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Sphingoid bases (SBs) are one of important components of cell membranes, playing important roles in cellular biology. Meanwhile, SBs are associated with various metabolic diseases such as Type 2 Diabetes mellitus (T2DM). Therefore, simultaneous quantitation of multiple SBs in biological samples could provide crucial information for uncovering underlying mechanisms of SBs related functions and diseases. However, existing methods are difficult to achieve simultaneous quantitation for multiple SBs due to the lack of isotope internal standards (ISs) of corresponding SBs. In the current study, we developed a highly sensitive method for the simultaneous detection of 26 SBs in biological samples by stable isotope labeling coupled with ultra-high performance liquid chromatography tandem mass spectrometry (SIL-UHPLC-MS/MS) analysis. In this respect, a pair of isotope labeling reagents, 3-(N, N -dimethylamino)propyl isothiocyanate (DMPI) and d 4 -3-(N, N -dimethylamino)propyl isothiocyanate (d 4 -DMPI), were synthesized and utilized to label SBs in biological samples and SB standards, respectively. The d 4 -DMPI labeled SB standards were used as ISs to calibrate quantitation deviation in MS analysis from the biological matrix. Using the developed method, we successfully quantitated 19 SBs in cells, 20 SBs in mice feces and 18 SBs in human serum samples. Three C17-SBs used as ISs in many reported works were even found in all prepared samples. In summary, the developed SIL-UHPLC-MS/MS analysis was demonstrated to be a promising method for the simultaneous determination of multiple SBs, which could facilitate the investigation of cellular function of SBs and pathogenesis of related diseases. Image 1 • DMPI and d 4 -DMPI were synthesized to label SBs. • d 4 -DMPI labeled SBs were used as ISs for simultaneous quantitation of SBs. • The developed method was applied in the quantitation of SBs from cells, mice feces and human serum samples. [ABSTRACT FROM AUTHOR]

Short-chain fatty acids (SCFAs) are one class of bacterial metabolites mainly formed by gut microbiota from undigested fibers and proteins. These molecules are able to mediate signal conduction processes of cells, acting as G protein-coupled receptors (GPR) activators and histone deacetylases (HDAC) inhibitors. It was reported that SCFAs were closely associated with various human diseases. However, it is still challenging to analyze SCFAs because of their diverse structures and broad range of concentrations. In this study, we developed a highly sensitive method for simultaneous detection of 34 SCFAs by stable isotope labeling coupled with ultra-high performance liquid chromatography-electrospray ionization-mass spectrometry (UHPLC-ESI-MS/MS) analysis. In this respect, a pair of isotope labeling reagents, N -(4-(aminomethyl)benzyl)aniline (4-AMBA) and N -(4-(aminomethyl)benzyl)aniline- d 5 (4-AMBA- d 5), were synthesized to label SCFAs from the feces of mice and SCFA standards, respectively. The 4-AMBA- d 5 labeled SCFAs were used as internal standards to compensate the ionization variances resulting from matrix effect and thus minimize quantitation deviation in MS detection. After 4-AMBA labeling, the retention of SCFAs on the reversed-phase column increased and the separation resolution of isomers were improved. In addition, the MS responses of most SCFAs were enhanced by up to three orders of magnitude compared to unlabeled SCFAs. The limits of detection (LODs) of SCFAs were as low as 0.005 ng/mL. Moreover, good linearity for 34 SCFAs was obtained with the coefficient of determination (R2) ranging from 0.9846 to 0.9999 and the intra- and inter-day relative standard deviations (RSDs) were <17.8% and 15.4%, respectively, indicating the acceptable reproducibility of the developed method. Using the developed method, we successfully quantified 21 SCFAs from the feces of mice. Partial least squares discriminant analysis (PLS-DA) and t -test analysis showed that the contents of 9 SCFAs were significantly different between Alzheimer's disease (AD) and wide type (WT) mice fecal samples. Compared to WT mice, the contents of propionic acid, isobutyric acid, 3-hydroxybutyric acid, and 3-hydroxyisocaleric acid were decreased in AD mice, while lactic acid, 2-hydroxybutyric acid, 2-hydroxyisobutyric acid, levulinic acid, and valpronic acid were increased in AD mice. These significantly changed SCFAs in the feces of AD mice may afford to a better understanding of the pathogenesis of AD. Taken together, the developed UHPLC-ESI-MS/MS method could be applied for the sensitive and comprehensive determination of SCFAs from complex biological samples. Image 1 • 4-AMBA and AMBA- d 5 were synthesized to label SCFAs. • The detection sensitivities of most SCFAs were enhanced by up to three orders of magnitude after 4-AMBA labeling. • The developed method was applied in the analysis of SCFAs from the feces of mice. [ABSTRACT FROM AUTHOR]

Perfluorocarboxylic acids (PFCAs) in cod liver oil was analyzed for the first time using newly designed and synthesized quaternary ammonium–functionalized magnetic nanoparticles (Fe3O4@SiO2@QTA). Fe3O4@SiO2@QTA was characterized by TEM, IR, and magnetic hysteresis curve. It can interact with perfluorocarboxylic acids through electrostatic interactions, hydrogen bonding, and hydrophobic effect. Stable isotope labeling (SIL)–assisted liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to evaluate the adsorption efficiency. The obtained recoveries for all compounds were in the range of 85.0–98.5%, with relative standard deviations of less than 8.1%. The sorbent amount was 20 mg. Desorption conditions were as follows: sample pH 5–7.0; desorption time, 5 min; and elution volume, 1.0 mL. The limits of detection were in the range of 1.5–20 ng/L, while the limits of quantitation were in the range of 5.0–70 ng/L. The proposed method was successfully applied to the selective adsorption of PFCAs from cod liver oil with no matrix effect observed because of the double assurance of selective adsorption and high accurate SIL strategy. [ABSTRACT FROM AUTHOR]

RNAs are key players in life as they connect the genetic code (DNA) with all cellular processes dominated by proteins. They contain a variety of chemical modifications and many RNAs fold into complex structures. Here, we review recent progress in the analysis of RNA modification and structure on the basis of stable isotope labeling techniques. Mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy are the key tools and many breakthrough developments were made possible by the analysis of stable isotope labeled RNA. Therefore, we discuss current stable isotope labeling techniques such as metabolic labeling, enzymatic labeling and chemical synthesis. RNA structure analysis by NMR is challenging due to two major problems that become even more salient when the size of the RNA increases, namely chemical shift overlaps and line broadening leading to complete signal loss. Several isotope labeling strategies have been developed to provide solutions to these major issues, such as deuteration, segmental isotope labeling or site-specific labeling. Quantification of modified nucleosides in RNA by MS is only possible through the application of stable isotope labeled internal standards. With nucleic acid isotope labeling coupled mass spectrometry (NAIL-MS), it is now possible to analyze the dynamic processes of post-transcriptional RNA modification and demodification. The trend, in both NMR and MS RNA analytics, is without doubt shifting from the analysis of snapshot moments towards the development and application of tools capable of analyzing the dynamics of RNA structure and modification profiles. [ABSTRACT FROM AUTHOR]

