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Data-dependent MS/MS for "A multi-omics exploration of biological responses upon high carotenoid intake"

ABSTRACT: Data-dependent Agilent 6546 UHPLC-QTOF-MS/MS experiments conducted on pooled treatment samples to aide in identification of features detected in blood plasma of healthy subjects following consumption of high lycopene tomato juice, high beta-carotene tomato juice, or control cucumber juice. Data dependent experiments of tomato juices are included. Blood plasma pools are labeled with "QC" and juice samples are labeled with "Juice."

INSTRUMENT(S): 6546 Q-TOF LC/MS

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Maria Sholola Jessica Cooperstone

PROVIDER: MSV000099373 | MassIVE | Fri Oct 03 10:33:00 BST 2025

REPOSITORIES: MassIVE

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Project description:Wounding due to mechanical injury or insect feeding causes a wide array of damage to the cell including cell disruption, desiccation, metabolite oxidation, and disruption of primary metabolism. In response, plants regulate a variety of genes and metabolic pathways to cope with injury. Tomato (Solanum lycopersicum) is a model for wound signaling but few studies have examined the comprehensive gene expression profiles in response to injury. A cross-species microarray approach using the TIGR potato 10-K cDNA array was analyzed for large-scale temporal (early and late) and spatial (locally and systemically) responses to mechanical wounding in tomato leaves. These analyses demonstrated that tomato regulates many primary and secondary metabolic pathways and this regulation is dependent on both timing and location. To determine if LAP-A, a known modulator of wound signaling, influences gene expression beyond the core of late wound-response genes, changes in RNAs from healthy and wounded Leucine aminopeptidase A-silenced (LapA-SI) and wild-type (WT) leaves were examined. While most of the changes in gene expression after wounding in LapA-SI leaves were similar to WT, overall responses were delayed in the LapA-SI leaves. Moreover, two pathogenesis-related 1 (PR-1c and PR-1a2) and two dehydrin (TAS14 and Dhn3) genes were negatively regulated by LAP-A. Collectively, this study has shown that tomato wound responses are complex and that LAP-A's role in modulation of wound responses extends beyond the well-described late-wound gene core. A reference design hybridization strategy was used with WT (0-hr) being the reference RNA. The reference RNA was a pool from five WT 0-hr RNAs. RNAs from wounded or unwounded leaves labeled with Cy3 and the reference RNA labeled with Cy5 were co-hybridized to the potato cDNA array. Three dye bias experiments were performed in which WT 0-hr RNAs were labeled with Cy3 and co-hybridized with the Cy5-labeled reference RNA (WT 0-hr RNAs from a different pool). After normalization, no dye bias was detected on these experiments (p-value<0.05).

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Data-dependent MS/MS for "A multi-omics exploration of biological responses upon high carotenoid intake"

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