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AbstractHydrolytic and oxidative damage to pyrimidine nucleobases in DNA represents a significant source of mutations in the human genome. To better understand how these lesions are incorporated and repaired in human cells, it is desirable to have ready access to isotopically enriched nucleosides for use in isotope tracing and mass spectrometry-based quantification experiments. Here we report on improved syntheses of deoxyuridine, deoxycytidine, 5-hydroxydeoxyuridine, and 5-hydroxydeoxycytidine nucleosides labeled with 13C and 15N. Deoxyuridine was synthesized from uracil in a direct glycosylation reaction with excellent stereoselectivity without the need to reduce a ribonucleoside intermediate. Deoxyuridine was further converted to deoxycytidine using mild O4 activation conditions with high efficiency. Finally, we document the synthetic details of preparative oxidation of deoxyuridine and deoxycytidine to their 5-hydroxy counterparts. Overall, our protocols avoid hazardous reagents and tedious conditions found in previous methods. [ABSTRACT FROM AUTHOR]

Mammalian cell culture processes are widely utilized for biotherapeutics production, disease diagnostics, and biosensors, and hence, should be optimized to support robust cell growth and viability. However, toxic by-products accumulate in cultures due to inefficiencies in metabolic activities and nutrient utilization. In this study, we applied comprehensive 13C stable-isotope tracing of amino acids and glucose to two Immunoglobulin G (IgG) producing Chinese Hamster Ovary (CHO) cell lines to identify secreted by-products and trace their origins. CHO cells were cultured in media formulations missing a single amino acid or glucose supplemented with a 13C-tracer of the missing substrate, followed by gas chromatography-mass spectrometry (GC-MS) analysis to track labeled carbon flows and identify by-products. We tracked the sources of all secreted by-products and verified the identity of 45 by-products, majority of which were derived from glucose, leucine, isoleucine, valine, tyrosine, tryptophan, methionine, and phenylalanine. In addition to by-products identified previously, we identified several metabolites including 2-hydroxyisovaleric acid, 2-aminobutyric acid, L-alloisoleucine, ketoisoleucine, 2-hydroxy-3-methylvaleric acid, desmeninol, and 2-aminobutyric acid. When added to CHO cell cultures at different concentrations, certain metabolites inhibited cell growth while others including 2-hydroxy acids, surprisingly, reduced lactate accumulation. In vitro enzymatic analysis indicated that 2-hydroxy acids were metabolized by lactate dehydrogenase suggesting a possible mechanism for lowered lactate accumulation, e.g., competitive substrate inhibition. The 13C-labeling assisted metabolomics pipeline developed and the metabolites identified will serve as a springboard to reduce undesirable by-products accumulation and alleviate inefficient substrate utilization in mammalian cultures used for biomanufacturing and other applications through altered media formulations and pathway engineering strategies. [ABSTRACT FROM AUTHOR]

The 5’ cap structure is crucial to mRNA function, with its diverse methylation patterns depending on the cellular state. Sensitive analytical methods are sought after to quantify this cap variety also referred to as cap epitranscriptome. To address a bottleneck for accurate and precise quantitation, we report a facile and fast access to high‐quality synthetic standards via a new route, involving P(III)‐amidite chemistry. A range of cap nucleotides and their stable heavy isotopic labeled analogues were derived from nucleoside diphosphates, which themselves were directly prepared in a one‐step reaction sequence starting from unprotected nucleosides using a triphosphorylating reagent in combination with ethylenediamine. Considering a wider scope, the route also enables direct access to magic spot nucleotides and diphosphates of isoprenyl‐alcohols. Stable‐isotope labeled cap nucleotides derived from this route paved the way for the development of a highly sensitive LC–MS/MS method, applied to the characterization of mouse brain cap epitranscriptomes, which turned out to be very different from those of cultured cell lines of widespread use in the life sciences. [ABSTRACT FROM AUTHOR]

The significance of small molecule metabolites as biomarkers for disease diagnosis and prognosis is growing increasingly evident, necessitating the development of highly sensitive qualitative and quantitative methods. Herein, multi‐chemoselective probes are synthesized and applied for profiling metabolites, including carboxyl, phosphate, hydroxyl, amino, thiol, and carbonyl compounds. This approach seamlessly integrates magnetic solid‐phase materials, orthogonal cleavage sites, isotopic tags, and selective coupling sites, minimizes matrix interference, and enhances quantitative accuracy. Meanwhile, a homemade program, High‐Resolution Isotope‐Assisted Identification and Quantitative (HRIAIQuant) is developed to process the data, which adeptly filters through 33,874 ion pairs present in human serum, leading to the identification of 701 known metabolites and a remarkable 1,062 potential novel ones. This method is successfully applied to analyze metabolites in multiple brain regions of SAMP8 and SAMR1 models, offering a novel tool for Alzheimer's disease research. [ABSTRACT FROM AUTHOR]

Aquaculture contributes to the sustainable development of food security, marine resource conservation, and economy. Shifting aquaculture feed from fish meal and oil to terrestrial plant derivatives may result in cost savings. However, many carnivorous fish cannot be sustained on plant-derived materials, necessitating the need for the identification of important factors for farmed fish growth and the identification of whether components derived from terrestrial plants can be used in feed. Herein, we focused on the carnivorous fish leopard coral grouper (P. leopardus) to identify the essential growth factors and clarify their intake timing from feeds. Furthermore, we evaluated the functionality of starch, which are easily produced by terrestrial plants. Results reveal that carbohydrates, which are not considered essential for carnivorous fish, can be introduced as a major part of an artificial diet. The development of artificial feed using starch offers the possibility of increasing the growth of carnivorous fish in aquaculture. [ABSTRACT FROM AUTHOR]

Plants have evolved numerous strategies for surviving the harsh conditions of the Arctic. One strategy for Arctic evergreen and semi‐evergreen species is to photosynthesize beneath the snow during spring. However, the prevalence of this photosynthesis and how recent photosynthates are used is still unknown. Here we ask, how is newly acquired carbon beneath the snow allocated? To answer this question, we delivered isotopically labeled 13CO2 to tussock tundra plants before snowmelt. Soluble sugars and starches were preferentially enriched with 13C in all five species tested, with lipids having comparatively low 13C enrichment. These results provide evidence of the recovery of metabolites used over the long winter. Additionally, these new soluble sugars may function in photoprotection and cold tolerance as plants release from snow cover. Climate change, by reducing the duration of subnivean photosynthesis of these species, will limit metabolite production before snowmelt, which may lead to a reduction in the ability of these species to compete effectively during the growing season, potentially leading to changes in community structure. [ABSTRACT FROM AUTHOR]

Abstract Changes in protein turnover play an important role in dynamic physiological processes, including skeletal muscle regeneration, which occurs as an essential part of tissue repair after injury. The inability of muscle tissue to recapitulate this regenerative process can lead to the manifestation of clinical symptoms in various musculoskeletal diseases, including muscular dystrophies and pathological atrophy. Here, we employed a workflow that couples deuterated water (2H2O) administration with mass spectrometry (MS) to systematically measure in-vivo protein turnover rates across the muscle proteome in 8-week-old male C57BL6/J mice. We compared the turnover kinetics of over 100 proteins in response to cardiotoxin (CTX) induced muscle damage and regeneration at unique sequential stages along the regeneration timeline. This analysis is compared to gene expression data from mRNA-sequencing (mRNA-seq) from the same tissue. The data reveals quantitative protein flux signatures in response to necrotic damage, in addition to sequential differences in cell proliferation, energy metabolism, and contractile gene expression. Interestingly, the mRNA changes correlated poorly with changes in protein synthesis rates, consistent with post-transcriptional control mechanisms. In summary, the experiments described here reveal the signatures and timing of protein flux changes during skeletal muscle regeneration, as well as the inability of mRNA expression measurements to reveal changes in directly measured protein turnover rates. The results of this work described here provide a better understanding of the muscle regeneration process and could help to identify potential biomarkers or therapeutic targets.

