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Metabolites
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Metabolic Pathway Profiling and Untargeted/Targeted Analysis of Metabolites
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Metabolic Pathway Profiling and Untargeted/Targeted Analysis of Metabolites

A special issue of Metabolites (ISSN 2218-1989). This special issue belongs to the section "Metabolomic Profiling Technology".

Deadline for manuscript submissions: closed (31 July 2022) | Viewed by 8949

Special Issue Editor

Dr. Dong-Hyun Kim

E-Mail Website
Guest Editor
Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University Park Campus, University of Nottingham, Nottingham NG7 2RD, UK
Interests: global metabolite profiling; metabolomics; lipidomics; metabolic pathway profiling; stable isotope assisted analysis; targeted quantitative analysis of metabolites; mass spectrometry; liquid chromatography-mass spectrometry

Special Issue Information

Dear Colleagues,

Metabolomics, including the untargeted and targeted analysis of it, as well as metabolic pathway profiling, have built a rich history for the analysis of small biomolecules which represent ‘metabolite and pathway profiles’ in biofluid, cell, and tissue extracts. Since metabolites provide the phenotypic outcome of gene expression or metabolic activities of a cell or organism, these analytical techniques can give a rapid snapshot of the cell physiology and provide insight into relationships between genotype and phenotype. Therefore, untargeted/targeted analysis and metabolic pathway profiles have been increasingly used in a variety of research areas, such as medicine, pharmaceutics, biotechnology, plant, food, microbiology, and nutrients.

Therefore, this Special Issue of Metabolites, “Metabolic Pathway Profiling and Untargeted/Targeted Analysis of Metabolites”, will be dedicated for publishing a wide range of applicatoins of metabolomics techniques to various research fileds mentioned above and a cutting-edge technology development to significantly enhance the sensitivity and selectivity of the detection of small molecules in a biological sample. Any research on computational tools to improve pre-processing of metabolomics data and metabolite identification is also highly desired.

Dr. Dong-Hyun Kim
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Metabolites is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • metabolite profiling
  • metabolic pathway profiling
  • global metabolic profiling
  • targeted quantitative analysis
  • metabolite identification
  • metabolomics data pre-processing tool
  • biomarker discovery

Published Papers (3 papers)

