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Metabolites, Volume 8, Issue 1

2018 March - 24 articles

Cover Story: We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters, accurate mass, MS/MS (MS2), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS2 approach facilitates the identification of metabolites that are not present in experimental NMR and MS metabolomics databases. View the paper
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Articles (24)

  • Communication
  • Open Access
12 Citations
6,554 Views
11 Pages

Identification of an Epoxide Metabolite of Lycopene in Human Plasma Using 13C-Labeling and QTOF-MS

  • Morgan J. Cichon,
  • Nancy E. Moran,
  • Ken M. Riedl,
  • Steven J. Schwartz and
  • Steven K. Clinton

The carotenoid lycopene is a bioactive component of tomatoes and is hypothesized to reduce risk of several chronic diseases, such as prostate cancer. The metabolism of lycopene is only beginning to be understood and some studies suggest that metaboli...

  • Article
  • Open Access
30 Citations
6,562 Views
15 Pages

GC-MS-Based Endometabolome Analysis Differentiates Prostate Cancer from Normal Prostate Cells

  • Ana Rita Lima,
  • Ana Margarida Araújo,
  • Joana Pinto,
  • Carmen Jerónimo,
  • Rui Henrique,
  • Maria De Lourdes Bastos,
  • Márcia Carvalho and
  • Paula Guedes de Pinho

Prostate cancer (PCa) is an important health problem worldwide. Diagnosis and management of PCa is very complex because the detection of serum prostate specific antigen (PSA) has several drawbacks. Metabolomics brings promise for cancer biomarker dis...

  • Review
  • Open Access
22 Citations
7,806 Views
14 Pages

Nanoparticle-Assisted Metabolomics

  • Bo Zhang,
  • Mouzhe Xie,
  • Lei Bruschweiler-Li and
  • Rafael Brüschweiler

Understanding and harnessing the interactions between nanoparticles and biological molecules is at the forefront of applications of nanotechnology to modern biology. Metabolomics has emerged as a prominent player in systems biology as a complement to...

  • Review
  • Open Access
54 Citations
7,578 Views
16 Pages

Carbonic anhydrases (CAs) are metalloenzymes that are omnipresent in nature. CAs catalyze the basic reaction of the reversible hydration of CO2 to HCO3 and H+ in all living organisms. Photosynthetic organisms contain six evolutionarily different cla...

  • Review
  • Open Access
49 Citations
5,799 Views
11 Pages

Hypoxia is a prominent feature of the tumor microenvironment (TME) and cancer cells must dynamically adapt their metabolism to survive in these conditions. A major consequence of metabolic rewiring by cancer cells in hypoxia is the accumulation of ac...

  • Review
  • Open Access
238 Citations
14,381 Views
31 Pages

Carbonic Anhydrases: Role in pH Control and Cancer

  • Mam Y. Mboge,
  • Brian P. Mahon,
  • Robert McKenna and
  • Susan C. Frost

28 February 2018

The pH of the tumor microenvironment drives the metastatic phenotype and chemotherapeutic resistance of tumors. Understanding the mechanisms underlying this pH-dependent phenomenon will lead to improved drug delivery and allow the identification of n...

  • Review
  • Open Access
41 Citations
6,484 Views
12 Pages

24 February 2018

In recent years, metabolomics has attracted great scientific attention. The metabolomics methodology might permit a view into transitional phases between healthy liver and nonalcoholic steatohepatitis. Metabolomics can help to analyze the metabolic a...

  • Article
  • Open Access
6 Citations
5,917 Views
28 Pages

Identifying Biomarkers of Wharton’s Jelly Mesenchymal Stromal Cells Using a Dynamic Metabolic Model: The Cell Passage Effect

  • Benoît Laflaquière,
  • Gabrielle Leclercq,
  • Chandarong Choey,
  • Jingkui Chen,
  • Sabine Peres,
  • Caryn Ito and
  • Mario Jolicoeur

24 February 2018

Because of their unique ability to modulate the immune system, mesenchymal stromal cells (MSCs) are widely studied to develop cell therapies for detrimental immune and inflammatory disorders. However, controlling the final cell phenotype and determin...

  • Article
  • Open Access
39 Citations
11,924 Views
15 Pages

RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites

  • Bofei Zhang,
  • Senyang Hu,
  • Elizabeth Baskin,
  • Andrew Patt,
  • Jalal K. Siddiqui and
  • Ewy A. Mathé

22 February 2018

The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms t...

  • Article
  • Open Access
10 Citations
7,169 Views
18 Pages

14 February 2018

Currently, changes in metabolic fluxes following consumption of stable isotope-enriched foods are usually limited to the analysis of postprandial kinetics of glucose. Kinetic information on a larger diversity of metabolites is often lacking, mainly d...

  • Article
  • Open Access
40 Citations
7,383 Views
17 Pages

Untargeted Metabolomics Profiling of an 80.5 km Simulated Treadmill Ultramarathon

  • Christopher C. F. Howe,
  • Ahmed Alshehri,
  • David Muggeridge,
  • Alexander B. Mullen,
  • Marie Boyd,
  • Owen Spendiff,
  • Hannah J. Moir and
  • David G. Watson

13 February 2018

Metabolomic profiling of nine trained ultramarathon runners completing an 80.5 km self-paced treadmill-based time trial was carried out. Plasma samples were obtained from venous whole blood, collected at rest and on completion of the distance (post-8...

