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Metabolites, Volume 9, Issue 4

2019 April - 21 articles

Cover Story: CFM-ID is a freely available software tool that implements the Competitive Fragmentation Modeling algorithm for the accurate prediction and annotation of mass-spectrometry (MS) spectra, as well as MS-based compound identification. Here we describe a newly updated version of the program called CFM-ID 3.0. This release implements a rule-based fragmentation approach to significantly improve the MS-spectra prediction accuracy for 21 classes of lipids. Moreover, a newly expanded spectral database, as well as an improved metadata-based scoring function have improved CFM-ID’s compound identification performance by 21%. Finally, a compound classification method is introduced, allowing CFM-ID to correctly classify chemical compounds based on their ESI-MS/MS-spectra in 80% of the cases. The CFM-ID 3.0 webserver and code base are freely accessible online. View this paper.
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Articles (21)

  • Article
  • Open Access
23 Citations
5,922 Views
14 Pages

Surfactant Lipidomics of Alveolar Lavage Fluid in Mice Based on Ultra-High-Performance Liquid Chromatography Coupled to Hybrid Quadrupole-Exactive Orbitrap Mass Spectrometry

  • Rui Yang,
  • Ying Zhang,
  • Wenjuan Qian,
  • Linxiu Peng,
  • Lili Lin,
  • Jia Xu,
  • Tong Xie,
  • Jianjian Ji,
  • Xiuqin Zhan and
  • Jinjun Shan

Surfactant lipid metabolism is closely related to pulmonary diseases. Lipid metabolism disorder can cause lung diseases, vice versa. With this rationale, a useful method was established in this study to determine the lipidome in bronchoalveolar lavag...

  • Article
  • Open Access
27 Citations
5,883 Views
15 Pages

An Integrative Multi-Omics Workflow to Address Multifactorial Toxicology Experiments

  • Víctor González-Ruiz,
  • Domitille Schvartz,
  • Jenny Sandström,
  • Julian Pezzatti,
  • Fabienne Jeanneret,
  • David Tonoli,
  • Julien Boccard,
  • Florianne Monnet-Tschudi,
  • Jean-Charles Sanchez and
  • Serge Rudaz

Toxicology studies can take advantage of omics approaches to better understand the phenomena underlying the phenotypic alterations induced by different types of exposure to certain toxicants. Nevertheless, in order to analyse the data generated from...

  • Article
  • Open Access
83 Citations
7,219 Views
13 Pages

Polyphenol Microbial Metabolites Exhibit Gut and Blood–Brain Barrier Permeability and Protect Murine Microglia against LPS-Induced Inflammation

  • Shelby L. Johnson,
  • Riley D. Kirk,
  • Nicholas A. DaSilva,
  • Hang Ma,
  • Navindra P. Seeram and
  • Matthew J. Bertin

Increasing evidence supports the beneficial effects of polyphenol-rich diets, including the traditional Mediterranean diet, for the management of cardiovascular disease, obesity and neurodegenerative diseases. However, a common concern when discussin...

  • Perspective
  • Open Access
560 Citations
28,542 Views
31 Pages

Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

  • Farhana R. Pinu,
  • David J. Beale,
  • Amy M. Paten,
  • Konstantinos Kouremenos,
  • Sanjay Swarup,
  • Horst J. Schirra and
  • David Wishart

The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological...

  • Article
  • Open Access
10 Citations
4,687 Views
14 Pages

Biomarker Discovery for Cytochrome P450 1A2 Activity Assessment in Rats, Based on Metabolomics

  • Xiao Pu,
  • Yiqiao Gao,
  • Ruiting Li,
  • Wei Li,
  • Yuan Tian,
  • Zunjian Zhang and
  • Fengguo Xu

Cytochrome P450 1A2 (CYP1A2) is one of the major CYP450 enzymes (CYPs) in the liver, and participates in the biotransformation of various xenobiotics and endogenous signaling molecules. The expression and activity of CYP1A2 show large individual diff...

