Stable isotope labeling-based two-step derivatization strategy for analysis of Phosphopeptides

Investigating site-specific protein phosphorylation remains a challenging task. The present study introduces a two-step chemical derivatization method for accurate identification of phosphopeptides. Methylamine neutralizes carboxyl groups, thus reducing the adsorption of non-phosphorylated peptides during enrichment, while dimethylamine offers a cost-effective reagent for stable isotope labeling of phosphorylation sites. The derivatization improves the mass spectra obtained through liquid chromatography-tandem mass spectrometry. The product ions at m/z 58.07 and 64.10 Da, resulting from dimethylamine-d0 and dimethylamine-d6 labeled phosphorylation sites respectively, can serve as report ions. Derivatized phosphopeptides from casein demonstrate enhanced ionization and formation of product ions, yielding a significant increase in the number of identifiable peptides. When using the parallel reaction monitoring technique, it is possible to distinguish isomeric phosphopeptides with the same amino acid sequence but different phosphorylation sites. By employing a proteomic software and screening the report ions, we identified 29 endogenous phosphopeptides in 10 μL of human saliva with high reliability. These findings indicate that the two-step derivatization strategy has great potential in site-specific phosphorylation and large-scale phosphoproteomics research. SIGNIFICANCE: There is a significant need to improve the accuracy of identifying phosphoproteins and phosphopeptides and analyzing them quantitatively. Several chemical derivatization techniques have been developed to label phosphorylation sites, thus enabling the identification and relative quantification of phosphopeptides. Nevertheless, these methods have limitations, such as incomplete conversion or the need for costly isotopic reagents. Building upon previous contributions, our study moves the field forward due to high efficiency in site-specific labeling, cost-effectiveness, improved sensitivity, and comprehensive product ion coverage. Using the two-step derivatization approach, we successfully identified 29 endogenous phosphopeptides in 10 μL of human saliva with high reliability. The outcomes underscore the possibility of the method for site-specific phosphorylation and large-scale phosphoproteomics investigations.

A green-footprint approach for parallel multiclass analysis of contaminants in roasted coffee via LC-HRMS

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.

A Mechanism to Transform Complex Salicinoids with Caffeoylquinic Acids in Lepidopteran Specialist Herbivores (Notodontidae)

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.

Simultaneous quantification of seven B vitamins in human faeces by stable isotope label-based high-performance liquid chromatography-tandem mass spectrometry

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.

Stable isotope labeling differential glycans discovery in the serum of acute myocardial infarction by ultrahigh-performance liquid chromatography-quadrupole-Orbitrap high resolution mass spectrometry

Acute myocardial infarction (AMI) poses a grave threat to human life. However, most clinical biomarkers have limitations of low sensitivity and specificity. Therefore, screening novel glycan biomarkers with high sensitivity and specificity is crucial for the prevention and treatment of AMI. The novel method of ultrahigh-performance liquid chromatography coupled to quadrupole-Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) with d0/d5-BOTC probe labeling for relative quantification of glycans based on Pronase E digestion was established to screen novel glycan biomarkers in the serum of 34 AMI patients relative to healthy volunteers. The monosaccharide model D-glucosamine was used to investigate the effectiveness of the derivatization; the limit of detection (S/N = 3) was 10 amol. The accuracy was verified based on the consistency of different theoretical molar ratios (d0/d5 = 1:2, 2:1) and intensity ratios following digestion of glycoprotein ribonuclease B. Expressions of H4N4F3SA, H4N6F2, H4N6SA, H4N6F3 and H5N4FSA in the serum were significantly different (p < 0.0005) between AMI patients and healthy volunteers. The area under the receiver operating characteristic curve (AUC) for H4N6SA, H5N4FSA, and H4N6F2 was greater than 0.9039. Based on the proposed method, H4N6SA, H5N4FSA, and H4N6F2 in human serum showed high accuracy and specificity and may serve as potential glycan biomarkers, crucial for the diagnosis and treatment monitoring of AMI.

Reductive Conversion Leads to Detoxification of Salicortin-like Chemical Defenses (Salicortinoids) in Lepidopteran Specialist Herbivores (Notodontidae)

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.

Pyridinium and ammonium stable isotope labeling agents and their performance in the analysis of alkylamines in food and food packaging materials

Two pairs of stable isotope labeling (SIL) agents, (4-carboxyphenyl)trimethylammonium iodide (d₀-CPTA) and its deuterated counterpart d₃-CPTA, 1-methyl-nicotinamide iodide (d₀-MNA) and its deuterated counterpart d₃-MNA, were designed and synthesized. Their mass spectrometry (MS) sensitivity enhancement effect was studied and compared with commercial dansyl chloride to provide inspiration for labeling agent design. CPTA with quaternary ammonium group showed much higher MS sensitivity enhancement effect and was applied to the SIL analysis of alkylamines in food and food packaging materials. The matrix effect was minimized due to the SIL strategy and the permanent charge of the CPTA. The limits of detection (LODs) were in the range of 2.9-5.1 ng/L, and the limits of quantitation (LOQs) were in the range of 9.6-16.8 ng/L. The recoveries ranged from 91.2 % to 97.1 % with relative standard deviations of less than 6.6 %, and the matrix effect ranged from -1.8 % to -4.9 %.

Tracer or toxicant: Does stable isotope labeling affect central processes in aquatic food webs?