Changes in protein turnover play an important role in dynamic physiological processes, including skeletal muscle regeneration, which occurs as an essential part of tissue repair after injury. The inability of muscle tissue to recapitulate this regenerative process can lead to the manifestation of clinical symptoms in various musculoskeletal diseases, including muscular dystrophies and pathological atrophy. Here, we employed a workflow that couples deuterated water (2H2O) administration with mass spectrometry (MS) to systematically measure in-vivo protein turnover rates across the muscle proteome in 8-week-old male C57BL6/J mice. We compared the turnover kinetics of over 100 proteins in response to cardiotoxin (CTX) induced muscle damage and regeneration at unique sequential stages along the regeneration timeline. This analysis is compared to gene expression data from mRNA-sequencing (mRNA-seq) from the same tissue. The data reveals quantitative protein flux signatures in response to necrotic damage, in addition to sequential differences in cell proliferation, energy metabolism, and contractile gene expression. Interestingly, the mRNA changes correlated poorly with changes in protein synthesis rates, consistent with post-transcriptional control mechanisms. In summary, the experiments described here reveal the signatures and timing of protein flux changes during skeletal muscle regeneration, as well as the inability of mRNA expression measurements to reveal changes in directly measured protein turnover rates. The results of this work described here provide a better understanding of the muscle regeneration process and could help to identify potential biomarkers or therapeutic targets. [ABSTRACT FROM AUTHOR]

The rapidly expanding market for regenerative medicines and cell therapies highlights the need to advance the understanding of cellular metabolisms and improve the prediction of cultivation production process for human induced pluripotent stem cells (iPSCs). In this paper, a metabolic kinetic model was developed to characterize the underlying mechanisms of iPSC culture process, which can predict cell response to environmental perturbation and support process control. This model focuses on the central carbon metabolic network, including glycolysis, pentose phosphate pathway, tricarboxylic acid cycle, and amino acid metabolism, which plays a crucial role to support iPSC proliferation. Heterogeneous measures of extracellular metabolites and multiple isotopic tracers collected under multiple conditions were used to learn metabolic regulatory mechanisms. Systematic cross‐validation confirmed the model's performance in terms of providing reliable predictions on cellular metabolism and culture process dynamics under various culture conditions. Thus, the developed mechanistic kinetic model can support process control strategies to strategically select optimal cell culture conditions at different times, ensure cell product functionality, and facilitate large‐scale manufacturing of regenerative medicines and cell therapies. [ABSTRACT FROM AUTHOR]

Abstract Plants have evolved numerous strategies for surviving the harsh conditions of the Arctic. One strategy for Arctic evergreen and semi‐evergreen species is to photosynthesize beneath the snow during spring. However, the prevalence of this photosynthesis and how recent photosynthates are used is still unknown. Here we ask, how is newly acquired carbon beneath the snow allocated? To answer this question, we delivered isotopically labeled 13CO2 to tussock tundra plants before snowmelt. Soluble sugars and starches were preferentially enriched with 13C in all five species tested, with lipids having comparatively low 13C enrichment. These results provide evidence of the recovery of metabolites used over the long winter. Additionally, these new soluble sugars may function in photoprotection and cold tolerance as plants release from snow cover. Climate change, by reducing the duration of subnivean photosynthesis of these species, will limit metabolite production before snowmelt, which may lead to a reduction in the ability of these species to compete effectively during the growing season, potentially leading to changes in community structure.

Abstract Efficient protein turnover is essential for cellular homeostasis and organ function. Loss of proteostasis is a hallmark of aging culminating in severe dysfunction of protein turnover. To investigate protein turnover dynamics as a function of age, we performed continuous in vivo metabolic stable isotope labeling in mice along the aging continuum. First, we discovered that the brain proteome uniquely undergoes dynamic turnover fluctuations during aging compared to heart and liver tissue. Second, trends in protein turnover in the brain proteome during aging showed sex-specific differences that were tightly tied to cellular compartments. Next, parallel analyses of the insoluble proteome revealed that several cellular compartments experience hampered turnover, in part due to misfolding. Finally, we found that age-associated fluctuations in proteasome activity were associated with the turnover of core proteolytic subunits, which was recapitulated by pharmacological suppression of proteasome activity. Taken together, our study provides a proteome-wide atlas of protein turnover across the aging continuum and reveals a link between the turnover of individual proteasome subunits and the age-associated decline in proteasome activity.

The development and validation of a simple, comprehensive, and environment-friendly procedure to determine pesticide residues, naturally occurring and processing contaminants in roasted coffee is presented. A solid-liquid extraction of pesticides and mycotoxins with ethyl acetate and the concurrent partition of acrylamide to an aqueous phase follows a parallel analytical strategy that requires a single analytical portion to determine contaminants that are typically analyzed by dedicated single residue methods. The partition rules the lipids out of the aqueous extract before an "in-tube" dispersive solid phase microextraction (dSPME) for acrylamide retention. This is followed by the elution with buffer prior to injection. This extract is independently introduced into the system front end followed by the injection of the compounds from the organic phase, yet all spotted in the same run. A novel liquid chromatography high-resolution mass spectrometry (LC-HRMS) method setup enables the quantification of 186 compounds at 10 µg/kg, 226 at 5 µg/kg, and the acrylamide at 200 µg/kg for a total of 414 molecules, with acceptable recoveries (70–120%) and precision (RSD < 20%) making this strategy significantly faster and cost-effective than the dedicated single residue methods. Even though the presence of chlorpyrifos, acrylamide, and ochratoxin A was confirmed on samples of different origins, the findings were below the limit of quantification. During the storage of raw coffee, no proof of masking of OTA was found; however, condensation with glucose was evidenced during thermal processing experiments with sucrose by using stable isotope labeling (SIL). No detected conjugates were found in roasted nor in commercial sugar-added torrefacto samples, an industrial processing usually carried out above the decomposition temperature of the disaccharide. [ABSTRACT FROM AUTHOR]

A simple and convenient synthesis of 9-hydroxy[13C6]phenanthrene has been developed from one-ring labeled [13C6]phenanthrene in three steps, involving a copper-ethyl acetate catalyzed "Ullmann-type" reaction. The mild conditions of this nucleophilic aromatic substitution are particularly advantageous in the case of expensive labeled material. Stable-labeled 9-hydroxy[13C6]phenanthrene has proven to be an ideal [M + 6]isotopomer for use as an internal standard for quantification of OH-polycyclic aromatic hydrocarbons by gas chromatography with tandem mass spectrometry (GC-MS/MS) in human urines. [ABSTRACT FROM AUTHOR]

Larvae of the Salicaceae-adapted Notodontidae have developed a unique mechanism to metabolize the chemical defenses of their Salicaceae host plants. Salicinoids and salicortinoids are enzymatically transformed into salicyloyl, benzoyl and mixed salicyloyl-benzoyl quinates. The source of quinates and benzoates was previously unknown. To elucidate the origin of quinate and benzoate in the metabolic end-products, we fed Cerura vinula caterpillars with 13C-labelled poplar defense compounds. Caffeoylquinic acids (CQAs), such as chlorogenic acid, neochlorogenic acid and their methyl esters, were identified as the source of quinates in the caterpillar's metabolism. Benzoyl substituents in the quinate end-products were found to originate from compounds such as tremulacin or trichocarpin. Salicaceae-adapted Notodontidae caterpillars have the ability to overcome their host plant's chemical defense by metabolizing CQAs and salicinoids, both abundant defense compounds in Salicacea plants, by a strategy of transformation and recombination. We believe that our study opens up avenues for understanding salicortinoid biotransformation at the enzymatic level. [ABSTRACT FROM AUTHOR]