  • Review
  • Open Access
70 Citations
10,921 Views
18 Pages

Carbonic Anhydrase IX (CAIX), Cancer, and Radiation Responsiveness

  • Carol Ward,
  • James Meehan,
  • Mark Gray,
  • Ian H. Kunkler,
  • Simon P. Langdon and
  • David J. Argyle

10 February 2018

Carbonic anhydrase IX has been under intensive investigation as a therapeutic target in cancer. Studies demonstrate that this enzyme has a key role in pH regulation in cancer cells, allowing these cells to adapt to the adverse conditions of the tumou...

  • Article
  • Open Access
3 Citations
5,580 Views
13 Pages

Anaerobic Degradation of Bicyclic Monoterpenes in Castellaniella defragrans

  • Edinson Puentes-Cala,
  • Manuel Liebeke,
  • Stephanie Markert and
  • Jens Harder

7 February 2018

The microbial degradation pathways of bicyclic monoterpenes contain unknown enzymes for carbon–carbon cleavages. Such enzymes may also be present in the betaproteobacterium Castellaniella defragrans, a model organism to study the anaerobic monoterpen...

  • Article
  • Open Access
38 Citations
7,864 Views
12 Pages

23 January 2018

We evaluated the metabolic alterations in maternal and fetal placental tissues from non-labored women undergoing cesarean section using samples collected from 5 min to 24 h following delivery. Using 1H-NMR, we identified 14 metabolites that significa...

  • Article
  • Open Access
17 Citations
5,866 Views
12 Pages

18 January 2018

Identifying non-annotated peaks may have a significant impact on the understanding of biological systems. In silico methodologies have focused on ESI LC/MS/MS for identifying non-annotated MS peaks. In this study, we employed in silico methodology to...

  • Article
  • Open Access
68 Citations
11,144 Views
12 Pages

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

  • Rene M. Boiteau,
  • David W. Hoyt,
  • Carrie D. Nicora,
  • Hannah A. Kinmonth-Schultz,
  • Joy K. Ward and
  • Kerem Bingol

17 January 2018

We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS2), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studi...

  • Article
  • Open Access
39 Citations
8,091 Views
13 Pages

Impact of Prolonged Blood Incubation and Extended Serum Storage at Room Temperature on the Human Serum Metabolome

  • Beate Kamlage,
  • Sebastian Neuber,
  • Bianca Bethan,
  • Sandra González Maldonado,
  • Antje Wagner-Golbs,
  • Erik Peter,
  • Oliver Schmitz and
  • Philipp Schatz

13 January 2018

Metabolomics is a powerful technology with broad applications in life science that, like other -omics approaches, requires high-quality samples to achieve reliable results and ensure reproducibility. Therefore, along with quality assurance, methods t...

  • Review
  • Open Access
138 Citations
15,198 Views
16 Pages

11 January 2018

Machine learning uses experimental data to optimize clustering or classification of samples or features, or to develop, augment or verify models that can be used to predict behavior or properties of systems. It is expected that machine learning will...

  • Article
  • Open Access
9 Citations
6,765 Views
14 Pages

11 January 2018

Vitamin D deficiency is a common problem worldwide. In particular, it is an issue in the Northern Hemisphere where UVB radiation does not penetrate the atmosphere as readily. There is a correlation between vitamin D deficiency and colorectal cancer i...

  • Article
  • Open Access
5 Citations
7,665 Views
17 Pages

Constraining Genome-Scale Models to Represent the Bow Tie Structure of Metabolism for 13C Metabolic Flux Analysis

  • Tyler W. H. Backman,
  • David Ando,
  • Jahnavi Singh,
  • Jay D. Keasling and
  • Héctor García Martín

Determination of internal metabolic fluxes is crucial for fundamental and applied biology because they map how carbon and electrons flow through metabolism to enable cell function. 13 C Metabolic Flux Analysis ( 13 C MFA) and Two-Scale...

  • Review
  • Open Access
55 Citations
7,689 Views
20 Pages

Rethinking the Combination of Proton Exchanger Inhibitors in Cancer Therapy

  • Elisabetta Iessi,
  • Mariantonia Logozzi,
  • Davide Mizzoni,
  • Rossella Di Raimo,
  • Claudiu T. Supuran and
  • Stefano Fais

23 December 2017

Microenvironmental acidity is becoming a key target for the new age of cancer treatment. In fact, while cancer is characterized by genetic heterogeneity, extracellular acidity is a common phenotype of almost all cancers. To survive and proliferate un...

  • Article
  • Open Access
52 Citations
8,729 Views
19 Pages

Methanol Generates Numerous Artifacts during Sample Extraction and Storage of Extracts in Metabolomics Research

  • Claudia Sauerschnig,
  • Maria Doppler,
  • Christoph Bueschl and
  • Rainer Schuhmacher

22 December 2017

Many metabolomics studies use mixtures of (acidified) methanol and water for sample extraction. In the present study, we investigated if the extraction with methanol can result in artifacts. To this end, wheat leaves were extracted with mixtures of n...

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Metabolites - ISSN 2218-1989