We have developed a system that combines mass spectrometric and biological metadata to achieve this goal. First, the SetupX system enables entering biological metadata for steering laboratory workflows by generating ‘classes’ that reflect experimental designs. After data acquisition, a relational database system (BinBase) is employed for automated metabolite annotation.
- Query BinBase for compounds
- This wss the main site to compare mass spectra by compound names, by BinBase identifiers or even by your GC/MS spectra that you have acquired on a different platform! The site also gives overview about positive detection of metabolites in the diverse set of species and organs analyzed at the UC Davis Genome Center (over 15,000 samples of more than 40 species)
- [publication] Setup and Annotation of Metabolomic Experiments
- Unbiased metabolomic surveys are used for physiological, clinical and genomic studies to infer genotype-phenotype relationships. Long term reusability of metabolomic data needs both correct metabolite annotations and consistent biological classifications. We have developed a system that combines mass spectrometric and biological metadata to achieve this goal. [...]
- [publication] A Public Study Design Database for Metabolomic Projects
- Metabolomic databases are useless without accurate description of the biological study design and accompanying metadata reporting on the laboratory workflow from sample preparation to data processing. Here we report on the implementation of a database system that enables investigators to detail and set up a biological experiment, and that also steers laboratory workflows by direct access to the data acquisition instrument.[...]
- [publication] A Public Study Design Database for Metabolomic Projects
- Metabolomic databases are useless without accurate description of the biological study design and accompanying metadata reporting on the laboratory workflow from sample preparation to data processing. Here we report on the implementation of a database system that enables investigators to detail and set up a biological experiment, and that also steers laboratory workflows by direct access to the data acquisition instrument.[...]
- [HowTo] BinBase - features, documentaion and FAQ
- Documentation of the features, documentation and FAQ regarding BinBase
- [publication] Current Progress in computational metabolomics
- David S.Wishart wrote: "SetupX, developed by the Fiehn laboratory at UCD, is an excellent example of a web-based metabolomics LIMS. It is XML compatible and built around a relational database management core. It is particularly oriented towards the capture and display of GC–MS metabolomic data through its metabolic annotation database called BinBase."
- SetupX Poster Boston 2008
- SetupX Poster shown at the Boston Metabolomics Conference 2008
- BinBase Download
- the BinBase database system download link