Efficient protein turnover is essential for cellular homeostasis and organ function. Loss of proteostasis is a hallmark of aging culminating in severe dysfunction of protein turnover. To investigate protein turnover dynamics as a function of age, we performed continuous in vivo metabolic stable isotope labeling in mice along the aging continuum. First, we discovered that the brain proteome uniquely undergoes dynamic turnover fluctuations during aging compared to heart and liver tissue. Second, trends in protein turnover in the brain proteome during aging showed sex-specific differences that were tightly tied to cellular compartments. Next, parallel analyses of the insoluble proteome revealed that several cellular compartments experience hampered turnover, in part due to misfolding. Finally, we found that age-associated fluctuations in proteasome activity were associated with the turnover of core proteolytic subunits, which was recapitulated by pharmacological suppression of proteasome activity. Taken together, our study provides a proteome-wide atlas of protein turnover across the aging continuum and reveals a link between the turnover of individual proteasome subunits and the age-associated decline in proteasome activity. Synopsis: Continuous pulse-step metabolic labeling with quantitative proteomics in mice reveals sex-specific differences in protein turnover linked to subcellular compartments. Age-related changes in protein turnover result in part from altered proteasome activity and subunit turnover. Brain protein turnover trends during aging display sex-specific differences tied to subcellular compartments. Misfolded proteins contribute to differential turnover trends in the brain. Reduced proteasome activity is associated with slowed turnover of proteasome subunits during aging. Continuous pulse-step metabolic labeling with quantitative proteomics in mice reveals sex-specific differences in protein turnover linked to subcellular compartments. Age-related changes in protein turnover result in part from altered proteasome activity and subunit turnover. [ABSTRACT FROM AUTHOR]

Protein phosphorylation is a critical post-translational modification involved in the regulation of numerous cellular processes from signal transduction to modulation of enzyme activities. Knowledge of dynamic changes of phosphorylation levels during biological processes, under various treatments or between healthy and disease models is fundamental for understanding the role of each phosphorylation event. Thereby, LC-MS/MS based technologies in combination with quantitative proteomics strategies evolved as a powerful strategy to investigate the function of individual protein phosphorylation events. State-of-the-art labeling techniques including stable isotope and isobaric labeling provide precise and accurate quantification of phosphorylation events. Here, we review the strengths and limitations of recent quantification methods and provide examples based on current studies, how quantitative phosphoproteomics can be further optimized for enhanced analytic depth, dynamic range, site localization, and data integrity. Specifically, reducing the input material demands is key to a broader implementation of quantitative phosphoproteomics, not least for clinical samples. Despite quantitative phosphoproteomics is one of the most thriving fields in the proteomics world, many challenges still have to be overcome to facilitate even deeper and more comprehensive analyses as required in the current research, especially at single cell levels and in clinical diagnostics. [ABSTRACT FROM AUTHOR]

Traditional strategies for the metabolic profiling of doping are limited by the unpredictable metabolic pathways and the numerous proportions of background and chemical noise that lead to inadequate metabolism knowledge, thereby affecting the selection of optimal detection targets. Thus, a stable isotope labeling-based nontargeted strategy combined with ultra-high-performance liquid chromatography–high-resolution mass spectrometry (UHPLC-HRMS) was first proposed for the effective and rapid metabolism analysis of small-molecule doping agents and demonstrated via its application to a novel doping BPC-157. Using 13C/15N-labeled BPC-157, a complete workflow including automatic 13C0,15N0-13C6,15N2 m/z pair picking based on the characteristic behaviors of isotope pairs was constructed, and one metabolite produced by a novel metabolic pathway plus eight metabolites produced by the conventional amide-bond breaking metabolic pathway were successfully discovered from two incubation models. Furthermore, a specific method for the detection of BPC-157 and the five main metabolites in human urine was developed and validated with satisfactory detection limits (0.01~0.11 ng/mL) and excellent quantitative ability (linearity: 0.02~50 ng/mL with R2 > 0.999; relative error (RE)% < 10% and relative standard deviation (RSD)% < 5%; recovery > 90%). The novel metabolic pathway and the in vitro metabolic profile could provide new insights into the biotransformation of BPC-157 and improved targets for doping control. [ABSTRACT FROM AUTHOR]

Rhizonin A and B are hepatotoxic cyclopeptides produced by bacterial endosymbionts (Mycetohabitans endofungorum) of the fungus Rhizopus microsporus. Their toxicity critically depends on the presence of 3‐furylalanine (Fua) residues, which also occur in pharmaceutically relevant cyclopeptides of the endolide and bingchamide families. The biosynthesis and incorporation of Fua by non‐ribosomal peptide synthetases (NRPS), however, has remained elusive. By genome sequencing and gene inactivation we elucidated the gene cluster responsible for rhizonin biosynthesis. A suite of isotope labeling experiments identified tyrosine and l‐DOPA as Fua precursors and provided the first mechanistic insight. Bioinformatics, mutational analysis and heterologous reconstitution identified dioxygenase RhzB as necessary and sufficient for Fua formation. RhzB is a novel type of heme‐dependent aromatic oxygenases (HDAO) that enabled the discovery of the bingchamide biosynthesis gene cluster through genome mining. [ABSTRACT FROM AUTHOR]

Mass spectrometry has been an essential technique for the investigation of the metabolic pathways of living organisms since its appearance at the beginning of the 20th century. Due to its capability to resolve isotopically labeled species, it can be applied together with stable isotope tracers to reveal the transformation of particular biologically relevant molecules. However, low-resolution techniques, which were used for decades, had limited capabilities for untargeted metabolomics, especially when a large number of compounds are labelled simultaneously. Such untargeted studies may provide new information about metabolism and can be performed with high-resolution mass spectrometry. Here, we demonstrate the capabilities of high-resolution mass spectrometry to obtain insights on the metabolism of a model plant, Lepidium sativum, germinated in D2O and H218O-enriched media. In particular, we demonstrated that in vivo labeling with heavy water helps to identify if a compound is being synthesized at a particular stage of germination or if it originates from seed content, and tandem mass spectrometry allows us to highlight the substructures with incorporated isotope labels. Additionally, we found in vivo labeling useful to distinguish between isomeric compounds with identical fragmentation patterns due to the differences in their formation rates that can be compared by the extent of heavy atom incorporation. [ABSTRACT FROM AUTHOR]

Over the last 50 years, advances in the production of stable isotopes and mass spectrometry instrumentation have fueled elucidation of endogenous biochemical pathways and underpinned quantitative methodology in analytical chemistry, to name but two areas impacted. The topic covering the use of stable isotopes in pharmacological research is very broad, but the scope of the current manuscript is more restricted, and will focus on the application of 2H, 13C and 18O to elucidate mechanisms of drug metabolism since the early 1980s. In keeping with the commemorative nature of this collection of papers, many of the examples are drawn from the work of Dr. Thomas Baillie and his colleagues. In the latter part of this review, we will also consider the development of stable-label forms of drugs that have recently been approved or are under development. [ABSTRACT FROM AUTHOR]

Saccharides in our diet are major sources of carbon for the formation of biomass such as proteins, lipids, nucleic acids and glycans. Among the dietary monosaccharides, glucose occupies a central role in metabolism, but human blood contains regulated levels of other monosaccharides as well. Their influence on metabolism and how they are utilized have not been explored thoroughly. Applying metabolic flux analysis on glycan synthesis can reveal the pathways that supply glycosylation precursors and provide a snapshot of the metabolic state of the cell. In this study, we traced the incorporation of six 13C uniformly labeled monosaccharides in the N-glycans, O-glycans and glycosphingolipids of both pluripotent and neural NTERA-2 cells. We gathered detailed isotopologue data for hundreds of glycoconjugates using mass spectrometry methods. The contributions of de novo synthesis and direct incorporation pathways for glucose, mannose, fructose, galactose, N-acetylglucosamine and fucose were determined based on their isotope incorporation. Co-feeding studies revealed that fructose incorporation is drastically decreased by the presence of glucose, while mannose and galactose were much less affected. Furthermore, increased sialylation slowed down the turnover of glycans, but fucosylation attenuated this effect. Our results demonstrated that exogenous monosaccharide utilization can vary markedly depending on the cell differentiation state and monosaccharide availability, and that the incorporation of carbons can also differ among different glycan structures. We contend that the analysis of metabolic isotope labeling of glycans can yield new insights about cell metabolism.

