Integrated quantification and identification of aldehydes and ketones in biological samples

Girard Derivatization-Based Enrichment Strategy for Profiling the Carbonyl Submetabolome in Biological Samples

Numerous bioactive compounds containing carbonyl groups, including aldehydes and ketones, are widely acknowledged as potential biomarkers for several diseases and are implicated in the development of metabolic disorders. However, the detection of carbonyl metabolites is hindered by challenges, such as poor ionization efficiency, low biological concentration, instability, and complexity of the sample matrix. To overcome these limitations, we developed a Girard derivatization-based enrichment (GDBE) strategy for capturing and comprehensively profiling carbonyl metabolites in biological samples. A functionalized resin, named carbonyl capture and reporter-ion installation (CCRI) resins, was synthesized to selectively capture carbonyl metabolites via a Girard reaction. After unwanted metabolites were removed, the hydrazone derivatives were cleaved from the solid-phase resins and subjected to LC-MS analysis. The proposed GDBE strategy exhibits exceptional selectivity for capturing and enriching carbonyl metabolites. Moreover, this method surpasses current detection limits by enhancing the MS sensitivity and facilitating structural characterization of hydrazone derivatives by a specific MS/MS fragmentation signature. Using the GDBE method, 957 potential carbonyl metabolites were successfully identified in liver tissue from alcohol-fed mice. Among them, 76 carbonyl metabolites were annotated, indicating the potential of this strategy for the efficient nontargeted profiling of the carbonyl submetabolome in complex biological samples.

Deciphering polymer degradation chemistry via integrating new database construction into suspect screening analysis

Water-soluble synthetic polymers and their environmental degradation products are overlooked but important industrial pollutants in wastewater. However, the detection of degradation products is limited to bulk solution chemistry and molecular-level analysis remains unreachable. In this work, we assessed the feasibility of current suspect screening and nontarget workflow using liquid chromatography-high resolution mass spectrometry (LC-HRMS) to elucidate molecular level information about polyacrylamide (PAM) and its degraded products by free radicals. Radical chain scission of PAM (10 kDa) using heat-activated persulfate was conducted to simulate hydraulic fracturing conditions in the deep subsurface. We found that the current workflows in the commercial software generated predicted formulae with low accuracy, due to limited capability of peak picking and formula prediction for high mass and charge features. By modeling literature-reported degradation pathways, we constructed a degradation product database of over 463 000 unique formulae, which improved the accuracy of the predicted formula. For the matched features, the ratio of aldehyde/ketone terminating molecule abundance was found to increase over 24 h degradation time, suggesting increasing content of aldehydes by radical-induced oxidative chain scission of PAM. This is contradictory to previously proposed ratios of carbon-centered radical position on polymer backbone initiated by hydroxyl radicals. Using in silico fragmentation of MS1 features, we identified 11 structures with confidence levels 2b and 3 using their MS2 information. This is the first attempt to resolve complex polymer degradation chemistry using HRMS that can advance our ability to detect water-soluble polymer pollutants and their transformation products in environmental samples.

Improved quantification of carbonyl sub-metabolome by liquid chromatography mass spectrometry using a fragment controlled multiplexed isotopic tag

BACKGROUND

Carbonyl-containing metabolites are a class of key intermediate in metabolism, which has potentials to be biomarkers. Since their poor ionization, derivatization reagents, such as dansylhydrazine, are usually used to improve the sensitivity and/or to facilitate quantification. However, most current carbonyl derivatization reagents only have two channels, one is isotopically labeled and the other one is non-labeled. To quantify more samples in a run and using data-independent acquisition (DIA) mode to get comprehensive and unbiased mass fragmentation, we proposed a fragment-controlled isotopic tag, called DiMe-FP-NHNH2 (FP) which has five channels: Δ0, Δ3, Δ6, Δ9, and Δ12, thus up to 5 samples can be analyzed in a run.

RESULTS

The most important improvement is that the FP tag can produce multiple characteristic signals in tandem mass, diagnostic ions and neutral losses, which helps to selectively detect aldehydes/ketones for targeted and untargeted analysis. To exhibit all capabilities of the FP tag, we mimicked an untargeted metabolomics experiment, which comprises two steps. First, discovery step, using Data-Independent Analysis (SWATH-MS) and the labeling of two channels (Δ0 and Δ3), we picked out aldehyde/ketone from the pooled urine samples based on three characteristic signals, including isotope patterns, diagnostic ions, and neutral losses. Second, five-plex quantification, relative and absolute quantification were achieved in a single LC-MS analysis. Notably, because of different nominal masses, the FP tag can be used on any low or high resolution mass spectrometers.

SIGNIFICANCE

The benefits and performance of the FP tag are demonstrated by the analysis of urine samples collected from patients from a prostate cancer study, in which more than a thousand features were found based on MS1 fingerprint, but only around 120 aldehyde/ketone candidates were confirmed with characteristic signals and nine of which were quantified showing significant differences from healthy and reference urine samples.

Isotope-coded derivatization with designed Girard-type reagent as charged isobaric mass tags for non-targeted profiling and discovery of natural aldehydes by liquid chromatography-tandem mass spectrometry

Aldehyde-containing metabolites are reactive electrophiles that have attracted extensive attention due to their widespread occurrence in organisms and natural foods. Herein we described a newly-designed Girard's reagent, 1-(4-hydrazinyl-4-oxobutyl)pyridin-1-ium bromide (HBP), as charged tandem mass (MS/MS) tags to facilitate selective capture, sensitive detection and semi-targeted discovery of aldehyde metabolites via hydrazone formation. After HBP labeling, the detection signals of the test aldehydes were increased by 21-2856 times, with the limits of detection were 2.5-7 nM. Upon isotope-coded derivatization with a pair of labeling reagents, HBP-d₀ and its deuterium-labeled counterpart HBP-d₅, the aldehyde analytes were converted to hydrazone derivatives, which generated characteristic neutral fragments of 79 Da and 84 Da, respectively. The isobaric HBP-d₀/HBP-d₅ labeling based LC-MS/MS method was validated by relative quantification of human urinary aldehydes (slope=0.999, R² > 0.99, RSDs ≤ 8.5%) and discrimination analysis between diabetic and control samples. The unique isotopic doubles (Δm/z = 5 Da) by dual neutral loss scanning (dNLS) provided a generic reactivity-based screening strategy that allowed non-targeted profiling and identification of endogenous aldehydes even amidst noisy data. The LC-dNLS-MS/MS screening of cinnamon extracts led to finding 61 possible natural aldehydes and guided discovery of 10 previously undetected congeners in this medicinal plant.

