nitrogen containing disinfection by-products (DBPs) and to assess their presence in potable water. Nine water samples were taken in the Llobregat river, in the context of a water reuse trial, near the catchment of a drinking water treatment plant (DWTP) in 2019. River samples were disinfected with chlorine under controlled formation potential tests conditions and analysed with a non-target approach. The peak lists of raw and chlorinated samples were compared exhaustively, resulting in an extensive list of 495 DBPs that include bromine and/or chlorine atoms. 172 of these species were found frequently, in three or more chlorinated samples. The empirical formulae of these DBPs were unambiguously annotated on the basis of accurate m/z measurements, isotopic patterns and common heuristic rules. Most of the annotated species (310) contained bromide, which is consistent with the relatively high bromide content of the Llobregat basin (>0.3 mg/l). Drinking water samples were taken at the outlet of the DWTP during the same sampling period. According to their analysis, a large portion of the DBPs detected after the formation potential tests do not reach real-life drinking water, which suggests that the treatment train successfully removes a significant fraction of DBP precursors. However, 131 DBPs could still be detected in the final product water. A larger sampling was carried in the Barcelona water distribution network, during six consecutive weeks, and it revealed the presence of 78 halogenated DBPs in end-consumer water, most of which were nitrogen-containing. MS/MS fragmentation and retention times were employed to tentatively suggest molecular structure for these recalcitrant DBPs.

Mass Difference Matching Unfolds Hidden Molecular Structures of Dissolved Organic Matter

Ultrahigh-resolution Fourier transform mass spectrometry (FTMS) has revealed unprecedented details of natural complex mixtures such as dissolved organic matter (DOM) on a molecular formula level, but we lack approaches to access the underlying structural complexity. We here explore the hypothesis that every DOM precursor ion is potentially linked with all emerging product ions in FTMS² experiments. The resulting mass difference (Δm) matrix is deconvoluted to isolate individual precursor ion Δm profiles and matched with structural information, which was derived from 42 Δm features from 14 in-house reference compounds and a global set of 11 477 Δm features with assigned structure specificities, using a dataset of ∼18 000 unique structures. We show that Δm matching is highly sensitive in predicting potential precursor ion identities in terms of molecular and structural composition. Additionally, the approach identified unresolved precursor ions and missing elements in molecular formula annotation (P, Cl, F). Our study provides first results on how Δm matching refines structural annotations in van Krevelen space but simultaneously demonstrates the wide overlap between potential structural classes. We show that this effect is likely driven by chemodiversity and offers an explanation for the observed ubiquitous presence of molecules in the center of the van Krevelen space. Our promising first results suggest that Δm matching can both unfold the structural information encrypted in DOM and assess the quality of FTMS-derived molecular formulas of complex mixtures in general.

The identification of antioxidant and ACE-I peptides in different turkish ripened cheeses

The principal purpose of this study was to determine antioxidant and ACE-inhibitory (angiotensin converting enzyme) activities of 5 ripened Turkish cheese varieties (Kashar, Erzincan Tulum, Izmir Tulum Gruyere, Mihalic). Among the water-soluble extracts with a molecular weight smaller than 3 kDa Gruyere and Erzincan Tulum exhibited the highest free radical scavenger activity in FRAP (Ferric Reducing Ability of Plasma) and ABTS [2,20-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid)] assays, respectively. For the inhibition of ACE, Mihalic was more effective than others. The water-soluble extracts of five cheese were analyzed with liquid chromatography-tandem mass spectrometry to identify the peptide sequences. Totally 394 peptides were sequenced; of these, 134 from αs1-casein, 44 from αs2-casein, 198 from β-casein, and 18 from κ-casein. Among these sequences, 48 peptides were reported as bioactive with the activities including ACE-inhibitory, antioxidant, antimicrobial, DPP-IV inhibitory, antidiabetic, immunomodulating, antithrombotic, anti-inflammatory, and inhibition of cholesterol solubility. These results showed that Turkish cheeses are good sources of bioactive peptides.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13197-022-05414-3.