Stable isotope analysis (SIA) is an elementary technique in food web ecology, but its insights become increasingly ambiguous in complex systems. One approach to elevate the utility of SIA in such systems is the use of heavy isotope tracers (i.e., labeling). However, the fundamental assumption that the addition of such tracers does not affect in situ conditions has been challenged. This study tests if labeling is suitable for autotrophy-based and detritus-based aquatic food webs. For the former, the survival and reproduction of Daphnia magna fed with phytoplankton cultured at different levels of ¹⁵N addition were assessed. For the latter, the microbial decomposition of leaf litter was assessed at the same tracer levels. While no significant differences were observed, effect patterns were comparable to a previous study, supporting the isotopic redundancy hypothesis that postulates discrete quantum mechanical states at which the reaction speeds of metabolic processes are altered. Although physiology (reproduction) and activity (microbial decomposition) might not be altered to an ecologically significant level, labeling with heavy stable isotopes could potentially affect isotopic fractionation in biochemical processes and bias conclusions drawn from resulting SI ratios.

Choline supplementation for preterm infants: metabolism of four Deuterium-labeled choline compounds

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.

Site-Specific Isotope Labeling of FliG for Studying Structural Dynamics Using Nuclear Magnetic Resonance Spectroscopy

To understand flagella-driven motility of bacteria, it is important to understand the structure and dynamics of the flagellar motor machinery. We have conducted structural dynamics analyses using solution nuclear magnetic resonance (NMR) to elucidate the detailed functions of flagellar motor proteins. Here, we introduce the analysis of the FliG protein, which is a flagellar motor protein, focusing on the preparation method of the original stable isotope-labeled protein.

Investigation of the Quinone-quinone and Quinone-catechol products using 13C labeling, UPLC-Q-TOF/MS and UPLC-Q-Exactive Orbitrap/MS

Quinones are highly reactive oxidants and play an essential role in inducing quality deterioration of fruit and vegetable products. Here, a novel stable isotope-labeling approach in combination with high-resolution tandem mass spectrometry UPLC-Q-TOF/MS and UPLC-Q-Exactive Orbitrap/MS, was successfully applied in tracking quinone reaction pathways in both real wines and model reaction systems. Unexpectedly, the binding products of quinone-quinone and quinone-catechol that are not derived from either nucleophilic reaction or redox reaction were discovered and showed the significant high peak area.Self-coupling reactions of semiquinone radicals might provide a possible interpretation for the formation of quinone-quinone products, and a charge transfer reaction coupled with a complementary donor-acceptor interaction is feasibly responsible for the products with a quinone-catechol structure. These findings endow a new perspective for quinone metabolic pathway in foods.

Preclinical pharmacokinetics, biodistribution, excretion, and plasma protein binding study of 58Fe-labeled hemin by ICP-MS

BACKGROUND

Hemin, a stable form of heme iron, is a potential iron supplement for the treatment of iron deficiency. To date, the pharmacokinetics and in vivo ADME properties of hemin are to be elucidated.

METHODS

In this study, a rapid, sensitive, and validated inductively coupled plasma mass spectrometry (ICP-MS) method was used in combination with ⁵⁸Fe stable isotope labeling to systemically investigate the plasma pharmacokinetics, biodistribution, excretion, and plasma binding profiles of hemin in animals.

RESULTS

Results showed that the ICP-MS method is accurate and sensitive enough to quantitatively determine the in vivo disposition process of ⁵⁸Fe derived from ⁵⁸Fe-labeled hemin. Following intra-gastric administration, ⁵⁸Fe was rapidly absorbed in gastrointestinal tract, with C_max of 41.1 ± 23.1 ng/mL, T_max of 1.38 ± 0.48 h, and bioavailability of 1.12 ± 0.45 % in beagle dogs. Moreover, ⁵⁸Fe was distributed to various organs including stomach, small intestine, spleen, and liver, within a few hours after intra-gastric administration in rats. Excretion of ⁵⁸Fe in rats was predominantly via feces (76.3 ± 15.1 % of dosage), whereas minimally via urine (0.14 ± 0.08 % of dosage). Protein binding study revealed majority of ⁵⁸Fe in plasma was bound to proteins, with average binding rates of 81.0 % and 92.7 % in human and rat plasma, respectively.

CONCLUSION

In conclusion, the present study validated the work-flow of preclinical pharmacokinetic studies of iron-containing drug candidates with using ICP-MS and stable (trace) isotope labeling strategy. It also provided useful information to support the further development of hemin as a drug/nutrition supplement candidate.

Combination of long-term 13CO2 labeling and isotopolog profiling allows turnover analysis of photosynthetic pigments in Arabidopsis leaves

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.

Relative quantitation of glycans in cetuximab using ultra-high-performance liquid chromatography-high-resolution mass spectrometry by Pronase E digestion

Glycans play important roles in the activity and function of monoclonal antibodies (mAbs). In this study, an isotope labeling method for the relative quantitative analysis of glycans in cetuximab, a chimeric human/mouse IgG1 monoclonal antibody that specifically targets epidermal growth factor receptor, via hydrophilic interaction LC-ultra-high-performance LC-HRMS was established based on Pronase E digestion. To this aim, novel isotope MS probes, i.e., 3-benzoyl-2-oxothiazolidine-4-carboxylic acid (d0-BOTC) and 3-(2,3,4,5,6-pentadeuterio-benzoyl)-2-oxothiazolidine-4-carboxylate acid (d5-BOTC), which include a carboxyl group to target the amino functional group in glycosylamine, were developed. The nonspecific Pronase E enzyme could simultaneously digest the peptide bound to the N- and O-glycans into glycosylamine having only one amino acid. Since the mass difference between the light- and heavy-labeled glycans was 5.0 Da, the relative abundance of their MS peaks was used to achieve the qualitative and relative quantitative analysis of glycans. Sialylglycopeptide was used as a complex glycan model to validate the accuracy of the method. The results demonstrated the good linearity (R² ≥ 0.9994) between the experimentally detected MS intensity ratios and the theoretical molar ratios of the d0-BOTC to the corresponding d5-BOTC derivatives in the dynamic range of 0.03-10 and 0.03-20 of three orders magnitude for the d5-BOTC/d0-BOTC ratios. The reproducibility was between 0.16% and 10.70%, and the limit of detection was 13 fmol. The feasibility of the relative quantification method was investigated by analyzing the glycan content in cetuximab, finding good consistency between experimental and theoretical molar ratios (5:1, 3:1, 1:1, 1:3, 1:5) of d0/d5-BOTC-labeled glycans. Finally, 13 glycans were successfully identified in cetuximab by applying this method using an in-house Tracefinder database. This study provides a novel strategy for the high throughput analysis, identification, and functional study of glycans in mAbs.

