Gas Chromatography-mass Spectrometry Metabolite Research Articles

Changes in GC-MS metabolite profile, antioxidant capacity and anthocyanins content during fermentation of fine-flavor cacao beans from Ecuador.

The fermentation of fine-flavor cacao beans is a key process contributing to the enhancement of organoleptic attributes and monetary benefits for cacao farmers. This work aimed to describe the dynamics of the gas chromatography-mass spectrometry (GC-MS) metabolite profile as well as the antioxidant capacity and anthocyanin contents during fermentation of fine-flavor cacao beans. Samples of Nacional x Trinitario cacao beans were obtained after 0, 24, 48, 72, 96, and 120 hours of spontaneous fermentation. Total phenolic content (TPC), ferric reducing antioxidant power (FRAP), and total anthocyanin content were measured by ultraviolet-visible (UV-Vis) spectrophotometry. Volatiles were adsorbed by headspace solid phase microextraction (HS-SPME) while other metabolites were assessed by an extraction-derivatization method followed by gas chromatography-mass spectrometry (GC-MS) detection and identification. Thirty-two aroma-active compounds were identified in the samples, including 17 fruity, and 9 floral-like volatiles as well as metabolites with caramel, chocolate, ethereal, nutty, sweet, and woody notes. Principal components analysis and Heatmap-cluster analysis of volatile metabolites grouped samples according to the fermentation time. Additionally, the total anthocyanin content declined during fermentation, and FRAP-TPC values showed a partial correlation. These results highlight the importance of fermentation for the improvement of the fine-flavor characteristics of cacao beans.

Evaluating Retention Index Score Assumptions to Refine GC-MS Metabolite Identification.

As metabolomics grows into a high-throughput and high demand research field, current metrics for the identification of small molecules in gas chromatography-mass spectrometry (GC-MS) still require manual verification. Though steps have been taken to improve scoring metrics by combining spectral similarity (SS) and retention index (RI), the problem persists. A large body of literature has analyzed and refined SS scores, but few studies have explicitly studied improvements to RI scores. Here, we examined whether uninvestigated assumptions of the RI score are valid and propose ways to improve them. Query RIs were matched to library RI with a generous window of ±35 to avoid unintentional removal of valid compound identifications. Each match was manually verified as a true positive (TP), true negative, or unknown. Metabolites with at least 30 TP identifications were included in downstream analyses, resulting in a total of 87 metabolites from samples of varying complexity and type (e.g., amino acid mixtures, human urine, fungal species, and so on.). Our results showed that the RI score assumptions of normality, consistent variance across metabolites, and a mean error centered at 0 are often violated. We demonstrated through a cross-validation analysis that modifying these underlying assumptions according to empirical metabolite-specific distributions improved the TP and negative rankings. Further, we statistically determined the minimum number of samples required to estimate distributional parameters for scoring metrics. Overall, this work proposes a robust statistical pipeline to reduce the time bottleneck of metabolite identification by improving RI scores and thus minimize the effort to complete manual verification.

Microsatellite Markers and Metabolite Profiles of Salt-Tolerant Rice: Inpari Unsoed 79 Agritan