UHPLC-Q-Orbitrap /MS2 identification of (+)-Catechin oxidation reaction dimeric products in red wines and grape seed extracts

B-type procyanidin dimers and (+)-catechin dimeric oxidation products were analyzed in grape seed extracts and red wines (UHPLC-Q-Orbitrap MS). The different dimers had different fragmentation patterns according to their interflavan linkage position. Oxidation dimeric compounds had a specific fragment ion at m/z 393, missing for B-Type dimers fragmentations. A fragment ion at m/z 291 occurred and was specific for oxidation dimeric compounds with a COC linkage. Higher level oxidation products had abundant specific fragments: m/z 425, 397 and 245. These fragmentations were useful to identify them in complex samples such as grape seed extracts and wines. Three grape varieties and three ripening stages were selected and the corresponding seed extracts were obtained. The analyses revealed an increasing trend for the oxidation markers during grape ripening. The analysis of Syrah wines (2018, 2014, 2010) showed a decreasing trend of these molecules during wine ageing which might be due to further oxidation.

Characterization of the Time-Domain Isotopic Beat Patterns of Monoclonal Antibodies in Fourier Transform Mass Spectrometry

The time-domain transients in the Fourier transform mass spectrometry (FTMS) analysis of monoclonal antibodies (mAbs) are known to exhibit characteristic isotopic beat patterns. These patterns are defined by the isotopic distributions of all gaseous mAb ions present in the FTMS mass analyzer, originating from single or multiple charge states, and from single or multiple proteoforms. For an isolated charge state of a single proteoform, the mAb isotopic beat pattern resembles narrow splashes of signal amplitude (beats), spaced periodically in the time-domain transient, with broad (often exceeding 1 s) "valleys" between them. Here, we reinforce the importance of isotopic beat patterns for the accurate interpretation and presentation of FTMS data in the analysis of mAbs and other large biopolymers. An updated, mAb-grade version of the transient-mediated FTMS data simulation and visualization tool, FTMS Simulator is introduced and benchmarked. We then apply this tool to evaluate the charge-state dependent characteristics of isotopic beats in mAbs analyses with modern models of Orbitrap and ion cyclotron resonance (ICR) FTMS instruments, including detection of higher-order harmonics. We demonstrate the impact of the isotopic beat patterns on the analytical characteristics of the resulting mass spectra of individual and overlapping mAb proteoforms. The results reported here detail highly nonlinear dependences of resolution and signal-to-noise ratio on the time-domain transient period, absorption or magnitude mode spectra representation, and apodization functions. The provided description and the demonstrated ability to routinely conduct accurate simulations of FTMS data for large biopolymers should aid the end-users of Orbitrap and ICR FTMS instruments in the analysis of mAbs and other biopolymers, including viruses.

Field Detection of Highly Oxygenated Organic Molecules in Shanghai by Chemical Ionization-Orbitrap

Secondary organic aerosol, formed through atmospheric oxidation processes, plays an important role in affecting climate and human health. In this study, we conducted a comprehensive campaign in the megacity of Shanghai during the 2019 International Import Expo (EXPO), with the first deployment of a chemical ionization─Orbitrap mass spectrometer for ambient measurements. With the ultrahigh mass resolving power of the Orbitrap mass analyzer (up to 140,000 Th/Th) and capability in dealing with massive spectral data sets by positive matrix factorization, we were able to identify the major gas-phase oxidation processes leading to the formation of oxygenated organic molecules (OOM) in Shanghai. Nine main factors from three independent sub-range analysis were identified. More than 90% of OOM are of anthropogenic origin and >60% are nitrogen-containing molecules, mainly dominated by the RO₂ + NO and/or NO₃ chemistry. The emission control during the EXPO showed that even though the restriction was effectual in significantly lowering the primary pollutants (20-70% decrease), the secondary oxidation products responded less effectively (14% decrease), or even increased (50 to >200%) due to the enhancement of ozone and the lowered condensation sink, indicating the importance of a stricter multi-pollutant coordinated strategy in primary and secondary pollution mitigation.