Mass Spectrometry-Based Proteomics for Biomarker Discovery

Proteomics plays a pivotal role in systems medicine, in which pharmacoproteomics and toxicoproteomics have been developed to address questions related to efficacy and toxicity of drugs. Mass spectrometry is the core technology for quantitative proteomics, providing the capabilities of identification and quantitation of thousands of proteins. The technology has been applied to biomarker discovery and understanding the mechanisms of drug action. Both stable isotope labeling of proteins or peptides and label-free approaches have been incorporated with multidimensional LC separation and tandem mass spectrometry (LC-MS/MS) to increase the coverage and depth of proteome analysis. A protocol of such an approach exemplified by dimethyl labeling in combination with 2D-LC-MS/MS is described. With further development of novel proteomic tools and increase in sample throughput, the full spectrum of mass spectrometry-based proteomic research will greatly advance systems medicine.

Production and stability of Oxygen-18 labeled Caribbean ciguatoxins and gambierones

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.

A simultaneous identification and quantification strategy for determination of sulfhydryl-containing metabolites in normal- and high-fat diet hamsters using stable isotope labeling combined with LC-MS

Sulfur-containing metabolites are related to several physiologic disorders and metabolic diseases. In this study, a simultaneous identification and quantification strategy in one batch for determination of sulfhydryl-containing metabolites was developed using stable isotope labeling combined with liquid chromatography-tandem mass spectrometry (SIL-LC-MS). In the proposed method, a pair of isotope labeling reagents, D₀/D₅-N-ethylmaleimide (D₀/D₅-NEM), was used to derivatize sulfhydryl-containing metabolites in blood and plasma of normal- and high-fat-diet (NFD and HFD) hamsters for reduced (-SH) and total (-SH, -S-S-, S-glutathionylated proteins) analysis. Quality control (QC) samples and test samples were prepared for LC-MS analysis. First, both QC samples and stable isotope labeled internal standards were used to monitor the status of the instrument and ensure the reliability of the analysis. Subsequently, an inhouse database containing 45 sulfhydryl-containing metabolites was established by MS¹ based on QC samples. Then, qualitatively differential sulfhydryl-containing metabolites were found by MS² between the NFD and HFD hamsters of the test samples, including 3 in reduced and 8 in total analysis of blood samples, and 2 in reduced and 2 in total analysis of plasma samples. Next, in quantitative analysis, satisfied linearities for 6 sulfhydryl-containing metabolites were obtained with the correlation coefficient (R²) > 0.99 and absolute quantification was carried out. The results showed that glutathione and cysteine have different concentrations in blood and plasma of hamsters. Finally, the correlation of sulfhydryl-containing metabolites with blood lipid and oxidative stress levels was determined, which provided insight into the hyperlipidemia-related oxidative stress. Taken together, the developed method of simultaneous identification with the inhouse database and MS² and quantification with standards in one batch provides a promising strategy for the analysis of sulfhydryl-containing metabolites in biological samples, which may promote the in-depth investigation on sulfhydryl-containing metabolites and related diseases.

Tracing the fate of phosphorus fertilizer derived cadmium in soil-fertilizer-wheat systems using enriched stable isotope labeling

Applying mineral phosphorus (P) fertilizers introduces a considerable input of the toxic heavy metal cadmium (Cd) into arable soils. This study investigates the fate of P fertilizer derived Cd (Cd_dff) in soil-wheat systems using a novel combination of enriched stable Cd isotope mass balances, sequential extractions, and Bayesian isotope mixing models. We applied an enriched ¹¹¹Cd labeled mineral P fertilizer to arable soils from two long-term field trials with distinct soil properties (a strongly acidic pH and a neutral pH) and distinct past mineral P fertilizer application rates. We then cultivated wheat in a pot trial on these two soils. In the neutral soil, Cd concentrations in the soil and the wheat increased with increasing past mineral P fertilizer application rates. This was not the case in the strongly acidic soil. Less than 2.3% of freshly applied Cd_dff was taken up by the whole wheat plant. Most of the Cd_dff remained in the soil and was predominantly (>95% of freshly applied Cd_dff) partitioned into the easily mobilizable acetic acid soluble fraction (F1) and the potentially mobile reducible fraction (F2). Soil pH was the determining factor for the partitioning of Cd_dff into F1, as revealed through a recovery of about 40% of freshly applied Cd_dff in F1 in the neutral pH soil compared with about 60% in the strongly acidic soil. Isotope mixing models showed that F1 was the predominant source of Cd for wheat on both soils and that it contributed to over 80% of the Cd that was taken up by wheat. By tracing the fate of Cd_dff in entire soil-plant systems using different isotope source tracing approaches, we show that the majority of Cd_dff remains mobilizable and is potentially plant available in the subsequent crop cycle.