A synthesis route for stable isotope-labeled sulfamethoxazole-benzene ring-13C6 has been developed. In this strategy, 13C6-benzene was used as the source and starting material for stable isotope labeling and starting material to synthesize sulfachloropyridazine-benzene ring-13C6 through 6 steps of nitration, nitroreduction, acylation, sulfonation, condensation and hydrolysis. The product structure was confirmed through characterization techniques such as nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS), which the purity of the product was higher than 98.0% and the isotopic enrichment was higher than 99.0atom%13C. Sulfachloropyridazine-benzene ring-13C6 can be used as an internal standard reagent for qualitative and quantitative analysis of sulfachlorpyridazine.

In order to improve the stable isotope utilization rate, a simple and inexpensive synthesis method was developed. The synthesis of levofloxacin is based on piperazine as the starting material, and the reaction with carbobenzoxy chloride (CBZ-Cl) to get CBZ-piperazine-CD3, and then the reaction with iodomethane-D3 to get CBZ-piperazine-CD3, after the removal of CBZ protection to get methylpiperazine-D3, and finally the reaction with levofloxacin carboxylic acid to get levofloxin-D3. The yield of levofloxacin-D3 was 37.0% based on the amount of iodomethane-D3. The synthesized Levofloxacin-D3 product was characterized by nuclear magnetic resonance spectroscopy, high performance liquid chromatography and mass spectrometry. The chemical purity was 98.5% and the isotope abundance was 99.5atom% D. It can be used as the internal standard for the quantitative determination of levofloxacin residue in animal food.

Abstract Background Living cells maintain and adjust structural and functional integrity by continual synthesis and degradation of metabolites and macromolecules. The maintenance and adjustment of thylakoid membrane involve turnover of photosynthetic pigments along with subunits of protein complexes. Quantifying their turnover is essential to understand the mechanisms of homeostasis and long-term acclimation of photosynthetic apparatus. Here we report methods combining whole-plant long-term 13CO2 labeling and liquid chromatography - mass spectrometry (LC–MS) analysis to determine the size of non-labeled population (NLP) of carotenoids and chlorophylls (Chl) in leaf pigment extracts of partially 13C-labeled plants. Results The labeling chamber enabled parallel 13CO2 labeling of up to 15 plants of Arabidopsis thaliana with real-time environmental monitoring ([CO2], light intensity, temperature, relative air humidity and pressure) and recording. No significant difference in growth or photosynthetic pigment composition was found in leaves after 7-d exposure to normal CO2 (~ 400 ppm) or 13CO2 in the labeling chamber, or in ambient air outside the labeling chamber (control). Following chromatographic separation of the pigments and mass peak assignment by high-resolution Fourier-transform ion cyclotron resonance MS, mass spectra of photosynthetic pigments were analyzed by triple quadrupole MS to calculate NLP. The size of NLP remaining after the 7-d 13CO2 labeling was ~ 10.3% and ~ 11.5% for all-trans- and 9-cis-β-carotene, ~ 21.9% for lutein, ~ 18.8% for Chl a and 33.6% for Chl b, highlighting non-uniform turnover of these pigments in thylakoids. Comparable results were obtained in all replicate plants of the 13CO2 labeling experiment except for three that were showing anthocyanin accumulation and growth impairment due to insufficient water supply (leading to stomatal closure and less 13C incorporation). Conclusions Our methods allow 13CO2 labeling and estimation of NLP for photosynthetic pigments with high reproducibility despite potential variations in [13CO2] between the experiments. The results indicate distinct turnover rates of carotenoids and Chls in thylakoid membrane, which can be investigated in the future by time course experiments. Since 13C enrichment can be measured in a range of compounds, long-term 13CO2 labeling chamber, in combination with appropriate MS methods, facilitates turnover analysis of various metabolites and macromolecules in plants on a time scale of hours to days.

Lepidopteran specialist herbivores of the Notodontidae family have adapted to thrive on poplar and willow species (Salicaceae). Previous research showed that Cerura vinula, a member of the Notodontidae family occurring throughout Europe and Asia, uses a unique mechanism to transform salicortinoids, the host plant's defense compounds, into quinic acid-salicylate conjugates. However, how the production of this conjugates relates to the detoxification of salicortinoids and how this transformation proceeds mechanistically have remained unknown. To find the mechanisms, we conducted gut homogenate incubation experiments with C. vinula and re-examined its metabolism by analyzing the constituents of its frass. To estimate the contribution of spontaneous degradation, we examined the chemical stability of salicortinoids and found that salicortinoids were degraded very quickly by midgut homogenates and that spontaneous degradation plays only a marginal role in the metabolism. We learned how salicortinoids are transformed into salicylate after we discovered reductively transformed derivatives, which were revealed to play key roles in the metabolism. Unless they have undergone the process of reduction, salicortinoids produce toxic catechol. We also studied constituents in the frass of the Notodontidae species Cerura erminea, Clostera anachoreta, Furcula furcula, Notodonta ziczac, and Pheosia tremula, and found the same metabolites as those described for C. vinula. We conclude that the process whereby salicortinoids are reductively transformed represents an important adaption of the Notodontidae to their Salicaceae host species. [ABSTRACT FROM AUTHOR]

Background: Supply of choline is not guaranteed in current preterm infant nutrition. Choline serves in parenchyma formation by membrane phosphatidylcholine (PC), plasma transport of poly-unsaturated fatty acids (PUFA) via PC, and methylation processes via betaine. PUFA-PC concentrations are high in brain, liver and lung, and deficiency may result in developmental disorders. We compared different deuterated (D9-) choline components for kinetics of D9-choline, D9-betaine and D9-PC. Methods: Prospective study (1/2021–12/2021) in 32 enterally fed preterm infants (28 0/7–32 0/7 weeks gestation). Patients were randomized to receive enterally a single dose of 2.7 mg/kg D9-choline-equivalent as D9-choline chloride, D9-phosphoryl-choline, D9-glycerophosphorylcholine (D9-GPC) or D9-1-palmitoyl-2-oleoyl-PC(D9-POPC), followed by blood sampling at 1 + 24 h or 12 + 60 h after administration. Plasma concentrations were analyzed by tandem mass spectrometry. Results are expressed as median (25th/75th percentile). Results: At 1 h, plasma D9-choline was 1.8 (0.9/2.2) µmol/L, 1.3 (0.9/1.5) µmol/L and 1.2 (0.7/1.4) µmol/L for D9-choline chloride, D9-GPC and D9-phosphoryl-choline, respectively. D9-POPC did not result in plasma D9-choline. Plasma D9-betaine was maximal at 12 h, with lowest concentrations after D9-POPC. Maximum plasma D9-PC values at 12 h were the highest after D9-POPC (14.4 (9.1/18.9) µmol/L), compared to the other components (D9-choline chloride: 8.1 [5.6/9.9] µmol/L; D9-GPC: 8.4 (6.2/10.3) µmol/L; D9-phosphoryl-choline: 9.8 (8.6/14.5) µmol/L). Predominance of D9-PC comprising linoleic, rather than oleic acid, indicated fatty-acyl remodeling of administered D9-POPC prior to systemic delivery. Conclusion: D9-Choline chloride, D9-GPC and D9-phosphoryl-choline equally increased plasma D9-choline and D9-betaine. D9-POPC shifted metabolism from D9-betaine to D9-PC. Combined supplementation of GPC and (PO) PC may be best suited to optimize choline supply in preterm infants. Due to fatty acid remodeling of (PO) PC during its assimilation, PUFA co-supplementation with (PO) PC may increase PUFA-delivery to critical organs. This study was registered (22.01.2020) at the Deutsches Register Klinischer Studien (DRKS) (German Register for Clinical Studies), DRKS00020502. Study registration: This study was registered at the Deutsches Register Klinischer Studien (DRKS) (German Register for Clinical Studies), DRKS00020502. [ABSTRACT FROM AUTHOR]