We report the recombinant preparation from Escherichia coli cells of samples of two closely related, small, secreted cysteine‐rich plant peptides: rapid alkalinization factor 1 (RALF1) and rapid alkalinization factor 8 (RALF8). Purified samples of the native sequence of RALF8 exhibited well‐resolved nuclear magnetic resonance (NMR) spectra and also biological activity through interaction with a plant receptor kinase, cytoplasmic calcium mobilization, and in vivo root growth suppression. By contrast, RALF1 could only be isolated from inclusion bodies as a construct containing an N‐terminal His‐tag; its poorly resolved NMR spectrum was indicative of aggregation. We prepared samples of the RALF8 peptide labeled with 15N and 13C for NMR analysis and obtained near complete 1H, 13C, and 15N NMR assignments; determined the disulfide pairing of its four cysteine residues; and examined its solution structure. RALF8 is mostly disordered except for the two loops spanned by each of its two disulfide bridges. PDB Code(s): 6NU4; [ABSTRACT FROM AUTHOR]

Sepsis induces heparanase-mediated degradation of the endothelial glycocalyx, a heparan sulfate-enriched endovascular layer critical to vascular homeostasis, releasing highly sulfated domains of heparan sulfate into the circulation. These domains are oligosaccharides rich in heparin-like trisulfated disaccharide repeating units. Using a chemoenzymatic approach, an undecasaccharide containing a uniformly 13C-labeled internal 2-sulfoiduronic acid residue was synthesized on a p-nitrophenylglucuronide acceptor. Selective periodate cleavage afforded a heparin nonasaccharide having a natural structure. This 13C-labeled nonasaccharide was intravenously administered to septic (induced by cecal ligation and puncture, a model of polymicrobial peritonitis-induced sepsis) and nonseptic (sham) mice. Selected tissues and biological fluids from the mice were harvested at various time points over 4 hours, and the 13C-labeled nonasaccharide was recovered and digested with heparin lyases. The resulting 13C-labeled trisulfated disaccharide was quantified, without interference from endogenous mouse heparan sulfate/heparin, using liquid chromatography-mass spectrometry with sensitive and selective multiple reaction monitoring. The 13C-labeled heparin non-asaccharide appeared immediately in the blood and was rapidly cleared through the urine. Plasma nonasaccharide clearance was only slightly prolonged in septic mice (t1/2 ~ 90 minutes). In septic mice, the nonasaccharide penetrated into the hippocampus but not the cortex of the brain; no hippocampal or cortical brain penetration occurred in sham mice. The results of this study suggest that circulating heparan sulfates are rapidly cleared from the plasma during sepsis and selectively penetrate the hippocampus, where they may have functional consequences. [ABSTRACT FROM AUTHOR]

In order to study the effects of straw C on the contents of dissolved organic carbon（DOC）, microbial biomass carbon（MBC）and particulate organic carbon（POC）in low-fertility soil at different nitrogen application rates, 13C-labeled wheat straw was mixed with low fertility soils in the carborundum tube at different nitrogen application rates（0, 120, 240 kg·hm-2, pure nitrogen content）. Soils were sampled periodically to analyze carbon component contents and its relative δ13C value. Straw C transformation rate and contribution to soil C pool was also calculated. The results showed that straw C was transformed rapidly within the first 7 days, thereafter the decomposition rate slowed down and was dependent on transformation to POC. Compared with DOC, straw C preferred transforming into MBC and POC, with the transformation rate of 0.12%~0.38%, 4.01%~6.25% and 4.74%~9.54% on 60 d after straw addition, respectively. Soil DOC, MBC, and POC contents were increased significantly by straw addition, with 0.29%~15.01%, 13.20%~32.85% and 33.62%~59.69% of respective carbon derived from straw, respectively. Compared with 0, 240 kg·hm-2 application rates, 120 kg hm-2 could increase the active and slow organic C pool of the experimental soil simultaneously. All results suggest that straw return with moderate nitrogen application is more conducive to both soil fertility improvement and C sequestration of low fertility soil. [ABSTRACT FROM AUTHOR]

Abstract Profiling of carboxyl-containing metabolites in smokers and non-smokers provides insight into the smoking-related biological events and causal relationships between exposure and adverse events. However, more comprehensive analysis of carboxyl-containing metabolites in bio-matrices with high sensitivity and accuracy is challenging. In this work, stable isotope labeling in combination with liquid chromatography-tandem mass spectrometry was used for untargeted profiling and relative quantification of carboxyl-containing metabolites in plasma of smokers and non-smokers. A pair of isotope labeling reagents, N , N -dimethylethylenediamine (DMED) and d 4 -DMED was used to label carboxyl-containing metabolites. Since the isotope labeled dimethylamino moieties of DMED and d 4 -DMED are easily fragmented and lost as characteristic neutral fragments of 45 and 49 Da, respectively, double neutral loss scans can be used to profiling of carboxyl-containing metabolites. Subsequently, based on the ion pair parameters obtained from double neutral loss scans, relative quantification method was developed. As a result, 269 carboxyl-containing metabolite candidates were discovered, and 88 metabolite candidates were found to have significant alterations between smokers and non-smokers. 7Z, 10Z-hexadecadienoic acid, myristic acid and 3β-hydroxy-5-cholestenoic acid with significant differences confirmed by standard comparison are linked to smoking related inflammation, abnormal bile acid synthesis and cholesterol metabolism. Highlights • Stable isotope labeling combined with double neutral loss scans was developed for untargeted profiling of carboxyl-containing metabolites.Stable isotope labeling combined with neutral loss scan was developed for profiling of carboxyl-containing metabolites. • 269 carboxyl-containing metabolite candidates were discovered in the human plasma. • 88 carboxyl-containing metabolite candidates with significantly difference between smokers and non-smokers were found. [ABSTRACT FROM AUTHOR]

