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Literature DB >> 26819880

Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees.

Kai Dührkop¹, Franziska Hufsky¹, Sebastian Böcker¹.

Abstract

We present the results of a fully automated de novo approach for identification of molecular formulas in the CASMI 2013 contest. Only results for Category 1 (molecular formula identification) were submitted. Our approach combines isotope pattern analysis and fragmentation pattern analysis and is completely independent from any (spectral and structural) database. We correctly identified the molecular formula for ten out of twelve challenges, being the best automated method competing in this category.

Keywords: CASMI 2013; fragmentation patterns; fragmentation trees; isotope patterns; mass spectrometry; molecular formula identification; small molecules

Year: 2014 PMID： 26819880 PMCID： PMC4321342 DOI： 10.5702/massspectrometry.S0037

Source DB: PubMed Journal: Mass Spectrom (Tokyo) ISSN： 2186-5116

16 in total

Review 1. Metabolite profiling: from diagnostics to systems biology.

Authors: Alisdair R Fernie; Richard N Trethewey; Arno J Krotzky; Lothar Willmitzer
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2. Identifying the unknowns by aligning fragmentation trees.

Authors: Florian Rasche; Kerstin Scheubert; Franziska Hufsky; Thomas Zichner; Marco Kai; Aleš Svatoš; Sebastian Böcker
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3. In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids.

Authors: Lars J Kangas; Thomas O Metz; Giorgis Isaac; Brian T Schrom; Bojana Ginovska-Pangovska; Luning Wang; Li Tan; Robert R Lewis; John H Miller
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4. DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem.

Authors: Sebastian Böcker; Zsuzsanna Lipták; Marcel Martin; Anton Pervukhin; Henner Sudek
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5. Finding maximum colorful subtrees in practice.

Authors: Imran Rauf; Florian Rasche; François Nicolas; Sebastian Böcker
Journal: J Comput Biol Date: 2013-03-19 Impact factor: 1.479

6. MetFusion: integration of compound identification strategies.

Authors: Michael Gerlich; Steffen Neumann
Journal: J Mass Spectrom Date: 2013-03 Impact factor: 1.982

7. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets.

Authors: Carsten Kuhl; Ralf Tautenhahn; Christoph Böttcher; Tony R Larson; Steffen Neumann
Journal: Anal Chem Date: 2011-12-12 Impact factor: 6.986

Molecular Formula Identification Using Isotope Pattern Analysis and Calculation of Fragmentation Trees.

Review 1. Metabolite profiling: from diagnostics to systems biology.

2. Identifying the unknowns by aligning fragmentation trees.

3. In silico identification software (ISIS): a machine learning approach to tandem mass spectral identification of lipids.

4. DECOMP--from interpreting Mass Spectrometry peaks to solving the Money Changing Problem.

5. Finding maximum colorful subtrees in practice.

6. MetFusion: integration of compound identification strategies.

7. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets.

8. From genomics to chemical genomics: new developments in KEGG.

9. Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry.

10. Molecular Formula Identification with SIRIUS.

1. Searching molecular structure databases with tandem mass spectra using CSI:FingerID.

2. Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data.

3. Machine learning for identification of silylated derivatives from mass spectra.