Chromatography High-resolution Tandem Mass Spectrometry Research Articles

Transcriptomic and Weighted Gene Co-expression Correlation Network Analysis Reveal Resveratrol Biosynthesis Mechanisms Caused by Bud Sport in Grape Berry

Resveratrol is a natural polyphenol compound produced in response to biotic and abiotic stresses in grape berries. However, changes in resveratrol caused by bud sport in grapes are scarcely reported. In this study, trans-resveratrol and cis-resveratrol were identified and quantified in the grape berries of ‘Summer Black’ and its bud sport ‘Nantaihutezao’ from the veraison to ripening stages using ultra performance liquid chromatography-high resolution tandem mass spectrometry (UPLC-HRMS). We found that bud sport accumulates the trans-resveratrol earlier and increases the contents of cis-resveratrol in the earlier stages but decreases its contents in the later stages. Simultaneously, we used RNA-Seq to identify 51 transcripts involved in the stilbene pathways. In particular, we further identified 124 and 19 transcripts that negatively correlated with the contents of trans-resveratrol and cis-resveratrol, respectively, and four transcripts encoding F3'5'H that positively correlated with the contents of trans-resveratrol by weighted gene co-expression network analysis (WGCNA). These transcripts may play important roles in relation to the synergistic regulation of metabolisms of resveratrol. The results of this study can provide a theoretical basis for the genetic improvement of grapes.

Herbal Medicine Must Be Treated with Care—A Case Report on Aconitine

Pathologists usually only request a screening for natural toxic substances if plant material has been observed during autopsy or if there exists a hint in the police investigation file. This situation is aggravated by the fact that most toxins are not covered by typical immunoassays and gas chromatography–mass spectrometry (GC–MS) profiling systems. In addition, only a few forensic toxicological libraries based on liquid chromatography coupled to high-resolution tandem mass spectrometry (LC–HRMS/MS) exist. In the following case, femoral blood and urine were applied to systematic toxicological analysis (STA). However, the concentrations determined in blood did not lead to death. Consequently, a liquid chromatography high-resolution tandem mass spectrometry (LC–HRMS/MS) screening approach was applied. Aconitine was quantitated in all specimens taken during autopsy and urine and bile fluid screened for aconitine metabolites. Aconitine, jesaconitine, hypaconitine, and mesaconitine were found in the root piece collected from the duodenum. Apart from aconitine, no other alkaloids were detected in the urine or in the femoral blood sample. The highest concentrations of aconitine were found in gastric content (55.2 μg/mL), bile fluid (11.7 μg/mL), and liver (9.14 μg/g), and least in femoral blood (0.15 μg/mL) and cerebrospinal fluid (0.07 μg/mL). The liver/peripheral blood ratio amounted to 61 L/kg and indicated that aconitine undergoes postmortem redistribution. During our metabolism investigation, we found 3-dehydrogen-aconitine in the urine and bile fluid sample and N-deethyl-aconitine only in the bile fluid sample. If the routine GC–MS screening approach does not come up with a toxin, then LC–HRMS/MS profiling could represent the method of choice. In this case aconitine was identified. The concentrations determined were compared to those reported in literature and clearly indicate that the deceased died due to an aconitine overdose.

Sponge-associated sp. RM66 metabolome induction with N-acetylglucosamine: Antibacterial, antifungal and anti-trypanosomal activities.

The marine sponge Amphimedon sp., collected from Hurghada (Egypt) was investigated for its sponge-derived actinomycetes diversity. Nineteen actinomycetes were cultivated and phylogenetically identified using 16S rDNA gene sequencing were carried out. The strains belong to genera Kocuria, Dietzia, Micrococcus, Microbacterium and Streptomyces. Many silent biosynthetic genes clusters were investigated using genome sequencing of actinomycete strains and has revealed in particular the genus Streptomyces that has indicated their exceptional capacity for the secondary metabolites production that not observed under classical cultivation conditions. In this study, the effect of N-acetylglucosamine on the metabolome of Streptomyces sp. RM66 was investigated using three actinomycetes media (ISP2, M1 and MA). In total, twelve extracts were produced using solid and liquid fermentation approaches. Liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) data were analysed using metabolomics tools to compare natural product production across all crude extracts. Our study highlighted the elicitation effect of N-acetylglucosamine on the secondary metabolite profiles of Streptomyces sp. RM66. These results highlight the of N-acetylglucosamine application as an elicitor to induce the cryptic metabolites and for increasing the chemical diversity. All the twelve extracts were tested for their antibacterial activity was tested against Staphylococcus aureus NCTC 8325, antifungal activity against Candida albicans 5314 (ATCC 90028) and anti-trypanosomal activity against Trypanosoma brucei brucei. Extract St1 showed the most potent one with activities 2.3, 3.2 and 4.7 ug/ml as antibacterial, antifungal and anti-trypanosomal, respectively.