Objective: The aim of this study was to investigate the proteome of the gingival crevicular fluid comparing the relative abundance of proteins from type 2 diabetes mellitus (2DM) individuals and chronic periodontitis (CP) affected sites, subjects affected by both conditions and healthy individuals. Material and Methods: Twenty individuals were equally allocated in four groups, 2DM with CP, 2DM periodontally healthy, CP without 2DM, and periodontally healthy without 2DM. The relative quantification of proteins was accessed with iTRAQ labeling and mass spectrometry. Results and Conclusion: A total of 104 proteins showed significant differences in abundance in pairwise comparisons. Some presented different levels in all diseased groups as compared to control, either increasing (rap guanine nucleotide exchange factor, S100A8, S100A9, and immunoglobulins) or decreasing (actins, myristoylated alanine‐rich C‐kinase substrate, and glutathione S‐transferase). Other differences were specific for a given condition: Titin, neutrophil elastase, and myeloperoxidase levels were higher in the DP group, cathelicidin antimicrobial peptide decreased in CP, and annexin decreased in DH. These differences in the proteome can provide clues for further studies that will validate the variation in their levels and their role in both diseases. [ABSTRACT FROM AUTHOR]

Abstract Increasing nitrogen (N) availability in Arctic soils could stimulate the growth of both plants and microorganisms by relieving the constraints of nutrient limitation. It was hypothesized that organic N addition to anoxic tundra soil would increase CH 4 production by stimulating the fermentation of labile substrates, which is considered the rate-limiting step in anaerobic C mineralization. We tested this hypothesis through both field and lab-based experiments. In the field experiment, we injected a solution of 13C- and 15N-labeled glutamate 35 cm belowground at a site near Nome on the Seward Peninsula, Alaska, and observed the resulting changes in porewater geochemistry and dissolved greenhouse gas concentrations. The concentration of free glutamate declined rapidly within hours of injection, and the 15N label was recovered almost exclusively as dissolved organic N within 62 h. These results indicate rapid microbial assimilation of the added N and transformation into novel organic compounds. We observed increasing concentrations of dissolved CH 4 and Fe(II), indicating rapid stimulation of methanogenesis and Fe(III) reduction. Low molecular weight organic acids such as acetate and propionate accumulated despite increasing consumption through anaerobic C mineralization. A laboratory soil column flow experiment using active layer soil collected from the same site further supported these findings. Glutamate recovery was low compared to a conservative bromide tracer, but concentrations of NO 3 − and NH 4 + remained low, consistent with microbial uptake of the added N. Similar to the field experiment, we observed both increasing Fe(II) and organic acid concentrations. Together, these results support our hypothesis of increased fermentation in response to organic N addition and suggest that increasing N availability could accelerate CH 4 production in tundra soils. Graphical abstract Image 1 Highlights • Field and lab experiments measured the effect of N addition on CH 4 production. • N addition increased fermentation in all experiments. • Increasing Fe(II), DIC, and CH 4 indicated increasing anaerobic C mineralization. • Non-aromatic DOC was selectively degraded following N addition. • Increasing N availability could increase tundra CH 4 emissions. [ABSTRACT FROM AUTHOR]

Abstract Synthetic isotope labeled phosphopeptides are valuable tools for the quantification and validation of phosphoproteome data. Here, we report that the same set of phosphopeptides, which are used as spike-in standards, can be successfully applied for identification of stimulus specific protein-protein interactions mediated by the respective phosphorylation sites. As a proof-of-concept, binding of two γ H2AX (pS139) phosphosite specific interaction partners, MDC1 and 53BP1, was confirmed and elevated binding affinity was revealed in response to ionizing radiation. Our strategy is generally applicable and enables multiplexed validation and functional analysis of phosphorylation sites offering great potential for the follow-up of phosphoproteome studies. [ABSTRACT FROM AUTHOR]

Background: The investigation of intracellular metabolism is the mainstay in the biotechnology and physiology settings. Intracellular metabolic rates are commonly evaluated using labeling pattern of the identified metabolites obtained from stable isotope labeling experiments. The labeling pattern or mass distribution vector describes the fractional abundances of all isotopologs with different masses as a result of isotopic labeling, which are typically resolved using mass spectrometry. Because naturally occurring isotopes and isotopic impurity also contribute to measured signals, the measured patterns must be corrected to obtain the labeling patterns. Since contaminant isotopologs with the same nominal mass can be resolved using modern mass spectrometers with high mass resolution, the correction process should be resolution dependent. Results: Here we present a software tool, ElemCor, to perform correction of such data in a resolution-dependent manner. The tool is based on mass difference theory (MDT) and information from unlabeled samples (ULS) to account for resolution effects. MDT is a mathematical theory and only requires chemical formulae to perform correction. ULS is semi-empirical and requires additional measurement of isotopologs from unlabeled samples. We validate both methods and show their improvement in accuracy and comprehensiveness over existing methods using simulated data and experimental data from Saccharomyces cerevisiae. The tool is available at https://github.com/4dsoftware/elemcor. Conclusions: We present a software tool based on two methods, MDT and ULS, to correct LC-MS data from isotopic labeling experiments for natural abundance and isotopic impurity. We recommend MDT for low-mass compounds for cost efficiency in experiments, and ULS for high-mass compounds with relatively large spectral inaccuracy that can be tracked by unlabeled standards. [ABSTRACT FROM AUTHOR]

B vitamins in the human distal gut are primarily derived from the gut microbiota because daily dietary vitamins are fully absorbed in the small intestine under normal dietary and physiological conditions. Quantitative determination of B vitamins in the distal gut and faecal samples is crucial for understanding the intricate relationship between gut B vitamins, gut microbiota, and host health. In this study, we developed a rapid, robust, and reliable method with a simple extraction procedure for the simultaneous analysis of seven B vitamins in human faeces using high-performance liquid chromatography-electrospray ionisation-tandem mass spectrometry (HPLC-ESI-MS/MS) with stable isotope-labelled internal standards. A protein precipitation approach using methanol as the precipitant was employed to extract vitamin B from human faecal samples. Seven B vitamins were adequately separated and quantified within 9 min by HPLC-ESI-MS/MS with a Pursuit PFP column (2.0 ×150 mm, 3.0 µm), including vitamins B1, B2, B3, B5, pyridoxic acid, pyridoxine, and B7. The lower limits of quantification were within the range of 0.1–25 ng mL−1. The intra-day and inter-day precision and accuracy were both within 15 %. The validated method was successfully applied to 55 faecal samples collected from healthy individuals, patients with type 2 diabetes, and obese patients. Compared with healthy controls, obese patients had lower faecal concentrations of vitamins B1 and B3 and pyridoxic acid, whereas patients with type 2 diabetes had lower faecal concentrations of vitamins B1 and B5. [Display omitted] • Development of an HPLC-MS/MS method for quantification of faecal B vitamins. • Application to faecal samples collected from healthy volunteers and patients. • Changes in faecal B vitamins profile in obesity and type 2 diabetes. [ABSTRACT FROM AUTHOR]