  • Review
  • Open Access
29 Citations
5,828 Views
15 Pages

Carbonic Anhydrases in Photosynthesizing Cells of C3 Higher Plants

  • Lyudmila Ignatova,
  • Natalia Rudenko,
  • Elena Zhurikova,
  • Maria Borisova-Mubarakshina and
  • Boris Ivanov

The review presents data on the location, nature, properties, number, and expression of carbonic anhydrase genes in the photosynthesizing cells of C3 plants. The available data about the presence of carbonic anhydrases in plasma membrane, cytoplasm,...

  • Article
  • Open Access
24 Citations
6,418 Views
15 Pages

Cyanobacteria have many defence strategies to overcome harmful ultraviolet (UV) stress including the production of secondary metabolites. Metabolomics can be used to investigate this altered metabolism via targeted and untargeted techniques. In this...

  • Article
  • Open Access
27 Citations
6,627 Views
21 Pages

Propolis Exerts an Anti-Inflammatory Effect on PMA-Differentiated THP-1 Cells via Inhibition of Purine Nucleoside Phosphorylase

  • Abdulmalik M. Alqarni,
  • Kanidta Niwasabutra,
  • Muhamad Sahlan,
  • Hugo Fearnley,
  • James Fearnley,
  • Valerie A. Ferro and
  • David G. Watson

Previous research has shown that propolis has immunomodulatory activity. Propolis extracts from different geographic origins were assessed for their anti-inflammatory activities by investigating their ability to alter the production of tumour necrosi...

  • Article
  • Open Access
12 Citations
6,193 Views
20 Pages

Plasma Free Fatty Acids Metabolic Profile with LC-MS and Appetite-Related Hormones in South Asian and White European Men in Relation to Adiposity, Physical Activity and Cardiorespiratory Fitness: A Cross-Sectional Study

  • Simone Benedetti,
  • Naser F. Al-Tannak,
  • Mansour Alzharani,
  • Hannah J. Moir,
  • David J. Stensel,
  • Alice E. Thackray,
  • Declan P. Naughton,
  • Mehmet T. Dorak,
  • Owen Spendiff and
  • Judith Allgrove
  • + 2 authors

South Asians have a greater cardiovascular disease (CVD) and type 2 diabetes (T2D) risk than white Europeans, but the mechanisms are poorly understood. This study examined ethnic differences in free fatty acids (FFAs) metabolic profile (assessed usin...

  • Article
  • Open Access
224 Citations
23,698 Views
23 Pages

CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification

  • Yannick Djoumbou-Feunang,
  • Allison Pon,
  • Naama Karu,
  • Jiamin Zheng,
  • Carin Li,
  • David Arndt,
  • Maheswor Gautam,
  • Felicity Allen and
  • David S. Wishart

Metabolite identification for untargeted metabolomics is often hampered by the lack of experimentally collected reference spectra from tandem mass spectrometry (MS/MS). To circumvent this problem, Competitive Fragmentation Modeling-ID (CFM-ID) was de...

  • Article
  • Open Access
15 Citations
4,510 Views
13 Pages

Role of Intestinal Microbiota in Metabolism of Gastrodin In Vitro and In Vivo

  • Mahesh Raj Nepal,
  • Ki Sun Jeong,
  • Geon Ho Kim,
  • Dong Ho Cha,
  • Mi Jeong Kang,
  • Jin Sung Kim,
  • Ju-Hyun Kim and
  • Tae Cheon Jeong

Alteration in the number and composition of intestinal microbiota affects the metabolism of several xenobiotics. Gastrodin, isolated from Gastrodia elata, is prone to be hydrolyzed by intestinal microbiota. In the present study, the role of intestina...

  • Communication
  • Open Access
19 Citations
5,022 Views
8 Pages

We report here that a straightforward change of the standard derivatization procedure for GC–MS metabolomics is leading to a strong increase in metabolite signal intensity. Drying samples between methoxymation and trimethylsilylation significan...

