Metabolomics Work Flow and Analytics in Systems Biology

2021 ◽  
Vol 22 ◽  
Author(s):  
Sanoj Chacko ◽  
Yumna B. Haseeb ◽  
Sohaib Haseeb
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Systems Biology ◽  
Nmr Spectroscopy ◽  
Magnetic Resonance ◽  
Large Scale ◽  
Biochemical Analysis ◽  
Data Extraction ◽  
Work Flow ◽  
Metabolic Profiles

: Metabolomics is an omics approach of systems biology that involves the development and assessment of large-scale, comprehensive biochemical analysis tools for metabolites in biological systems. This review describes the metabolomics workflow and provides an overview of current analytic tools used for the quantification of metabolic profiles. We explain analytic tools such as mass spectrometry (MS), nuclear magnetic resonance (NMR) spectroscopy, ionization techniques, and approaches for data extraction and analysis.

Data Analysis and Interpretation in Metabolomics

2013 ◽  
pp. 1494-1521
Author(s):  
Jose M. Garcia-Manteiga
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Data Analysis ◽  
Systems Biology ◽  
Magnetic Resonance ◽  
Biological System ◽  
Analytical Techniques ◽  
Point Of View ◽  
The Other ◽  
Top Down

Metabolomics represents the new ‘omics’ approach of the functional genomics era. It consists in the identification and quantification of all small molecules, namely metabolites, in a given biological system. While metabolomics refers to the analysis of any possible biological system, metabonomics is specifically applied to disease and physiopathological situations. The data collected within these approaches is highly integrative of the other higher levels and is hence amenable to be explored with a top-down systems biology point of view. The aim of this chapter is to give a global view of the state of the art in metabolomics describing the two analytical techniques usually used to give rise to this kind of data, nuclear magnetic resonance, NMR, and mass spectrometry. In addition, the author will focus on the different data analysis tools that can be applied to such studies to extract information with special interest at the attempts to integrate metabolomics with other ‘omics’ approaches and its relevance in systems biology modeling.

Data Analysis and Interpretation in Metabolomics

2011 ◽  
pp. 29-56
Author(s):  
Jose M. Garcia-Manteiga
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Data Analysis ◽  
Systems Biology ◽  
Magnetic Resonance ◽  
Biological System ◽  
Analytical Techniques ◽  
Point Of View ◽  
The Other ◽  
Top Down

Metabolomics represents the new ‘omics’ approach of the functional genomics era. It consists in the identification and quantification of all small molecules, namely metabolites, in a given biological system. While metabolomics refers to the analysis of any possible biological system, metabonomics is specifically applied to disease and physiopathological situations. The data collected within these approaches is highly integrative of the other higher levels and is hence amenable to be explored with a top-down systems biology point of view. The aim of this chapter is to give a global view of the state of the art in metabolomics describing the two analytical techniques usually used to give rise to this kind of data, nuclear magnetic resonance, NMR, and mass spectrometry. In addition, the author will focus on the different data analysis tools that can be applied to such studies to extract information with special interest at the attempts to integrate metabolomics with other ‘omics’ approaches and its relevance in systems biology modeling.

Comparison of hydrogenolysis with thioacidolysis for lignin structural analysis

Holzforschung ◽  
2014 ◽  
Vol 68 (2) ◽  
pp. 151-155 ◽  
Author(s):  
Daniel J. van de Pas ◽  
Bernadette Nanayakkara ◽  
Ian D. Suckling ◽  
Kirk M. Torr
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Gas Chromatography ◽  
Nmr Spectroscopy ◽  
Structural Analysis ◽  
Magnetic Resonance ◽  
Gas Chromatography Mass Spectrometry ◽  
Aryl Ether ◽  
Chromatography Mass Spectrometry

Abstract Mild hydrogenolysis has been compared with thioacidolysis as a method for degrading lignins in situ and in isolated form before analysis by gas chromatography/mass spectrometry and quantitative 31P nuclear magnetic resonance (NMR) spectroscopy. Both degradation methods gave similar levels of β-aryl ether-linked phenylpropane units that were released as monomers. Degradation by hydrogenolysis generally gave lower levels of total phenylpropane units when analyzed by 31P NMR, especially in the case of lignins with high levels of condensed units. Overall, these results indicate that mild hydrogenolysis could offer an alternative to thioacidolysis for probing lignin structure.