Free fatty acids serve as important bioactive molecules in the brain. They are involved in message transfer in the brain. There are many reports available in the literature regarding the role of cerebral fatty acids in message transfer; however, most of the studies are mainly focused on limited fatty acid species or only a few specific brain regions. To understand the relationship between cerebral functions and free fatty acids, it is necessary to investigate the distribution of the free fatty acids among different regions in the whole brain. In this study, free fatty acids were extracted from different brain regions and analyzed qualitatively and quantitatively using the stable isotopic labeling liquid chromatography–mass spectrometry approach. In total, 1008 potential free fatty acids were detected in the whole brain out of which 38 were found to be commonly present in all brain regions. Among different brain regions, the highest and the smallest amounts of potential free fatty acids were detected in the olfactory bulb and cerebellum, respectively. From a statistical point of view, 4-methyl-2-oxovaleric acid, cis-11, 14-eicosadienoic acid, tridecanoic acid, myristic acid, nonadecanoic acid, and arachidic acid were found to significantly vary among the four different brain regions (olfactory bulb, occipital lobe, hippocampus, and cerebellum). The variation in the composition of free fatty acids among different brain regions may be very important for investigating the relationship between free fatty acids and functions of cerebral regions.

Stable isotopic tracer analysis is a technique used to determine carbon or nitrogen atom incorporation into biological systems. A number of mass spectrometry based approaches have been developed for this purpose, including high-resolution tandem mass spectrometry (HR-LC-MS/MS), selected reaction monitoring (SRM) and parallel reaction monitoring (PRM). We have developed an approach for analyzing untargeted metabolomic and lipidomic datasets using high-resolution mass spectrometry with polarity switching and implemented our approach in the open-source R script IsoSearch and in Scaffold Elements software. Using our strategy, which requires an unlabeled reference dataset and isotope labeled datasets across various biological conditions, we traced metabolic isotopomer alterations in breast cancer cells (MCF-7) treated with the metabolic drugs 2-deoxy-glucose, 6-aminonicotinamide, compound 968, and rapamycin. Metabolites and lipids were first identified by the commercial software Scaffold Elements and LipidSearch, then IsoSearch successfully profiled the 13C-isotopomers extracted metabolites and lipids from 13C-glucose labeled MCF-7 cells. The results interpreted known models, such as glycolysis and pentose phosphate pathway inhibition, but also helped to discover new metabolic/lipid flux patterns, including a reactive oxygen species (ROS) defense mechanism induced by 6AN and triglyceride accumulation in rapamycin treated cells. The results suggest the IsoSearch/Scaffold Elements platform is effective for studying metabolic tracer analysis in diseases, drug metabolism, and metabolic engineering for both polar metabolites and non-polar lipids.

Memory T-cells are essential to maintain long-term immunological memory. It is widely thought that the bone marrow (BM) plays an important role in the long-term maintenance of memory T-cells. There is controversy however on the longevity and recirculating kinetics of BM memory T-cells. While some have proposed that the BM is a reservoir for long-lived, non-circulating memory T-cells, it has also been suggested to be the preferential site for memory T-cell self-renewal. In this study, we used in vivo deuterium labeling in goats to simultaneously quantify the average turnover rates—and thereby expected lifespans—of memory T-cells from BM, blood and lymph nodes (LN). While the fraction of Ki-67 positive cells, a snapshot marker for recent cell division, was higher in memory T-cells from blood compared to BM and LN, in vivo deuterium labeling revealed no substantial differences in the expected lifespans of memory T-cells between these compartments. Our results support the view that the majority of memory T-cells in the BM are self-renewing as fast as those in the periphery, and are continuously recirculating between the blood, BM, and LN.

Metabolomics has been used in unraveling metabolites that play essential roles in plant–microbe (including pathogen) interactions. However, the problem of profiling a plant metabolome with potential contaminating metabolites from the coexisting microbes has been largely ignored. To address this problem, we implemented an effective stable isotope labeling approach, where the metabolome of a plant bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 was labeled with heavy isotopes. The labeled bacterial cells were incubated with Arabidopsis thaliana epidermal peels (EPs) with guard cells, and excessive bacterial cells were subsequently removed from the plant tissues by washing. The plant metabolites were characterized by liquid chromatography mass spectrometry using multiple reactions monitoring, which can differentiate plant and bacterial metabolites. Targeted metabolomic analysis suggested that Pst DC3000 infection may modulate stomatal movement by reprograming plant signaling and primary metabolic pathways. This proof-of-concept study demonstrates the utility of this strategy in differentiation of the plant and microbe metabolomes, and it has broad applications in studying metabolic interactions between microbes and other organisms.

Ammonia tepida is a common and abundant benthic foraminifer in intertidal mudflats. Benthic foraminifera are primary consumers and detritivores and act as key players in sediment nutrient fluxes. In this study, laboratory feeding experiments using isotope-labeled phytodetritus were carried out with A. tepida collected at the German Wadden Sea, to investigate the response of A. tepida to varying food supply. Feeding mode (single pulse, constant feeding; different incubation temperatures) caused strong variations in cytoplasmic carbon and nitrogen cycling, suggesting generalistic adaptations to variations in food availability. To study the influence of intraspecific size to foraminiferal carbon and nitrogen cycling, three size fractions (125–250 µm, 250–355 µm, >355 µm) of A. tepida specimens were separated. Small individuals showed higher weight specific intake for phytodetritus, especially for phytodetrital nitrogen, highlighting that size distribution within foraminiferal populations is relevant to interpret foraminiferal carbon and nitrogen cycling. These results were used to extrapolate the data to natural populations of living A. tepida in sediment cores, demonstrating the impact of high abundances of small individuals on phytodetritus processing and nutrient cycling. It is estimated that at high abundances of individuals in the 125–250 µm size fraction, Ammonia populations can account for more than 11% of phytodetritus processing in intertidal benthic communities.

