Analyzing LC/MS Metabolic Profiling Data in the Context of Existing Metabolic Networks

Yu, Tianwei; Bai, Yun

doi:10.2174/2213235x130107

Cited by 8 publications

(13 citation statements)

References 55 publications

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“…Przy interpretacji wyników nale ży uwzględniać wiele czynników, takich jak wiek, uwarunkowania genetyczne, sprawność fizyczną, mikroflorę jelitową, dietę. Innymi bazami danych zawierającymi informację na temat metabolitów są: The Kyoto Encyclopedia of Genes end Genomes (KEGG), The Small Molecule Pathway Database (SMPDB), Madison Metabolomics Consortium Database (MMCD) oraz The METLIN Metabolite Database [8].…”

Section: Wstępunclassified

“…Do najpopularniejszych metod należą spektroskopia magnetycznego rezonansu jądrowego (nuclear magneticm resonance, NMR) oraz spektrometria mas (mass spectrometry, MS) [3]. Spektrometria mas opiera się na pomiarze stosunku masy do ładunku elektrycznego danego jonu, co pozwala na identyfikacje danej substancji [8]. Połączenie spektrometrii mas z metodami chro matografii pozwoliło stworzyć dwie techniki wykorzystywane do oznaczania związków chemicznych w płynach ustrojowych.…”

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The use of metabolomics in medicine – some examples of oncological and metabolic diseases

Zimny¹,

Szatkowska²,

Połubok³

et al. 2014

Pediatr Endocrino Diabetes Metab

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Metabolomics is a new field of medicine focused on examining and analyzing metabolites produced in biological cells. Biological fluids primarily used in this method include: plasma, cerebrospinal fluid, saliva and urine. The most common methods of evaluating the composition involve nuclear magnetic resonance (NMR) and magnetic resonance (MR) with addition of gas chromatography (GC-MS) or liquid chromatography (LC-MS). Metabolomics is used in a wide variety of medicine disciplines. The variability of biochemical processes in tumor cells in comparison to normal cells is the starting point of such studies. The metabolomic changes are observed not only in solid tumors, like the mammary tumor, ovarian cancer, prostate cancer but also in tumors of the hematopoietic and lymphoid tissues. Nowadays, the aim of studies is to find biomarkers which would help to diagnose a disease quickly, assess its progression, and implement effective treatment. Metabolomics is also widely applied in metabolic diseases, mainly the diabetes. The list of examined metabolites gives promising chances for a successful prognosis, diagnosis and comprehensive monitoring of the progression of this civilization disease. The development of metabolomics will also contribute to the individualization of treatment, proper drugs adjustment, which will make a therapy more successful, cause less side effects and improve the quality of patient's life.

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Section: Wstępunclassified

The use of metabolomics in medicine – some examples of oncological and metabolic diseases

Zimny¹,

Szatkowska²,

Połubok³

et al. 2014

Pediatr Endocrino Diabetes Metab

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show abstract

“…High‐performance liquid chromatography‐mass spectrometry (HPLC‐MS) has become a favored technique in metabolic profiling with good specificity and sensitivity, which has laid a foundation for the qualitative and quantitative analysis of chemical components in complex samples (Liao, Jia, Sun, Qi, & Li, ; Nian, Li, Liu, & Li, ; Sun et al, ; Wu et al, ; Yu & Bai, ). It is very helpful to identify compounds without the limitation of using standards.…”

Section: Introductionmentioning

confidence: 99%

Quality evaluation of Panax ginseng adventitious roots based on ginsenoside constituents, functional genes, and ferric‐reducing antioxidant power

et al. 2019

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In the study, six adventitious root lines of Panax ginseng have been successfully established. HPLC‐ESI‐MS analysis showed that 20 ginsenosides were identified in root lines, notoginsenoside Fa and notoginsenoside R2 were not found in AR lines. In AR lines, the highest accumulation of total ginsenosides was obtained in five‐year main AR (24.87 mg/g). Principal component analysis classified root lines into three groups. Five‐year ginseng was mostly similar with five‐year main AR, five‐year rootlet AR, and four‐year rootlet AR in ginsenosides composition of group 1. Besides, gene expressions were consistent with the production of total ginsenosides, and correlation analysis revealed that total ginsenosides biosynthesis was significantly positively correlated with the gene expression of dammarenediol synthase. Five‐year rootlet AR showed the highest activity on ferric‐reducing antioxidant power test among samples. It provides a scientific evidence for the further exploitation and large‐scale production of P. ginseng. Practical applications This study provides valuable information for the commercial scale culture of ginseng adventitious roots. This report combines morphology, ginsenoside composition and content, gene expression, and ferric‐reducing antioxidant power test to evaluate the quality of P. ginseng adventitious root, and combined with principal component analysis to screen out the high yield and stable ginseng adventitious roots. It would be profitable to use adventitious root culture of P. ginseng instead of field cultivation.

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“…The metabolome is, thereby, the most predictive of phenotype [ 1 , 4 ]. Metabolic profiling refers to the comprehensive identification and quantification of metabolites in a biological system [ 14 , 15 ]. Systems biology-based metabolome profiling is a new and promising field, which is still puzzled by several aspects, such as sample preparation, identification, standardization, and translating results into biological meaningful data.…”

Section: Introductionmentioning

confidence: 99%

Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

Aretz

Meierhofer

2016

IJMS

132

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Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

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Analyzing LC/MS Metabolic Profiling Data in the Context of Existing Metabolic Networks

Cited by 8 publications

References 55 publications

The use of metabolomics in medicine – some examples of oncological and metabolic diseases

The use of metabolomics in medicine – some examples of oncological and metabolic diseases

Quality evaluation of Panax ginseng adventitious roots based on ginsenoside constituents, functional genes, and ferric‐reducing antioxidant power

Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

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