Cucumis sativu (Cucumber) Metabolomics Analysis

Cucumis sativu (Cucumber) Metabolomics Analysis

Service Details Case Study

What is Cucumis sativu (Cucumber)?

Cucumis sativus, commonly known as the cucumber, is a widely cultivated plant species belonging to the Cucurbitaceae family. This plant is renowned for its edible fruit, which is classified as a pepo, characterized by a tough outer rind. Cucumbers are a popular vegetable enjoyed for their crisp texture, mild flavor, and high water content, making them a refreshing addition to various culinary dishes worldwide.

Cucumber Metabolism

Cucumber metabolism encompasses a intricate web of biochemical processes that are essential for the growth, development, and sustenance of the cucumber plant. Cucumber plants engage in photosynthesis, a fundamental metabolic process that uses sunlight to convert carbon dioxide and water into glucose and oxygen. This provides the necessary energy for the plant's growth and releases oxygen into the atmosphere. Respiration is another pivotal metabolic process in cucumbers. It involves the breakdown of glucose and other organic molecules to release energy for various cellular activities, ensuring the plant's vital functions. The uptake of essential nutrients from the soil through the cucumber's root system is a critical metabolic process. This nutrient absorption, in conjunction with water absorption, is fundamental for plant growth, nutrient assimilation, and overall health. Cucumbers also produce secondary metabolites, such as cucurbitacins and flavonoids, as part of their metabolic pathways. These compounds can have various functions, including acting as antioxidants, serving as natural defense mechanisms against herbivores, or contributing to the flavor and aroma of the cucumber fruit.

Specific Cucumber Analysis Projects by Creative Proteomics

Identification of Cucumber Secondary Metabolites:

Profiling and characterization of secondary metabolites in cucumbers, including cucurbitacins, flavonoids, and phenolic compounds.

Quantitative analysis of these compounds to understand their abundance and variations among different cucumber varieties and growth conditions.

Investigation of the potential health benefits and applications of cucumber secondary metabolites, such as their antioxidant properties or medicinal uses.

Metabolic Profiling of Cucumber Varieties:

Comparative metabolomic analysis of different cucumber cultivars to identify metabolic differences related to taste, aroma, and nutritional content.

Discovering specific metabolite profiles associated with unique cucumber varieties, aiding in quality control and flavor optimization.

Stress Response Metabolomics:

Study of cucumber metabolite changes in response to environmental stresses, such as drought, salinity, or temperature fluctuations.

Identification of stress-responsive metabolites and metabolic pathways to develop strategies for stress-resistant cucumber varieties.

Disease Resistance and Pathogen Metabolomics:

Investigation of cucumber metabolic responses to pathogen infections, including viruses, fungi, and bacteria.

Discovery of metabolites involved in disease resistance and the development of strategies for breeding cucumbers with enhanced resistance.

Nutritional Metabolomics:

Comprehensive analysis of the nutritional composition of cucumbers, including vitamins, minerals, amino acids, and carbohydrates.

Profiling of metabolites related to cucumber nutritional quality and their variations based on cultivation methods and environmental factors.

Metabolomics of Cucumber Fruit Ripening:

Monitoring the changes in metabolite profiles during cucumber fruit ripening.

Identification of metabolites associated with flavor development, sugar accumulation, and texture changes during ripening.

Cucumber Metabolomics for Crop Improvement:

Integration of metabolomics data with genomics to identify metabolic markers linked to desirable traits, such as disease resistance, flavor, and shelf-life.

Development of molecular breeding strategies for improving cucumber varieties based on metabolic traits.

Metabolomics for Cucumber Post-Harvest Quality:

Analysis of metabolite changes in cucumbers during post-harvest storage and transportation.

Identification of metabolites linked to freshness, shelf-life, and quality deterioration, enabling better post-harvest management.

Cucumber Metabolomics in Pickling Processes:

Metabolomic profiling of cucumbers before and after pickling to understand the chemical changes that occur during preservation.

Optimization of pickling processes for flavor, texture, and nutritional retention.

Metabolomics for Cucumber-Based Product Development:

Metabolomic analysis of cucumber-derived products, such as juices, sauces, and cosmetics, to ensure product quality and authenticity.

Verification of label claims and nutritional content in cucumber-based products.

Cucumber Metabolomics Analysis Techniques

Sample Preparation:

  • Harvesting: Cucumber plant tissues are collected at specific growth stages or under various conditions.
  • Quenching: Samples are rapidly frozen or immersed in liquid nitrogen to stop metabolic activity.
  • Extraction: Metabolites are extracted from plant tissues using suitable solvents.

Metabolite Profiling:

Liquid Chromatography-Mass Spectrometry (LC-MS):

  • High-Performance Liquid Chromatography (HPLC) systems, such as the Agilent 1290 Infinity II LC system.
  • Mass spectrometers, such as the Agilent 6545 Q-TOF mass spectrometer.
  • Thermo Scientific™ Q Exactive™ Plus high-resolution mass spectrometers coupled with liquid chromatography systems.