Ozonation of lake water and wastewater: Identification of carbonous and nitrogenous carbonyl-containing oxidation byproducts by non-target screening

Ozonation of drinking water and wastewater is accompanied by the formation of disinfection byproducts (DBPs) such as low molecular weight aldehydes and ketones from the reactions of ozone with dissolved organic matter (DOM). By applying a recently developed non-target workflow, 178 carbonous and nitrogenous carbonyl compounds were detected during bench-scale ozonation of two lake waters and three secondary wastewater effluent samples and full-scale ozonation of secondary treated wastewater effluent. An overlapping subset of carbonyl compounds (20%) was detected in all water types. Moreover, wastewater effluents showed a significantly higher fraction of N-containing carbonyl compounds (30%) compared to lake water (17%). All carbonyl compounds can be classified in 5 main formation trends as a function of increasing specific ozone doses. Formation trends upon ozonation and comparison of results in presence and absence of the ^•OH radical scavenger DMSO in combination with kinetic and mechanistic information allowed to elucidate potential carbonyl structures. A link between the detected carbonyl compounds and their precursors was established by ozonating six model compounds (phenol, 4-ethylphenol, 4-methoxyphenol, sorbic acid, 3-buten-2-ol and acetylacetone). About one third of the detected carbonous carbonyl compounds detected in real waters was also detected by ozonating model compounds. Evaluation of the non-target analysis data revealed the identity of 15 carbonyl compounds, including hydroxylated aldehydes and ketones (e.g. hydroxyacetone, confidence level (CL) = 1), unsaturated dicarbonyls (e.g. acrolein, CL = 1; 2-butene-1,4-dial, CL = 1; 4-oxobut-2-enoic acid, CL = 2) and also a nitrogen-containing carbonyl compound (2-oxo-propanamide, CL =1). Overall, this study shows the formation of versatile carbonous and nitrogenous carbonyl compounds upon ozonation involving ozone and ^•OH reactions. Carbonyl compounds with unknown toxicity might be formed, and it could be demonstrated that acrolein, malondialdehyde, methyl glyoxal, 2-butene-1,4-dial and 4-oxo-pentenal are degraded during biological post-treatment.

Formation of carbonyl compounds during ozonation of lake water and wastewater: Development of a non-target screening method and quantification of target compounds

Ozonation of natural waters is typically associated with the formation of carbonyl compounds (aldehydes, ketones and ketoacids), a main class of organic disinfection byproducts (DBPs). However, the detection of carbonyl compounds in water and wastewater is challenged by multiple difficulties inherent to their physicochemical properties. A non-target screening method involving the derivatisation of carbonyl compounds with p-toluenesulfonylhydrazine (TSH) followed by their analysis using liquid chromatography coupled to electrospray ionisation high-resolution mass spectrometry (LC-ESI-HRMS) and an advanced non-target screening and data processing workflow was developed. The workflow was applied to investigate the formation of carbonyl compounds during ozonation of different water types including lake water, aqueous solutions containing Suwannee River Fulvic acid (SRFA), and wastewater. A higher sensitivity for most target carbonyl compounds was achieved compared to previous derivatisation methods. Moreover, the method allowed the identification of known and unknown carbonyl compounds. 8 out of 17 target carbonyl compounds were consistently detected above limits of quantification (LOQs) in most ozonated samples. Generally, the concentrations of the 8 detected target compounds decreased in the order: formaldehyde > acetaldehyde > glyoxylic acid > pyruvic acid > glutaraldehyde > 2,3-butanedione > glyoxal > 1-acetyl-1-cyclohexene. The DOC concentration-normalised formation of carbonyl compounds during ozonation was higher in wastewater and SRFA-containing water than in lake water. The specific ozone doses and the type of the dissolved organic matter (DOM) played a predominant role for the extent of formation of carbonyl compounds. Five formation trends were distinguished for different carbonyl compounds. Some compounds were produced continuously upon ozonation even at high ozone doses, while others reached a maximum concentration at a certain ozone dose above which they decreased. Concentrations of target and peak areas of non-target carbonyl compounds during full-scale ozonation at a wastewater treatment plant showed an increase as a function of the specific ozone dose (sum of 8 target compounds ∼ 280 µg/L at 1 mgO₃/mgC), followed by a significant decrease after biological sand filtration (> 64-94% abatement for the different compounds). This highlights the biodegradability of target and non-target carbonyl compounds and the importance of biological post-treatment.

Reconstruction of Glutathione Metabolism in the Neuronal Model of Rotenone-Induced Neurodegeneration Using Mass Isotopologue Analysis with Hydrophilic Interaction Liquid Chromatography-Zeno High-Resolution Multiple Reaction Monitoring

Accurate reconstruction of metabolic pathways is an important prerequisite for interpreting metabolomics changes and understanding the diverse biological processes in disease models. A tracer-based metabolomics strategy utilizes stable isotope-labeled precursors to resolve complex pathways by tracing the labeled atom(s) to downstream metabolites through enzymatic reactions. Isotope enrichment analysis is informative and achieved by counting total labeled atoms and acquiring the mass isotopologue distribution (MID) of the intact metabolite. However, quantitative analysis of labeled metabolite substructures/moieties (MS² fragments) can offer more valuable insights into the reaction connections through measuring metabolite transformation. In order to acquire the isotopic labeling information at the intact metabolite and moiety level simultaneously, we developed a method that couples hydrophilic interaction liquid chromatography (HILIC) with Zeno trap-enabled high-resolution multiple reaction monitoring (MRM^HR). The method enabled accurate and reproducible MID quantification for intact metabolites as well as their fragmented moieties, with notably high sensitivity in the MS² fragmentation mode based on the measurement of ¹³C- or ¹⁵N-labeled cellular samples. The method was applied to human-induced pluripotent stem cell-derived neurons to trace the fate of ¹³C/¹⁵N atoms from D-¹³C₆-glucose/L-¹⁵N₂-glutamine added to the media. With the MID analysis of both intact metabolites and fragmented moieties, we validated the pathway reconstruction of de novo glutathione synthesis in mid-brain neurons. We discovered increased glutathione oxidization from both basal and newly synthesized glutathione pools under neuronal oxidative stress. Furthermore, the significantly decreased de novo glutathione synthesis was investigated and associated with altered activities of several key enzymes, as evidenced by suppressed glutamate supply via glucose metabolism and a diminished flux of glutathione synthetic reaction in the neuronal model of rotenone-induced neurodegeneration.

Comprehensive Online Reversed-Phase × Chiral Two-Dimensional Liquid Chromatography-Mass Spectrometry with Data-Independent Sequential Window Acquisition of All Theoretical Fragment-Ion Spectra-Acquisition for Untargeted Enantioselective Amino Acid Analysis

