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What Is Metabolomics

Metabolomics refers to the systematic identification and quantification of the metabolome of a biological system at a specific point in time. And metabolome means the complete set of small-molecule chemicals found within a biological sample. Its main goal is to qualitatively and quantitatively study the diverse dynamic responses of living organisms to external stimuli, physiological and pathological changes, and genetic mutations, focusing on the levels of endogenous metabolites. The research primarily involves small molecule substances with a relative molecular mass ≤1000 Da, such as organic acids, amino acids, nucleotides, sugars, lipids, vitamins, etc.

Advantages of Metabolomics

Small changes in gene and protein expression can be amplified in metabolites, making detection easier.

Metabolomics research does not require the establishment of databases for whole genome sequencing or large-scale expressed sequence tags (ESTs).

The number of metabolites studied is much smaller than the number of proteins; the quantity of metabolites varies significantly among species: plants (200,000 species), animals (2,500 species), microorganisms (1,500 species).

The techniques used in this research are more versatile.

Metabolomics Service

Metabolomics Service at Creative Proteomics

At Creative Proteomics, we can provide a wide range of metabolomics services from discovery to targeted analysis.

As the platform construction and project accumulation progressed, Creative Proteomics has established a metabolite library of nearly 4000 standard compounds on its metabolomics platform. The company boasts a professional metabolomics team and a comprehensive detection and management platform.

Metabolomics Research Platforms

Commonly used research platforms in metabolomics include Nuclear Magnetic Resonance Spectroscopy (NMR), Gas Chromatography-Mass Spectrometry (GC-MS), and Liquid Chromatography-Mass Spectrometry (LC-MS). Among them, GC-MS is more suitable for analyzing volatile substances, while LC-MS is more suitable for analyzing polar molecules, which is currently more commonly used in metabolomics.

PlatformApplicable Sample TypesSensitivityQuantitative Accuracy
NMRFew and Complex Substances10^-6Targeted Analysis - Absolute Quantification
Segmental Integration - Relative Quantification
GC-MSSmall Molecules, Volatile Substances10^-9Broad Screening: Provides Relative Quantification
Targeted Analysis: Standard Samples - Absolute Quantification
LC-MSUnstable and Non-volatile Substances10^-9Broad Screening: Provides Relative Quantification
Targeted Analysis: Standard Samples - Absolute Quantification

Metabolomics Service

Applications of Metabolomics

Our metabolomics services can be applied to various fields, including but not limited to the agricultural industry, food industry, biomedical area, and pharmaceutical area.

  • Agricultural industry: plant metabolomics, the development of new pesticides, etc
  • Food industry: fruits, vegetables, dairy products, olive oil, etc
  • Biomedical area: metabolomic profiling, biomarker discovery, etc
  • Pharmaceutical area: drug toxicity, drug metabolism, etc

Advantages Our Metabolomics Service

  • The compounds we test are widely covered, ranging from small water-soluble molecules to large lipids.
  • We can analyze any biological materials, including but not limited to biofluids and tissues from animals, cell cultures and humans.
  • A comprehensive platform contains advanced instruments, including MS, GC-MS, LC-MS, NMR, and so on.
  • A complete analysis report is offered, including method interpretation, data, and result files.

Our experts with years of experience in metabolomics, bioinformatics, statistics and various application fields ranging from food to pharmacy can help you plan, conduct, and report your metabolomics studies. Whether you want to study the whole metabolome, complex lipids, or just a few metabolites or pathways, we will closely work with you to define research purpose and develop customized plans. If you have any questions or specific requirements, please don’t hesitate to contact us.

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Research Steps in Metabolomics

Metabolomics research generally involves the collection of samples, acquisition of metabolomics data, pre-processing of data, multivariate data analysis, biomarker identification, and pathway analysis.

Research Methods in Metabolomics

Untargeted metabolomics research is often implemented as an initial comprehensive screening method. Following the analysis of experimental results and metabolite variance across different groups, potential target metabolites are selected. Subsequently, targeted metabolomics research is performed on these selected metabolites for further verification. If the research specifically focuses on a particular type of metabolite, targeted metabolomics research can be carried out first to confirm the presence of metabolic variations, followed by Untargeted research to explore a broader spectrum of metabolite concentration differences.

Levels of Metabolomics

In the field of metabolomics, metabolites in biological systems can be divided into four levels depending on the research subjects and objectives: (1) Target metabolite analysis - for particular or partial analysis of components; (2) Metabolite profiling - a quantitative study of a predetermined limited number of metabolites; (3) Metabolomics - qualitative and quantitative analysis of all endogenous metabolite components in a biological sample under specific conditions; (4) Metabolic fingerprinting - quickly categorizing samples based on the comparison of difference in metabolic fingerprints rather than identifying a single component.

Characteristics of Metabolomics

1) Emphasizes the study of endogenous compounds.