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

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

Heparin is a highly sulfated, complex polysaccharide and widely used anticoagulant pharmaceutical. In this work, we chemoenzymatically synthesized perdeuteroheparin from biosynthetically enriched heparosan precursor obtained from microbial culture in deuterated medium. Chemical de-N-acetylation, chemical N-sulfation, enzymatic epimerization, and enzymatic sulfation with recombinant heparin biosynthetic enzymes afforded perdeuteroheparin comparable to pharmaceutical heparin. A series of applications for heavy heparin and its heavy biosynthetic intermediates are demonstrated, including generation of stable isotope labeled disaccharide standards, development of a non-radioactive NMR assay for glucuronosyl-C5-epimerase, and background-free quantification of in vivo half-life following administration to rabbits. We anticipate that this approach can be extended to produce other isotope-enriched glycosaminoglycans.

Advancements in liquid chromatography and mass spectrometry over the last decades have led to a significant development in mass spectrometry‐based proteome quantification approaches. An increasingly attractive strategy is multiplex isotope labeling, which significantly improves the accuracy, precision and throughput of quantitative proteomics in the data‐dependent acquisition mode. Isotope labeling‐based approaches can be classified into MS1‐based and MS2‐based quantification. In this review, we give an overview of approaches based on chemical isotope labeling and discuss their principles, benefits, and limitations with the goal to give insights into fundamental questions and provide a useful reference for choosing a method for quantitative proteomics. As a perspective, we discuss the current possibilities and limitations of multiplex, isotope labeling approaches for the data‐independent acquisition mode, which is increasing in popularity. [ABSTRACT FROM AUTHOR]

A pair of permanently positively charged stable isotope labeling (SIL) agents, 2-(4-(((2,5-dioxopyrrolidin-1-yl)oxy)carbonyl)phenyl)-1,3-dimethyl-benzimidazolium iodides (d0-DPDBM) and its deuterated counterpart d6-DPDBM, were designed and synthesized for the analysis of bisphenols with the aid of ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC–MS/MS). The UHPLC–MS/MS sensitivity of bisphenols was enhanced due to the introduction of positively charged DPDBM moiety into the molecules. Bisphenols were purified by a simple n-hexane extraction and subsequent alkaline back-extraction method, which could remove both hydrophilic and hydrophobic matrices. Matrix effect was effectively minimized by this strategy and the SIL strategy during which samples and standards experienced identical ionization process. The developed method was applied to the simultaneous determination of bisphenols in food and food contact materials with limits of detection (LODs) of 1.5–6.5 ng·L−1, and the limits of quantitation (LOQs) of 4.9 − 21.5 ng·L−1. Correlation coefficients for all analytes were higher than 0.9964. The intra-day precision for all analytes was in the range of 2.7–4.1%, whereas the inter-day precision was in the range of 4.6–6.3%. The recoveries were in the range of 90.2 − 96.4%, and the matrix effects for all analytes ranged from –5.6 to 4.5%. [ABSTRACT FROM AUTHOR]

Although interactions of small molecular drugs with serum proteins have been widely studied from pharmacokinetic and pharmacodynamic perspectives, there have been few reports on the effects of serum components on therapeutic antibody functions. This study reports the effect of abundant serum proteins on antibody-dependent cellular cytotoxicity (ADCC) mediated by rituximab and Fcg receptor III (FcγRIII). Human serum albumin (HSA) and the Fab fragment from the pooled serum polyclonal IgG were found to compromise ADCC as noncompetitive inhibitors. Our nuclear magnetic resonance data provided direct evidence for the interactions of HSA with both the Fab and Fc regions of rituximab and also with the extracellular region of FcγRIII (sFcγRIII). The degree of involvement in the interaction decreased in the order of rituximab-Fab > rituximab-Fc > sFcγRIII, suggesting preferential binding of HSA to net positively charged proteins. Although much less pronounced than the effect of HSA, polyclonal IgG-Fab specifically interacted with rituximab-Fc. The NMR data also showed that the serum protein interactions cover the Fc surface extensively, suggesting that they can act as pan-inhibitors against various Fc receptormediated functions and pharmacokinetics. Our findings highlight the importance of considering serum–protein interactions in the design and application of antibody-based drugs with increased efficacy and safety. [ABSTRACT FROM AUTHOR]

Stable isotope labeling (SIL) is a powerful tool for probing cellular metabolism and has been increasingly employed for metabolite annotation in mass spectrometry-based metabolomics. Herein, we outline the principles and methods of designing and performing SIL-based experiments in metabolomics studies. Further, we summarize different SIL approaches and highlight recent examples of their use for metabolite annotation, including biological feature recognition, degenerate feature annotation, elemental composition determination and metabolite structure elucidation, across diverse biological systems. Throughout, the opportunities, open challenges, and potential pitfalls of each SIL workflow are discussed. Finally, we summarize and compare the recently developed software tools for the analysis of SIL-based metabolomics data. • Various stable isotope labeling (SIL)-based workflows have been developed for metabolite annotation. • SIL aids in biological feature recognition, degenerate feature annotation, elemental composition determination and metabolite structure elucidation. • The design of SIL experiments is crucial to maximize the information extracted for metabolite annotation. [ABSTRACT FROM AUTHOR]

Stable isotope labeled standards of all major human lens crystallins were created to measure the abundance of lens endogenous crystallins from birth to adulthood. All major human crystallins (αA, αB, βA2, βA3/A1, βA4, βB1, βB2, βB3, γA, γB, γC, γD, γS) were cloned with N-terminal 6 x His tagged SUMO for ease of purification and the ability to generate natural N-termini by SUMO protease cleavage when producing crystallins for structure/function studies. They were then expressed in 15N-enriched media, quantified by mass spectrometry, and mixed in proportions found in young human lens to act as an artificial lens standard. The absolute quantification method was tested using soluble protein from 5-day, 23-day, 18-month, and 18-year-old human lenses spiked with the 15N artificial lens standard. Proteins were trypsinized, relative ratios of light and heavy labeled peptides determined using high-resolution precursor and data independent MS2 scans, and data analysis performed using Skyline software. Crystallin abundances were measured in both human donor lenses and in transgenic mouse αA N101D cataract lenses. Technical replicates of human crystallin abundance measurements were performed with average coefficients of variation of approximately 2% across all 13 crystallins. αA crystallin comprised 27% of the soluble protein of 5-day-old lens and decreased to 16% by 18-years of age. Over this time period αB increased from 6% to 9% and the αA/αB ratio decreased from 4.5/1 to 2/1. γS-crystallin also increased nearly 2-fold from 7% to 12%, becoming the 3rd most abundant protein in adult lens, while βB1 increased from 14% to 20%, becoming the most abundant crystallin of adult lens. Minor crystallins βA2, βB3, and γA comprised only about 1% each of the newborn lens soluble protein, and their abundance dropped precipitously by adulthood. While 9 of the SUMO tagged crystallins were useful for purification of crystallins for structural studies, γA, γB, γC, and γD were resistant to cleavage by SUMO protease. The abundance of WT and N101D human αA in transgenic mouse lenses was approximately 40-fold lower than endogenous mouse αA, but the deamidation mimic human αA N101D was less soluble than human WT αA. The high content of αA and the transient abundance of βA2, βB3, and γA in young lens suggest these crystallins play a role in early lens development and growth. βB1 becoming the most abundant crystallin may result from its role in promoting higher order β-crystallin oligomerization in mature lens. The full set of human crystallin expression vectors in the Addgene repository should be a useful resource for future crystallin studies. 15N labeling of these crystallins will be useful to accurately quantify crystallins in lens anatomic regions, as well as measure the composition of insoluble light scattering crystallin aggregates. The standards will also be useful to measure the abundance of crystallins expressed in transgenic animal models. [Display omitted] • Expression and purification of all major crystallins in human lens. • Labeling with 15N to use as standards to measure crystallin abundance. • Changes in human crystallin abundance measured from newborn to adult lens. • Human αA-crystallin abundance measurements in wild type and N101D transgenic mice. [ABSTRACT FROM AUTHOR]