This work presents an advanced analytical platform for untargeted enantioselective amino acid analysis (eAAA) by comprehensive achiral × chiral 2D-LC hyphenated to ESI-QTOF-MS/MS utilizing data-independent SWATH (sequential window acquisition of all theoretical fragment-ion spectra) technology. The methodology involves N-terminal pre-column derivatization with 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC; AccQ) as retention, selectivity, and MS tag, supporting retention and UV detection in RPLC (¹D), chiral recognition, and thus enantioselectivity by the core-shell tandem column composed of a quinine carbamate weak anion exchanger (QN-AX) and a zwitterionic chiral ion-exchanger (ZWIX(+)) (²D) as well as the ionization efficiency during positive electrospray ionization due to a high proton affinity of the AQC label. Furthermore, the urea-type MS tag gives rise to the generation of AQC-tag characteristic signature fragments in MS². The latter allows the chemoselective mass spectrometric filtering of targeted and untargeted N-derivatized amino acids or related labeled species. The chiral core-shell tandem column provides a complete enantioselective amino acid profile of all proteinogenic amino acids within 1 min, with full baseline separation of all enantiomers, but without resolution of isomeric Ile/allo-Ile (aIle)/Leu, which can be resolved by RPLC. The entire LC × LC separation occurs within a total run time of 60 min (¹D), with the chiral ²D operated in gradient elution mode and a cycle time of 60 s. A strategy to mine the 2D-LC-SWATH data is presented and demonstrated for the qualitative eAAA of two peptide hydrolysate samples of therapeutic peptides containing common and uncommon as well as primary and secondary amino acids. Absolute configuration assignment of amino acids using template matching for all proteinogenic amino acids was made feasible due to method robustness and the inclusion of an isotopically labeled L-[U-¹³C¹⁵N]-AA standard. The quantification performance of this LC × LC-MS/MS assay was also evaluated. Accuracies were acceptable for the majority of AAs enabling AA composition determination in peptide hydrolysates simultaneously with configuration assignment, as exemplified by oxytocin. This methodology represents a step toward truly untargeted 2D enantioselective amino acid analysis and metabolomics.

A high-specificity aniline-based mass tag for aldehyde detection

RATIONALE

We studied an aldehyde-labeling reagent, N-{2-[(4-aminophenoxy)methyl]benzyl}-N,N-diethylethanaminium bromide (CAX-A), containing an aniline functional group for the detection of aldehydes with high specificity.

METHODS

Six standard aldehydes were labeled by CAX-A and analyzed using LC-ESI-Orbitrap-MS. The aldehydes (each 40 nmol) were derivatized with CAX-A in the presence of sodium cyanoborohydride at room temperature overnight. The labeling reaction was applied to two urine samples for the detection of putative aldehydes.

RESULTS

All six standard CAX-aldehyde derivatives were detected as precursor ions by dilution to 830 fmol/injection (signal-to-noise [S/N] ratio 587-1573). A total of 2184 MS1 features were detected overall in urine and blanks, of which 14 were putative aldehydes found only in urine.

CONCLUSIONS

CAX-A can provide three levels of specificity for aldehyde detection. First is the known labeling specificity of the aniline functional group for aldehydes, which we confirmed here by observing a significant peak only from the aldehyde (S/N = 3388) when a mixture of an aldehyde, a ketone (no peak), and a quinone (S/N = 2.3) was tested. Second is the ease of formation of an analyte-characteristic first product ion (via anchimeric-assisted loss of triethylamine as a neutral) in MS2 from a CAX-labeled analyte. Third is the formation of a characteristic second product ion via loss of CO in MS3. CAX-A enables the specific, convenient detection of putative aldehydes in urine.

Integrated Chemical Interpretation and Network Pharmacology Analysis to Reveal the Anti-Liver Fibrosis Effect of Penthorum chinense

Liver fibrosis is a disease with complex pathological mechanisms. Penthorum chinense Pursh (P. chinense) is a traditional Chinese medicine (TCM) for liver injury treatment. However, the pharmacological mechanisms of P. chinense on liver fibrosis have not been investigated and clarified clearly. This study was designed to investigate the chemicals in P. chinense and explore its effect on liver fibrosis. First, we developed a highly efficient method, called DDA-assisted DIA, which can both broaden mass spectrometry (MS) coverage and MS² quality. In DDA-assisted DIA, data-dependent acquisition (DDA) and data-independent acquisition (DIA) were merged to construct a molecular network, in which 1,094 mass features were retained in Penthorum chinense Pursh (P. chinense). Out of these, 169 compounds were identified based on both MS¹ and MS² analysis. After that, based on a network pharmacology study, 94 bioactive compounds and 440 targets of P. chinense associated with liver fibrosis were obtained, forming a tight compound–target network. Meanwhile, the network pharmacology experimental results showed that multiple pathways interacted with the HIF-1 pathway, which was first identified involved in P. chinense. It could be observed that some proteins, such as TNF-α, Timp1, and HO-1, were involved in the HIF-1 pathway. Furthermore, the pharmacological effects of P. chinense on these proteins were verified by CCl₄-induced rat liver fibrosis, and P. chinense was found to improve liver functions through regulating TNF-α, Timp1, and HO-1 expressions. In summary, DDA-assisted DIA could provide more detailed compound information, which will help us to annotate the ingredients of TCM, and combination with computerized network pharmacology provided a theoretical basis for revealing the mechanism of P. chinense.

Progress and Challenges in Quantifying Carbonyl-Metabolomic Phenomes with LC-MS/MS

Carbonyl-containing metabolites widely exist in biological samples and have important physiological functions. Thus, accurate and sensitive quantitative analysis of carbonyl-containing metabolites is crucial to provide insight into metabolic pathways as well as disease mechanisms. Although reversed phase liquid chromatography electrospray ionization mass spectrometry (RPLC-ESI-MS) is widely used due to the powerful separation capability of RPLC and high specificity and sensitivity of MS, but it is often challenging to directly analyze carbonyl-containing metabolites using RPLC-ESI-MS due to the poor ionization efficiency of neutral carbonyl groups in ESI. Modification of carbonyl-containing metabolites by a chemical derivatization strategy can overcome the obstacle of sensitivity; however, it is insufficient to achieve accurate quantification due to instrument drift and matrix effects. The emergence of stable isotope-coded derivatization (ICD) provides a good solution to the problems encountered above. Thus, LC-MS methods that utilize ICD have been applied in metabolomics including quantitative targeted analysis and untargeted profiling analysis. In addition, ICD makes multiplex or multichannel submetabolome analysis possible, which not only reduces instrument running time but also avoids the variation of MS response. In this review, representative derivatization reagents and typical applications in absolute quantification and submetabolome profiling are discussed to highlight the superiority of the ICD strategy for detection of carbonyl-containing metabolites.

Simultaneous 3-Nitrophenylhydrazine Derivatization Strategy of Carbonyl, Carboxyl and Phosphoryl Submetabolome for LC-MS/MS-Based Targeted Metabolomics with Improved Sensitivity and Coverage

Metabolomics is a powerful and essential technology for profiling metabolic phenotypes and exploring metabolic reprogramming, which enables the identification of biomarkers and provides mechanistic insights into physiology and disease. However, its applications are still limited by the technical challenges particularly in its detection sensitivity for the analysis of biological samples with limited amount, necessitating the development of highly sensitive approaches. Here, we developed a highly sensitive liquid chromatography tandem mass spectrometry method based on a 3-nitrophenylhydrazine (3-NPH) derivatization strategy that simultaneously targets carbonyl, carboxyl, and phosphoryl groups for targeted metabolomic analysis (HSD^ccp-TM) in biological samples. By testing 130 endogenous metabolites including organic acids, amino acids, carbohydrates, nucleotides, carnitines, and vitamins, we showed that the derivatization strategy resulted in significantly improved detection sensitivity and chromatographic separation capability. Metabolic profiling of merely 60 oocytes and 5000 hematopoietic stem cells primarily isolated from mice demonstrated that this method enabled routine metabolomic analysis in trace amounts of biospecimens. Moreover, the derivatization strategy bypassed the tediousness of inferring the MS fragmentation patterns and simplified the complexity of monitoring ion pairs of metabolites, which greatly facilitated the metabolic flux analysis (MFA) for glycolysis, the tricarboxylic acid (TCA) cycle, and pentose phosphate pathway (PPP) in cell cultures. In summary, the novel 3-NPH derivatization-based method with high sensitivity, good chromatographic separation, and broad coverage showed great potential in promoting metabolomics and MFA, especially in trace amounts of biospecimens.