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Research

12 pages, 856 KiB  
Article
Untargeted Metabolomic Assay of Prefrail Older Adults after Nutritional Intervention
by Alina Jaroch, Mariusz Kozakiewicz, Karol Jaroch, Emilia Główczewska-Siedlecka, Barbara Bojko and Kornelia Kędziora-Kornatowska
Metabolites 2022, 12(5), 378; https://doi.org/10.3390/metabo12050378 - 21 Apr 2022
Viewed by 1790
Abstract
Frailty is a geriatric syndrome causing a reduction in the body’s functional reserves. Proper nutrition may be helpful in delaying transitioning older adults from pre-frail to frailty syndrome. The present study evaluates the nutritional status of pre-frail patients who underwent nutritional intervention and [...] Read more.
Frailty is a geriatric syndrome causing a reduction in the body’s functional reserves. Proper nutrition may be helpful in delaying transitioning older adults from pre-frail to frailty syndrome. The present study evaluates the nutritional status of pre-frail patients who underwent nutritional intervention and metabolomic changes resulting from this intervention. Sixteen pre-frail patients (68.4 ± 5.5 years old; 81.3% women) were enrolled for nutritional intervention, and twenty-nine robust elderly people (69.3 ± 5.3 years old; 82.8% women) were the control group. Pre-frail patients consumed 1.0 g protein/kg BW/day for eight weeks through diet modification and an additional daily intake of a protein powder formula. Taken measurements included: Nutritional anthropometry, assessment of food intake, and blood serum analysis with an untargeted metabolomic assessment. Protein consumption increased by 25.8%; moreover, significant increases in body weight (+1.2 kg; p = 0.023) and muscle mass index (+0.1 kg/m2; p = 0.042) were also observed. The untargeted metabolomic assay showed a significant increase in arachidonic acid (p = 0.038), and valine (p = 0.008) among pre-frail patients. Increased protein consumption is reflected in improved anthropometric and biochemical parameters of pre-frail patients. Moreover, metabolomic assay can be a useful tool in determining compliance with dietary recommendations. Full article
(This article belongs to the Special Issue Metabolic Pathway Profiling and Untargeted/Targeted Analysis of Metabolites)
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23 pages, 4488 KiB  
Article
Metabolic Footprinting of Microbial Systems Based on Comprehensive In Silico Predictions of MS/MS Relevant Data
by Alexander Reiter, Jian Asgari, Wolfgang Wiechert and Marco Oldiges
Metabolites 2022, 12(3), 257; https://doi.org/10.3390/metabo12030257 - 17 Mar 2022
Cited by 3 | Viewed by 2280
Abstract
Metabolic footprinting represents a holistic approach to gathering large-scale metabolomic information of a given biological system and is, therefore, a driving force for systems biology and bioprocess development. The ongoing development of automated cultivation platforms increases the need for a comprehensive and rapid [...] Read more.
Metabolic footprinting represents a holistic approach to gathering large-scale metabolomic information of a given biological system and is, therefore, a driving force for systems biology and bioprocess development. The ongoing development of automated cultivation platforms increases the need for a comprehensive and rapid profiling tool to cope with the cultivation throughput. In this study, we implemented a workflow to provide and select relevant metabolite information from a genome-scale model to automatically build an organism-specific comprehensive metabolome analysis method. Based on in-house literature and predicted metabolite information, the deduced metabolite set was distributed in stackable methods for a chromatography-free dilute and shoot flow-injection analysis multiple-reaction monitoring profiling approach. The workflow was used to create a method specific for Saccharomyces cerevisiae, covering 252 metabolites with 7 min/sample. The method was validated with a commercially available yeast metabolome standard, identifying up to 74.2% of the listed metabolites. As a first case study, three commercially available yeast extracts were screened with 118 metabolites passing quality control thresholds for statistical analysis, allowing to identify discriminating metabolites. The presented methodology provides metabolite screening in a time-optimised way by scaling analysis time to metabolite coverage and is open to other microbial systems simply starting from genome-scale model information. Full article
(This article belongs to the Special Issue Metabolic Pathway Profiling and Untargeted/Targeted Analysis of Metabolites)
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16 pages, 2108 KiB  
Article
Systematic Evaluation of HILIC Stationary Phases for Global Metabolomics of Human Plasma
by Farideh Hosseinkhani, Luojiao Huang, Anne-Charlotte Dubbelman, Faisa Guled, Amy C. Harms and Thomas Hankemeier
Metabolites 2022, 12(2), 165; https://doi.org/10.3390/metabo12020165 - 9 Feb 2022
Cited by 15 | Viewed by 4345
Abstract
Polar hydrophilic metabolites have been identified as important actors in many biochemical pathways. Despite continuous improvement and refinement of hydrophilic interaction liquid chromatography (HILIC) platforms, its application in global polar metabolomics has been underutilized. In this study, we aimed to systematically evaluate polar [...] Read more.
Polar hydrophilic metabolites have been identified as important actors in many biochemical pathways. Despite continuous improvement and refinement of hydrophilic interaction liquid chromatography (HILIC) platforms, its application in global polar metabolomics has been underutilized. In this study, we aimed to systematically evaluate polar stationary phases for untargeted metabolomics by using HILIC columns (neutral and zwitterionic) that have been exploited widely in targeted approaches. To do so, high-resolution mass spectrometry was applied to thoroughly investigate selectivity, repeatability and matrix effect at three pH conditions for 9 classes of polar compounds using 54 authentic standards and plasma matrix. The column performance for utilization in untargeted metabolomics was assessed using plasma samples with diverse phenotypes. Our results indicate that the ZIC-c HILIC column operated at neutral pH exhibited several advantages, including superior performance for different classes of compounds, better isomer separation, repeatability and high metabolic coverage. Regardless of the column type, the retention of inorganic ions in plasma leads to extensive adduct formation and co-elution with analytes, which results in ion-suppression as part of the overall plasma matrix effect. In ZIC-c HILIC, the sodium chloride ion effect was particularly observed for amino acids and amine classes. Successful performance of HILIC for separation of plasma samples with different phenotypes highlights this mode of separation as a valuable approach in global profiling of plasma sample and discovering the metabolic changes associated with health and disease. Full article
(This article belongs to the Special Issue Metabolic Pathway Profiling and Untargeted/Targeted Analysis of Metabolites)
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