[Display omitted] • A click chemistry-based stable isotope labeling technique was developed to determine steroid hormones in food samples. • A novel pair of chemoselective probe ABI and d 5 -ABI was designed and synthesized. • The ethynyl group at the C-17 position of synthetic steroid hormones was labeled via the CuAAC reaction. • The ionization efficiencies of steroid hormones were increased by 17–4532 folds after labeling. • The matrix effects can be effectively improved by using d 5 -ABI labeled steroid hormone standards as internal standards. Steroid hormone residues in food are a significant sources of endocrine disrupting chemicals (EDCs) that can adversely affect public health. However, the current analytical methods for determining steroid hormones using liquid chromatography-tandem mass spectrometry (LC-MS/MS) can be challenging due to the poor ionization efficiency of steroid hormones and the matrix effect of complex food samples. Herein, based on Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction and stable isotope labeling (SIL) technique, a novel pair of chemoselective probes ABI / d 5 -ABI was precisely designed and synthesized. This pair of probes comprises a H/D isotope tag, a linker, a reactive site azido group (N 3) and a MS tag (imidazolium salt). The probe ABI was employed to label ethynyl-containing steroid hormones in real samples and d 5 -ABI was applied to label standards, respectively, followed by mixing the two labeled samples for high performance (HP)LC-MS/MS analysis. It was found that the ionization efficiencies of target analytes were increased by 17–4532 folds after ABI labeling. More importantly, the heavy labeled samples serving as internal standards (ISs) can effectively compensate matrix effect during HPLC-MS/MS analysis. Finally, the proposed SIL-HPLC-MS/MS method was successfully used to highly sensitive determine four synthetic steroid hormones in food samples (milk, pork and egg). Furthermore, the good detection limits (0.015–0.020 ng/mL), satisfactory recoveries (75.7–122.9 %), and precisions (RSDs less than 9.2 %) were obtained. Hence, the established method not only provides new insights in designing SIL probes for determination of ethynyl-containing analytes within complex matrix, but also extends the application of CuAAC reaction in the field of food chemistry. [ABSTRACT FROM AUTHOR]

Sugar consumption increases the fecundity and longevity in many species of parasitic wasps (parasitoids) but whether these insects use sugars to synthesize significant amounts of fatty acids and storage fat de novo (lipogenesis) is discussed controversially. It has long been assumed that parasitic wasps lost this ability during evolution, mainly because in several species wasps with ad libitum access to sugar did not increase teneral lipid levels. Recent studies demonstrated that many species are nonetheless capable of synthesizing fatty acids de novo from glucose. It is unclear, however, whether also other sugars are used for fatty acid biosynthesis and whether an increase of sugar concentration to levels occurring in natural sugar sources translates into higher fatty acid production. Furthermore, it has been suggested that fatty acid production in parasitoids is negligible compared to species increasing teneral fat reserves such as Drosophila melanogaster. Here we show by stable isotope labeling experiments that females of Nasonia vitripennis convert D-glucose, D-fructose, sucrose, and α,α-trehalose, major sugars consumed by adult parasitoids in nature, equally well to palmitic, stearic, oleic, and linoleic acid. Lipogenesis from D-galactose occurs as well albeit to a lesser extent. Sugar concentration is crucial for lipogenic activity, and almost 80% of de novo synthesized fatty acids were incorporated into storage fat (triacylglycerides). Comparison of fatty acid biosynthesis within a 48-h feeding period with D. melanogaster revealed that N. vitripennis produced approximately half as many fatty acids per body mass unit. Both species fed equal amounts of the glucose offered. We conclude that lipogenesis is far from negligible in N. vitripennis and plays an important role for the energy balance when teneral lipid reserves deplete. [Display omitted] • It has long been assumed that parasitic wasps are unable to synthesize fatty acids de novo. • Nasonia vitripennis uses glucose, fructose, galactose, sucrose, and trehalose for fatty acid biosynthesis. • Galactose is less suitable for fatty acid biosynthesis by N. vitripennis. • almost 80% of the fatty acids were used to synthesize triacylglycerides. • N. vitripennis synthesized within 48 h ca. 50% of the fatty acids produced by Drosophila melanogaster. [ABSTRACT FROM AUTHOR]

It is well understood that fatty acids can be synthesized, imported, and modified to meet requisite demands in cells. However, following the movement of fatty acids through the multiplicity of these metabolic steps has remained difficult. To better address this problem, we developed Fatty Acid Source Analysis (FASA), a model that defines the contribution of synthesis, import, and elongation pathways to fatty acid homeostasis in saturated, monounsaturated, and polyunsaturated fatty acid pools. Application of FASA demonstrated that elongation can be a major contributor to cellular fatty acid content and showed that distinct pro-inflammatory stimuli (e.g., Toll-like receptors 2, 3, or 4) specifically reprogram homeostasis of fatty acids by differential utilization of synthetic and elongation pathways in macrophages. In sum, this modeling approach significantly advances our ability to interrogate cellular fatty acid metabolism and provides insight into how cells dynamically reshape their lipidomes in response to metabolic or inflammatory signals.

Background: Living cells maintain and adjust structural and functional integrity by continual synthesis and degradation of metabolites and macromolecules. The maintenance and adjustment of thylakoid membrane involve turnover of photosynthetic pigments along with subunits of protein complexes. Quantifying their turnover is essential to understand the mechanisms of homeostasis and long-term acclimation of photosynthetic apparatus. Here we report methods combining whole-plant long-term 13CO2 labeling and liquid chromatography - mass spectrometry (LC–MS) analysis to determine the size of non-labeled population (NLP) of carotenoids and chlorophylls (Chl) in leaf pigment extracts of partially 13C-labeled plants. Results: The labeling chamber enabled parallel 13CO2 labeling of up to 15 plants of Arabidopsis thaliana with real-time environmental monitoring ([CO2], light intensity, temperature, relative air humidity and pressure) and recording. No significant difference in growth or photosynthetic pigment composition was found in leaves after 7-d exposure to normal CO2 (~ 400 ppm) or 13CO2 in the labeling chamber, or in ambient air outside the labeling chamber (control). Following chromatographic separation of the pigments and mass peak assignment by high-resolution Fourier-transform ion cyclotron resonance MS, mass spectra of photosynthetic pigments were analyzed by triple quadrupole MS to calculate NLP. The size of NLP remaining after the 7-d 13CO2 labeling was ~ 10.3% and ~ 11.5% for all-trans- and 9-cis-β-carotene, ~ 21.9% for lutein, ~ 18.8% for Chl a and 33.6% for Chl b, highlighting non-uniform turnover of these pigments in thylakoids. Comparable results were obtained in all replicate plants of the 13CO2 labeling experiment except for three that were showing anthocyanin accumulation and growth impairment due to insufficient water supply (leading to stomatal closure and less 13C incorporation). Conclusions: Our methods allow 13CO2 labeling and estimation of NLP for photosynthetic pigments with high reproducibility despite potential variations in [13CO2] between the experiments. The results indicate distinct turnover rates of carotenoids and Chls in thylakoid membrane, which can be investigated in the future by time course experiments. Since 13C enrichment can be measured in a range of compounds, long-term 13CO2 labeling chamber, in combination with appropriate MS methods, facilitates turnover analysis of various metabolites and macromolecules in plants on a time scale of hours to days. [ABSTRACT FROM AUTHOR]