Discovery of Polyhydroxyalkyl Pyrazine Generation upon Coffee Roasting by In-Bean Labeling Experiments

The major non-volatile reaction products formed from free amino acids during the early stage of coffee roasting were investigated using biomimetic in-bean experiments with labeled and unlabeled free amino acids. Comprehensive untargeted screening by ultra-high performance liquid chromatography-electrospray-ionization-quadrupole time-of-flight-tandem mass spectrometry (UHPLC-ESI-QToF-MS) in data-independent acquisition (DIA) mode was carried out and modeling by orthogonal partial least-squares discriminant analysis (OPLS-DA) helped in revealing 11 pyrazine structures identified in coffee for the first time. 2-(2',3',4'-Trihydroxybutyl)-(5/6)-methyl-pyrazine (1) and 2,(5/6)-bis(2',3',4'-trihydroxybutyl)-pyrazine (2) were the most prominent compounds, while 2-(3',4'-dihydroxybutyl)-(5/6)-methyl-pyrazine (5) and 2-(2',3',4'-trihydroxybutyl)-(5/6)-(2'-hydroxyethyl)-pyrazine (10) were not even previously identified in other food matrices. The structures could be verified by means of additional biomimetic in-bean experiments with labeled sucrose leveraging the carbon module labeling (CAMOLA) approach. Based on these results, plausible formation pathways could be formulated fitting into the known Maillard reaction mechanisms. Sucrose was highlighted as the predominant precursor of the carbon backbone of all identified pyrazines butonly 33-55% of the nitrogen atoms originated from free amino acids.

Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry

The inclusion of preliminary chemical labeling (derivatization) in the analysis process by such powerful and widespread methods as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a popular and widely used methodological approach. This is due to the need to remove some fundamental limitations inherent in these powerful analytic methods. Although a number of special reviews has been published discussing the utilization of derivatization approaches, the purpose of the present critical review is to comprehensively summarize, characterize and evaluate most of the previously developed and practically applied, as well as recently proposed representative derivatization reagents for ESI-MS and MALDI-MS platforms in their mostly sensitive positive ion mode and frequently hyphenated with separation techniques. The review is focused on the use of preliminary chemical labeling to facilitate the detection, identification, structure elucidation, quantification, profiling or MS imaging of compounds within complex matrices. Two main derivatization approaches, namely the introduction of permanent charge-fixed or highly proton affinitive residues into analytes are critically evaluated. In situ charge-generation, charge-switch and charge-transfer derivatizations are considered separately. The potential of using reactive matrices in MALDI-MS and chemical labeling in MS-based omics sciences is given.

Genetically encoded formaldehyde sensors inspired by a protein intra-helical crosslinking reaction

Formaldehyde (FA) has long been considered as a toxin and carcinogen due to its damaging effects to biological macromolecules, but its beneficial roles have been increasingly appreciated lately. Real-time monitoring of this reactive molecule in living systems is highly desired in order to decipher its physiological and/or pathological functions, but a genetically encoded FA sensor is currently lacking. We herein adopt a structure-based study of the underlying mechanism of the FA-responsive transcription factor HxlR from Bacillus subtilis, which shows that HxlR recognizes FA through an intra-helical cysteine-lysine crosslinking reaction at its N-terminal helix α1, leading to conformational change and transcriptional activation. By leveraging this FA-induced intra-helical crosslinking and gain-of-function reorganization, we develop the genetically encoded, reaction-based FA sensor-FAsor, allowing spatial-temporal visualization of FA in mammalian cells and mouse brain tissues.

Chemical Isotope Labeling LC-MS for Metabolomics

Due to the great diversity of chemical and physical properties of metabolites as well as a wide range of concentrations of metabolites present in metabolomic samples, performing comprehensive and quantitative metabolome analysis is a major analytical challenge. Conventional approach of combining various techniques and methods with each detecting a fraction of the metabolome can lead to the increase in overall metabolomic coverage. However, this approach requires extensive investment in equipment and analytical expertise with still relatively low coverage and low sample throughput. Chemical isotope labeling (CIL) liquid chromatography mass spectrometry (LC-MS) offers an alternative means of increasing metabolomic coverage while maintaining high quantification precision and accuracy. This chapter describes the CIL LC-MS method and its key features for metabolomic analysis.

Stochastic dynamic mass spectrometric quantification of steroids in mixture - Part II

This paper deals with quantification of the following steroids in mixture: hydrocortisone (1), deoxycorticosterone (2), progesterone (3) and methyltestosterone (4) by means of mass spectrometry and implementing our innovative stochatic dynamic functional relationship between the analyte concentration in solution and the experimental variable intensity. The mass spectrometric data are correlated independently using chromatography. Chemometric analysis is carried out.

A Comprehensive Review on Source, Types, Effects, Nanotechnology, Detection, and Therapeutic Management of Reactive Carbonyl Species Associated with Various Chronic Diseases

Continuous oxidation of carbohydrates, lipids, and amino acids generate extremely reactive carbonyl species (RCS). Human body comprises some important RCS namely hexanal, acrolein, 4-hydroxy-2-nonenal, methylglyoxal, malondialdehyde, isolevuglandins, and 4-oxo-2- nonenal etc. These RCS damage important cellular components including proteins, nucleic acids, and lipids, which manifests cytotoxicity, mutagenicity, multitude of adducts and crosslinks that are connected to ageing and various chronic diseases like inflammatory disease, atherosclerosis, cerebral ischemia, diabetes, cancer, neurodegenerative diseases and cardiovascular disease. The constant prevalence of RCS in living cells suggests their importance in signal transduction and gene expression. Extensive knowledge of RCS properties, metabolism and relation with metabolic diseases would assist in development of effective approach to prevent numerous chronic diseases. Treatment approaches for RCS associated diseases involve endogenous RCS metabolizers, carbonyl metabolizing enzyme inducers, and RCS scavengers. Limited bioavailability and bio efficacy of RCS sequesters suggest importance of nanoparticles and nanocarriers. Identification of RCS and screening of compounds ability to sequester RCS employ several bioassays and analytical techniques. Present review describes in-depth study of RCS sources, types, properties, identification techniques, therapeutic approaches, nanocarriers, and their role in various diseases. This study will give an idea for therapeutic development to combat the RCS associated chronic diseases.