Novel Strategy for Untargeted Chiral Metabolomics using Liquid Chromatography-High Resolution Tandem Mass Spectrometry.

Stereospecific recognition of metabolites plays a significant role in the detection of potential disease biomarkers thereby providing new insights in diagnosis and prognosis. D-Hdroxy/amino acids are recognized as potential biomarkers in several metabolic disorders. Despite continuous advances in metabolomics technologies, the simultaneous measurement of different classes of enantiomeric metabolites in a single analytical run remains challenging. Here, we develop a novel strategy for untargeted chiral metabolomics of hydroxy/amine groups (-OH/-NH2) containing metabolites, including all hydroxy acids (HAs) and amino acids (AAs), by chiral derivatization coupled with liquid chromatography-high resolution tandem mass spectrometry (LC-HR-MS/MS). Diacetyl-tartaric anhydride (DATAN) was used for the simultaneous derivatization of-OH/-NH2 containing metabolites as well as the resulting diastereomers, and all the derivatized metabolites were resolved in a single analytical run. Data independent MS/MS acquisition (DIA) was applied to positively identify DATAN-labeled metabolites based on reagent specific diagnostic fragment ions. We discriminated chiral from achiral metabolites based on the reversal of elution order of D and L isomers derivatized with the enantiomeric pair (±) of DATAN in an untargeted manner. Using the developed strategy, a library of 301 standards that consisted of 214 chiral and 87 achiral metabolites were separated and detected in a single analytical run. This approach was then applied to investigate the enantioselective metabolic profile of the bone marrow (BM) and peripheral blood (PB) plasma samples from patients with acute myeloid leukemia (AML) at diagnosis and following completion of the induction phase of chemotherapeutic treatment. The sensitivity and selectivity of the developed method enabled the detection of trace levels of the D-enantiomer of HAs and AAs in primary plasma patient samples. Several of these metabolites were significantly altered in response to chemotherapy. The developed LC-HR-MS method entails a valuable step forward in chiral metabolomics.

New bioactive constituents characterized by LC–MS/MS in optimized microwave extract of jujube seeds (Zizyphus lotus L.)

The present study was aimed to optimize the extraction conditions of total phenolic contents (TPC) from Zizyphus lotus seeds (Zls) samples by microwave procedure using response surface methodology in order to obtain maximum extraction yields. Central Composite Design was employed with three factors defined as solvent concentration (X1), irradiation power (X2) and microwave power (X3) at three coded levels on the TPC recovery. The optimal conditions for X1, X2 and X3 were: ethanol 60%, 210 s and 600 W, respectively. The experimental value of TPC yields was for 6709.01 ± 2.20 mg GAE/100 g which is in close agreement with the predicted value indicating the model success. Results showed that optimized Zls extract exhibited a high inhibitory effect on some biological activities including antioxidants and enzyme inhibition. The liquid chromatography-high resolution tandem mass spectrometry profile revealed 47 active compounds where 21 were never been detected in Zizyphus genus. The Zls extract was found to contain significant major compounds comprised 6-methyl-2-O-glucoside xanthone, jasminoside isomer, citric acid, gallocatechin, imidazole carboxylate derivative, kaempferol-3-O-robinobioside, 6-gingerol, 2-hydroxy-2-methyl-1-[4-[3-(2,4,5-trihydroxyhexan-3-yloxy)propyl]phenyl]propan-1-one, 3-(decyloxy)-2-hydroxy-propyl prop-2-enoate, tenasogenin and some small peptides. The findings demonstrated the beneficial application of microwave method for an increase extraction of TPC amounts from Zls extracts that could be valorized in food and pharmaceutical industries.