Simultaneous determination of short-chain fatty alcohols in aged oil and biodiesels by stable isotope labeling assisted liquid chromatography-mass spectrometry

Short-chain fatty alcohols (SCFAs) are one of the reactants for the production of biodiesels. The SCFA residues at the trace level have a significant impact on biodiesel quality. However, the analysis of SCFAs in aged biodiesels has not been reported so far, which is probably due to the unavailability of an appropriate analytical method for the simultaneous determination of SCFAs. Herein, we developed a novel analytical approach with high sensitivity and selectivity for the simultaneous identification and determination of SCFAs in seed oil and biodiesel samples during the simulated real-time aging by stable isotope labeling assisted liquid chromatography-mass spectrometry (SIL-LC-MS). A pair of isotope labeling reagents, pyridine (Py) and [²H₅]pyridine ([²H₅]Py), were used to label SCFAs in biodiesels and standards, respectively. The [²H₅]Py labeled SCFAs were used as internal standards to compensate for the detection of variances. The simultaneous determination of SCFAs was performed by LC-MS with an improved detection selectivity and sensitivity. The limits of detection (LODs) values were ranged from 0.2 to 0.5 ng mL^-1 for the investigated SCFAs. Good linearity was observed in the studied ranges (R² > 0.99) and good precision with relative standard deviations (RSDs) was in the range of 4.9-18.1%. Average recoveries were obtained in the range of 80.3%-115.4%. The matrix effects were in the range of 70.0-104.3%. The validated SIL-LC-MS method was applied to the simultaneous quantitative analysis of SCFAs in seed oil and biodiesel samples and the LC-MS analysis could be done within 3 min. The formation mechanism of SCFAs in aged oil and biodiesel samples was also investigated by this method. The results suggest that SCFAs were formed and their composition changed during the simulated real-time aging of long-chain fatty acid (LCFA), long-chain fatty acid methyl ester (FAME), seed oil, and biodiesels. Moreover, we found that the formation of 1-pentanol and 1-hexanol was associated with the number and position of double bonds in LCFAs and FAMEs.

Protocol: analytical methods for visualizing the indolic precursor network leading to auxin biosynthesis

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.

Novel acquisition strategies for metabolomics using drift tube ion mobility-quadrupole resolved all ions time-of-flight mass spectrometry (IM-QRAI-TOFMS)

The focus of this work was the implementation of ion mobility (IM) and a prototype quadrupole driver within data independent acquisition (DIA) using a drift tube IM-QTOFMS aiming to improve the level of confidence in identity confirmation workflows for non-targeted metabolomics. In addition to conventional all ions (IM-AI) acquisition, quadrupole resolved all ions (IM-QRAI) acquisition allows a drift time-directed precursor ion isolation in DIA using sequential isolation of precursor ions using mass windows of up to 100 Da which can be rapidly ramped across single ion mobility transients (i.e., <100 ms) according to the arrival times of precursor ions. Both IM-AI and IM-QRAI approaches were used for identity confirmation and relative quantification of metabolites in cellular extracts of the cell factory host Pichia pastoris. Samples were spiked with a uniformly ¹³C-labeled (U¹³C) internal standard and LC with low-field drift tube IM separation was used in combination with IM-AI and IM-QRAI. Combining excellent hardware performance and correlation of IM arrival times of natural (^natC) and U¹³C metabolites enabled alignment of signals in the arrival time domain (^DTCCS_N2 differences ≤0.3%), and, in the case of IM-QRAI operation, maintenance of quantitative signals in comparison to IM-AI. The combination of tailored IM-QRAI methods for precursor ion isolation and IM separation also minimized the occurrence of spectral interferences in complex DIA datasets. Combined use of the software tools MS-DIAL, MS-Finder and Skyline for peak picking, feature alignment, reconciliation of ^natC and U¹³C isotopologue pairs, deconvolution of fragment spectra from DIA data, identity confirmation (including ^DTCCS_N2) and targeted re-extraction of datafiles were employed for the data processing workflow. Overall, the combined new acquisition and data processing approaches enabled 87 metabolites to be identified between Level 1 (identified by standard compound) and Level 3.2 (accurate mass spectrum and number of carbons confirmed). The developed methods constitute promising metabolomics discovery tools and can be used to elucidate the number of carbon atoms present in unknown metabolites in stable isotope-supported metabolomics.

Isotope ratio-based quantification of carbon assimilation highlights the role of plastidial isoprenoid precursor availability in photosynthesis

BACKGROUND

We report a method to estimate carbon assimilation based on isotope ratio-mass spectrometry (IRMS) of ¹³CO₂ labeled plant tissue. Photosynthetic carbon assimilation is the principal experimental observable which integrates important aspects of primary plant metabolism. It is traditionally measured through gas exchange. Despite its centrality in plant research, gas exchange performs poorly with rosette growth habits typical of Arabidopsis thaliana, mutant lines with limited biomass, and accounts poorly for leaf shading.