Microalgae are active producers of various compounds, including toxic substances. However, their metabolism is very diverse and insufficiently known. We demonstrate an approach that includes growing a new strain of cyanobacterium Leptolyngbya sp. (IPPAS B-1204) on an isotopically labeled medium (D 2 O) and evaluating the metabolomic composition of these microorganisms after deuterium uptake. Despite the low resolution of the GC-MS method, the interpretation of the obtained spectra allowed us to find out not only the amount of the embedded isotope label but also to assume the position in the structure where the label is embedded. We present the results of reliably detecting more than 30 compounds with isotope labels belonging to various classes of biological compounds produced by this cyanobacterium, revealing the metabolic pathways of entry of this label. We also demonstrate that the synthesis of unsaturated fatty acids is suppressed under the growth on D 2 O medium. In addition, we found an isotopic effect in the chromatographic separation of isotopically labeled compounds in gas chromatography. These data can be used in the future both for the identification of compounds and the analysis of the biosynthesis pathways of secondary biologically active compounds and in the analysis of the production of isotopically labeled standards of compounds., Competing Interests: Conflicts of interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.)

Advanced liquid chromatogram-mass spectrometry (LC-MS) and automated large-scale data processing have made MS-based quantitative analysis increasingly useful for research in fields such as biology, medicine, food safety, and beyond. This is because MS-based quantitative analysis can accurately and sensitively analyze thousands of proteins and peptides in a single experiment. However, the precision, coverage, complexity, and resilience of conventional quantification methods vary as a result of the modifications to the analytic environment and the physicochemical characteristics of analytes. Therefore, specially designed approaches are necessary for sample preparation. Dozens of methods have been developed and adapted for these needs based on stable isotopic labeling or isobaric tagging, each with distinct characteristics. In this review, we will summarize the leading strategies and techniques used thus far for MS-based protein quantification as well as analyze the advantages and shortcomings of different approaches. Additionally, we provide an overview of protein metrology development.

Targeted protein degradation (TPD) has emerged as a powerful strategy to selectively eliminate cellular proteins using small-molecule degraders, offering therapeutic promise for targeting proteins that are otherwise undruggable. However, a remaining challenge is to unambiguously identify primary TPD targets that are distinct from secondary downstream effects in the proteome. Here we introduce an approach for selective analysis of protein degradation by mass spectrometry (DegMS) at proteomic scale, which derives its specificity from the exclusion of confounding effects of altered transcription and translation induced by target depletion. We show that the approach efficiently operates at the timescale of TPD (hours) and we demonstrate its utility by analyzing the cyclin K degraders dCeMM2 and dCeMM4, which induce widespread transcriptional downregulation, and the GSPT1 degrader CC-885, an inhibitor of protein translation. Additionally, we apply DegMS to characterize a previously uncharacterized degrader, and identify the zinc-finger protein FIZ1 as a degraded target., Competing Interests: Declaration of interests G.E.W. is scientific founder and shareholder of Proxygen and Solgate. The Winter lab received funding from Pfizer., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

A reliable method for metabolite extraction is central to mass spectrometry-based metabolomics. However, existing methods are lengthy, mostly due to the step of scraping cells from cell culture vessels, which restricts metabolomics in broader application such as lower cell numbers and high-throughput studies. Here, we present a simplified metabolite extraction (SiMeEx) method, to efficiently and quickly extract metabolites from adherent mammalian cells. Our method excludes the cell scraping step and therefore allows for a more efficient extraction of polar metabolites in less than 30 min per 12-well plate. We demonstrate that SiMeEx achieves the same metabolite recovery as using a standard method containing a scraping step, in various immortalized and primary cells. Omitting cell scraping does not compromise the performance of non-targeted and targeted GC-MS analysis, but enables metabolome analysis of cell culture on smaller well sizes down to 96-well plates. Therefore, SiMeEx demonstrates advantages not only on time and resources, but also on the applicability in high-throughput studies.

In this work a rapid RNA assignment approach by combining chemical and enzymatic 13C and 15N stable isotope labeling is introduced. We exemplify the assignment strategy for imino N1H1 purine and N3H3 pyrimidine and aromatic C6H6 pyrimidine, C8H8 purine and C2H2 adenine resonances for a non-coding RNA comprising 66 nucleotides. The assignment strategy is based on position specific labeling by chemical solid phase synthesis and dilute stable isotope 13C/15N-labeling by mixing labeled and commercially available unlabeled RNA phosphoramidites. The assignment process is further facilitated by nucleotide specific labeling using T7 RNA polymerase in vitro transcription with in house produced atom specific 13C labeled ribonucleotide triphosphates. The approach is fast with a total NMR measurement time of only 22 h and also competitive in terms of costs as compared to the standard methodology relying on in vitro transcription using 2H, 15N and 13C/15N uniformly labeled ribonucleotide triphosphates. Furthermore, the assignment procedure revealed a slow exchange process on the NMR chemical shift time scale in the 66 nt non-coding RNA with possible biological implications in the regulation of bacterial competence.

Dissolved organic nitrogen (DON) is actively involved in N cycling and transformation processes in the ocean, yet how this large N pool is formed remains elusive. Here we incubated 15N‐labeled individual amino acids (Ala, Val, and Phe) in seawater and monitored their fates over 21 days. About 25%–45% of Phe‐N and Val‐N were transformed to "uncharacterizable DON," as compared to only about 6% for Ala‐N, indicating the formation of refractory DON is related to specific amino acids. Through a stable isotope probing approach, 5 Phe‐derived DON molecules from the incubations were found to be present in natural waters, and their possible structures were proposed. These results shed new lights on the formation mechanisms of refractory DON, including the roles of specific amino acids and particular chemical structures that may resist decomposition in millennial time scales. Plain Language Summary: The formation of refractory dissolved organic nitrogen through microbial degradation was investigated through a series of lab incubations using amino acids as substrates. We found that a higher fraction of nitrogen (25%–45%) from phenylalanine and valine was transformed into refractory dissolved organic nitrogen, as compared to alanine (6%). Such contrasting results suggest that the formation of refractory dissolved organic nitrogen may be tightly connected with specific amino acids. We also constructed a database with possible structures of the amino acids‐derived dissolved organic nitrogen molecules based on stable isotope and high‐resolution mass spectrometry techniques. With the database, we further confirmed that at least five of amino acids‐derived dissolved organic nitrogen molecules were present in natural waters (including the deep ocean). Overall, our study offered new insights into the formation mechanisms of refractory dissolved organic nitrogen, demonstrating the roles of specific amino acids and particular chemical structures in the long‐term stability of dissolved organic nitrogen in the ocean. Key Points: More nitrogen from phenylalanine or valine formed uncharacterizable dissolved organic nitrogen (DON) via microbial processing than that from alanineStable isotope probing coupled with advanced mass spectrometry was applied to build a database of amino acid‐derived DON moleculesSome DON molecules derived from phenylalanine are also present in natural waters [ABSTRACT FROM AUTHOR]