Formation and Fate of Carbonyls in Potable Water Reuse Systems

Low molecular weight, uncharged compounds have been the subject of considerable study at advanced treatment plants employed for potable water reuse. However, previously identified compounds only account for a small fraction of the total dissolved organic carbon remaining after reverse osmosis treatment. Uncharged carbonyl compounds (e.g., aldehydes and ketones) formed during oxidation have rarely been monitored in potable water reuse systems. To determine the relative importance of these compounds to final product water quality, samples were collected from six potable water reuse facilities and one conventional drinking water treatment plant. Saturated carbonyl compounds (e.g., formaldehyde, acetone) and α,β-unsaturated aldehydes (e.g., acrolein, crotonaldehyde) were quantified with a sensitive new analytical method. Relatively high concentrations of carbonyls (i.e., above 7 μM) were observed after ozonation of wastewater effluent. Biological filtration reduced concentrations of carbonyls by over 90%. Rejection of the carbonyls during reverse osmosis was correlated with molecular weight, with concentrations decreasing by 33% to 58%. Transformation of carbonyls resulted in decreases in concentration of 10% to 90% during advanced oxidation, with observed decreases consistent with rate constants for reactions of the compounds with hydroxyl radicals. Overall, carbonyl compounds accounted for 19% to 38% of the dissolved organic carbon in reverse osmosis-treated water.

Ring-Cleavage Products Produced during the Initial Phase of Oxidative Treatment of Alkyl-Substituted Aromatic Compounds

Chemical oxidation with hydroxyl radical (HO^•) and sulfate radical (SO₄^•-) is often used to treat water contaminated with aromatic compounds. Although oxidation of aromatics by these radicals has been studied for decades, the commonly accepted transformation pathway-sequential hydroxylation of the ring followed by ring cleavage and mineralization of the resulting products-does not account for the loss of the parent compound observed during the initial phase of the process. To assess the importance of pathways for aromatic compound oxidation that do not result in ring hydroxylation, we identified products formed after the initial reaction between HO^• or SO₄^•- and benzene, toluene, ethylbenzene, and (BTEX) xylene isomers. We quantified products of ring hydroxylation and oxidation of alkyl substituents as well as a suite of ring-cleavage products, including acetaldehyde, formic acid, 6-, 7-, or 8-carbon oxoenals and oxodials. Other ring-cleavage products, which were most likely aldehydes and organic acids, were observed but not quantified. When SO₄^•- was used as the oxidant, aromatic organosulfates also were formed. Our results indicated that the initial phase of the oxidation process involves radical addition, hydrogen abstraction, or one-electron transfer to the ring followed by reaction with O₂. The hydroxycyclohexadienylperoxy radical produced in this reaction can eliminate hydroperoxyl radical (HO₂^•) to produce a phenolic compound or it can rearrange to form a bicyclic peroxy intermediate that subsequently undergoes ring cleavage. Hydroxylation of the ring and oxidation of the alkyl substituent accounted for approximately 15-40% of the reacted mass of the parent compound. Ring-cleavage products for which quantification was possible accounted for approximately 2 to 10% of the reacted mass. Our results raise concerns about the formation of toxic ring-cleavage products during the initial stage of oxidation whenever HO^• or SO₄^•- is used for the treatment of water containing benzene or alkylbenzenes.

Sensitive mass spectrometric analysis of carbonyl metabolites in human urine and fecal samples using chemoselective modification

Metabolites with ketone or aldehyde functionalities comprise a large proportion of the human metabolome, most notably in the form of sugars. However, these reactive molecules are also generated through oxidative stress or gut microbiota metabolism and have been linked to disease development. The discovery and structural validation of this class of metabolites over the large concentration range found in human samples is crucial to identify their links to pathogenesis. Herein, we have utilized an advanced chemoselective probe methodology alongside bioinformatic analysis to identify carbonyl-metabolites in urine and fecal samples. In total, 99 metabolites were identified in urine samples and the chemical structure for 40 metabolites were unambiguously validated using a co-injection procedure. We also describe the preparation of a metabolite-conjugate library of 94 compounds utilized to efficiently validate these ketones and aldehydes. This method was used to validate 33 metabolites in a pooled fecal sample extract to demonstrate the potential for rapid and efficient metabolite detection over a wide metabolite concentration range. This analysis revealed the presence of six metabolites that have not previously been detected in either sample type. The constructed library can be utilized for straightforward, large-scale, and expeditious analysis of carbonyls in any sample type.

SWATH-MS for metabolomics and lipidomics: critical aspects of qualitative and quantitative analysis

INTRODUCTION

While liquid chromatography coupled to mass spectrometric detection in the selected reaction monitoring detection mode offers the best quantification sensitivity for omics, the number of target analytes is limited, must be predefined and specific methods developed. Data independent acquisition (DIA), including SWATH using quadrupole time of flight or orbitrap mass spectrometers and generic acquisition methods, has emerged as a powerful alternative technique for quantitative and qualitative analyses since it can cover a wide range of analytes without predefinition.

OBJECTIVES

Here we review the current state of DIA, SWATH-MS and highlight novel acquisition strategies for metabolomics and lipidomics and opportunities for data analysis tools.

METHOD

Different databases were searched for papers that report developments and applications of DIA and in particular SWATH-MS in metabolomics and lipidomics.

RESULTS

DIA methods generate digital sample records that can be mined retrospectively as further knowledge is gained and, with standardized acquisition schemes, used in multiple studies. The different chemical spaces of metabolites and lipids require different specificities, hence different acquisition and data processing approaches must be considered for their analysis.

CONCLUSIONS

Although the hardware and acquisition modes are well defined for SWATH-MS, a major challenge for routine use remains the lack of appropriate software tools capable of handling large datasets and large numbers of analytes.

Chemoselective probe for detailed analysis of ketones and aldehydes produced by gut microbiota in human samples

New strategies are required for the discovery of unknown bioactive molecules produced by gut microbiota in the human host. Herein, we utilize a chemoselective probe immobilized to magnetic beads for analysis of carbonyls in human fecal samples. We identified 112 metabolites due to femtomole analysis and an increased mass spectrometric sensitivity by up to six orders of magnitude.

Bioanalytical and Mass Spectrometric Methods for Aldehyde Profiling in Biological Fluids

Human exposure to aldehydes is implicated in multiple diseases including diabetes, cardiovascular diseases, neurodegenerative disorders (i.e., Alzheimer’s and Parkinson’s Diseases), and cancer. Because these compounds are strong electrophiles, they can react with nucleophilic sites in DNA and proteins to form reversible and irreversible modifications. These modifications, if not eliminated or repaired, can lead to alteration in cellular homeostasis, cell death and ultimately contribute to disease pathogenesis. This review provides an overview of the current knowledge of the methods and applications of aldehyde exposure measurements, with a particular focus on bioanalytical and mass spectrometric techniques, including recent advances in mass spectrometry (MS)-based profiling methods for identifying potential biomarkers of aldehyde exposure. We discuss the various derivatization reagents used to capture small polar aldehydes and methods to quantify these compounds in biological matrices. In addition, we present emerging mass spectrometry-based methods, which use high-resolution accurate mass (HR/AM) analysis for characterizing carbonyl compounds and their potential applications in molecular epidemiology studies. With the availability of diverse bioanalytical methods presented here including simple and rapid techniques allowing remote monitoring of aldehydes, real-time imaging of aldehydic load in cells, advances in MS instrumentation, high performance chromatographic separation, and improved bioinformatics tools, the data acquired enable increased sensitivity for identifying specific aldehydes and new biomarkers of aldehyde exposure. Finally, the combination of these techniques with exciting new methods for single cell analysis provides the potential for detection and profiling of aldehydes at a cellular level, opening up the opportunity to minutely dissect their roles and biological consequences in cellular metabolism and diseases pathogenesis.