RESULTS

IRMS-based carbon assimilation values from plants labeled at different light intensities were compared to those obtained by gas exchange, and the two methods yielded similar values. Using this method, we observed a strong correlation between ¹³C content and labeling time (R² = 0.999) for 158 wild-type plants labeled for 6 to 42 min. Plants cultivated under different light regimes showed a linear response with respect to carbon assimilation, varying from 7.38 nmol ¹³C mg^-1 leaf tissue min^-1 at 80 PAR to 19.27 nmol ¹³C mg^-1 leaf tissue min^-1 at 500 PAR. We applied this method to examine the link between inhibition of the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway and suppression of photosynthesis. A significant decrease in carbon assimilation was observed when metabolic activity in the MEP pathway was compromised by mutation or herbicides targeting the MEP pathway. Mutants affected in MEP pathway genes 1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE (DXS) or 1-HYDROXY-2-METHYL-2-(E)-BUTENYL 4-DIPHOSPHATE SYNTHASE (HDS) showed assimilation rates 36% and 61% lower than wild type. Similarly, wild type plants treated with the MEP pathway inhibitors clomazone or fosmidomycin showed reductions of 52% and 43%, respectively, while inhibition of the analogous mevalonic acid pathway, which supplies the same isoprenoid intermediates in the cytosol, did not, suggesting inhibition of photosynthesis was specific to disruption of the MEP pathway.

CONCLUSIONS

This method provides an alternative to gas exchange that offers several advantages: resilience to differences in leaf overlap, measurements based on tissue mass rather than leaf surface area, and compatibility with mutant Arabidopsis lines which are not amenable to gas exchange measurements due to low biomass and limited leaf surface area. It is suitable for screening large numbers of replicates simultaneously as well as post-hoc analysis of previously labeled plant tissue and is complementary to downstream detection of isotopic label in targeted metabolite pools.

Quantification of Modified Nucleosides in the Context of NAIL-MS

Recent progress in epitranscriptome research shows an interplay of enzymes modifying RNAs and enzymes dedicated for RNA modification removal. One of the main techniques to study RNA modifications is liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) as it allows sensitive detection of modified nucleosides. Although RNA modifications have been found to be highly dynamic, state-of-the-art LC-MS/MS analysis only gives a static view on modifications and does not allow the investigation of temporal modification placement. Here, we present the principles of nucleic acid isotope labeling coupled with mass spectrometry, termed NAIL-MS, which overcomes these limitations by stable isotope labeling in human cell culture and gives detailed instructions on how to label cells and process samples in order to get reliable results. For absolute quantification in the context of NAIL-MS, we explain the production of internal standards in detail. Furthermore, we outline the requirements for stable isotope labeling in cell culture and all subsequent steps to receive nucleoside mixtures of native RNA for NAIL-MS analysis. In the final section of this chapter, we describe the distinctive features of NAIL-MS data analysis with a special focus toward absolute quantification of modified nucleosides.

Formation of formaldehyde as an artifact peak in head space GC analysis resulting from decomposition of sample diluent DMSO: A GC-MS investigation with deuterated DMSO

During our method development for residual formaldehyde detection in a drug substance, unusually high levels of formaldehyde were detected when using a mixed solvent of EtOH/DMSO (4:1, v/v) as sample diluent in headspace GC analysis (HS-GC). Initial investigation found that formaldehyde is used in the preparation for one of the starting materials of the drug substance. Nevertheless, there is neither other source of formaldehyde in the manufacturing process of the drug substance, nor would formaldehyde be generated during the process. In the ensuing root cause investigation, it was found that once the solvent DMSO is replaced by other solvent [e.g., N,N-dimethylformamide (DMF)], while keeping other method parameters unchanged in the HS-GC analysis, the level of formaldehyde in the same batch of the drug substance became undetectable (LOD: 3 ppm). All the evidence suggested that the observed formaldehyde in the HS-GC analysis might be due to the decomposition of DMSO, which could be facilitated by the presence of this particular drug substance. In other words, the presence of the drug substance (in the form of HCl salt) would cause a minor decomposition of DMSO to produce formaldehyde. To prove this hypothesis, a GC-MS experiment of the drug substance was conducted in which deuterated DMSO (DMSO-_d6) was used in place of regular DMSO; the expected deuterated derivatization product, i.e., diethoxymethane-_d2 (C₂H₅OCD₂OC₂H₅), was observed in the HS-GC-MS analysis. Therefore, it became clear that this drug substance facilitates the minor decomposition of DMSO in the HS-GC analysis. In such a case, formaldehyde is an artifact peak, or ghost peak, rather than a true impurity of the drug substance. The false positive results of formaldehyde were also found in other four compounds (three drug substances and one reagent) which are all in the form of HCl or HBr salts, suggesting that generation of formaldehyde from DMSO could be a widely occurred phenomenon in HS-GC analysis of alkyl amines in the form of HCl or HBr salts, when DMSO-containing diluents are used during sample preparation.

Understanding Muscle Protein Dynamics: Technical Considerations for Advancing Sarcopenia Research

Sarcopenia, which is the loss of muscle mass and strength that occurs with aging, involves imbalanced muscle protein turnover (i.e., protein breakdown exceeding synthesis), which in turn exacerbates other clinical conditions such as type 2 diabetes mellitus, obesity, osteoporosis, and cancer, thereby worsening the quality of life in older adults. This imbalance is attributed in part to the resistance of aged muscle to anabolic stimuli such as dietary protein/amino acids and resistance exercise known as anabolic resistance. Despite research efforts, no practical therapeutics have been successfully discovered possibly because of a lack of understanding of the dynamic nature of muscle protein, and the use of indirect assessments of muscle mass. Herein, we briefly discuss the regulation of protein turnover in response to the abovementioned anabolic stimuli with respect to anabolic resistance and optimal protein intake, followed by methodological considerations for advancing sarcopenia research, including assessments of muscle mass and dynamics.