  • Review
  • Open Access
31 Citations
7,219 Views
18 Pages

Metabolomics uses quantitative analyses of metabolites from tissues or bodily fluids to acquire a functional readout of the physiological state. Complex diseases arise from the influence of multiple factors, such as genetics, environment and lifestyl...

  • Review
  • Open Access
16 Citations
4,389 Views
8 Pages

The Metabolomic Signatures of Weight Change

  • Amrita Vijay and
  • Ana M Valdes

Obesity represents a major health concern, not just in the West but increasingly in low and middle income countries. In order to develop successful strategies for losing weight, it is essential to understand the molecular pathogenesis of weight chang...

  • Article
  • Open Access
17 Citations
6,687 Views
21 Pages

The Effect of Pre-Analytical Conditions on Blood Metabolomics in Epidemiological Studies

  • Diana L. Santos Ferreira,
  • Hannah J. Maple,
  • Matt Goodwin,
  • Judith S. Brand,
  • Vikki Yip,
  • Josine L. Min,
  • Alix Groom,
  • Debbie A. Lawlor and
  • Susan Ring

Serum and plasma are commonly used in metabolomic-epidemiology studies. Their metabolome is susceptible to differences in pre-analytical conditions and the impact of this is unclear. Participant-matched EDTA-plasma and serum samples were collected fr...

  • Article
  • Open Access
33 Citations
4,916 Views
12 Pages

Extra-Virgin Olive Oils from Nine Italian Regions: An 1H NMR-Chemometric Characterization

  • Cinzia Ingallina,
  • Antonella Cerreto,
  • Luisa Mannina,
  • Simone Circi,
  • Silvia Vista,
  • Donatella Capitani,
  • Mattia Spano,
  • Anatoly P. Sobolev and
  • Federico Marini

Extra-virgin olive oil (383 samples; EVOOs) of three consecutive harvesting years from nine Italian regions were collected and submitted to an 1H NMR-chemometric protocol to characterize the samples according to their origin (geographical area and va...

  • Article
  • Open Access
3 Citations
4,114 Views
13 Pages

Identification of N-Oxide-Containing Aromatic Heterocycles as Pharmacophores for Rumen Fermentation Modifiers

  • Carla Bonifacino,
  • Gonzalo Rodríguez,
  • Analía Pérez-Ruchel,
  • José Luis Repetto,
  • Hugo Cerecetto,
  • Cecilia Cajarville and
  • Mercedes González

Different strategies have been used to mitigate greenhouse gas emissions from domesticated ruminants, including the removal of protozoa (defaunation). The objective of the present work was to analyze the potential of different N-oxide-containing arom...

  • Article
  • Open Access
33 Citations
6,192 Views
21 Pages

Dynamic 13C-tracer-based flux analyses of in vivo reaction networks still require a continuous development of advanced quantification methods applying state-of-the-art mass spectrometry platforms. Utilizing alkaline HILIC chromatography, we adapt str...

  • Article
  • Open Access
41 Citations
7,392 Views
19 Pages

Metabolomics Identifies Novel Blood Biomarkers of Pulmonary Function and COPD in the General Population

  • Bing Yu,
  • Claudia Flexeder,
  • Robert W. McGarrah,
  • Annah Wyss,
  • Alanna C. Morrison,
  • Kari E. North,
  • Eric Boerwinkle,
  • Gabi Kastenmüller,
  • Christian Gieger and
  • Stephanie J. London
  • + 7 authors

Determination of metabolomic signatures of pulmonary function and chronic obstructive pulmonary disease (COPD) in the general population could aid in identification and understanding of early disease processes. Metabolome measurements were performed...

  • Article
  • Open Access
17 Citations
5,108 Views
16 Pages

Begomoviruses, such as the Tomato curly stunt virus (ToCSV), pose serious economic consequences due to severe crop losses. Therefore, the development and screening of possible resistance markers is imperative. While some tomato cultivars exhibit diff...

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Metabolites - ISSN 2218-1989