Advancing untargeted metabolomics using data-independent acquisition mass spectrometry technology

Metabolomics quantitatively measures metabolites in a given biological system and facilitates the understanding of physiological and pathological activities. With the recent advancement of mass spectrometry (MS) technology, liquid chromatography-mass spectrometry (LC-MS) with data-independent acquisition (DIA) has been emerged as a powerful technology for untargeted metabolomics due to its capability to acquire all MS2 spectra and high quantitative accuracy. In this trend article, we first introduced the basic principles of several common DIA techniques including MS^E, all ion fragmentation (AIF), SWATH, and MSX. Then, we summarized and compared the data analysis strategies to process DIA-based untargeted metabolomics data, including metabolite identification and quantification. We think the advantages of the DIA technique will enable its broad application in untargeted metabolomics.

A combined targeted/untargeted LC-MS/MS-based screening approach for mammalian cell lines treated with ionic liquids: Toxicity correlates with metabolic profile

This work presents the development and validation of a quantitative HILIC UHPLC-ESI-QTOF-MS/MS method for amino acids combined with untargeted metabolic profiling of human corneal epithelial (HCE) cells after treatment with ionic liquids. The work included a preliminary metabotoxicity screening of 14 different ionic liquids, of which 9 carefully selected ionic liquids were chosen for a metabolomics study. This study is focused on the correlation between the toxicity of the ionic liquids and their metabolic profiles. The method development included the comparison of different MS/MS acquisition modes. A sequential window acquisition of all theoretical fragment ion mass spectra (SWATH) method with variable Q1 window widths and narrow Q1 target windows of 5 Da for most of the amino acids was selected as the optimal acquisition mode. Due to the absence of a true blank matrix, ¹³C,¹⁵N-isotopically labelled amino acids were utilized as surrogate calibrants, instead of proteinogenic amino acids. Partial least squares (PLS) analysis of the median effective concentrations (EC₅₀) of 9 selected ionic liquids showed a correlation with their metabolic profile measured by the untargeted screening.

Quantitative analysis of chemoresistance-inducing fatty acid in food supplements using UHPLC-ESI-MS/MS

Polyunsaturated fatty acids are important signaling molecules. A recent study reported hexadeca-4Z,7Z,10Z,13Z-tetraenoic acid, 12-oxo-5Z,8E,10E-heptadecatrienoic acid, and (12S)-hydroxy-5Z,8E,10E-heptadecatrienoic acid as chemotherapy resistance-inducing factors when tumor cells were treated with cisplatin. Marine-based food supplements like fish oil or algae extracts are rich in polyunsaturated fatty acids and can contain large amounts of hexadeca-4Z,7Z,10Z,13Z-tetraenoic acid. Thus, it was concluded that oral uptake of hexadeca-4Z,7Z,10Z,13Z-tetraenoic acid might induce chemoresistance as shown in a mouse model. Cancer patients tend to consume food supplements containing polyunsaturated fatty acids on a regular basis. The uptake of hexadeca-4Z,7Z,10Z,13Z-tetraenoic acid and (12S)-hydroxy-5Z,8E,10E-heptadecatrienoic acid should be controlled, because even low concentrations of 0.5 ng mL^-1 showed chemoresistance-inducing effects in animal experiments. For accurate analysis of hexadeca-4Z,7Z,10Z,13Z-tetraenoic acid and (12S)-hydroxy-5Z,8E,10E-heptadecatrienoic acid a validated method was developed by using ultrahigh-performance liquid chromatography hyphenated to quadrupole time of flight mass spectrometry via electrospray ionization and sample preparation by solid-phase extraction (SPE) with 3-aminopropyl silica. A combined targeted/untargeted approach was utilized using MS/MS by data-independent acquisition with SWATH and applied to commercial food supplements (refined fish oil, fish oil capsules, algae oil capsules, and flaxseed capsules). Accurate quantification of hexadeca-4Z,7Z,10Z,13Z-tetraenoic acid and (12S)-hydroxy-5Z,8E,10E-heptadecatrienoic acid on the MS/MS level with simultaneous untargeted fatty acid screening revealed additional information. The LODs for hexadeca-4Z,7Z,10Z,13Z-tetraenoic acid and (12S)-hydroxy-5Z,8E,10E-heptadecatrienoic acid were 0.036 ng mL^-1 and 0.054 ng mL^-1, respectively. Since hexadeca-4Z,7Z,10Z,13Z-tetraenoic acid was present in the samples in large amounts and (12S)-hydroxy-5Z,8E,10E-heptadecatrienoic was not expected to be present in high concentrations, two calibration ranges, namely, 0.5-20 ng mL^-1 and 5-200 ng mL^-1, were validated. An untargeted screening identified 18-39 free fatty acids being present in the lipid extracts of the food supplement samples. Graphical abstract ᅟ.

Redox Signaling by Reactive Electrophiles and Oxidants

The concept of cell signaling in the context of nonenzyme-assisted protein modifications by reactive electrophilic and oxidative species, broadly known as redox signaling, is a uniquely complex topic that has been approached from numerous different and multidisciplinary angles. Our Review reflects on five aspects critical for understanding how nature harnesses these noncanonical post-translational modifications to coordinate distinct cellular activities: (1) specific players and their generation, (2) physicochemical properties, (3) mechanisms of action, (4) methods of interrogation, and (5) functional roles in health and disease. Emphasis is primarily placed on the latest progress in the field, but several aspects of classical work likely forgotten/lost are also recollected. For researchers with interests in getting into the field, our Review is anticipated to function as a primer. For the expert, we aim to stimulate thought and discussion about fundamentals of redox signaling mechanisms and nuances of specificity/selectivity and timing in this sophisticated yet fascinating arena at the crossroads of chemistry and biology.

Comprehensive MS/MS profiling by UHPLC-ESI-QTOF-MS/MS using SWATH data-independent acquisition for the study of platelet lipidomes in coronary artery disease

A non-targeted lipidomics workflow based on C8 core-shell particle ultra high-performance liquid chromatography (UHPLC) hyphenated to ESI-QTOF-MS in data-independent acquisition (DIA) mode with sequential window acquisition of all theoretical fragment ion spectra (SWATH) was developed and applied to differential platelet lipidomics profiling of cardiovascular disease patients (stable angina pectoris (n = 10), ST-elevated myocardial infarction (n = 13)) against healthy controls (n = 10). DIA with SWATH generates comprehensive MS and MS/MS data throughout the entire chromatograms and all study samples. Hence, chromatograms can be extracted based on precursors or fragments which provided some benefits in terms of assay specificity in some cases. SWATH acquisition offers flexible experimental design with variable Q1 isolation windows. Liquid chromatography as well as SWATH settings were optimized to cover the lipidome of human platelets. The flexibility of the SWATH experiment design was utilized to implement target SWATH windows with narrow 5 Da Q1 precursor ion selection width (multiple reaction monitoring (MRM)-like SWATH windows) for the detection of low abundant oxidized phospholipids. Data processing was performed with MS-DIAL, and its feasibilities and caveats are discussed by illustrative examples. Thereby, identification of lipids is still a bottleneck in non-targeted lipidomics workflow. MS-DIAL, however, offers automatic identification via spectral matching using an in silico library. In total 1971 molecular features were detected cross the samples of which 611 were identified (total score >70%). The quality of the acquired data was validated with embedded quality control samples (n = 11). 80.3% of all features detected in the QC samples showed a coefficient of variation of below 30%. Multivariate statistics were used to visualize differences in the lipidome of distinct sample groups at a false discovery rate of 5%.