Medusae of the widely distributed upside-down jellyfish Cassiopea release autonomous, mobile stinging structures. These so-called cassiosomes play a role in predator defense and prey capture, and are major contributors to "contactless" stinging incidents in (sub-)tropical shallow waters. While the presence of endosymbiotic dinoflagellates in cassiosomes has previously been observed, their potential contribution to the metabolism and long-term survival of cassiosomes is unknown. Combining stable isotope labeling and correlative scanning electron microscopy and nanoscale secondary ion mass spectrometry imaging with a long-term in vitro experiment, our study reveals a mutualistic symbiosis based on nutritional exchanges in dinoflagellate-bearing cassiosomes. We show that organic carbon input from the dinoflagellates fuels the metabolism of the host tissue and enables anabolic nitrogen assimilation. This symbiotic nutrient exchange enhances the life span of cassiosomes for at least one month in vitro . Overall, our study demonstrates that cassiosomes, in analogy with Cassiopea medusae, are photosymbiotic holobionts. Cassiosomes, which are easily accessible under aquarium conditions, promise to be a powerful new miniaturized model system for in-depth ultrastructural and molecular investigation of cnidarian photosymbioses.IMPORTANCEThe upside-down jellyfish Cassiopea releases autonomous tissue structures, which are a major cause of contactless stinging incidents in (sub-) tropical coastal waters. These so-called cassiosomes frequently harbor algal symbionts, yet their role in cassiosome functioning and survival is unknown. Our results show that cassiosomes are metabolically active and supported by algal symbionts. Algal photosynthesis enhances the cassiosomes long-term survival in the light. This functional understanding of cassiosomes thereby contributes to explaining the prevalence of contactless stinging incidents and the ecological success of some Cassiopea species. Finally, we show that cassiosomes are miniaturized symbiotic holobionts that can be used to study host-microbe interactions in a simplified system., Competing Interests: The authors declare no conflict of interest.

Quantitative proteomics approaches based on stable isotopic labeling and mass spectrometry have been widely applied to disease research, drug target discovery, biomarker identification, and systems biology. One of the notable stable isotopic labeling approaches is trypsin-catalyzed 18 O/ 16 O labeling, which has its own advantages of low sample consumption, simple labeling procedure, cost-effectiveness, and absence of chemical reactions that potentially generate by-products. In this chapter, a protocol for 18 O/ 16 O labeling-based quantitative proteomics approach is described with an application to the identification of proteomic biomarkers of acetaminophen (APAP)-induced hepatotoxicity in rats. The protocol involves first the extraction of proteins from liver tissues of control and APAP-treated rats and digestion into peptides by trypsin. After cleaning of the peptides by solid-phase extraction, equal amounts of peptides from the APAP treatment and the control groups are then subject to trypsin-catalyzed 18 O/ 16 O labeling. The labeled peptides are combined and fractionated by off-line strong cation exchange liquid chromatography (SCXLC), and each fraction is then analyzed by nanoflow reversed-phase LC coupled online with tandem mass spectrometry (RPLC-MS/MS) for identification and quantification of differential protein expression between APAP-treated rats and controls. The protocol is applicable to quantitative proteomic analysis for a variety of biological samples., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Abstract Brassinosteroids (BRs) play crucial roles in a variety of physiological processes in plants. The full elucidation of the functions of RBs relies on sensitive detection and accurate measurement of BRs in plants. However, the identification and quantification of BRs are challenging due to their low abundance as well as poor ionization efficiencies during mass spectrometry-based analysis. Herein, we developed a highly sensitive and selective strategy for profiling potential BRs in plants by stable isotope labeling liquid chromatography multiple reaction monitoring scan mass spectrometry (SIL-LC-MRM-MS) analysis. In the strategy, we used a pair of stable isotope labeling reagents 4-phenylaminomethyl-benzeneboronic acid (4-PAMBA) and d 5 -4-phenylaminomethyl-benzeneboronic acid (4-PAMBA- d 5) that can react with C22-C23 cis-diol on BRs for profiling potential BRs in plant tissues. The 4-PAMBA and 4-PAMBA- d 5 labeled BRs could generate two characteristic neutral loss under collision induced dissociation (CID), respectively, which is used to establish the MRM-based detection and screening. The precursor ions of BRs labeled with 4-PAMBA and 4-PAMBA- d 5 were set according to the reported structures of BRs, and the corresponding product ions were predicted by subtracting the lost neutral loss. In this respect, corresponding precursor ions and product ions in MRM transitions are formed. The peak pairs with a fixed mass difference, similar retention times and intensities were assigned as potential BRs. Using the developed SIL-LC-MRM-MS strategy, we successfully found 13 potential BR in different tissues of rape flower. Taken together, the SIL-LC-MRM-MS analytical strategy is promising for profiling potential BRs as well as other compounds that have the same functional moiety from complex biological samples. Graphical abstract Image 1 [ABSTRACT FROM AUTHOR]

Abstract A pair of stable isotope labeling (SIL) reagents, N -(4-(carbazole-9-yl)-phenyl)- N -maleimide (NCPM-d 0) and its heavy analogue NCPM-d 2 , were used for labeling thiol-containing drugs. On basis of SIL, a global isotope internal standard quantitative method for the detection of five thiol-containing drugs by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) was developed. The NCPM-d 0 and NCPM-d 2 can easily label thiol-containing drugs under mild conditions within 10 min at 40 °C. The NCPM-d 0 and NCPM-d 2 labeled thiol-containing drugs can generate two characteristic product ions (m / z at 372.5 and 374.5) under collision induced dissociation, respectively, which is used to establish the multiple reaction monitoring (MRM) based detection. The NCPM labeling combined with MRM analysis not only allowed trace detection of thiol-containing drugs due to the extremely high sensitivity, but also efficiently corrected the matrix effects during HPLC-MS/MS and the instrument fluctuation in the MS/MS signal intensity. The detection sensitivities of thiol-containing drugs improved by 14.5–650.5-fold due to NCPM-labeling, while the matrix and ion suppression effects were markedly minimized by the SIL strategy. The limits of detection (LODs) and the limits of quantitation (LOQs) were in the range 10.0–15.0 ng·mL−1 and 31.0–50.0 ng·mL−1, respectively. The proposed method was used for the simultaneous determination of five thiol-containing drugs in plasma samples with satisfactory recoveries in the range of 95.0–97.5%. Highlights • A stable isotope labeling strategy for analyzing thiol-containing drugs has been developed. • A pair of SIL reagents NCPM-d 0 and NCPM-d 2 were used to label thiol-containing drugs. • The detection sensitivities of thiol-containing drugs improved by 14.5–650.5-fold. • The proposed method was successfully applied to pharmacokinetic study of captopril. [ABSTRACT FROM AUTHOR]

Abstract Information about the distributions of cholesterol and sphingolipids within the plasma membranes of mammalian cells provides insight into the roles of these molecules in membrane function. In this report, high-resolution secondary ion mass spectrometry was used to image the distributions of metabolically incorporated rare isotope-labeled sphingolipids and cholesterol on the surfaces of nonpolarized epithelial cells. Sphingolipid domains that were not enriched with cholesterol were detected in the plasma membranes of subconfluent Madin-Darby canine kidney cells. Surprisingly, cholesterol-enriched sphingolipid patches were observed on the substrate adjacent to these cells. Based on the shapes of these cholesterol-enriched sphingolipid patches on the substrate and their proximity to cellular projections, we hypothesize that they are deposits of membranous particles released by the cell. Highlights • Plasma membranes of nonpolarized MDCK cells contain sphingolipid domains. • Uniform cholesterol distribution in the plasma membranes of nonpolarized MDCK cells • Cholesterol-rich sphingolipid patches detected on the substrate next to MDCK cells • No cholesterol-sphingolipid domains in the plasma membranes of nonpolarized MDCK cells [ABSTRACT FROM AUTHOR]