Rapid Identification of Chemical Constituents in Hericium erinaceus Based on LC-MS/MS Metabolomics

Hericium erinaceus is a precious edible and medicinal fungus with high nutritional value. It has many functions, such as enhancing immunity, antitumor antioxidation, antihyperglycemic, antihyperlipidemic, and protecting gastric mucosa. However, there are few researches about the H. erinaceus compounds. In this paper, ultraperformance liquid chromatography tandem high-resolution mass spectrometry (UPLC-Q-exactive-MS/MS) was used to isolate and identify the compounds in H. erinaceus. 102 compounds were identified in H. erinaceus by comparing with standard databases such as MZVault, MZCloud, and BGI Library (self-built standard Library by BGI Co., Ltd), including flavonoids, terpenoids, phenolic acids, phenylpropanoids, steroids, organic acids, and amino acids.

Identification of LC-HRMS nontarget signals in groundwater after source related prioritization

Groundwater is a major drinking water resource but its quality with regard to organic micropollutants (MPs) is insufficiently assessed. Therefore, we aimed to investigate Swiss groundwater more comprehensively using liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). First, samples from 60 sites were classified as having high or low urban or agricultural influence based on 498 target compounds associated with either urban or agricultural sources. Second, all LC-HRMS signals were related to their potential origin (urban, urban and agricultural, agricultural, or not classifiable) based on their occurrence and intensity in the classified samples. A considerable fraction of estimated concentrations associated with urban and/or agricultural sources could not be explained by the 139 detected targets. The most intense nontarget signals were automatically annotated with structure proposals using MetFrag and SIRIUS4/CSI:FingerID with a list of >988,000 compounds. Additionally, suspect screening was performed for 1162 compounds with predicted high groundwater mobility from primarily urban sources. Finally, 12 nontargets and 11 suspects were identified unequivocally (Level 1), while 17 further compounds were tentatively identified (Level 2a/3). amongst these were 13 pollutants thus far not reported in groundwater, such as: the industrial chemicals 2,5-dichlorobenzenesulfonic acid (19 detections, up to 100 ng L−1), phenylphosponic acid (10 detections, up to 50 ng L−1), triisopropanolamine borate (2 detections, up to 40 ng L−1), O-des[2-aminoethyl]-O-carboxymethyl dehydroamlodipine, a transformation product (TP) of the blood pressure regulator amlodipine (17 detections), and the TP SYN542490 of the herbicide metolachlor (Level 3, 33 detections, estimated concentrations up to 100–500 ng L−1). One monitoring site was far more contaminated than other sites based on estimated total concentrations of potential MPs, which was supported by the elucidation of site-specific nontarget signals such as the carcinogen chlorendic acid, and various naphthalenedisulfonic acids. Many compounds remained unknown, but overall, source related prioritisation proved an effective approach to support identification of compounds in groundwater.

Degradation of benzo[a]pyrene by halophilic bacterial strain Staphylococcus haemoliticus strain 10SBZ1A.

The exploitation of petroleum oil generates a considerable amount of "produced water or petroleum waste effluent (PWE)" that is contaminated with polycyclic aromatic hydrocarbons (PAHs), including Benzo[a]pyrene (BaP). PWE is characterised by its high salinity, which can be as high as 30% NaCl, thus the exploitation of biodegradation to remove PAHs necessitates the use of active halophilic microbes. The strain 10SBZ1A was isolated from oil contaminated soils, by enrichment experiment in medium containing 10% NaCl (w/v). Homology analyses of 16S rRNA sequences identified 10SBZ1A as a Staphylococcus haemoliticus species, based on 99.99% homology (NCBI, accession number GI: MN388897). The strain could grow in the presence of 4-200 μmol l-1 of BaP as the sole source of carbon, with a doubling time of 17-42 h. This strain optimum conditions for growth were 37 oC, 10% NaCl (w/v) and pH 7, and under these conditions, it degraded BaP at a rate of 0.8 μmol l-1 per day. The strain 10SBZ1A actively degraded PAHs of lower molecular weights than that of BaP, including pyrene, phenanthrene, anthracene. This strain was also capable of removing 80% of BaP in the context of soil spiked with BaP (10 μmol l-1 in 100 g of soil) within 30 days. Finally, a metabolic pathway of BaP was proposed, based on the identified metabolites using liquid chromatography-high resolution tandem mass spectrometry. To the best of our knowledge, this is the first report of a halophilic BaP degrading bacterial strain at salinity > 5% NaCl.