2) Conducts qualitative and quantitative analyses of small metabolite compounds within biological entities.

3) Changes in the upregulation and downregulation of metabolites reflect the impacts of diseases, toxins, genetic modifications, or environmental factors.

4) Utilizing knowledge of these endogenous compounds can facilitate disease diagnosis and drug selection.

How many biological replicates are generally required in metabolomics studies?

In metabolomic research, there are certain requirements for the number of biological repeat samples. Recommended standards are as follows: not less than 30 clinical samples, not less than 10 animal samples, not less than 8 cell samples, not less than 8 plant samples, and not less than 8 microbial samples. Metabolomics is downstream of systems biology and the amplification of biological processes may lead to amplified individual differences. Influencing factors are numerous, such as age, gender, and the physicochemical property differences of metabolites. To ensure analytical result accuracy and minimize individualized spectral error introduced by sample variability, the sample size should be maximized. Too few biological replicates may led to poor model building in later stages and possibly make statistical analysis impossible, thereby limiting the discovery of differential metabolites.

Why is High Resolution Mass Spectrometry Essential for LC-MS Metabolomics?

In present-day metabolomics research, LC-MS plays a vital role with the primary method of metabolite annotation involving a database search based on accurate molecular weight and secondary fragment information. Accurate molecular weight serves as an indispensable parameter in this procedure. To acquire the accurate molecular weight of substances, the application of high-resolution mass spectrometry is vital. Conventional high-resolution mass spectrometers can ensure the precise mass error of substances is controlled within 5 ppm, and even as low as 3 ppm, thereby significantly enhancing the accuracy of annotation.

What Are TOF, QQQ, QTRAP, and Orbitrap in Mass Spectrometry?

Mass spectrometers can be classified based on their mass analyzers, with TOF, QQQ, QTRAP, and Orbitrap representing different types of such analyzers: TOF (Time-of-Flight); QQQ (Triple Quadrupole); QTRAP (Quadrupole TRAP); Orbitrap (Orbitrap Analyzer).

Serum samples or plasma samples?

Extant research has demonstrated different metabolic varieties and abundances between the two. However, in terms of research objectives, no specific sample type has been definitively proved as superior. Consequently, when deciding to use either serum or plasma, the primary concern should be to ensure consistency in the collection process. In selecting blood samples, plasma anticoagulated with EDTA or heparin is preferable. During the collection process, it is vital to minimize hemolysis. After collection, samples should be stored at -80℃ to prevent any degradation and repeated freeze-thaw cycles should be strictly avoided to maintain sample integrity.

Are the metabolites detected by mass spectrometry all truly existing metabolites?

Qualitative assessment in untargeted metabolomics necessitates aligning the metabolite's tandem mass spectrometry (MS/MS) fragmentation information with database fragment data. Given the variance in fragment patterns for the same substance across different instruments and conditions, a nuanced matching discrepancy arises during data correlation. To mitigate the risk of false positives in substance identification, Creative Proteomics consistently advocates for a stringent matching criterion, emphasizing high concordance in the matching process. This approach underscores the commitment to meticulous data analysis and strives to uphold the integrity of metabolite identification in the pursuit of scientific rigor.

Why are some commonly metabolites sometimes undetectable?

The limitations of untargeted metabolite detection stem from its inherent lack of specificity. For metabolites with low signal intensity, untargeted metabolomics techniques may introduce interference, potentially masking signals and impeding accurate identification. In situations where research objectives are clearly defined, investigators often opt for targeted metabolomics, a method tailored to the specific detection of chosen metabolites, yielding more desirable outcomes. However, it is important to note that, currently, no single technique exists capable of simultaneously identifying all metabolites.

In metabolomics, the query emerging frequently is why, despite detecting thousands of metabolic feature peaks, does the final qualification of compounds remain relatively low?

Conventionally, the range for metabolite identification falls within approximately 300 to 400 species. During data analysis, a stringent standard reference database is applied, thereby contributing to a low rate of false-positive results. Yet, certain metabolites are not included in the standard reference library, hence undetectable. The public database, relying on molecular weight for matching, might propose numerous candidate metabolites, but the probability of false positives is elevated.

Moreover, a single metabolite, detected multiple times, can manifest itself in various charged (ionic) forms, such as protonated, deprotonated, adduct ions, isotopic peaks, dimers, trimers, and specific ionic forms. This phenomenon elucidates why numerous ionic peaks could be detected yet eventually be qualified as a singular metabolite.

In instances of insufficient fecal sample collection, is it permissible to supplement with intestinal contents?

The answer is negative. Research indicates significant disparities between metabolites found in intestinal contents and those in feces, with notable variations even among different segments of the intestine. In the context of metabolomic investigations, only samples collected beyond the colon can be considered representative of fecal material. This distinction underscores the importance of precision in sample selection for metabolomics examinations and highlights the necessity of drawing distinct boundaries when characterizing samples in scientific studies.