Recombinantly expressed proteins are susceptible to oxidation during expression, purification, storage, and analysis; the residue most susceptible to oxidation is methionine. Methionine oxidation can be overestimated using current quantitative analysis methods because oxidation can occur during sample preparation, and researchers often do not use methods that account for this possibility. An experimental strategy had been developed previously to solve this problem through the use of an 18O-labeled hydrogen peroxide reagent. However, the method did not address the analysis of peptides that contained multiple methionine residues. Herein, we develop and validate a new analysis method that uses theoretical isotope distributions and experimental spectra to quantify methionine oxidation that is present prior to sample preparation. The newly described approach is more rapid than the previously described method, and it needs only half the amount of protein for analysis. This method was validated using model proteins; then, it was applied to the analysis of recombinant HIV-1 Env, the key protein in HIV vaccine candidates. While Met oxidation of this protein could not be analyzed using previous methods, the approach described herein was useful for determining the oxidation state of HIV-Env.ᅟ [ABSTRACT FROM AUTHOR]

Memory T-cells are essential to maintain long-term immunological memory. It is widely thought that the bone marrow (BM) plays an important role in the long-term maintenance of memory T-cells. There is controversy however on the longevity and recirculating kinetics of BM memory T-cells. While some have proposed that the BM is a reservoir for long-lived, non-circulating memory T-cells, it has also been suggested to be the preferential site for memory T-cell self-renewal. In this study, we used in vivo deuterium labeling in goats to simultaneously quantify the average turnover rates—and thereby expected lifespans—of memory T-cells from BM, blood and lymph nodes (LN). While the fraction of Ki-67 positive cells, a snapshot marker for recent cell division, was higher in memory T-cells from blood compared to BM and LN, in vivo deuterium labeling revealed no substantial differences in the expected lifespans of memory T-cells between these compartments. Our results support the view that the majority of memory T-cells in the BM are self-renewing as fast as those in the periphery, and are continuously recirculating between the blood, BM, and LN. [ABSTRACT FROM AUTHOR]

NMR studies of human integral membrane proteins provide unique opportunities to probe structure and dynamics at specific locations and on multiple timescales, often with significant implications for disease mechanism and drug development. Since membrane proteins such as G protein-coupled receptors (GPCRs) are highly dynamic and regulated by ligands or other perturbations, NMR methods are potentially well suited to answer basic functional questions (such as addressing the biophysical basis of ligand efficacy) as well as guiding applications (such as novel ligand design). However, such studies on eukaryotic membrane proteins have often been limited by the inability to incorporate optimal isotopic labels for NMR methods developed for large protein/lipid complexes, including methyl TROSY. We review the different expression systems for production of isotopically labeled membrane proteins and highlight the use of the yeast Pichia pastoris to achieve perdeuteration and 13C methyl probe incorporation within isoleucine sidechains. We further illustrate the use of this method for labeling of several biomedically significant GPCRs. [ABSTRACT FROM AUTHOR]

Methyl-detected NMR spectroscopy is a useful tool for investigating the structures and interactions of large macromolecules such as membrane proteins. The procedures for preparation of methyl-specific isotopically-labeled proteins were established for the Escherichia coli (E. coli) expression system, but typically it is not feasible to express eukaryotic proteins using E. coli. The Pichia pastoris (P. pastoris) expression system is the most common yeast expression system, and is known to be superior to the E. coli system for the expression of mammalian proteins, including secretory and membrane proteins. However, this system has not yet been optimized for methyl-specific isotope labeling, especially for Val/Leu-methyl specific isotope incorporation. To overcome this difficulty, we explored various culture conditions for the yeast cells to efficiently uptake Val/Leu precursors. Among the searched conditions, we found that the cultivation pH has a critical effect on Val/Leu precursor uptake. At an acidic cultivation pH, the uptake of the Val/Leu precursor was increased, and methyl groups of Val and Leu in the synthesized recombinant protein yielded intense 1H-13C correlation signals. Based on these results, we present optimized protocols for the Val/Leu-methyl-selective 13C incorporation by the P. pastoris expression system. [ABSTRACT FROM AUTHOR]

Summary: Arbuscular mycorrhiza (AM) fungi establish symbiotic interactions with plants, providing the host plant with minerals, i.e. phosphate, in exchange for organic carbon. Arbuscular mycorrhiza fungi of the order Glomerales produce vesicles which store lipids as an energy and carbon source. Acyl‐acyl carrier protein (ACP) thioesterases (Fat) are essential components of the plant plastid‐localized fatty acid synthase and determine the chain length of de novo synthesized fatty acids. In addition to the ubiquitous FatA and FatB thioesterases, AM‐competent plants contain an additional, AM‐specific, FatM gene. Here, we characterize FatM from Lotus japonicus by phenotypically analyzing fatm mutant lines and by studying the biochemical function of the recombinant FatM protein. Reduced shoot phosphate content in fatm indicates compromised symbiotic phosphate uptake due to reduced arbuscule branching, and the fungus shows reduced lipid accumulation accompanied by the occurrence of smaller and less frequent vesicles. Lipid profiling reveals a decrease in mycorrhiza‐specific phospholipid forms, AM fungal signature fatty acids (e.g. 16:1ω5, 18:1ω7 and 20:3) and storage lipids. Recombinant FatM shows preference for palmitoyl (16:0)‐ACP, indicating that large amounts of 16:0 fatty acid are exported from the plastids of arbuscule‐containing cells. Stable isotope labeling with [13C2]acetate showed reduced incorporation into mycorrhiza‐specific fatty acids in the fatm mutant. Therefore, colonized cells reprogram plastidial de novo fatty acid synthesis towards the production of extra amounts of 16:0, which is in agreement with previous results that fatty acid‐containing lipids are transported from the plant to the fungus. [ABSTRACT FROM AUTHOR]

