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Documents authored by Hufsky, Franziska

Document
Complete Volume
DOI: 10.4230/OASIcs.GCB.2012
OASIcs, Volume 26, GCB'12, Complete Volume

Authors: Sebastian Böcker, Franziska Hufsky, Kerstin Scheubert, Jana Schleicher, and Stefan Schuster

Published in: OASIcs, Volume 26, German Conference on Bioinformatics 2012

Abstract
OASIcs, Volume 26, GCB'12, Complete Volume
Cite as

German Conference on Bioinformatics 2012. Open Access Series in Informatics (OASIcs), Volume 26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@Proceedings{bocker_et_al:OASIcs.GCB.2012,
  title =	{{OASIcs, Volume 26, GCB'12, Complete Volume}},
  booktitle =	{German Conference on Bioinformatics 2012},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{B\"{o}cker, Sebastian and Hufsky, Franziska and Scheubert, Kerstin and Schleicher, Jana and Schuster, Stefan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2012},
  URN =		{urn:nbn:de:0030-drops-37269},
  doi =		{10.4230/OASIcs.GCB.2012},
  annote =	{Keywords: Life and Medical Sciences}
}
Document
Front Matter
DOI: 10.4230/OASIcs.GCB.2012.i
Frontmatter, Table of Contents, Preface, Programm Committee, Supportes and Sponsors, Index of Authors

Authors: Sebastian Böcker, Franziska Hufsky, Kerstin Scheubert, Jana Schleicher, and Stefan Schuster

Published in: OASIcs, Volume 26, German Conference on Bioinformatics 2012

Abstract
Frontmatter, Table of Contents, Preface, Programm Committee, Supportes and Sponsors, Index of Authors
Cite as

German Conference on Bioinformatics 2012. Open Access Series in Informatics (OASIcs), Volume 26, pp. i-xiv, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@InProceedings{bocker_et_al:OASIcs.GCB.2012.i,
  author =	{B\"{o}cker, Sebastian and Hufsky, Franziska and Scheubert, Kerstin and Schleicher, Jana and Schuster, Stefan},
  title =	{{Frontmatter, Table of Contents, Preface, Programm Committee, Supportes and Sponsors, Index of Authors}},
  booktitle =	{German Conference on Bioinformatics 2012},
  pages =	{i--xiv},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{B\"{o}cker, Sebastian and Hufsky, Franziska and Scheubert, Kerstin and Schleicher, Jana and Schuster, Stefan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2012.i},
  URN =		{urn:nbn:de:0030-drops-37121},
  doi =		{10.4230/OASIcs.GCB.2012.i},
  annote =	{Keywords: Frontmatter, Table of Contents, Preface, Programm Committee, Supportes and Sponsors, Index of Authors}
}
Document
DOI: 10.4230/OASIcs.GCB.2012.12
Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways

Authors: Franziska Hufsky and Sebastian Böcker

Published in: OASIcs, Volume 26, German Conference on Bioinformatics 2012

Abstract
Electron impact ionization (EI) is the most common form of ionization for GC-MS analysis of small molecules. This ionization method results in a mass spectrum not necessarily containing the molecular ion peak. The fragmentation of small compounds during EI is well understood, but manual interpretation of mass spectra is tedious and time-consuming. Methods for automated analysis are highly sought, but currently limited to database searching and rule-based approaches. With the computation of hypothetical fragmentation trees from high mass GC-MS data the high-throughput interpretation of such spectra may become feasible. We compare these trees with annotated fragmentation pathways. We find that fragmentation trees explain the origin of the ions found in the mass spectra in accordance to the literature. No peak is annotated with an incorrect fragment formula and 78.7% of the fragmentation processes are correctly reconstructed.
Cite as

Franziska Hufsky and Sebastian Böcker. Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways. In German Conference on Bioinformatics 2012. Open Access Series in Informatics (OASIcs), Volume 26, pp. 12-22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@InProceedings{hufsky_et_al:OASIcs.GCB.2012.12,
  author =	{Hufsky, Franziska and B\"{o}cker, Sebastian},
  title =	{{Comparing Fragmentation Trees from Electron Impact Mass Spectra with Annotated Fragmentation Pathways}},
  booktitle =	{German Conference on Bioinformatics 2012},
  pages =	{12--22},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{B\"{o}cker, Sebastian and Hufsky, Franziska and Scheubert, Kerstin and Schleicher, Jana and Schuster, Stefan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2012.12},
  URN =		{urn:nbn:de:0030-drops-37146},
  doi =		{10.4230/OASIcs.GCB.2012.12},
  annote =	{Keywords: metabolomics, GC-MS, computational mass spectrometry, fragmentation trees}
}
Document
DOI: 10.4230/OASIcs.GCB.2012.23
Finding Characteristic Substructures for Metabolite Classes

Authors: Marcus Ludwig, Franziska Hufsky, Samy Elshamy, and Sebastian Böcker

Published in: OASIcs, Volume 26, German Conference on Bioinformatics 2012

Abstract
We introduce a method for finding a characteristic substructure for a set of molecular structures. Different from common approaches, such as computing the maximum common subgraph, the resulting substructure does not have to be contained in its exact form in all input molecules. Our approach is part of the identification pipeline for unknown metabolites using fragmentation trees. Searching databases using fragmentation tree alignment results in hit lists containing compounds with large structural similarity to the unknown metabolite. The characteristic substructure of the molecules in the hit list may be a key structural element of the unknown compound and might be used as starting point for structure elucidation. We evaluate our method on different data sets and find that it retrieves essential substructures if the input lists are not too heterogeneous. We apply our method to predict structural elements for five unknown samples from Icelandic poppy.
Cite as

Marcus Ludwig, Franziska Hufsky, Samy Elshamy, and Sebastian Böcker. Finding Characteristic Substructures for Metabolite Classes. In German Conference on Bioinformatics 2012. Open Access Series in Informatics (OASIcs), Volume 26, pp. 23-38, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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@InProceedings{ludwig_et_al:OASIcs.GCB.2012.23,
  author =	{Ludwig, Marcus and Hufsky, Franziska and Elshamy, Samy and B\"{o}cker, Sebastian},
  title =	{{Finding Characteristic Substructures for Metabolite Classes}},
  booktitle =	{German Conference on Bioinformatics 2012},
  pages =	{23--38},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{B\"{o}cker, Sebastian and Hufsky, Franziska and Scheubert, Kerstin and Schleicher, Jana and Schuster, Stefan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2012.23},
  URN =		{urn:nbn:de:0030-drops-37157},
  doi =		{10.4230/OASIcs.GCB.2012.23},
  annote =	{Keywords: metabolites, substructure prediction, mass spectrometry, FT-BLAST}
}
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