Salinity is a challenge in crop production. High salinity affects soil osmotic pressure and the balance of nutrients that inhibit plant growth. In such case, utilization of salt-tolerant rice varieties could be an alternative. This study aims to identify microsatellite markers associated with salt tolerance, compare the Inpari Unsoed 79 Agritan variety with ten other rice genotypes based on microsatellite markers and determine the qualitative composition metabolites in Inpari Unsoed 79 Agritan associated with the plant response to salinity. This research was carried out at the Laboratory of Plant Breeding and Biotechnology Universitas Jenderal Soedirman and Indonesian Institute of Sciences, Bogor. This research used eleven rice varieties and ten microsatellite markers. The identification of microsatellite markers consisted of genomic DNA extraction, quantification and qualification of DNA, amplification of microsatellite DNA and data analysis. Metabolite profiling was conducted on Gas Chromatography-Mass Spectrometry (GC-MS) instrument. The results showed that microsatellite markers RM 241, RM 515, RM 519 and RM 528 differentiate the Inpari Unsoed 79 Agritan from the IR 29 genotype. Microsatellite markers RM 129 and RM 292 distinguished the Nona Bokra from the IR 29 genotypes. The genetic relationship of eleven rice genotypes resulted in two clusters. The GC-MS metabolite compounds in Inpari Unsoed 79 Agritan are β-Alanine and trimethylsilyl ester β-Alanine, a derivative compound of β-Alanine. These findings suggested that microsatellite markers RM 129, RM 292, RM 241, RM 515, RM 519 and RM 528 were associated with salt-tolerant in the seedling stage.

GC-MS Metabolite and Transcriptome Analyses Reveal the Differences of Volatile Synthesis and Gene Expression Profiling between Two Apple Varieties.

Aroma is a key quality attribute of apples, making major contributions to commercial value and consumer choice. However, the mechanism underlying molecular regulation of aroma formation genes and transcription factors remains poorly understood in apples. Here, we investigated the aroma volatile profiles of two apple varieties with distinctive flavors using headspace solid-phase microextraction (HS-SPME) combined with gas chromatography–mass spectrometry (GC-MS). A total of 35 volatile compounds were identified in Granny Smith and Jonagold apples. Aldehydes were the most abundant volatiles contributing to the aroma in Granny Smith apple while esters were the dominant volatile compounds in Jonagold apple. In order to know more about the expression levels of aroma-related genes involved in the metabolic pathways, transcriptome sequencing of these two different apple varieties was conducted utilizing the Illumina platform. In total, 94 differentially expressed genes (DEGs) were found in the fatty acid metabolism, amino acid metabolism, the mevalonate pathway and phenylpropanoid pathway. Furthermore, compared to the Granny Smith apple, the expression of multiple genes and transcription factors were upregulated in the Jonagold apple, which might play important roles in the synthesis of aroma volatile compounds. Our study contributes toward better understanding on the molecular mechanism of aroma synthesis in apples and provides a valuable reference for metabolic engineering and flavor improvement in the future.

Physiology and metabolism of grafted bell pepper in response to low root-zone temperature.

Low temperature is a prominent limiting factor for tropical originated crops production in temperate regions, particularly during cool-season production. The diverse response of two rootstocks (Canon-sensitive and S103-tolerant to low root-zone temperature) was studied when exposed to aeroponically different temperature regimes at the root zone: constant low temperature of 14°C low root-zone temperature (LRZT), transient exposure to LRZT of 27-14-27°C and control temperature of 27°C. Gas exchange, shoot dry mass, and root morphology were measured. Shifts in central and secondary metabolite levels in the leaves and roots were examined by gas chromatography-mass spectrometry (GC-MS). Low root-zone temperature inhibited photosynthesis and transpiration of both grafted bell pepper plants; however, self-grafted Canon physiology was impeded to a greater extent compared with Canon grafted onto rootstock S103. Rootstock S103 demonstrated higher sink potential contributing to milder reduction of photosynthesis and transpiration during stress compared with self-grafted Canon. This reduction of gas exchange led to a significant reduction of root maximum length and root dry mass in self-grafted Canon in response to the stress at 14°C compared with Canon grafted onto rootstock S103. In response to stress, GC-MS metabolite profiling showed enhance metabolism in both cultivars' leaves, as well as in the roots irrespective of the developmental stage of the plant. This evidence combined indicates enhance gas exchange and carbon assimilation when bell pepper is grafted on S103 under low root-zone temperature.

GC-MS Metabolite Profiling of Extreme Southern Pinot noir Wines: Effects of Vintage, Barrel Maturation, and Fermentation Dominate over Vineyard Site and Clone Selection.