Heavy and radioisotope labeling are commonly used methods to trace the pharmacological activity and metabolic fate of a biochemical or pharmaceutical in vivo . Recent years witnessed increased demand for molecules uniformly labeled with heavy carbon-13 (U- 13 C) or radioactive carbon-14 (U- 14 C) isotopes over singly labeled isotopic versions. Polyunsaturated fatty acids (PUFAs) represent one classic example where uniform 13 C or 14 C isotopic enrichment of the hydrocarbon backbone has numerous technical, metabolic and pharmacological advantages. PUFAs are usually produced in fungi or algae and uniform 13 C or 14 C enrichment of the hydrocarbon chain is achieved by feeding the microorganism a suitable U- 13 C or U- 14 C substrate. Previous literature methods describing the biosynthesis of U- 13 C or U- 14 C fatty acids reported variable isotopic enrichments that were less than anticipated and suffered from inconsistent growth of the microorganism due to radiotoxicity. In the present study, a single-tube method is described for the biosynthesis and extraction of U- 13 C and U- 14 C arachidonic acid (AA), a standard PUFA, from microcultures of the soil fungus Mortierella alpina . To produce U- 13 C-AA, a suspension of fungal spores and mycelial fragments was directly inoculated and grown into submerged cultures in a medium composed of U- 13 C-glucose and NaNO 3 as the respective and only sources of carbon and nitrogen. The total 13 C enrichment of AA was in excess of 95% and the percentage of U- 13 C-AA was in the range of 60–70%. These values have not been surpassed by previously reported methods. To produce U- 14 C-AA, the procedure was modified to limit the radiotoxic effects of 14 C on fungal growth. Submerged cultures were initially grown on common 12 C-glucose. Then, following glucose depletion, the biomass was collected and immediately cultured on U- 14 C-glucose. This approach is unprecedented in reported literature and has significantly limited the radiotoxic effects of 14 C on the microorganism. Biomass transfer from 12 C to 14 C substrates was timed to keep an uninterrupted supply of carbon required to sustain the microorganism in the fatty acid synthesis mode and suppress β-oxidation, a metabolic status that is prerequisite for enhanced isotopic purity of the 14 C product. The specific activity of 14 C enriched AA was estimated at 864 Ci/mol (range of 708–1020 Ci/mol) suggesting 69.2% (range of 56.7–81.7%) 14 C enrichment along the AA hydrocarbon backbone. The present method used a single tube for microbial culture and lipid extraction to minimize manipulative losses and oxidative degradation of the labeled products. Production cost is comparatively cheaper to custom labeling and yields of U- 13 C and U- 14 C-AA are comparable to literature methods and sufficient for small scale in vitro and in vivo pharmacological studies. [ABSTRACT FROM AUTHOR]

Glycoproteins are characterized by the heterogeneous and dynamic nature of their glycan moieties, which hamper crystallographic analysis. NMR spectroscopy provides potential advantages in dealing with such complicated systems, given that the target molecules can be isotopically labeled. Methods of metabolic isotope labeling in recombinant glycoproteins have been developed recently using a variety of eukaryotic production vehicles, including mammalian, yeast, insect, and plant cells, each of which has a distinct N-glycan diversification pathway. Yeast genetic engineering has enabled the overexpression of homogeneous high-mannose-type oligosaccharides with 13C labeling for NMR characterization of their conformational dynamics. The utility of stable isotope-assisted NMR spectroscopy has also been demonstrated using the Fc fragment of immunoglobulin G (IgG) as a model glycoprotein, providing useful information regarding intramolecular carbohydrate-protein interactions. Transverse relaxation optimization of intact IgG with a molecular mass of 150 kDa has been achieved by tailored deuteration of selected amino acid residues using a mammalian expression system. This offers a useful probe for the characterization of molecular interaction networks in multimolecular crowded systems typified by serum. Perspectives regarding the development of techniques for tailoring glycoform designs and isotope labeling of recombinant glycoproteins are also discussed. [ABSTRACT FROM AUTHOR]

Salicortin is a phenolic glucoside produced in Salicaceae as a chemical defense against herbivory. The specialist lepidopteran herbivorous larvae of Cerura vinula are able to overcome this defense. We examined the main frass constituents of C. vinula fed on Populus nigra leaves, and identified 11 quinic acid derivatives with benzoate and/or salicylate substitution. We asked whether the compounds are a result of salicortin breakdown and sought answers by carrying out feeding experiments with highly 13C-enriched salicortin. Using HRMS and NMR analyses, we were able to confirm that salicortin metabolism in C. vinula proceeds through deglucosylation and ester hydrolysis, after which saligenin is oxidatively transformed into salicylic acid and, eventually, conjugated to quinic acid. To the best of our knowledge, this is the first report of a detoxification pathway based on conjugation with quinic acid. [ABSTRACT FROM AUTHOR]

Low-molecular-weight thiols play important roles in a variety of pathological processes and are closely associated with a wide range of diseases. In this study, a selective and sensitive method was developed for the simultaneous determination of all the 7 thiols occurring in the transsulfuration pathway (Cysteine (Cys), homocysteine (Hcys), glutathione (GSH), N -acetylcysteine (Nac), cysteinylglycine (CysGly), glutamylcysteine (GluCys) and cysteamine (CA)) in human serum by in - vitro stable isotope labeling - dispersive solid phase extraction - liquid chromatography - tandem mass spectrometry analysis (IL-DSPE-LC-MS/MS). In the proposed method, a pair of stable isotope-labeling reagents, BQB ( ω -bromoacetonylquinolinium bromide) and BQB- D 7 , were utilized to label thiols in human serum samples and thiol standards, respectively. The BQB labeled thiols which carry a positive charge were extracted and purified with C 8 -SO 3 H-based DSPE followed by LC-MS/MS analysis. Good linearities for 7 thiols occurring in the transsulfuration pathway were obtained with the coefficient of determination ( R 2 ) >0.9901. The limits of detection (LODs) were in the range of 0.7–6.0 nmol/L. The method was further applied to investigate the contents change of 7 thiols in human serum samples of type 2 diabetes mellitus (T2DM) patients and breast cancer (BC) patients. The results showed that the contents of these thiols occurring in the transsulfuration pathway significantly changed and were highly diseases-related. In addition, partial least squares discriminant analysis (PLS-DA) suggested excellent classification performance between patients and healthy controls. The findings indicated that these significantly changed thiols occurring in the transsulfuration pathway in T2DM patients and BC patients might serve as the indicator for the diagnosis of T2DM and BC. Taken together, the developed IL-DSPE-LC-MS/MS method provides a promising tool for the sensitive analysis of thiols from complex biological samples, which may promote the in-depth investigation of the functions of thiols. [ABSTRACT FROM AUTHOR]

