Fragmentation Trees Reloaded

DOI10.1007/978-3-319-16706-0_10MaRDI QIDQ2814578zbMATH OpenOpenAlexWikidataFDO

Authors Kai Dührkop, Sebastian Böcker

Publication date 22 June 2016

Published in Lecture Notes in Computer Science (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1412.1929

zbMATH Keywords

fragmentation treesmetabolomicstandem mass spectometry

Mathematics Subject Classification ID

Applications of graph theory (05C90) Computational methods for problems pertaining to biology (92-08) Biochemistry, molecular biology (92C40)

Abstract: Metabolites, small molecules that are involved in cellular reactions, provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually relies on tandem mass spectrometry to identify the thousands of compounds in a biological sample. Today, the vast majority of metabolites remain unknown. Fragmentation trees have become a powerful tool for the interpretation of tandem mass spectrometry data of small molecules. These trees are found by combinatorial optimization, and aim at explaining the experimental data via fragmentation cascades. To obtain biochemically meaningful results requires an elaborate optimization function. We present a new scoring for computing fragmentation trees, transforming the combinatorial optimization into a maximum a posteriori estimator. We demonstrate the superiority of the new scoring for two tasks: Both for the de novo identification of molecular formulas of unknown compounds, and for searching a database for structurally similar compounds, our methods performs significantly better than the previous scoring, as well as other methods for this task. Our method can expedite the workflow for untargeted metabolomics, allowing researchers to investigate unknowns using automated computational methods.

Recommendations

• General fragmentation trees
• Gibbs fragmentation trees
• Fragmentation of random trees
• Trees within trees. II: Nested fragmentations
• Breakage and restoration in recursive trees
• And/Or Trees Revisited
• On reconstructing rooted trees
• Reconstructing trees from traces
• Reconstruction of hypertrees

Cites work

• Partitions and Their Representative Graphs

Cited in

(6)

• Finding characteristic substructures for metabolite classes
• Speedy colorful subtrees
• Towards mechanistic prediction of mass spectra using graph transformation
• Heuristic algorithms for the maximum colorful subtree problem
• The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution
• Determination of Glycan Structure from Tandem Mass Spectra

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