Metabolism of 17β-estradiol by Novosphingobium sp. ES2-1 as probed via HRMS combined with 13C3-labeling

This study investigated the biodegradation and metabolic mechanisms of 17β-estradiol (E2) by Novosphingobium sp. ES2-1 isolated from the activated sludge in a domestic sewage treatment plant (STP). It could degrade 97.1% E2 (73.5 μmol/L) in 7 d with a biodegradation half-life of 1.29 d. E2 was initially converted to estrone (E1), then to 4-hydroxyestrone (4-OH-E1), before subsequent monooxygenation reactions cleaved 4-OH-E1 into a metabolite with long-chain ketones structure (metabolite P8). However, when 4-OH-E1 was cleaved through the 4,5-seco pathway, the resulting phenol ring cleavage product could randomly condense with NH₃ to yield a pyridine derivative, accompanied by the uncertain loss of a carboxy group at C4 before the condensation. The derivative was further oxidized into the metabolites with both pyridine and long-chain ketones structure (metabolite N5) through a similar formation mechanism as for P8 performed. This research presents several novel metabolites and shows that E2 can be biodegraded into the metabolite with long-chain structure through three optional pathways, thereby reducing E2 contamination.

Osmotrophic glucose and leucine assimilation and its impact on EPA and DHA content in algae

The uptake of dissolved organic compounds, that is, osmotrophy, has been shown to be an efficient nutritional strategy for algae. However, this mode of nutrition may affect the biochemical composition, for example, the fatty acid (FA) contents, of algal cells. This study focused on the osmotrophic assimilation of glucose and leucine by selected seven algal strains belonging to chlorophytes, chrysophytes, cryptophytes, dinoflagellates and euglenoids. Our laboratory experiments with stable isotope labeling showed that osmotrophy occurred in four of the selected seven strains. However, only three of these produced long chain omega-3 FAs eicosapentaenoic acid (EPA; 20:5ω3) and docosahexaenoic acid (DHA; 22:6ω3). High glucose content (5 mg L-1) affected negatively on the total FAs of Mallomonas kalinae and the total omega-3 FAs of Cryptomonas sp. Further, glucose assimilation explained 35% (negative effect) and leucine assimilation 48% (positive effect) of the variation of EPA, DHA and the FAs related to their synthesis in Cryptomonas sp. Moderate glucose concentration (2 mg L-1) was found to enhance the growth of Cryptomonas ozolinii, whereas low leucine (20 µg L-1) enhanced the growth of M. kalinae. However, no systematic effect of osmotrophy on growth rates was detected. Our study shows that osmotrophic assimilation of algae is species and compound specific, and that the effects of the assimilated compounds on algal metabolism also varies depending on the species.

Methods and Algorithms for Quantitative Proteomics by Mass Spectrometry

Protein quantitation by mass spectrometry has always been a resourceful technique in protein discovery, and more recently it has leveraged the advent of clinical proteomics. A single mass spectrometry analysis experiment provides identification and quantitation of proteins as well as information on posttranslational modifications landscape. By contrast, protein array technologies are restricted to quantitation of targeted proteins and their modifications. Currently, there are an overwhelming number of quantitative mass spectrometry methods for protein and peptide quantitation. The aim here is to provide an overview of the most common mass spectrometry methods and algorithms used in quantitative proteomics and discuss the computational aspects to obtain reliable quantitative measures of proteins, peptides and their posttranslational modifications. The development of a pipeline using commercial or freely available software is one of the main challenges in data analysis of many experimental projects. Recent developments of R statistical programming language make it attractive to fully develop pipelines for quantitative proteomics. We discuss concepts of quantitative proteomics that together with current R packages can be used to build highly customizable pipelines.

Multiplexed Profiling and Data Processing Methods to Identify Temperature-Regulated Primary Metabolites Using Gas Chromatography Coupled to Mass Spectrometry

This book chapter describes the analytical procedures required for the profiling of a metabolite fraction enriched for primary metabolites. The profiling is based on routine gas chromatography coupled to mass spectrometry (GC-MS). The generic profiling method is adapted to plant material, specifically to the analysis of plant material that was exposed to temperature stress. The method can be combined with stable isotope labeling and tracing experiments and is equally applicable to preparations of plant material and microbial photosynthetic organisms. The described methods are modular and can be multiplexed, that is, the same sample or a paired identical backup sample can be analyzed sequentially by more than one of the described procedures. The modules include rapid sampling and metabolic inactivation protocols for samples in a wide weight range, sample extraction procedures, chemical derivatization steps that are required to make the metabolite fraction amenable to gas chromatographic analysis, routine GC-MS methods, and procedures of data processing and data mining. A basic and extendable set of standardizations for metabolite recovery and retention index alignment of the resulting GC-MS chromatograms is included. The methods have two applications: (1) The rapid screening for changes of relative metabolite pools sizes under temperature stress and (2) the verification by exact quantification using GC-MS protocols that are extended by internal and external standardization.

Cellular Fatty Acid Analysis in Macrophage Using Stable Isotope Labeling

Fatty acids (FAs) are essential for building complex lipids, posttranslational modifications, and energetics. FAs can be imported from extracellular sources or synthesized by cells. The analysis of fatty acid methyl esters (FAMEs) by gas chromatography-mass spectrometry (GC-MS) allows for the quantitative analysis of long-chain and very-long-chain fatty acid content of cells. When coupled with isotopic labeling, this approach can elucidate the synthetic pathways being engaged by the cells, and the relative contribution of synthesis and import to maintain lipid content. Here, we describe a method for total cellular fatty acid analysis in macrophages.

Non-Targeted Mass Isotopolome Analysis Using Stable Isotope Patterns to Identify Metabolic Changes

Gas chromatography coupled with mass spectrometry can provide an extensive overview of the metabolic state of a biological system. Analysis of raw mass spectrometry data requires powerful data processing software to generate interpretable results. Here we describe a data processing workflow to generate metabolite levels, mass isotopomer distribution, similarity and variability analysis of metabolites in a nontargeted manner, using stable isotope labeling. Using our data analysis software, no bioinformatic or programming background is needed to generate results from raw mass spectrometry data.