Intact quantitative bioanalytical method development and fit-for-purpose validation of a monoclonal antibody and its related fab fragment in human vitreous and aqueous humor using LC-HRMS

Ranibizumab is an FDA-approved drug used to treat wet age-related macular degeneration (AMD), diabetic retinopathy, macular edema, and myopic choroidal neovascularization. Bevacizumab is another drug often used off-label to treat wet AMD. In order to reduce unwanted angiogenesis, ranibizumab and bevacizumab target circulating VEGF-A in the eye. Concentration levels in human vitreous and aqueous humor can be used to provide valuable efficacy information. However, vitreous and aqueous humor's aqueous environment, and vitreous humor's viscosity, as well as the stickiness of the analytes can provide bioanalytical challenges. In this manuscript, we describe the development, optimization, and fit-for-purpose validation of an LC-HRMS method designed for intact quantitative bioanalysis of ranibizumab and bevacizumab in human vitreous and aqueous humor following intravitreal administration. In order to fully develop this method, evaluations were conducted to optimize the conditions, including the data processing model (extracted ion chromatograms (XICs) vs deconvolution), carryover mitigation, sample preparation scheme optimization for surrogate and primary matrices, use of internal standard/immunocapture/deglycosylation, and optimization of the extraction and dilution procedure, as well as optimization of the liquid chromatography and mass spectrometry conditions. Once the method was fully optimized, a fit-for-purpose validation was conducted, including matrix parallelism, with a linear calibration range of 10 to 200 µg/mL. The development of this intact quantitative method using LC-HRMS provides a proof-of-concept template for challenging, but valuable new and exciting bioanalytical techniques.

High resolution Orbitrap mass spectrometry analysis of oxidized hydrocarbons found in freshwater following a simulated spill of crude oil

Negative ion electrospray Orbitrap mass spectrometry was used to analyze water samples taken from a pilot-scale spill tank test of conventional crude oil on freshwater. A 56-day spill test was performed, and water samples were taken at regular intervals throughout the test to determine what changes in water chemistry occur with time. Orbitrap mass spectrometry was used to measure oxidized species in water samples, and oxidized species are analyzed by carbon number, double bond equivalent and hydrocarbon class. Emphasis is placed on changes with time over the course of the spill test, to examine changes by weathering processes that could occur naturally in a field spill scenario. Results demonstrate that while the concentrations of polycyclic aromatic hydrocarbons decrease in the water phase over time, the concentrations of total organic carbon and oxidized species in the water increase with time, where quantities of O2 and O3 species have the highest abundance. Measurement of increasing concentrations and changing relative abundances of these oxidized compounds can be used to assess how oil behaves in a freshwater aquatic environment after a spill.

Identification and potential mechanism of different components from the aerial part of Bupleurum chinense DC. for epileptic treatment

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.

Non-targeted analysis of unknown volatile chemicals in medical masks

This paper reports the non-targeted analysis of unknown volatile chemicals in medical masks through headspace gas chromatography-Orbitrap high-resolution mass spectrometry. In view of the difficulties that may be encountered in the qualitative analysis of unknown substances, several typical cases and the corresponding reliable solutions are given from the perspective of comprehensive score and retention index, chemical ionization identification molecular formula, fragment ion detail comparison for distinguishing isomers, and identification of alkanes. With this method, 69 volatile substances were identified in 60 masks. The identified substances were divided into nine categories. Alkanes, esters, benzenes, and alcohols were the top four groups of substances identified in masks and accounted for 34.8%, 15.9%, 10.1%, and 7.2% of the total substances, respectively. In addition, ketones, ethers, phenolics, amides, and other substances were identified. Ethanol, 1,4-dichlorobenzene, toluene, m-xylene, dimethyl glutarate, and N,N-dimethylacetamide had high detection rates. The identified substances were further filtered and screened according to their detection rate, toxicity, and response intensity. Finally, 12 high-risk volatile chemicals in medical masks were listed. This study could serve as a reference for identifying unknown substances and a guide for monitoring volatile chemicals in masks and promoting chemical safety improvements in products.