A Systematic Pipeline to Enhance the Fecal Metabolome Coverage by LC-HRMS

The comprehended knowledge of the metabolic profile of the fecal matter has been recognized as an important point for understanding metabolic changes in the human systemic metabolism and it can provide precious information about host-gut microbiota interactions. However, few analytical strategies have been addressed for a broad analysis of metabolites with different chemical properties to better understand the chemical space of fecal samples. Here we report a systematic pipeline to achieve comprehensive coverage of the fecal metabolome, from high polar to nonpolar metabolites, using dog fecal samples as a proof-of-concept. This pipeline comprises a monophasic (ACN/H2O) and a biphasic extraction (methyl tert-butyl ether (MTBE)/MeOH/H2O) of the sample, followed by three liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) methods using HILIC-amide, RP-C18 and CSH-C18 columns, and a switch polarity acquisition mode in the electrospray ion source. This approach allowed the annotation of 376 metabolites from 70 different chemical classes. The chemical space analysis by molecular networking and the pathway analysis revealed the complexity of the fecal sample and the importance of combined methods to better understand biochemical pathways. This pipeline can be used as a valuable tool to comprehend the relationship between host-gut microbiota metabolites and the influence of diet, medication, or environmental changes.

Use of high resolution/accurate mass full scan/data-dependent acquisition for targeted/non-targeted screening in equine doping control.

High-resolution mass spectrometry (HRMS) is a very powerful technology for equine doping control analysis. The more recently developed hybrid type of Orbitrap-based HRMS instrument allows for both targeted and non-targeted screening analyses in a single liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) run. In the present study, an LC-HRMS/MS method was developed and validated to detect prohibited substances in equine sports. The substances were recovered from equine plasma by liquid-liquid extraction (LLE) using methyl tert-butyl ether and were separated on a C18 reversed-phase column using mobile phases of 5 mM ammonium formate and acetonitrile. A 7.5 min LC gradient was employed to elute substances and results indicated that the LC method generated sharp and symmetric chromatographic peaks. An in-house equine doping compound database and a spectral library were built to increase method specificity for substances of interest. Five criteria, i.e. accurate mass, retention time, isotope pattern, selected HRMS/MS fragment ions (compound database) and HRMS/MS spectra (spectral library), were employed for targeted screening. We utilized these criteria to validate targeted detection of 451 substances within our in-house equine doping compound database. By using all five criteria in screening, the false screening positive rate is significantly reduced. A screening strategy and a Microsoft Excel macro were developed to facilitate interpretation and reporting of results. As the simultaneous acquisition of the full scan HRMS data provides the opportunity for retrospective non-targeted analysis, our findings highlight the use of this novel methodology as a simple, rapid, and reliably reproducible strategy to meet the challenge of identifying an increasing number of doping substances that could potentially impact the integrity of the horse racing community.

Plasma proteomic changes in patients with non-valvular atrial fibrillation starting rivaroxaban treatment: A pilot study

IntroductionDirect oral anticoagulants (DOACs) also influence cell signaling in various cell types, thus affecting biological systems other than coagulation, whose markers are uncertain. Material and methodsTo perform a pilot study of variations in plasma protein by means of Liquid chromatography–high resolution tandem mass spectrometry (LC-HRMS/MS) in 5 patients with newly-diagnosed non-valvular atrial fibrillation (NVAF) starting rivaroxaban anti-FXa DOAC treatment. ResultsA total of 260 proteins could be identified in plasma samples obtained before treatment and at one month of treatment. A significant sustained variation in their concentrations (doubling or halving) was evidenced in at least one patient. These variations were heterogeneous and inconstant from one patient to another. Their most striking feature was the downregulation of proteins participating in the inflammatory system reaction, and of proteins related to intravascular hemolysis. Other variations were rarer and more erratic. ConclusionsIndividual rivaroxaban treatment-associated variations in protein were evidenced in patients with NVAF starting rivaroxaban. This should now be tested and confirmed with a large series of carefully annotated patients. Confirming these established variations would open the door to the search for clinically-relevant correlations and consequences, if any.

Pyrrolidinyl Synthetic Cathinones α-PHP and 4F-α-PVP Metabolite Profiling Using Human Hepatocyte Incubations.