Multiomics tools for the diagnosis and treatment of rare neurological disease

Conventional workup of rare neurological disease is frequently hampered by diagnostic delay or lack of diagnosis. While biomarkers have been established for many neurometabolic disorders, improved methods are required for diagnosis of previously unidentified or underreported causes of rare neurological disease. This would result in a higher diagnostic yield and increased patient numbers required for interventional studies. Recent studies using next-generation sequencing and metabolomics have led to identification of novel disease-causing genes and biomarkers. This combined approach can assist in overcoming challenges associated with analyzing and interpreting the large amount of data obtained from each technique. In particular, metabolomics can support the pathogenicity of sequence variants in genes encoding enzymes or transporters involved in metabolic pathways. Moreover, metabolomics can show the broader perturbation caused by inborn errors of metabolism and identify a metabolic fingerprint of metabolic disorders. As such, using "omics" has great potential to meet the current needs for improved diagnosis and elucidation of rare neurological disease.

Metabolomic spectral libraries for data-independent SWATH liquid chromatography mass spectrometry acquisition

High-quality mass spectral libraries have become crucial in mass spectrometry-based metabolomics. Here, we investigate a workflow to generate accurate mass discrete and composite spectral libraries for metabolite identification and for SWATH mass spectrometry data processing. Discrete collision energy (5-100 eV) accurate mass spectra were collected for 532 metabolites from the human metabolome database (HMDB) by flow injection analysis and compiled into composite spectra over a large collision energy range (e.g., 10-70 eV). Full scan response factors were also calculated. Software tools based on accurate mass and predictive fragmentation were specially developed and found to be essential for construction and quality control of the spectral library. First, elemental compositions constrained by the elemental composition of the precursor ion were calculated for all fragments. Secondly, all possible fragments were generated from the compound structure and were filtered based on their elemental compositions. From the discrete spectra, it was possible to analyze the specific fragment form at each collision energy and it was found that a relatively large collision energy range (10-70 eV) gives informative MS/MS spectra for library searches. From the composite spectra, it was possible to characterize specific neutral losses as radical losses using in silico fragmentation. Radical losses (generating radical cations) were found to be more prominent than expected. From 532 metabolites, 489 provided a signal in positive mode [M+H]⁺ and 483 in negative mode [M-H]^-. MS/MS spectra were obtained for 399 compounds in positive mode and for 462 in negative mode; 329 metabolites generated suitable spectra in both modes. Using the spectral library, LC retention time, response factors to analyze data-independent LC-SWATH-MS data allowed the identification of 39 (positive mode) and 72 (negative mode) metabolites in a plasma pool sample (total 92 metabolites) where 81 previously were reported in HMDB to be found in plasma. Graphical abstract Library generation workflow for LC-SWATH MS, using collision energy spread, accurate mass, and fragment annotation.

Quantitative profiling of carbonyl metabolites directly in crude biological extracts using chemoselective tagging and nanoESI-FTMS

The extensive range of chemical structures, wide range of abundances, and chemical instability of metabolites present in the metabolome pose major analytical challenges that are difficult to address with existing technologies. To address these issues, one approach is to target a subset of metabolites that share a functional group, such as ketones and aldehydes, using chemoselective tagging. Here we report a greatly improved chemoselective method for the quantitative analysis of hydrophilic and hydrophobic carbonyl-containing metabolites directly in biological samples. This method is based on direct tissue or cells extraction with simultaneous derivatization of stable and labile carbonylated metabolites using N-[2-(aminooxy)ethyl]-N,N-dimethyl-1-dodecylammonium (QDA) and 13CD3 labeled QDA. We combined innovations of direct quenching of biological sample with frozen derivatization conditions under the catalyst N,N-dimethyl-p-phenylenediamine, which facilitated the formation of oxime stable-isotope ion pairs differing by m/z 4.02188 while minimizing metabolite degradation. The resulting oximes were extracted by HyperSep C8 tips to remove interfering compounds, and the products were detected using nano-electrospray ionization interfaced with a Thermo Fusion mass spectrometer. The quaternary ammonium tagging greatly increased electrospray MS detection sensitivity and the signature ions pairs enabled simple identification of carbonyl compounds. The improved method showed the lower limits of quantification for carbonyl standards to be in the range of 0.20-2 nM, with linearity of R2 > 0.99 over 4 orders of magnitude. We have applied the method to assign 66 carbonyls in mouse tumor tissues, many of which could not be assigned solely by accurate mass and tandem MS. Fourteen of the metabolites were quantified using authentic standards. We also demonstrated the suitability of this method for determining 13C labeled isotopologues of carbonyl metabolites in 13C6-glucose-based stable isotope-resolved metabolomic (SIRM) studies.

Practical application of in silico fragmentation based residue screening with ion mobility high-resolution mass spectrometry

RATIONALE

A screening concept for residues in complex matrices based on liquid chromatography coupled to ion mobility high-resolution mass spectrometry LC/IMS-HRMS is presented. The comprehensive four-dimensional data (chromatographic retention time, drift time, mass-to-charge and ion abundance) obtained in data-independent acquisition (DIA) mode was used for data mining. An in silico fragmenter utilizing a molecular structure database was used for suspect screening, instead of targeted screening with reference substances.

METHODS

The utilized data-independent acquisition mode relies on the MS^E concept; where two constantly alternating HRMS scans (low and high fragmentation energy) are acquired. Peak deconvolution and drift time alignment of ions from the low (precursor ion) and high (product ion) energy scan result in relatively clean product ion spectra. A bond dissociation in silico fragmenter (MassFragment) supplied with mol files of compounds of interest was used to explain the observed product ions of each extracted candidate component (chromatographic peak).

RESULTS

Two complex matrices (fish and bovine liver extract) were fortified with 98 veterinary drugs. Out of 98 screened compounds 94 could be detected with the in silico based screening approach. The high correlation among drift time and m/z value of equally charged ions was utilized for an orthogonal filtration (ranking). Such an orthogonal ion mobility based filter removes multiply charged ions (e.g. peptides and proteins from the matrix) as well as noise and artefacts. Most significantly, this filtration dramatically reduces false positive findings but hardly increases false negative findings.

CONCLUSIONS

The proposed screening approach may offer new possibilities for applications where reference compounds are hardly or not at all commercially available. Such areas may be the analysis of metabolites of drugs, pyrrolizidine alkaloids, marine toxins, derivatives of sildenafil or novel designer drugs (new psychoactive substances). Copyright © 2017 John Wiley & Sons, Ltd.

