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Metabolites, Volume 9, Issue 4

April 2019 - 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
22 Citations
5,553 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
26 Citations
5,639 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
79 Citations
6,871 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
526 Citations
27,350 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
9 Citations
4,439 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
28 Citations
5,619 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
6,163 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
6,238 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
6,031 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
  • Natasha Hill
  • + 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
218 Citations
22,853 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...

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Metabolites - ISSN 2218-1989