For more than ten years, new synthetic cathinones (SCs) mimicking the effects of controlled cocaine-like stimulants have flooded the illegal drug market, causing numerous intoxications and fatalities. There are often no data on the pharmacokinetics of these substances when they first emerge onto the market. However, the detection of SC metabolites is often critical in order to prove consumption in clinical and forensic settings. In this research, the metabolite profile of two pyrrolidinyl SCs, α-pyrrolidinohexaphenone (α-PHP) and 4′′-fluoro-α-pyrrolidinovalerophenone (4F-α-PVP), were characterized to identify optimal intake markers. Experiments were conducted using pooled human hepatocyte incubations followed by liquid chromatography–high-resolution tandem mass spectrometry and data-mining software. We suggest α-PHP dihydroxy-pyrrolidinyl, α-PHP hexanol, α-PHP 2′-keto-pyrrolidinyl-hexanol, and α-PHP 2′-keto-pyrrolidinyl as markers of α-PHP use, and 4F-α-PVP dihydroxy-pyrrolidinyl, 4F-α-PVP hexanol, 4F-α-PVP 2′-keto-pyrrolidinyl-hexanol, and 4F-α-PVP 2′-keto-pyrrolidinyl as markers of 4F-α-PVP use. These results represent the first data available on 4F-α-PVP metabolism. The metabolic fate of α-PHP was previously studied using human liver microsomes and urine samples from α-PHP users. We identified an additional major metabolite (α-PHP dihydroxy-pyrrolidinyl) that might be crucial for documenting exposure to α-PHP. Further experiments with suitable analytical standards, which are yet to be synthesized, and authentic specimens should be conducted to confirm these results.

In Vitro Metabolism of Five Bisphenol A Analogs Studied by LC-HRMS/MS.

Bisphenol A (BPA) structural analogs are increasingly used as alternatives in many industrial applications, due to growing evidence of BPA-related toxicity. Despite their widespread use, little is known about the biotransformation of these BPA analogs in the body. In this study, the in vitro metabolism of five BPA analogs (bisphenol AF, bisphenol F, bisphenol S, cumylphenol, and tetramethylbisphenol F) were investigated, using human and rat liver fractions, to evaluate the formation of phase I and phase II metabolites. Liquid chromatography high-resolution tandem mass spectrometry was employed to separate and characterize over 50 metabolites, many of which were not previously reported. The structures of all detected oxidative metabolites, dimers, GSH adducts, glucuronide, and sulfate conjugates were elucidated. A biphenyl solid-core chromatographic column was utilized for the separation of all metabolites, with a subsequent method, on a F5 column, specifically optimized for the separation of dimers formed via oxidative metabolism. There are several examples in this work where the combination of high chromatographic resolution and tandem mass spectrometry were necessary to distinguish between isomeric metabolites and conjugates.

Understanding the Fate of Almond (Prunus dulcis (Mill.) D.A. Webb) Oleosomes during Simulated Digestion.

Background: Almond kernels contain phytochemicals with positive health effects in relation to heart disease, diabetes and obesity. Several studies have previously highlighted that almond cell wall encapsulation during digestion and particle size are factors associated with these benefits. In the present study, we have characterized almond oleosomes, natural oil droplets abundant in plants, and we have investigated their integrity during simulated gastrointestinal digestion. Methods: Oleosomes were visualized on the almond seed surface by imaging mass spectrometry analysis, and then characterized in terms of droplet size distribution by dynamic light scattering and protein profile by liquid chromatography high-resolution tandem mass spectrometry analysis. Results: The almond oleosomes’ distribution remained monomodal after in vitro mastication, whereas gastric and duodenal digestion led to a bimodal distribution, albeit characterized mainly by a prevalent population with a droplet size decrease related to a rearrangement of the protein profile. Oleosins, structural proteins found in plant oil bodies, persisted unchanged during simulated mastication, with the appearance of new prunin isoforms after gastric and duodenal digestion. Conclusions: The rearrangement of the protein profile could limit lipid bioaccessibility. The data improve our understanding of the behavior of almond lipids during gastrointestinal digestion, and may have implications for energy intake and satiety imparted by almonds.