Transformation of bitumen-derived naphthenic acid fraction compounds across surface waters of wetlands in the Athabasca Oil Sands region

Bitumen is extracted from oil sands in the Athabasca Oil Sands region (AOSR) of Alberta, Canada. Much of the bitumen-derived toxicity in mine waste is attributable to naphthenic acid fraction compounds (NAFCs). Mines in the AOSR are required to be returned to a natural state after closure; thus, cost-effective strategies are needed to reduce toxicity from NAFCs. Previous studies have demonstrated the capability of constructed wetlands to attenuate NAFCs. However, the capacity of wetlands in the natural environment to degrade and transform NAFCs to less toxic components is poorly understood. To better understand the spatial distribution and fate of NAFCs in natural wetlands, samples were collected across the surfaces of two mature opportunistic wetlands near active oil sands mines. The first wetland has a well-defined surface flow pathway and inflows affected by overburden containing lean bitumen ore. The second wetland, in contrast, is a stagnant water body with raw bitumen visible along its edges. For the wetland with a well defined flow path, NAFCs decreased in concentration down gradient, while oxidized NAFCs constituted a greater proportion of NAFCs with increase in flow path. Likewise there was a decrease in the molecular weights of NAFCs, similar to trends observed in constructed wetland treatment systems. In comparison, NAFCs were more uniformly distributed across the relatively stagnant wetland. Overall, these data provide new evidence that mature opportunistic wetlands in the AOSR can promote the degradation and oxidation of bitumen-derived naphthenic acids into less toxic compounds.

Biomass magnetic porous carbon prepared from mangosteen shell for the preconcentration of 3 bisphenols from beverages followed by liquid chromatographyquadrupoleorbitrap high-resolution mass spectrometry determination

Natural biomass magnetic porous carbon was successfully prepared via a cost-effective and green route using mangosteen shell as raw material. The prepared magnetic porous carbon was used as a magnetic solid phase extraction adsorbent for bisphenols enrichment from beverages followed by high-performance liquid chromatographyquadrupole Orbitrap high-resolution mass spectrometry. Parameters affecting extraction efficiency including sample solutionpH, adsorbent amount, extraction time, eluent type and volume were optimized. Results showed that biomass magnetic porous carbon had excellent adsorption properties for bisphenols due to its large specific surface area and abundant functional groups, which could form hydrogen bonding and π-π stacking with bisphenols. The enrichment factor of 3 bisphenolswere in the range of15∼19. Under optimum conditions, favorable linearity for all analytes was obtained with correlation coefficients higher than 0.998. Recoveries of spiked samples were in the range of 88.5%∼105.1% with relative standard deviation of 3.4%∼5.5%. These results demonstrated thatmagnetic porous carbon may be a promising adsorbent for enrichment of aromatic compounds. This article is protected by copyright. All rights reserved.

TOF-SIMS Imaging of Biological Tissue Sections and Structural Determination Using Tandem MS

Over the past couple of years, imaging mass spectrometry (IMS) has arisen as a powerful tool to answer research questions in the biomedical field. Imaging mass spectrometry allows for label-free chemical imaging by providing full molecular information. The IMS technique best positioned for cell and tissue analysis is time-of-flight secondary ion mass spectrometry (ToF-SIMS) because it has the best spatial resolution of all the molecular IMS techniques and can detect many biochemical species and especially lipids with high sensitivity. Because one must rely on the mass and isotopic pattern of an ion in combination with positive correlations with lower mass fragments to help identify its structure, one major problem during ToF-SIMS experiments is the ambiguity when assigning a molecule to a certain mass peak. The solution are instruments with tandem MS capabilities as was already the case for many MALDI-ToF instruments more than a decade ago. It has been a few years since instruments with this capability were introduced and a number of interesting publications have been produced highlighting the advantages in biological SIMS work. Here, we present a protocol describing how tandem MS can be used to elucidate the structure of unknown or ambiguous mass peaks in biological tissue samples observed during ToF-SIMS imaging based on our experiences.

Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics

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.[Figure: see text].

Occurrence, spatial distribution and risk assessment of high concern endocrine-disrupting chemicals in Jiangsu Province, China

Endocrine-disrupting chemicals (EDCs) have attracted much concern because of the environmental and health risks they pose. Here we used liquid chromatography coupled with quadrupole-Orbitrap high-resolution mass spectrometry to quantify 10 types of EDCs at 118 sampling sites in Jiangsu Province, China, and then evaluated their respective environmental risk using a conservative risk quotient method. The results show that, in surface water, the targeted nonylphenol (NP), 4-tert-octylphenol (4-t-OP), and (2-ethylhexyl)phthalate (DEHP) were ranked highest, having mean concentrations above 300 ng/L. In comparison, both 4-t-OP and DEHP were also ranked highest, with mean concentrations above 100 ng/g, in the sediment samples. Moreover, the ∑₁₀EDCs concentration in the Huai River Basin was similar to that in the Yangtze River Basin. Notably, Huai'an city had the maximum mean concentration for EDCs in the Huai River Basin, followed by Xuzhou city and Suqian city, while Yangzhou city ranked highest in the Yangtze River Basin. Furthermore, the corresponding risk distribution revealed that (1) NP, bisphenol A (BPA), and 4-t-OP are of medium to high risk in 70%, 100% and 95% of the surface water samples, and likewise in 45%, 88% and 100% of the sediment samples, respectively; the maximum RQ value for NP in surface water samples reached 74.9; (2) DEHP belongs to the high-risk category in all samples (100%), whose maximum RQ reached 54.7. To our best knowledge, this is the first study to report on the occurrence, spatial distribution, and risk assessment of EDCs of high concern in Jiangsu Province, China.

Ravulizumab: Characterization and quantitation of a new C5 inhibitor using isotype specific affinity purification and high-resolution mass spectrometry

Introduction

Ravulizumab (RAVUL) is a new complement inhibitor, with a difference of 4 amino acids in the heavy chain from a predecessor compound, eculizumab (ECUL).

Objectives

First, to utilize mass spectrometry (MS) to characterize RAVUL and verify differences from its predecessor and, second, to validate and implement a lab developed test (LDT) for RAVUL that will allow for quantitative therapeutic monitoring.

Methods

A time-of-flight mass spectrometer (TOF-MS) was used to characterize and differentiate the molecular weight differences between RAVUL and ECUL by both digest and reduction experiments. In parallel, an LDT for RAVUL was validated and implemented utilizing IgG4 enrichment with light chain detection and quantitation on a high throughput orbitrap MS platform.

Results

The TOF-MS platform allowed for the mass difference between RAVUL and ECUL to be verified along with providing a proof of concept for a new intact protein quantitation software. An LDT on an orbitrap MS was validated and implemented using intact light chain quantitation, with the limitation that it cannot differentiate between ECUL and RAVUL. The LDT has an analytical measuring range from 5 to 600 mcg/mL, inter-assay imprecision of ≤13% CV (n = 13) and accuracy with <4% error from expected values (n = 20).

Conclusion

The TOF-MS is a versatile development platform that can be used to characterize and verify the molecular weight differences between the ECUL and RAVUL heavy chains. Routine laboratory testing for RAVUL was viable using an orbitrap-MS to quantitate using the mass of the intact light chain. These two platforms, combined, provide incomparable value in development of LDTs for the clinical laboratory.