scholarly journals Special Issue: NMR-Based Metabolomics

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3283
Author(s):  
Miriam Pérez-Trujillo ◽  
Toby J. Athersuch
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Nmr Spectroscopy ◽  
Magnetic Resonance ◽  
Dynamic Range ◽  
Chemical Information ◽  
Special Issue ◽  
The Core ◽  
Analytical Platforms ◽  
Nuclear Magnetic

Nuclear magnetic resonance (NMR) spectroscopy remains one of the core analytical platforms for metabolomics, providing complementary chemical information to others, such as mass spectrometry, and offering particular advantages in some areas of research on account of its inherent robustness, reproducibility, and phenomenal dynamic range [...]

scholarly journals Dudley Howard Williams. 25 May 1937 — 3 November 2010

2017 ◽  
Vol 63 ◽  
pp. 567-583
Author(s):  
Jeremy K. M. Sanders ◽  
Dame Carol V. Robinson
Keyword(s):  
Organic Chemistry ◽  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Nmr Spectroscopy ◽  
Magnetic Resonance ◽  
Molecular Recognition ◽  
Mode Of Action ◽  
Academic Research ◽  
Spectroscopic Methods ◽  
Structural Problems

Dudley Williams was a pioneer in using nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) to solve important structural problems in Chemistry and Biology. His 35-year quest to understand the structure and mode of action of the vancomycin antibiotics led him to fundamental thinking about the nature and thermodynamics of molecular recognition, in particular the roles of solvation, flexibility, entropy, enthalpy and cooperativity. He was always keen that his expertise be used for practical benefit through his academic research and industrial consulting. His legacy also includes a set of textbooks that transformed the use of spectroscopic methods in organic chemistry, and a school of former PhD students and postdoctoral colleagues who have themselves made major contributions across a broad swathe of science.

Separation and Identification of Bridgehead-Substituted Methyl and Ethyl Adamantanes

1968 ◽  
Vol 22 (2) ◽  
pp. 115-120 ◽  
Author(s):  
R. W. Warren ◽  
Abraham Schneider ◽  
E. J. Janoski
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Gas Chromatography ◽  
Nmr Spectroscopy ◽  
Magnetic Resonance ◽  
Mass Spectra ◽  
Nmr Spectra ◽  
Adamantane Derivatives ◽  
Saturated Hydrocarbons ◽  
Aluminum Halide

A combination of gas chromatography, infrared and nuclear magnetic resonance (NMR) spectroscopy, and mass spectrometry was used to characterize the products obtained from aluminum halide-catalyzed isomerizations of tricyclic saturated hydrocarbons. Six compounds were isolated and identified as methyl and ethyl bridgehead-substituted adamantane derivatives. In addition to supplying evidence pertinent to the structural proof of these derivatives, the data provide useful correlations between infrared, NMR, and mass spectra and methyl and ethyl bridgehead substitution of the adamantane nucleus. A complex splitting pattern which was observed in the NMR spectra of the ethyl-substituted derivatives was shown to be due to the unique A2B3 splitting of the bridgehead-ethyl group.

scholarly journals Revisiting marine bioprospecting of tropical Indonesian macroalgae from West Timor

2021 ◽  
Author(s):  
◽  
Wem Turupadang
Keyword(s):  
Mass Spectrometry ◽  
Nuclear Magnetic Resonance ◽  
Liquid Chromatography ◽  
Nmr Spectroscopy ◽  
Magnetic Resonance ◽  
Natural Product ◽  
Marine Algae ◽  
Liquid Chromatography Mass Spectrometry ◽  
Molecular Networking ◽  
West Timor

<p>Marine algae are an important and historically rich source of new marine-based natural products. This thesis describes the screening of 40 Indonesian macroalgal samples using liquid chromatography-mass spectrometry (LC-MS) based molecular networking, and the subsequent nuclear magnetic resonance (NMR)-guided isolation and structural elucidation of a 6-deoxy-6-aminoglycoglyrecolipid (60). Molecular networking was performed using LC-MS/MS data through the online Global Natural Product Social Molecular Networking (GNPS) platform directly from crude extracts. NMR spectroscopy-guided screening was also employed targeting unique peaks detected by 1H NMR to validate any hits from GNPS. Out of 40 macroalgae specimens collected from West Timor waters, six samples were prioritised by the molecular networking screening. Proton NMR revealed three specimens with significantly interesting peaks but only one specimen, Laurencia snackeyi was purified further, which yielded compound 60.</p>

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