Gas Chromatography-Mass Spectrometry (GC-MS):

  • Gas chromatographs, such as the Agilent 7890B gas chromatograph.
  • Mass spectrometers, such as the Agilent 5977B mass spectrometer.
  • Shimadzu GCMS-QP2020 high-sensitivity gas chromatograph-mass spectrometer.

Data Acquisition:

  • In LC-MS and GC-MS, raw data files are generated containing mass spectra and chromatograms.
  • Data preprocessing includes noise reduction, peak detection, alignment, and normalization.

Data Analysis:

  • Metabolites are annotated by comparing data with reference libraries.
  • Statistical techniques like principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) identify patterns and metabolite changes.

Metabolite Identification and Verification:

  • Metabolites are identified through comparisons with authentic standards, chemical databases, and spectral databases.
  • Verification may involve tandem MS (MS/MS) for LC-MS or spiking samples with standards for GC-MS.

Pathway Analysis:

  • Bioinformatics tools and databases like Kyoto Encyclopedia of Genes and Genomes (KEGG) are used for pathway enrichment analysis.


  • Metabolite quantification is done using external standard curves or internal standards.

Validation and Biological Interpretation:

  • Identified metabolites and pathways are validated through biological experiments.
  • Data integration with other 'omics' data (genomics, transcriptomics, proteomics) provides a holistic understanding.

Reporting and Visualization:

  • Results are reported with graphical representations, such as heatmaps and pathway diagrams.

Workflow for Metabolomics ServiceWorkflow for Metabolomics Service

Sample Requirements for Cucumber Metabolomics

Sample Type Tissue or Organ Growth Stage Sample Quantity Storage Conditions Additional Notes
Cucumber Leaves Mature leaves Vegetative stage 100 g Flash-frozen in liquid nitrogen Remove excess moisture before freezing.
Cucumber Fruits Mature fruits Fruiting stage 100 g Flash-frozen in liquid nitrogen Include both peel and flesh portions.
Cucumber Roots Root tissue Vegetative stage 50 g Flash-frozen in liquid nitrogen Ensure minimal soil contamination.
Cucumber Seedlings Whole seedlings Seedling stage 50 seedlings Flash-frozen in liquid nitrogen Harvest at uniform growth stage.
Cucumber Cell Cultures Cultured cells As needed Cell pellet Freeze at -80°C in suitable buffer Maintain consistent cell culture conditions.
Cucumber Extracts/Extracts Metabolite extracts As needed Varies based on assay Store at -80°C Precise quantity depends on downstream analysis.


  • Sample quantity may vary based on the specific downstream analysis methods and instruments used.
  • For flash-freezing, liquid nitrogen or dry ice is recommended for rapid quenching of metabolic activity.
  • Remove excess moisture from samples before freezing to prevent ice crystal formation.
  • Ensure minimal soil contamination when harvesting root samples.
  • Maintain consistent cell culture conditions for reproducible results.
  • Store metabolite extracts at -80°C for long-term preservation.

Case. Metabolic Response of Cucumber Plants to Copper Exposure: Implications for Agriculture and Environmental Safety


Copper is a widely used component in agricultural fungicides, making it crucial to understand its effects on plant metabolism. This study aims to elucidate the metabolic responses of cucumber plants to different doses of copper exposure and their implications for agricultural practices and environmental safety.


Cucumber plants subjected to various copper doses via foliar application were used as the experimental samples. The study investigated the metabolic changes in cucumber leaves in response to copper exposure.

Technological Methods

The study employed gas chromatography-quadrupole time-of-flight mass spectrometry (GC-QTOF-MS) for the comprehensive analysis of metabolites in cucumber leaves. A total of 149 metabolites from primary and secondary metabolic pathways were identified and quantified. Partial least squares-discriminant analysis (PLS-DA) was conducted to assess differences in metabolic profiles among control and copper-exposed plants. PLS-DA was applied separately for low, medium, and high copper doses. Polyphenols were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to investigate secondary metabolite changes.


  • Copper exposure induced dose-dependent metabolic alterations in cucumber plants.
  • Even at low copper doses, changes in tricarboxylic acid (TCA) cycle intermediates suggested disruption of energy metabolism.
  • Low copper doses triggered the accumulation of antioxidant-related metabolites such as threonic acid, phenylalanine, and tyrosine.
  • Higher copper doses led to significant changes in polyphenol levels, potentially accelerating leaf senescence.
  • The study provides insights into the molecular mechanisms of copper-induced effects on cucumber plants, with implications for safe and effective copper-containing fungicide use in agriculture and environmental conservation.

Schematic representation of phenylpropanoid/flavonoid pathway as affected by copper ionsSchematic representation of phenylpropanoid/flavonoid pathway as affected by copper ions


  1. Zhao, Lijuan, et al. "Metabolomics reveals the molecular mechanisms of copper induced cucumber leaf (Cucumis sativus) senescence." Environmental science & technology 52.12 (2018): 7092-7100.