Post-translational modification of proteins is complex and diverse, with the phosphorylation regulated by kinases and phosphatases being one of the most widespread and important modifications. Dynamic change of quantitative analysis of phosphorylated proteins is helpful to clarify the mechanism of phosphorylation regulating life activities and understand its role in achieving biological functions. Mass spectrometry is the most commonly used strategy for the quantitative analysis of post-translational modification, involving label-free quantification, internal standard absolute quantification, and chemical labeling, etc. In this paper, a chemical labeling approach which has been used for protein glycosylation profiling was applied to the relative quantitative analysis of phosphopeptides. Using the method, carboxyl groups were located on the side chain of aspartic acid and glutamic acid residues, and the C-terminus of peptide were allowed to react with dimethylamine (d0-DMA)/deuterated dimethylamine (d6-DMA). As a result, the carboxyl groups were neutralized, and all enzymatic peptides were labeled with light/heavy tags. After the samples with different tags were mixed, the phosphopeptides were enriched using TiO2 magnetic particles and then analyzed qualitatively and relatively quantitatively by liquid chromatography-mass spectrometry (LC-MS). Amidation could shield the negatively charged carboxyl groups of non-phosphorylated and phosphorylated peptides, so that the peptides with phosphate groups mainly exhibited negative charge property, thus improving the enrichment specificity of TiO2 for phosphopeptides as well as its detection sensitivity in LC-MS analysis. Using 0.2 mg casein as a standard, 8 phosphopeptides were detected in the derivatized samples. A high abundance of b and y ions indicated that the amidation by dimethylamine was highly specific and usually occurs only at the carboxyl group without a significant effect on the phosphate group of peptides. A series of molar ratios (5∶1, 2∶1, 1∶1, 1∶2, 1∶5) of samples were derivatized using d0-DMA and d6-DMA, respectively. The results showed that the error was less than 20% for each ratio, indicating that the method possessed good relative quantitative range and accuracy. However, too many derivative sites in the peptides could result in incomplete derivatization, and the C-terminal lysine residues might self-condense to form lactam during the derivatization process. By selecting some individualized proteases during protein digestion, such as GluC, the number of derivative sites might be in an appropriate range and lysine residue could be avoided at the terminal of peptides, which should be useful for improving identification efficiency and quantitative accuracy of phosphopeptides. In summary, the chemical labeling method based on dimethylamine derivatization presents advantages for high-throughput relative quantitative analysis of phosphopeptides and it is expected to be a powerful tool for protein phosphorylation profiling in biological tissues. [ABSTRACT FROM AUTHOR]

Stable isotope labeling has become an important methodology for determining lipid metabolic parameters of normal and neoplastic cells. Conventional methods for fatty acid and cholesterol analysis have one or more issues that limit their utility for in vitro stable isotope-labeling studies. To address this, we developed a method optimized for measuring both fatty acids and cholesterol from small numbers of stable isotope-labeled cultured cells. We demonstrate quantitative derivatization and extraction of fatty acids from a wide range of lipid classes using this approach. Importantly, cholesterol is also recovered, albeit at a modestly lower yield, affording the opportunity to quantitate both cholesterol and fatty acids from the same sample. Although we find that background contamination can interfere with quantitation of certain fatty acids in low amounts of starting material, our data indicate that this optimized method can be used to accurately measure mass isotopomer distributions for cholesterol and many fatty acids isolated from small numbers of cultured cells. Application of this method will facilitate acquisition of lipid parameters required for quantifying flux and provide a better understanding of how lipid metabolism influences cellular function.

Abstract Dissolved organic nitrogen (DON) is actively involved in N cycling and transformation processes in the ocean, yet how this large N pool is formed remains elusive. Here we incubated 15N‐labeled individual amino acids (Ala, Val, and Phe) in seawater and monitored their fates over 21 days. About 25%–45% of Phe‐N and Val‐N were transformed to “uncharacterizable DON,” as compared to only about 6% for Ala‐N, indicating the formation of refractory DON is related to specific amino acids. Through a stable isotope probing approach, 5 Phe‐derived DON molecules from the incubations were found to be present in natural waters, and their possible structures were proposed. These results shed new lights on the formation mechanisms of refractory DON, including the roles of specific amino acids and particular chemical structures that may resist decomposition in millennial time scales.

Abstract Background The plant hormone auxin plays a central role in regulation of plant growth and response to environmental stimuli. Multiple pathways have been proposed for biosynthesis of indole-3-acetic acid (IAA), the primary auxin in a number of plant species. However, utilization of these different pathways under various environmental conditions and developmental time points remains largely unknown. Results Monitoring incorporation of stable isotopes from labeled precursors into proposed intermediates provides a method to trace pathway utilization and characterize new biosynthetic routes to auxin. These techniques can be aided by addition of chemical inhibitors to target specific steps or entire pathways of auxin synthesis. Conclusions Here we describe techniques for pathway analysis in Arabidopsis thaliana seedlings using multiple stable isotope-labeled precursors and chemical inhibitors coupled with highly sensitive liquid chromatography-mass spectrometry (LC–MS) methods. These methods should prove to be useful to researchers studying routes of IAA biosynthesis in vivo in a variety of plant tissues.

We report the use of a novel technology based on optical photothermal infrared (O-PTIR) spectroscopy for obtaining simultaneous infrared and Raman spectra from the same location of the sample allowing us to study bacterial metabolism by monitoring the incorporation of 13C- and 15N-labeled compounds. Infrared data obtained from bulk populations and single cells via O-PTIR spectroscopy were compared to conventional Fourier transform infrared (FTIR) spectroscopy in order to evaluate the reproducibility of the results achieved by all three approaches. Raman spectra acquired were concomitant with infrared data from bulk populations as well as infrared spectra collected from single cells, and were subjected to principal component analysis in order to evaluate any specific separation resulting from the isotopic incorporation. Similar clustering patterns were observed in infrared data acquired from single cells via O-PTIR spectroscopy as well as from bulk populations via FTIR and O-PTIR spectroscopies, indicating full incorporation of heavy isotopes by the bacteria. Satisfactory discrimination between unlabeled (viz. 12C14N), 13C14N- and 13C15N-labeled bacteria was also obtained using Raman spectra from bulk populations. In this report, we also discuss the limitations of O-PTIR technology to acquire Raman data from single bacterial cells (with typical dimensions of 1 × 2 µm) as well as spectral artifacts induced by thermal damage when analyzing very small amounts of biomass (a bacterium tipically weighs ~ 1 pg). [ABSTRACT FROM AUTHOR]

Ciguatoxins (CTXs) and gambierones are ladder-shaped polyethers associated with ciguatera poisoning and Gambierdiscus spp. Several of these compounds contain carbonyl or hemiketal groups, which have the potential to exchange with 18O-labeled water under acidic conditions. The effects of solvent composition and acid on the rate of exchange and on the stability of the labels at various pH values were assessed to optimize the incorporation of 18O into Caribbean ciguatoxin-1 and -2 (C-CTX1/2), gambierone, and 44-methylgambierone. LC−HRMS results showed that 18O-labeling occurred at the hydroxy group of the hemiketal at C-56 in C-CTX1/2, and at the hydroxy group of the hemiketal at C-4 and the ketone at C-40 in gambierones. Labeling occurred very rapidly (complete in <30 min) for C-CTX1/2, and more slowly (complete in ca. 16 h) for both gambierones. Labeled C-CTX1/2 was reduced with sodium borohydride to produce 18O-labeled C-CTX3/4. The incorporated 18O labels in the gambierones and C-CTXs were retained in aqueous solvent mixtures under neutral conditions in a short-term stability study, demonstrating that these 18O-labeled toxins have the potential to be used in isotope dilution and metabolism studies. [Display omitted] • Methodologies developed for 18O exchange with H 2 18O to produce labeled C-CTX1/2 and gambierones. • Borohydride reduction of [18O]C-CTX1/2 produced stable [18O]C-CTX3/4. • pH stability suggested 18O-labeled CTXs and gambierones maintained under neutral conditions. [ABSTRACT FROM AUTHOR]