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- Metabolomic database annotations via query of elemental compositions: Mass accuracy is insufficient even at less than 1 ppm (2006) (Online version)
Tobias Kind and Oliver Fiehn, UC Davis
Metabolomic studies are targeted at identifying and quantifying all metabolites in a given biological context. Among the tools used for metabolomic research, mass spectrometry is one of the most powerful tools. However, metabolomics by mass spectrometry always reveals a high number of unknown compounds which complicate in depth mechanistic or biochemical understanding. In principle, mass spectrometry can be utilized within strategies of de novo structure elucidation of small molecules...
- Metabolomics: building on a century of biochemistry to guide human health (2005) (Online version)
German et al., UC Davis
Medical diagnosis and treatment efficacy will improve significantly when a more personalized system for health assessment is implemented. This system will require diagnostics that provide sufficiently detailed information about the metabolic status of individuals such that assay results will be able to guide food, drug and lifestyle choices to maintain or improve distinct aspects of health without compromising others. Achieving this goal will use the new science of metabolomics – comprehensive metabolic profiling of individuals linked to the biological understanding of human integrative metabolism...
- Expansion of the BioCyc collection of pathway/genome databases to 160 genomes (2005) (Online version)
Karp et al., SRI International, California
The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from multiple organisms. In addition, each bacterial PGDB includes predicted operons for the corresponding species...
- Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops (2005) (Online version)
Catchpole et al., Max Planck Institute for Molecular Plant Physiology, Germany
There is current debate whether genetically modified (GM) plants might contain unexpected, potentially undesirable changes in overall metabolite composition. However, appropriate analytical technology and acceptable metrics of compositional similarity require development. We describe a comprehensive comparison of total metabolites in field-grown GM and conventional potato tubers using a hierarchical approach initiating with rapid metabolome “fingerprinting” to guide more detailed profiling of metabolites where significant differences are suspected...
- Processing methods for differential analysis of LC/MS profile data (2005) (Online version)
Katajamaa et al., Turku Centre for Biotechnology, Finland
We present a software package MZmine that enables differential LC/MS analysis of metabolomics data. This software is a toolbox containing methods for all data processing stages preceding differential analysis: spectral filtering, peak detection, alignment and normalization. Specifically, we developed and implemented a new recursive peak search algorithm and a secondary peak picking method for improving already aligned results, as well as a normalization tool that uses multiple internal standards...
- An integrated functional genomics and metabolomics approach for defining poor prognosis in human neuroendocrine cancers (2005) (Online version)
Ippolito et al., Washington University School of Medicine, St. Louis, MO
Human neuroendocrine (NE) cancers range from relatively indolent to highly aggressive. In this study, we combine functional genomics with metabolomics to identify features of NE cancers associated with a poor outcome. Analysis of GeneChip datasets of primary prostate tumors, as well as lymph node and liver metastases from transgenic mice with a NE cell cancer, plus derived NE cell lines yielded a signature of 446 genes whose expression is enriched in neoplastic mouse prostatic NE cells. This signature was used for in silico metabolic reconstructions of NE cell metabolism, directed liquid chromatography/tandem MS analysis of metabolites in prostatic NE tumors and cell lines, and analysis of GeneChip datasets of human NE tumors with good or poor prognoses...
- Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period (2005) (Online version)
Tarpley et al., Texas A&M, Beaumont, Texas
This study analyzes metabolomic data from a rice tillering (branching) developmental profile to define a set of biomarker metabolites that reliably captures the metabolite variance of this plant developmental event, and which has potential as a basis for rapid comparative screening of metabolite profiles in relation to change in development, environment, or genotype. Changes in metabolism, and in metabolite profile, occur as a part of, and in response to, developmental events...
- Toward Supportive Data Collection Tools for Plant Metabolomics (2005) (Online Version)
Jenkins et al., University of Wales at Ceredigion
Over recent years, a number of initiatives have proposed standard reporting guidelines for functional genomics experiments. Associated with these are data models that may be used as the basis of the design of software tools that store and transmit experiment data in standard formats. Central to the success of such data handling tools is their usability. Successful data handling tools are expected to yield benefits in time saving and in quality assurance. Here, we describe the collection of datasets that conform to the recently proposed data model for plant metabolomics known as ArMet...
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- Metabolic Pathways of Biochemistry - graphically presents all major metabolic pathways, primarily those important to human biochemistry
Note: MDL Chemscape CHIME plug-in required to view molecules in 3D.
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