Wine is an extremely complex beverage that contains a multitude of volatile and nonvolatile compounds. This study investiged the effect of vineyard site and grapevine clone on the volatile profiles of commercially produced Pinot noir wines from central Otago, New Zealand. Volatile metabolites in Pinot noir wines produced from five grapevine clones grown on six vineyard sites in close proximity, over two consecutive vintages, were surveyed using gas chromatography-mass spectrometry (GC-MS). The raw GC-MS data were processed using parallel factor analysis (PARAFAC2), and final metabolite data were analyzed by principal component analysis (PCA). Winemaking conditions, vintage, and barrel maturation were found to be the most dominant factors. The effects of vineyard site and clone were mostly vintage dependent. Although four compounds including β-citronellol, homovanillyl alcohol, N-(3-methylbutyl)acetamide, and N-(2-phenylethyl)acetamide discriminated the vineyard sites independent of vintage, Pinot noir wines from different clones were only partially discriminated by PCA, and marker compound selection remained challenging.

Altered Fatty Acid Metabolism Due to Rifampicin-Resistance Conferring Mutations in therpoBGene ofMycobacterium tuberculosis: Mapping the Potential of Pharmaco-metabolomics for Global Health and Personalized Medicine

Abstract We investigated the use of gas chromatography mass spectrometry (GC-MS) metabolomics to better characterize rifampicin-resistance by comparing the fatty acid metabolomes of two rpoB mutant Mycobacterium tuberculosis strains (S522L and S531L) to that of a fully susceptible wild-type parent strain. Using the generated GC-MS metabolite data, principal component analysis (PCA) showed a clear differentiation between all three sample groups analyzed. We subsequently identified those metabolites contributing most to the variation in the data using PCA and partial least squares discriminant analysis (PLS-DA). The altered metabolite markers detected in the rifampicin-resistant mutants indicate a decreased synthesis of various 10-methyl branched-chain fatty acids and cell wall lipids, and an increased use of the shorter-chain fatty acids as carbon sources. Furthermore, the rpoB S531L mutant, previously reported to occur in well over 70% of all clinical rifampicin-resistant M. tuberculosis strains, potentially showed a better capacity for using these alternative energy sources, compared to the less frequently detected rpoB S522L mutant. This study is the first of its kind to associate rifampicin resistance, rpoB mutations, and the β-subunit of RNA polymerase in M. tuberculosis, with an altered fatty acid metabolism, thereby demonstrating the role that pharmaco-metabolomics can play in identifying new markers associated with drug resistance.

Nontargeted Urinary Metabolite Profiling of a Mouse Model of Crohn’s Disease

Crohn's disease is an inflammatory disorder of the bowel, believed to arise from the dysregulation of intestinal mucosal immunity. The interleukin-10-deficient (IL10-/-) mouse, which develops intestinal inflammation in the presence of gut microflora, serves as a mouse model of Crohn's disease. Nontargeted urinary metabolite profiling was carried out to identify systemic metabolic changes associated with the development of intestinal inflammation caused by IL10-deficiency. Spot urine samples, collected from IL10-/- and wildtype mice at ages 5.5, 7, 8.5, and 10.5 weeks old were analyzed by gas chromatography-mass spectrometry (GCMS). The data were analyzed using XCMS software, multiple t tests, and ANOVA. Among the key metabolic differences detected were elevated urinary levels of xanthurenic acid and fucose in IL10-/- mice relative to wildtype, indicating upregulation of tryptophan catabolism and perturbed fucosylation in IL10-/- mice. Three short-chain dicarboxylic acid metabolites were decreased in urine of IL10-/- mice relative to wildtype, suggesting the downregulation of fatty acid oxidation in IL10-/- mice. These metabolic differences were reproducible in an independent set of mice. This study demonstrates that nontargeted GCMS metabolite profiling of IL10-/- mice can provide insights into the metabolic effects of IL10-deficiency and identify potential markers of intestinal inflammation.