Anion-Exchange Chromatography Coupled to High-Resolution Mass Spectrometry: A Powerful Tool for Merging Targeted and Non-targeted Metabolomics

In this work, simultaneous targeted metabolic profiling by isotope dilution and non-targeted fingerprinting is proposed for cancer cell studies. The novel streamlined metabolomics workflow was established using anion-exchange chromatography (IC) coupled to high-resolution mass spectrometry (MS). The separation time of strong anion-exchange (2 mm column, flow rate 380 μL min^-1, injection volume 5 μL) could be decreased to 25 min for a target list comprising organic acids, sugars, sugar phosphates, and nucleotides. Internal standardization by fully ¹³C labeled Pichia pastoris extracts enabled absolute quantification of the primary metabolites in adherent cancer cell models. Limits of detection (LODs) in the low nanomolar range and excellent intermediate precisions of the isotopologue ratios (on average <5%, N = 5, over 40 h) were observed. As a result of internal standardization, linear dynamic ranges over 4 orders of magnitude (5 nM-50 μM, R² > 0.99) were obtained. Experiments on drug-sensitive versus resistant SW480 cancer cells showed the feasibility of merging analytical tasks into one analytical run. Comparing fingerprinting with and without internal standard proved that the presence of the ¹³C labeled yeast extract required for absolute quantification was not detrimental to non-targeted data evaluation. Several interesting metabolites were discovered by accurate mass and comparing MS2 spectra (acquired in ddMS2 mode) with spectral libraries. Significant differences revealed distinct metabolic phenotypes of drug-sensitive and resistant SW480 cells.

Development of High-Performance Chemical Isotope Labeling LC-MS for Profiling the Carbonyl Submetabolome

Metabolites containing a carbonyl group represent several important classes of molecules including various forms of ketones and aldehydes such as steroids and sugars. We report a high-performance chemical isotope labeling (CIL) LC-MS method for profiling the carbonyl submetabolome with high coverage and high accuracy and precision of relative quantification. This method is based on the use of dansylhydrazine (DnsHz) labeling of carbonyl metabolites to change their chemical and physical properties to such an extent that the labeled metabolites can be efficiently separated by reversed phase LC and ionized by electrospray ionization MS. In the analysis of six standards representing different carbonyl classes, acetaldehyde could be ionized only after labeling and MS signals were significantly increased for other 5 standards with an enhancement factor ranging from ∼15-fold for androsterone to ∼940-fold for 2-butanone. Differential ¹²C- and ¹³C-DnsHz labeling was developed for quantifying metabolic differences in comparative samples where individual samples were separately labeled with ¹²C-labeling and spiked with a ¹³C-labeled pooled sample, followed by LC-MS analysis, peak pair picking, and peak intensity ratio measurement. In the replicate analysis of a 1:1 ¹²C-/¹³C-labeled human urine mixture (n = 6), an average of 2030 ± 39 pairs per run were detected with 1737 pairs in common, indicating the possibility of detecting a large number of carbonyl metabolites as well as high reproducibility of peak pair detection. The average RSD of the peak pair ratios was 7.6%, and 95.6% of the pairs had a RSD value of less than 20%, demonstrating high precision for peak ratio measurement. In addition, the ratios of most peak pairs were close to the expected value of 1.0 (e.g., 95.5% of them had ratios of between 0.67 and 1.5), showing the high accuracy of the method. For metabolite identification, a library of DnsHz-labeled standards was constructed, including 78 carbonyl metabolites with each containing MS, retention time (RT), and MS/MS information. This library and an online search program for labeled carbonyl metabolite identification based on MS, RT, and MS/MS matches have been implemented in a freely available Website, www.mycompoundid.org . Using this library, out of the 1737 peak pairs detected in urine, 33 metabolites were positively identified. In addition, 1333 peak pairs could be matched to the metabolome databases with most of them belonging to the carbonyl metabolites. These results show that ¹²C-/¹³C-DnsHz labeling LC-MS is a useful tool for profiling the carbonyl submetabolome of complex samples with high coverage.

Fluorescent probes for imaging formaldehyde in biological systems

Formaldehyde (FA) is a common environmental toxin but is also endogenously produced through a diverse array of essential biological processes, including mitochondrial one-carbon metabolism, metabolite oxidation, and nuclear epigenetic modifications. Its high electrophilicity enables reactivity with a wide variety of biological nucleophiles, which can be beneficial or detrimental to cellular function depending on the context. New methods that enable detection of FA in living systems can help disentangle the signal/stress dichotomy of this simplest reactive carbonyl species (RCS), and fluorescent probes for FA with high selectivity and sensitivity have emerged as promising chemical tools in this regard.

Hyphenated MS-based targeted approaches in metabolomics

Review of targeted metabolomics, with a focus on the description of analytical methods.

Bacterial persistence is an active σS stress response to metabolic flux limitation

While persisters are a health threat due to their transient antibiotic tolerance, little is known about their phenotype and what actually causes persistence. Using a new method for persister generation and high‐throughput methods, we comprehensively mapped the molecular phenotype of Escherichia coli during the entry and in the state of persistence in nutrient‐rich conditions. The persister proteome is characterized by σ^S‐mediated stress response and a shift to catabolism, a proteome that starved cells tried to but could not reach due to absence of a carbon and energy source. Metabolism of persisters is geared toward energy production, with depleted metabolite pools. We developed and experimentally verified a model, in which persistence is established through a system‐level feedback: Strong perturbations of metabolic homeostasis cause metabolic fluxes to collapse, prohibiting adjustments toward restoring homeostasis. This vicious cycle is stabilized and modulated by high ppGpp levels, toxin/anti‐toxin systems, and the σ^S‐mediated stress response. Our system‐level model consistently integrates past findings with our new data, thereby providing an important basis for future research on persisters.

SWATH acquisition mode for drug metabolism and metabolomics investigations

Aim: Sequential window acquisition of all theoretical fragment-ion spectra (SWATH) has recently emerged as a powerful high resolution mass spectrometric data independent acquisition technique. In the present work, the potential and challenges of an integrated strategy based on LC-SWATH/MS for simultaneous drug metabolism and metabolomics studies was investigated. Methodology: The richness of SWATH data allows numerous data analysis approaches, including: detection of metabolites by prediction; metabolite detection by mass defect filtering; quantification from high-resolution MS precursor chromatograms or fragment chromatograms. Multivariate analysis can be applied to the data from the full scan or SWATH windows and allows changes in endogenous metabolites as well as xenobiotic metabolites, to be detected. Principal component variable grouping detects intersample variable correlation and groups variables with similar profiles which simplifies interpretation and highlights related ions and fragments. Principal component variable grouping can extract product ion spectra from the data collected by fragmenting a wide precursor ion window. Conclusion: It was possible to characterize 28 vinpocetine metabolites in urine, mostly mono- and di-hydroxylated forms, and detect endogenous metabolite expression changes in urine after the administration of a single dose of a model drug (vinpocetine) to rats.