Cadmium allocation to grains in durum wheat exposed to low Cd concentrations in hydroponics

This study aims to characterize the response of durum wheat to different concentrations of Cd found in agricultural soils. One French durum wheat cultivar (i.e. Sculptur) was exposed to low concentrations of Cd (5 nM or 100 nM) in hydroponics. After anthesis, the plants were fed with a solution enriched with the stable isotope ¹¹¹Cd to trace the newly absorbed Cd. Plants were sampled at anthesis and grain maturity to assess how plant growth, Cd uptake and partitioning among organs, as well as Cd remobilization, differed between the two Cd exposure levels. Durum wheat did not show any visual symptoms of Cd toxicity, regardless of which Cd treatment was applied. However, post-anthesis durum wheat growth was 14% penalized at 100 nM due to the large transpiration-based accumulation of Cd in leaves at this stage. The allocation of Cd to the grains was not restricted but enhanced at 100 nM compared to 5 nM. Both the root-to-shoot Cd translocation and the fraction of aboveground Cd allocated to grains were higher in plants exposed to 100 nM. Cadmium was remobilized exclusively from roots and stems, and remobilized Cd contributed on average to 40-45% of the Cd accumulated in mature grains, regardless of which Cd treatment was applied. The relevance of these results to decreasing the concentration of Cd in durum wheat grains is discussed.

Profiling thiol metabolites in myocardial infarction human serum by stable isotope labeling assisted liquid chromatography-mass spectrometry

Myocardial Infarction (MI) is one of the most common causes of deaths worldwide. Thiols have been reported to play a key role in physiological and pathological processes of MI. Comprehensive analysis of thiols would be conducive to fully elucidate the relation between thiols and MI. In the current study, we analyze the metabolomic differences of thiols in serum between MI patients (n = 30) and healthy controls (HCs, n = 30) by stable isotope labeling-dispersive solid phase extraction-liquid chromatography-full scan-Orbitrap-mass spectrometry analysis (IL-DSPE-LC-full scan-Orbitrap MS) method. We detected 300 potential thiols in serum of MI patients and HCs, among which, 67 thiols were positively or putatively identified. Furthermore, we found that the levels of 71 thiols in serum exhibited significant difference between MI patients and HCs. In the transsulfuration pathway, we observed that Cys and Hcys were upregulated, while GSH were downregulated. Our results provide a comprehensive understanding of thiols metabolome in human serum between MI patients and HCs.

Metandem: An online software tool for mass spectrometry-based isobaric labeling metabolomics

Mass spectrometry-based stable isotope labeling provides the advantages of multiplexing capability and accurate quantification but requires tailored bioinformatics tools for data analysis. Despite the rapid advancements in analytical methodology, it is often challenging to analyze stable isotope labeling-based metabolomics data, particularly for isobaric labeling using MS/MS reporter ions for quantification. We report Metandem, a novel online software tool for isobaric labeling-based metabolomics, freely available at http://metandem.com/web/. Metandem provides a comprehensive data analysis pipeline integrating feature extraction, metabolite quantification, metabolite identification, batch processing of multiple data files, online parameter optimization for custom datasets, data normalization, and statistical analysis. Systematic evaluation of the Metandem tool was demonstrated on UPLC-MS/MS, nanoLC-MS/MS, CE-MS/MS and MALDI-MS platforms, via duplex, 4-plex, 10-plex, and 12-plex isobaric labeling experiments and the application to various biological samples.

High-sensitivity quantification of glycosphingolipid glycans by ESI-MS utilizing ozonolysis-based release and isotopic Girard's reagent labeling

Quantitative analysis of glycosphingolipids (GSLs) has been hindered by the lack of chromogenic groups for spectral detection or active functional groups for specific derivatization. In this study, a highly sensitive method based on ozonolysis-induced release and isotopic Girard's reagent P labeling of GSL glycans coupled with mass spectrometric detection for the quantification of animal tissue GSLs is developed. First, different approaches for the release of glycans from GSLs were compared with each other and the ozonolysis-based method was found to have the highest glycan yield under relative mild reaction conditions. Then a relative quantification method of ozonolysis-released GSL glycans based on stable isotope labeling using nondeuterated (d0-) and 2,3,4,5,6-pentadeuterated (d5-) Girard's reagent P (GP) was established, and its good linearity, accuracy and reproducibility were statistically verified. Finally, the new method was successfully applied to revealing the difference between porcine brain and liver as well as between the brain of normal and aging rats in GSL glycome by online hydrophilic interaction liquid chromatography coupling with ultraviolet detection and tandem mass spectrometry (HILIC-UV-MS/MS). This novel method is versatile and sensitive, enabling accurate quantitative analysis of tissue GSLs and showing great significance for glycomic studies.

Stable isotope labeling combined with liquid chromatography-tandem mass spectrometry for comprehensive analysis of short-chain fatty acids

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-d₅ (4-AMBA-d₅), were synthesized to label SCFAs from the feces of mice and SCFA standards, respectively. The 4-AMBA-d₅ 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.

Synthetic phosphopeptides: From spike-in standards to affinity tools for protein-protein interaction studies

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 γH2AX (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.

ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments

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.

A Guide to Mass Spectrometry-Based Quantitative Proteomics

Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.

Method for Quantifying Oxidized Methionines and Application to HIV-1 Env

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. Graphical Abstract ᅟ.

