Independent or integrative processing approach of metabolite datasets from different biospecimens potentially affects metabolic pathway recognition in metabolomics.
Abstract In metabolomics studies, metabolic pathway recognition (MPR) is performed by software tools to screen out the significant pathways disturbed by diseases or reinstated by drugs. To achieve MPR, the significantly changed metabolites determined in different biospecimens ( e.g. plasma and urine) are analyzed either independently (metabolites from each biospecimen as a dataset) or integratively (metabolites from all biospecimens as a dataset). However, whether the choice of these two processing approaches affects the results of MPR remains unknown. In this study, this issue was addressed by selecting evaluation of the effects of the herbal medicine Rehmanniae Radix (RR) on anemia and adrenal fatigue by UPLC-QTOF-MS/MS-based metabolomics as an example. The significant pathways disturbed by the modeling of anemia and adrenal fatigue and those reinstated by treatments with raw and processed RR were recognized using MetPA software tool ( MetaboAnalyst 3.0 ), and compared by independent and integrative processing of the significantly changed metabolites determined in plasma and urine. The results showed that the two processing approaches could yield different impact values of pathways and thereby recognize different significant pathways. The differences appear to happen more easily when metabolites from different biospecimens shared the same metabolic pathway. Such pathway could be recognized as a significant pathway by integrative processing but could be excluded by independent processing due to the converged and dispersed importance contributions of the involved metabolites to MPR in the two processing approaches. This issue should concern researchers because MPR is crucial not only to understanding metabolomics data but also to guiding subsequent mechanistic research.
: We present a new update to MetaboAnalyst (version 4.0) for comprehensive metabolomic data analysis, interpretation, and integration with other omics data. Since the last major update in 2015, MetaboAnalyst has continued to evolve based on user feedback and technological advancements in the field. For this year's update, four new key features have been added to MetaboAnalyst 4.0, including: (1) real-time R command tracking and display coupled with the release of a companion MetaboAnalystR packa...
#1Li Zhou(Nanjing University of Chinese Medicine)H-Index: 4
#2Jin-Di Xu(Nanjing University of Chinese Medicine)H-Index: 11
Last. Song-Lin Li(Nanjing University of Chinese Medicine)H-Index: 26
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Abstract Exploring processing chemistry, in particular the chemical transformation mechanisms involved, is a key step to elucidate the scientific basis in traditional processing of herbal medicines. Previously, taking Rehmanniae Radix (RR) as a case study, the holistic chemome (secondary metabolome and glycome) difference between raw and processed RR was revealed by integrating hyphenated chromatographic techniques-based targeted glycomics and untargeted metabolomics. Nevertheless, the complex c...
#1Li Zhou(Nanjing University of Chinese Medicine)H-Index: 4
#2Jin-Di Xu(Nanjing University of Chinese Medicine)H-Index: 11
Last. Song-Lin Li(Nanjing University of Chinese Medicine)H-Index: 26
view all 10 authors...
Abstract It is well-recognized that multiple components, the majority of which are secondary metabolites and carbohydrates, collectively contribute to the therapeutic effects of herbal medicines. The chemical characterization of herbal medicines has focused extensively on secondary metabolites but has largely overlooked carbohydrates. Here, we proposed an integrated chromatographic technique based targeted glycomics and untargeted metabolomics strategy simultaneously determining carbohydrates an...
Metabolomics is rapidly emerging as an important tool in understanding disease mechanisms and identifying novel therapeutic strategies. Here, Wishart explores recent developments in metabolomics technologies, focusing on the growing role of metabolomics in drug discovery and its potential effect on precision medicine.
Last. Gary Siuzdak(Scripps Research Institute)H-Index: 88
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Metabolomics has been utilized extensively for the identification of single metabolites and their use as biomarkers. Owing to recent technical advances, it is now possible to use metabolomics to better understand whole metabolic pathways and to more precisely pinpoint the involvement of metabolites in physiology and pathology.
Last. David S. Wishart(National Institute for Nanotechnology)H-Index: 116
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MetaboAnalyst (www.metaboanalyst.ca) is a web server designed to permit comprehensive metabolomic data analysis, visualization and interpretation. It supports a wide range of complex statistical calculations and high quality graphical rendering functions that require significant computational resources. First introduced in 2009, MetaboAnalyst has experienced more than a 50X growth in user traffic (>50 000 jobs processed each month). In order to keep up with the rapidly increasing computational d...
Last. Yi Feng(SHU: Shanghai University)H-Index: 22
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Liuwei Dihuang Pills (LDPs) are a well-known prescription of nourishing yin especially for invigorating kidney-yin. According to the deviation of the structural imbalance of intestinal flora in kidney-yin deficiency patients and the study about polysaccharides having significant added value on intestinal probiotics, it is indicated that there is a possible correlation between intestinal flora metabolism and the mechanism of LDPs intervening in kidney-yin deficiency. In this study, LDPs, a nouris...
Shenfu decoction (SFD) is a well-known important traditional Chinese medicine prescription that has been used to treat chronic heart failure (CHF) for many years in China. However, its holistic therapeutic effects and mechanism are not yet well understood. Here, a UPLC/TOF–MS-based metabonomic study was conducted to explore potential biomarkers to increase the understanding of CHF and to assess the integral efficacy of SFD for CHF in rats. Principal component analysis was used to investigate the...
#1Weixia Li(Nanjing University of Chinese Medicine)H-Index: 11
#2Yuping Tang(Nanjing University of Chinese Medicine)H-Index: 47
Last. Jin-Ao Duan(Nanjing University of Chinese Medicine)H-Index: 55
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The compatibility of Angelicae Sinensis Radix (Danggui, DG) and Chuanxiong Rhizoma (Chuanxiong, CX), a famous herb pair Gui-Xiong (GX), can produce synergistic and complementary hematopoiesis. In present study, global metabolic profiling with ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC–QTOF/MS) combined with pattern recognition method was performed to discover the underlying hematopoietic regulation mechanisms of DG, CX and GX on hem...
The citric acid cycle is the final common oxidative pathway for carbohydrates, fats and amino acids. It is the most important metabolic pathway for the energy supply to the body. TCA is the most important central pathway connecting almost all the individual metabolic pathways. In this review article, introduction, regulation and energetics of TCA cycle have been discussed. The present study was carried out to review literature on TCA cycle.
The therapeutic effects of water extract of ginseng (WEG) on exercise-induced fatigue (EF) have been reported in several previous studies, but the molecular mechanisms involved remain unexplored. In this study, the anti-EF effects of WEG were studied, and the potential mechanisms were discussed. We characterized the chemical components of WEG by ultra-high performance liquid chromatography-tandem triple quadrupole mass spectrometry (UHPLC-QqQ-MS/MS) and high performance liquid chromatography cou...
Last. Huijun Xu(Hebei Medical University)H-Index: 14
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Abstract Screening diagnostic biomarkers can be challenging due to the complexity of traditional Chinese medicine (TCM) and ambiguous pharmacological mechanisms. In this study, we reported an integrated strategy for accurately screening diagnostic biomarkers based on metabolomics coupled with network pharmacology. First, a feasible pharmacological model was established through systems pharmacology and based on metabolomics-based techniques to explore diagnostic biomarkers. While the components s...