Abstract
Metabolomics complements investigation of the genome, transcriptome, and proteome of an organism. Today, the vast majority of metabolites remain unknown, in particular for non-model organisms. Mass spectrometry is one of the predominant techniques for analyzing small molecules such as metabolites. A fundamental step for identifying a small molecule is to determine its molecular formula.
Here, we present and evaluate three algorithm engineering techniques that speed up the molecular formula determination. For that, we modify an existing algorithm for decomposing the monoisotopic mass of a molecule. These techniques lead to a four-fold reduction of running times, and reduce memory consumption by up to 94 %. In comparison to the classical search tree algorithm, our algorithm reaches a 1000-fold speedup.
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Dührkop, K., Ludwig, M., Meusel, M., Böcker, S. (2013). Faster Mass Decomposition. In: Darling, A., Stoye, J. (eds) Algorithms in Bioinformatics. WABI 2013. Lecture Notes in Computer Science(), vol 8126. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-40453-5_5
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DOI: https://doi.org/10.1007/978-3-642-40453-5_5
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