Journal article
A pre-processing strategy for liquid chromatography time-of-flight mass spectrometry metabolic fingerprinting data
Environmental Chemistry and Physics, Department of Basic Sciences and Environment, Faculty of Life Sciences, Københavns Universitet
Department of Agriculture & Ecology, Genetics & Microbiology, Department of Agriculture & Ecology, Faculty of Life Sciences, Københavns Universitet
Department of Systems Biology
Chemistry and Biochemistry, Department of Basic Sciences and Environment, Faculty of Life Sciences, Københavns Universitet
Dekanat, DJF
A series of simple and robust operations for handling large chromatographic time-of-flight mass spectrometry fingerprinting data has been established and applied to data from extracts of Fusarium graminearum genotypes modified in a non-ribosomal peptide synthase gene by over-expression and deletion.
It includes importing data into a computing environment by binning the m/z axis; baseline removal; data transformation and compression across retention times. Each sample represented by a total mass spectrum was normalized to unit sum and variables selected by partial least squares discriminant analysis.
Finally, principal component analysis was used for identification of high discriminatory power mass-to-charge ratios (m/z’s) separating over-expression, wildtype and deletion genotypes. Two compounds exhibiting a positive correlation to the expected levels in different genotypes were identified. The two compounds were represented by m/z 683.5 with retention time of 8.9 min, and m/z’s 774.5 and 775.5 with retention time of 14.1 min.
This methodology enables extraction of chemical information from large data sets (>108 entries), and provides a starting point for individual optimization in targeting small molecules from metabolomics data.
Language: | English |
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Publisher: | Springer US |
Year: | 2010 |
Pages: | 341-352 |
Journal subtitle: | An Official Journal of the Metabolomics Society |
ISSN: | 15733890 and 15733882 |
Types: | Journal article |
DOI: | 10.1007/s11306-010-0211-1 |
ORCIDs: | Tomasi, Giorgio , Giese, Henriette , Kristensen, Matilde, B. and Frandsen, Rasmus, J., N. |