Methyl-selective isotope labeling using α-ketoisovalerate for the yeast Pichia pastoris recombinant protein expression system

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.

On the use of Pichia pastoris for isotopic labeling of human GPCRs for NMR studies

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.

Stable isotope labeling approaches for NMR characterization of glycoproteins using eukaryotic expression systems

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.

A 13C isotope labeling method for the measurement of lignin metabolic flux in Arabidopsis stems

BACKGROUND

Metabolic fluxes represent the functional phenotypes of biochemical pathways and are essential to reveal the distribution of precursors among metabolic networks. Although analysis of metabolic fluxes, facilitated by stable isotope labeling and mass spectrometry detection, has been applied in the studies of plant metabolism, we lack experimental measurements for carbon flux towards lignin, one of the most abundant polymers in nature.

RESULTS

We developed a feeding strategy of excised Arabidopsis stems with 13C labeled phenylalanine (Phe) for the analysis of lignin biosynthetic flux. We optimized the feeding methods and found the stems continued to grow and lignify. Consistent with lignification profiles along the stems, higher levels of phenylpropanoids and activities of lignin biosynthetic enzymes were detected in the base of the stem. In the feeding experiments, 13C labeled Phe was quickly accumulated and used for the synthesis of phenylpropanoid intermediates and lignin. The intermediates displayed two different patterns of labeling kinetics during the feeding period. Analysis of lignin showed rapid incorporation of label into all three subunits in the polymers.

CONCLUSIONS

Our feeding results demonstrate the effectiveness of the stem feeding system and suggest a potential application for the investigations of other aspects in plant metabolism. The supply of exogenous Phe leading to a higher lignin deposition rate indicates the availability of Phe is a determining factor for lignification rates.

Cholesterol is enriched in the sphingolipid patches on the substrate near nonpolarized MDCK cells, but not in the sphingolipid domains in their plasma membranes

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.

Food supply and size class depending variations in phytodetritus intake in the benthic foraminifer Ammonia tepida

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.

Acylated Quinic Acids Are the Main Salicortin Metabolites in the Lepidopteran Specialist Herbivore Cerura vinula

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.

DeltaMS: a tool to track isotopologues in GC- and LC-MS data

INTRODUCTION

Stable isotopic labeling experiments are powerful tools to study metabolic pathways, to follow tracers and fluxes in biotic and abiotic transformations and to elucidate molecules involved in metal complexing.

OBJECTIVE

To introduce a software tool for the identification of isotopologues from mass spectrometry data.

METHODS

DeltaMS relies on XCMS peak detection and X¹³CMS isotopologue grouping and then analyses data for specific isotope ratios and the relative error of these ratios. It provides pipelines for recognition of isotope patterns in three experiment types commonly used in isotopic labeling studies: (1) search for isotope signatures with a specific mass shift and intensity ratio in one sample set, (2) analyze two sample sets for a specific mass shift and, optionally, the isotope ratio, whereby one sample set is isotope-labeled, and one is not, (3) analyze isotope-guided perturbation experiments with a setup described in X¹³CMS.

RESULTS

To illustrate the versatility of DeltaMS, we analyze data sets from case-studies that commonly pose challenges in evaluation of natural isotopes or isotopic signatures in labeling experiment. In these examples, the untargeted detection of sulfur, bromine and artificial metal isotopic patterns is enabled by the automated search for specific isotopes or isotope signatures.

CONCLUSION

DeltaMS provides a platform for the identification of (pre-defined) isotopologues in MS data from single samples or comparative metabolomics data sets.

Stable Isotope Quantitative N-Glycan Analysis by Liquid Separation Techniques and Mass Spectrometry

Liquid phase separation analysis and subsequent quantitation remains a challenging task for protein-derived oligosaccharides due to their inherent structural complexity and diversity. Incomplete resolution or co-detection of multiple glycan species complicates peak area-based quantitation and associated statistical analysis when optical detection methods are used. The approach outlined herein describes the utilization of stable isotope variants of commonly used fluorescent tags that allow for mass-based glycan identification and relative quantitation following separation by liquid chromatography (LC) or capillary electrophoresis (CE). Comparability assessment of glycoprotein-derived oligosaccharides is performed by derivatization with commercially available isotope variants of 2-aminobenzoic acid or aniline and analysis by LC- and CE-mass spectrometry. Quantitative information is attained from the extracted ion chromatogram/electropherogram ratios generated from the light and heavy isotope clusters.

Structure and Dynamics of Immunoglobulin G Glycoproteins

Immunoglobulin G (IgG) is a major serum glycoprotein that exerts the role of antibody in the immune system. This multifunctional glycoprotein couples antigen recognition with a variety of effector functions promoted via interactions with various IgG-binding proteins. Given its versatile functionality, IgG has recently been used for therapeutic interventions. Evidence indicates that the carbohydrate moieties of IgG glycoproteins critically affect their antibody functions, particularly the effector functions mediated by the interactions with Fcγ receptors (FcγRs). N-glycans at specific positions of FcγR also contribute both positively and negatively to the interactions with IgG. The integration of multilateral biophysical approaches, including X-ray crystallography, nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, has provided structural insights into the mechanisms underlying the glycofunctions of this interacting system. The N-glycans of IgG and FcγR mediate their interactions by either strengthening or weakening the affinity on the basis of their glycoforms. Moreover, the N-glycosylation of IgG-Fc is a prerequisite to maintain the integrity of the quaternary structure of the sites interacting with the effector molecules and can also control functionally relevant local conformations. The biopharmaceutical significance of these glycan functions is discussed from a structural point of view.