A metabolome—the collection of comprehensive quantitative data on metabolites in an organism—has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal), where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study onJatropha curcasis presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data.

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Commercial fruit juices are categorized into juice not from concentrate (JNFC) and juice from concentrate (JFC). Tomato juice is one of the most popular vegetable juices, and its aroma is an important factor in evaluating its quality. However, differences in the aroma characteristics of JNFC and JFC tomato juices have not been clearly identified. This study aimed to investigate the volatile organic compounds (VOCs) involved in distinguishing between JNFC and JFC using commercially available tomato juices. Furthermore, the effect of concentration on the VOC composition was evaluated using different procedures. Twenty-three commercial tomato juices were prepared for analysis of VOCs using headspace solid phase microextraction-gas chromatography mass spectrometry (HS-SPME-GC-MS). Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were used to discriminate the samples into JNFC and JFC groups. JNFC contained 43 VOCs, which was more than twice that contained in JFC, and the quantitative variation was larger in JNFC than in JFC. In particular, the JNFC group contained significantly more alcohol and phenol compounds. On the other hand, the JFC group contained more formyl pyrrole and Strecker aldehydes. Additional GC-MS/olfactometry (GC-MS/O) and odor active value analyses indicated that (Z)-3-hexenol and 3-methylbutanal were the best VOCs to distinguish between the JNFC and JFC groups. Furthermore, different concentration procedures, including heating concentration (HC), decompression concentration (DC), and freeze drying (FD), were performed, and the corresponding VOCs were compared. HC and DC reduced the levels of most of the compounds to the levels seen in commercial JFC. These results indicate that the concentration procedure is an important processing stage, in addition to the break process, that determines the quality of tomato juice.

Raspberry ketone is a valuable aromatic compound that occurs only at trace levels in natural sources. In this study, transgenic tomato fruits expressing benzalacetone synthase (BAS) from Rheum palmatum and raspberry ketone/zingerone synthase 1 (RZS1) from Rubus idaeus under the CaMV 35S promoter accumulated raspberry ketone (9.9-19.3 μg g^-1 fresh weight) together with minor amounts of rhododenol (2.7-4.4 μg g^-1 fresh weight), predominantly as glycosides during fruit ripening. LC-MS/MS analysis using an authentic standard identified raspberry ketone monoglucoside as a major glycosylated form present in transgenic fruits but absent in wild-type controls. Raspberry ketone glycosides were predominantly detected in the fruit peel, with negligible levels in the flesh, seeds, or leaves. Co-expression of the Arabidopsis thaliana R2R3-MYB transcription factor AtMYB12 further enhanced raspberry ketone production, reaching up to 88 μg g^-1 fresh weight. These results demonstrate effective metabolic redirection of phenylpropanoid flux in an edible fruit tissue and establish tomato as a viable heterologous host for raspberry ketone production. This metabolic engineering strategy highlights the potential of edible fleshy fruits as sustainable plant-based platforms for the biosynthesis of high-value aromatic phenolics.

Oxylipin carbonyls are chemically diverse lipid peroxidation-derived metabolites that function as cytotoxic agents and signaling molecules in plants. However, the intracellular and sub-organellar sites at which individual carbonyl species accumulate remain poorly defined. Here, we analyzed carbonyl compositions in spinach (Spinacia oleracea L.) leaves, isolated chloroplasts, and three chloroplast subcompartments: thylakoids, envelopes, and stroma. Across these samples, 26 carbonyl species were detected, of which 13 were identified. The carbonyl profile of chloroplasts differed markedly from that of whole leaves: phenylacetaldehyde and n-pentanal, both abundant in leaves, were absent or detected only at trace levels in chloroplasts, indicating that they are largely non-chloroplast-derived. Acetaldehyde was also much less abundant in chloroplasts than in leaves, although a minor chloroplast-associated pool was detected mainly in thylakoids and stroma. Within chloroplasts, the three subcompartments exhibited distinct carbonyl signatures. Formaldehyde was enriched in thylakoids and envelopes, suggesting a membrane-associated source consistent with formation from chloroplast lipid oxidation. By contrast, acetone was preferentially associated with envelope membranes, whereas several C6 aldehydes were abundant in thylakoids and stroma. Apparent local concentration estimates suggested that several carbonyls can reach millimolar ranges in chloroplast membranes, although these values should be interpreted as compartmental accumulation capacities rather than exact in vivo concentrations. These results provide a compartment-resolved chemical map of oxylipin carbonyls in chloroplasts and establish a spatial framework for investigating their formation mechanisms and potential metabolic and signaling functions in plant cells.