Phosphoenolpyruvate carboxykinase from T. cruzi magnetic beads affinity-based screening assays on crude plant extracts from Brazilian Cerrado

In T. cruzi, a causative agent of Chagas disease, phosphoenolpyruvate carboxykinase (TcPEPCK) is associated with carbohydrate catabolism. Due to its importance in the metabolism of the parasite, it has become a promising target for the development of new drugs against Chagas disease. Aiming to investigate different approaches for ligands screening, TcPEPCK was immobilized on amine-terminated magnetic beads (TcPEPCK-MB) and kinetically characterized by liquid chromatography tandem mass spectrometry activity assay with a KMapp value of 10 ± 1 μM to oxaloacetate as substrate. Natural products library affords highly diverse molecular frameworks through their secondary metabolites, herein a ligand fishing TcPEPCK-MB assay is described for prospecting ligands in four ethanolic extracts of Brazilian Cerrado plants: Qualea grandiflora (Vochysiaceae), Diospyros burchellii (Ebenaceae), Anadenanthera falcata (Fabaceae) and Byrsonima coccolobifolia (Malpighiaceae). The chemical characterization of eleven identified ligands was carried out by liquid chromatography tandem high-resolution mass spectrometry experiments. Senecic acid, syneilesinolide A, phytosphingosine and vanillic acid 4-glucopyranoside are herein reported for the first time for Q. grandiflora, D. burchellii, A. falcata, respectively. In addition, the specificity of the assay was observed since only catechin was fished out from the ethanolic extract of B. coccolobifolia leaves, despite the presence of epicatechin epimer.

Identification of Polyphenol Glucuronide Conjugates in Glechoma hederacea var. longituba Hot Water Extracts by High-Performance Liquid Chromatography-Tandem Mass Spectrometry (HPLC-MS/MS).

Glechoma hederacea var. longituba (GHL) is one of many herbal plants distributed worldwide and is known to contain various biologically useful antioxidant constituents. GHL has been used in folk remedies for various treatments and as favorable tea beverages. However, research on the precise analysis of ingredients in GHL extracts remains insufficient. In this study, compositional analysis has been conducted on polyphenolic ingredients in GHL hot water extracts. GHL samples collected from growing regions were incubated in hot water at 100 °C for 1 h. The polyphenolic constituents in the hot water extracts were analyzed using high performance liquid chromatography-high resolution mass spectrometry (HPLC-HR MS) and tandem mass spectrometry (HPLC-MS/MS) in negative ion mode. As a result, a total of seven compounds were identified as the major polyphenolic constituents. Interestingly, four constituents out of the identified substances were confirmed to be polyphenol glucuronide conjugates, in which glucuronidation was known to be an important metabolic process in polyphenol aglycone along with methylation and sulphation. This study can be applied for the quality control and standardization of GHL herbal samples and the monitoring of metabolic processes involved in the polyphenolic conjugates.

Extra-mitochondrial mouse frataxin and its implications for mouse models of Friedreich\u2019s ataxia

Mature frataxin is essential for the assembly of iron–sulfur cluster proteins including a number of mitochondrial enzymes. Reduced levels of mature frataxin (81-20) in human subjects caused by the genetic disease Friedreich’s ataxia results in decreased mitochondrial function, neurodegeneration, and cardiomyopathy. Numerous studies of mitochondrial dysfunction have been conducted using mouse models of frataxin deficiency. However, mouse frataxin that is reduced in these models, is assumed to be mature frataxin (78-207) by analogy with human mature frataxin (81-210). Using immunoaffinity purification coupled with liquid chromatography-high resolution tandem mass spectrometry, we have discovered that mature frataxin in mouse heart (77%), brain (86%), and liver (47%) is predominantly a 129-amino acid truncated mature frataxin (79-207) in which the N-terminal lysine residue has been lost. Mature mouse frataxin (78-207) only contributes 7–15% to the total frataxin protein present in mouse tissues. We have also found that truncated mature frataxin (79-207) is present primarily in the cytosol of mouse liver; whereas, frataxin (78-207) is primarily present in the mitochondria. These findings, which provide support for the role of extra-mitochondrial frataxin in the etiology of Friedreich’s ataxia, also have important implications for studies of mitochondrial dysfunction conducted in mouse models of frataxin deficiency.