Does a peak in the TIC/BPC diagram represent a distinct compound?

In TIC/BPC diagrams, a single peak does not always denote a unique compound. In fact, a single peak could potentially be composed of multiple substances.

Is it feasible to submit samples individually for separate testing and subsequently amalgamate them for joint analysis?

Within the experimental framework, assuring the accuracy and consistency of data mandates the concurrent testing of identical experiments. Routine recalibration of equipment remains indispensable. Processing samples in batches may introduce variability attributable to calibration disparities, thereby incurring a batch effect. Consequently, conducting collective tests for the identical experiment becomes imperative.

For experiments characterized by prolonged sampling periods, such as those spanning a year or more, the practice of dispatching samples in batches, conducting separate analyses, and subsequently consolidating results is ill-advised. The consequential batch effect could wield substantial influence on experimental outcomes. It is recommended to store completed samples in a -80℃ freezer to mitigate the impact of repeated freeze-thaw cycles. Upon the completion of sample collection, dispatching them for testing collectively ensures the uniformity of test conditions.

What iS QC?

In the process of metabolomics research based on mass spectrometry techniques, the implementation of quality control (QC) is usually necessary to ensure the acquisition of reliable and high-quality metabolomics data. A QC sample, composed by mixing 20 μL from each test sample, principally serves to rectify deviations in the analysis results of mixed samples and to correct errors caused by the analytical instrument itself.

What are primary mass spectrometry (MS) and secondary mass spectrometry (MS/MS)?

In the context of LC-MS metabolomic studies, the primary role of MS is to acquire accurate mass-to-charge ratio information for molecular ions, facilitating the determination of a compound's precise molecular weight for the inference of its molecular formula. However, this process only addresses a portion of the requirements for structural inference and alignment.

To enhance the accuracy of substance structural inference, it becomes necessary to fragment the molecular ions, acquiring fragment information through secondary mass spectrometry, denoted as MS/MS data. This secondary level of analysis contributes crucial insights into the structural elucidation of compounds, complementing the information obtained from primary mass spectrometry.

During the LC-MS detection process, why are there positive and negative ion modes?

Positive and negative ion modes represent two distinct scanning approaches within mass spectrometry (MS). Following ionization by the ESI source, the sample generates ions carrying positive charges (such as M+H, M+NH4, M+Na, etc.) and negative charges (such as M-H, M+Cl, M+CH3COO, etc.). Given the diversity in physicochemical properties of metabolites, some compounds exhibit positive charges, while others present negative charges.

To ensure a comprehensive profiling of the metabolome, it becomes imperative to scan both positive and negative ion states, recognizing the varied ionization behaviors of different metabolites. This dual-mode approach allows for a more thorough exploration of the metabolic landscape, acknowledging the nuanced characteristics of diverse metabolites.

How to assess the stability of the instrument system during the detection process?

In the course of detection, evaluating the stability of the instrument system involves several key considerations. Firstly, prior to sample analysis, meticulous calibration and correction of the instrument are essential to ensure that its response and quality accuracy meet the required standards. Secondly, during the injection process, validation of the analytical system can be achieved by employing Quality Control (QC) samples. Lastly, after obtaining data, assessing the stability of the analytical system during the analysis process can be done by examining the clustering pattern of QC samples in the Principal Component Analysis (PCA) score plot.

When dealing with a large volume of samples, how can the stability of the entire analysis process be ensured, and the impact of instrument fluctuations minimized?

To address this question, the initial step involves the incorporation of Quality Control (QC) samples. Subsequently, depending on the quantity of samples, the detection process can be divided into several batches. During the data processing stage, adopting batch normalization methods becomes crucial to reduce instrument errors and diminish differences between batches. This meticulous approach ensures the stability of the overall analysis process and mitigates the influence of instrument fluctuations.

What types of substances can be detected by LC-MS?

LC-MS technology is versatile in detecting various substance types in the analysis of biological samples. Utilizing the ESI source, as favored by Creative Proteomics, it is particularly suitable for the detection of moderately polar and highly polar compounds. Specific substance categories encompass fatty acids, alcohols, phenols, vitamins, organic acids, polyamines, nucleotides, polyphenols, terpenes, flavones, lipids, and more.

What types of substances can be primarily detected by GC-MS?

Gas Chromatography-Mass Spectrometry (GC-MS) is predominantly applicable for the detection of a spectrum of chemical substances, including short-chain fatty acids, organic acids, fatty acids, sugars, polyols, amines, and sugar phosphates. These substances are chiefly associated with amino acid metabolism, sugar metabolism, the tricarboxylic acid cycle (TCA), and other biological metabolic pathways. It is noteworthy that for water-soluble substances, GC-MS detection requires derivatization treatment. Direct GC-MS analysis is only feasible when the sample possesses volatility and thermal stability.

* For Research Use Only. Not for use in diagnostic procedures.
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