Abstract: In this study, we examined the impact of temperature on the carbon and nitrogen trophic transfers from a macroalga to a macro‐grazer by the use of dual 13C‐ and 15N‐labeling. Using an experimental approach in mesocosms, individuals of the urchin Psammechinus miliaris were maintained for 1 month at 17°C (mean summer temperature in the Bay of Brest) and at 20°C (maximum summer temperature) and fed with 13C‐ and 15N‐labeled Solieria chordalis. The results showed that the urchins’ 13C uptake was 0.30 µg13C g dry weight (DW)−1 at 17°C and 0.14 µg13C g DW−1 at 20°C at the end of the experiment. The lower uptake at the higher temperature may be attributed to a decrease in metabolic activity at 20°C, involving lower feeding and/or respiration rates. Conversely, no significant effect of temperature was detected on 15N uptake. At the end of the experiment, the urchins’ 15N uptake was 0.04 µg15N g DW−1 at 17°C and 0.03 µg15N g DW−1 at 20°C. This suggests that temperature may affect carbon and nitrogen trophic fluxes differently. The use of dual isotope labeling offers interesting prospects and needs to be further extended in order to better understand trophic interactions in marine communities and the consequences of current environmental changes, such as global warming. [ABSTRACT FROM AUTHOR]

Mucin-type O-glycans decorate >80% of secretory and cell surface proteins and contribute to health and disease. However, dynamic alterations in the O-glycome are poorly understood because current O-glycomic methodologies are not sufficiently sensitive nor quantitative. Here we describe a novel isotope labeling approach termed Isotope-Cellular O-glycome Reporter Amplification (ICORA) to amplify and analyze the O-glycome from cells. In this approach, cells are incubated with Ac3GalNAc- Bn (Ac3GalNAc-[1H7]Bn) or a heavy labeled Ac3GalNAc-BnD7 (Ac3GalNAc-[2D7]Bn) O-glycan precursor (7 Da mass difference), which enters cells and upon de-esterification is modified by Golgi enzymes to generate Bn-O-glycans secreted into the culture media. After recovery, heavy and light Bn-O-glycans from two separate conditions are mixed, analyzed by MS, and statistically interrogated for changes in O-glycan abundance using a semi-automated approach. ICORA enables ~100-1000-fold enhanced sensitivity and increased throughput compared to traditional O-glycomics. We validated ICORA with model cell lines and used it to define alterations in the O-glycome in colorectal cancer. ICORA is a useful tool to explore the dynamic regulation of the O-glycome in health and disease. [ABSTRACT FROM AUTHOR]

Aims: This study focuses on quantifying the contribution of remobilization to the amount of cadmium accumulated in durum wheat grains. The impact of post-anthesis N supply was tested in two cultivars that differ in their shoot biomass partitioning.Methods: Two French durum wheat cultivars were grown hydroponically and exposed to 100 nM Cd. After anthesis, the plants were fed with a solution enriched in the stable isotope 111Cd to trace the Cd newly absorbed, and subjected or not to nitrogen deprivation. Plants were sampled at anthesis and grain maturity to assess the post-anthesis fluxes of Cd and N among organs.Results: Cd remobilized from pre-anthesis stores contributed to more than half of the Cd accumulated in mature grains. Cd was mainly remobilized from stem and poorly remobilized from leaves. Stopping N supply during grain filling enhanced N remobilization but had no impact on post-anthesis uptake and remobilization of Cd, and thereby, on Cd concentration in grains. No difference was observed between the two cultivars in the contribution of Cd remobilization and its dependence toward post-anthesis N supply.Conclusions: Cd remobilization significantly contributes to the accumulation of Cd in durum wheat grains. Cd remobilization is not tightly linked with N remobilization and behaves like a senescent-independent process in durum wheat. [ABSTRACT FROM AUTHOR]

Currently, changes in metabolic fluxes following consumption of stable isotope-enriched foods are usually limited to the analysis of postprandial kinetics of glucose. Kinetic information on a larger diversity of metabolites is often lacking, mainly due to the marginal percentage of fully isotopically enriched plant material in the administered food product, and hence, an even weaker 13C enrichment in downstream plasma metabolites. Therefore, we developed an analytical workflow to determine weak 13C enrichments of diverse plasma metabolites with conventional gas chromatography-mass spectrometry (GC-MS). The limit of quantification was increased by optimizing (1) the metabolite extraction from plasma, (2) the GC-MS measurement, and (3) most importantly, the computational data processing. We applied our workflow to study the catabolic dynamics of 13C-enriched wheat bread in three human subjects. For that purpose, we collected time-resolved human plasma samples at 16 timepoints after the consumption of 13C-labeled bread and quantified 13C enrichment of 12 metabolites (glucose, lactate, alanine, glycine, serine, citrate, glutamate, glutamine, valine, isoleucine, tyrosine, and threonine). Based on isotopomer specific analysis, we were able to distinguish catabolic profiles of starch and protein hydrolysis. More generally, our study highlights that conventional GC-MS equipment is sufficient to detect isotope traces below 1% if an appropriate data processing is integrated. [ABSTRACT FROM AUTHOR]

The lack of a highly sensitive and simple method for the quantitative analysis of glycan has impeded the exploration of protein glycosylation patterns (glycomics), evaluation of antibody drug stability, and screening of disease glycan biomarkers. In this study, we describe a novel and simplified quantitative glycomics strategy. Quantitation by mutant enzyme reaction stable isotope labeling (QMERSIL) to label the N -glycans with either a nondeuterated (d0-) or deuterated (d8-) 4-(2,4-Dinitro-5-piperazin-1-yl-phenyl)-1,1-dimethyl-piperazin-1-ium (MPDPZ)-Boc-asparaginyl- N -acetyl- d -glucosamine (Boc-Asn-GlcNAc) acceptor of a positive charge structure through the glycosynthase (Endo-M-N175Q) transglycosylation reaction with mass spectrometry facilitates comparative glycomics. The sialylglycopeptide (SGP) of the complex type was used to demonstrate that QMERSIL facilitates the relative quantitation over a linear dynamic range (up to d0/d8 = 0.02:20) of 3 orders of magnitude. The area ratios of the N -glycan peaks from the QMERSIL method showed a good linearity (d0/d8, R 2 = 0.9999; d8/d0, R 2 = 0.9978). The reproducibility and accuracy assay precisions were all less than 6.12%, and the mean recoveries (%) of SGP spiked in the human plasma were 97.34%. Moreover, the QMERSIL using LC–MS/MS was evaluated with various molar ratios (1:1, 1:5, 5:1) of d0(d8)- MPDPZ-Boc-Asn-GlcNAc-labeled glycans from ribonuclease B, bovine fetuin, and ovalbumin. The ratios of the relative intensity between the isotopically MPDPZ-Boc-Asn-GlcNAc labeled N -glycans were almost equal a close to the theoretical values (1:1, 1:5, 5:1). Finally, this method was used for the relative quantitative comparison of the N -Linked oligosaccharides in human plasma. [ABSTRACT FROM AUTHOR]