Comprehensive lipid analysis of green Arabica coffee beans by LC-HRMS/MS

Lipids play an important role in coffee bean development, coffee brew and in the effects of coffee on human health. They account for around 17% of the dry bean weight and encompass different classes and subclasses, mostly triacylglycerols (TAG) and a minor quantity of phospholipids (PL) and βN-alkanoyl-5-hydroxytryptamides (C-5HT). To comprehensive profile these different lipids, it is important to evaluate extraction methods that provide high lipid coverage and to analyze the lipids in high-resolution techniques. In this work, liquid chromatography-high resolution tandem mass spectrometry (LC-HRMS/MS) was employed to comprehensive profile lipids from green Arabica coffee beans and to evaluate the extraction efficiency and lipid coverage of three methods: Bligh-Dyer (BD), Folch (FO), and Matyash (MA). The MA method yielded the greatest number of annotated compounds (131 lipids) compared to the other methods. In the positive electrospray ionization (ESI) mode, the main difference among extraction methods was observed for TAG and diacylglycerols, whereas for the negative ESI it was observed differences for phosphatidylinositol (PI), lysophosphatidylinositol and phosphatidic acid (p < 0.05). The analysis of coffees from different maturation stages and/or post-harvest processes were also performed using the MA method. Immature beans were discriminated from mature and overripe beans by its lower levels of C-5HT, PI, phosphatidylcholine, lysophosphatidylcholine, phosphatidylethanolamine, and lysophosphatidylethanolamine. These results can help to better understand the coffee lipid composition and its association with coffee quality.

MetIDfyR: An Open-Source R Package to Decipher Small-Molecule Drug Metabolism through High-Resolution Mass Spectrometry.

With recent advances in analytical chemistry, liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS) has become an essential tool for metabolite discovery and detection. Even if most of the common drug transformations have already been extensively described, manual search of drug metabolites in LC-HRMS/MS datasets is still a common practice in toxicology laboratories, complicating metabolite discovery. Furthermore, the availability of free open-source software for metabolite discovery is still limited. In this article, we present MetIDfyR, an open-source and cross-platform R package for in silico drug phase I/II biotransformation prediction and mass-spectrometric data mining. MetIDfyR has proven its efficacy for advanced metabolite identification in semi-complex and complex mixtures in in vitro or in vivo drug studies and is freely available at github.com/agnesblch/MetIDfyR.

LC-QTOF-MS Presumptive Identification of Synthetic Cannabinoids without Reference Chromatographic Retention/Mass Spectral Information. II. Evaluation of a Computational Approach for Predicting and Identifying Unknown High-Resolution Product Ion Mass Spectra.

Despite liquid chromatography-high-resolution tandem mass spectrometry (MS2) enables untargeted acquisition, data processing in toxicological screenings is almost invariably performed in targeted mode. We developed a computational approach based on open source chemometrics software that, starting from a suspected synthetic cannabinoid (SC) determined formula, searches for isomers in different new psychoactive substances web databases, predicts retention time (RT) and high-resolution MS2 spectrum, and compares them with the unknown providing a rank-ordered candidates list. R was applied on 105 SC measured data to develop and validate a multiple linear regression quantitative structure-activity relationship model predicting RT. Competitive Fragmentation Modeling for Metabolite Identification (CFM-ID) freeware was used to predict/compare spectra with Jaccard similarity index. Data-dependent acquisition was performed with an Agilent Infinity 1290 LC-6550 iFunnel Q-TOF MS with ZORBAX Eclipse-Plus C18 (100 × 2.1 mm2/1.8 µm) in water/acetonitrile/ammonium formate gradient. Ability of the combined RT/MS2 prediction to identify unknowns was evaluated on SC standards (with leave-one-out from the RT model) and on unexpected SC encountered in real cases. RT prediction reduced the number of isomers retrieved from a group of new psychoactive substances web databases to one-third (2,792 ± 3,358→845 ± 983) and differentiated between SC isomers when spectra were not selective (4F-MDMB-BUTINACA, 4F-MDMB-BUTINACA 2'-indazole isomer) or unavailable (4CN-Cumyl-B7AICA, 4CN-Cumyl-BUTINACA). When comparing 30/40 eV measured spectra of 99 SC against RT-selected, CFM-ID predicted spectra of isomers, the right candidate ranked 1st on median and 4th on average; 54% and 88% of times the right match ranked 1st or within the first 5 matches, respectively. To our knowledge, this is the first case of extensive chemometrics application to toxicological screening. In most cases, presumptive identification (being based on computation, it requires further information for confirmation) of unexpected SC was achieved without reference measured information. This method is currently the closest possible to true unbiased/untargeted screening. The bottleneck of the method is the processing time required to predict mass spectra (ca. 30-35 s/compound using a 64-bit 2.50-GHz Intel® Core™ i5-7200U CPU). However, strategies can be implemented to reduce prediction processing time.