Setup and annotation of metabolomic experiments by integrating biological and mass spectrometric metadata

Oliver Fiehn, Gert Wohlgemuth, Martin Scholz

Research output: Chapter in Book/Report/Conference proceedingConference contribution

142 Scopus citations

Abstract

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. First, an XML-based LIMS 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. It consists of a manifold filtering algorithm for matching and generating database objects by utilizing mass spectral metadata such as 'retention index', 'purity', 'signal/noise', and the biological information class. Once annotations and quantitations are complete for a specific larger experiment, this information is fed back into the LIMS system to notify supervisors and users. Eventually, qualitative and quantitative results are released to the public for downloads or complex queries.

Original languageEnglish (US)
Title of host publicationLecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science)
EditorsB. Ludascher, L. Raschid
Pages224-239
Number of pages16
Volume3615
StatePublished - 2005
EventSecond International Workshop on Data Integration in the Life Sciences, DILS 2005 - San Diego, CA, United States
Duration: Jul 20 2005Jul 22 2005

Other

OtherSecond International Workshop on Data Integration in the Life Sciences, DILS 2005
CountryUnited States
CitySan Diego, CA
Period7/20/057/22/05

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computer Science (miscellaneous)
  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

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    Fiehn, O., Wohlgemuth, G., & Scholz, M. (2005). Setup and annotation of metabolomic experiments by integrating biological and mass spectrometric metadata. In B. Ludascher, & L. Raschid (Eds.), Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science) (Vol. 3615, pp. 224-239)