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DOI: 10.4230/OASIcs.GCB.2013.56
Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics

Authors: Anna Katharina Hildebrandt, Ernst Althaus, Hans-Peter Lenhof, Chien-Wen Hung, Andreas Tholey, and Andreas Hildebrandt

Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013

Abstract
Mass spectrometry is the major analytical tool for the identification and quantification of proteins in biological samples. In so-called top-down proteomics, separation and mass spectrometric analysis is performed at the level of intact proteins, without preparatory digestion steps. It has been shown that the tandem mass tag (TMT) labeling technology, which is often used for quantification based on digested proteins (bottom-up studies), can be applied in top-down proteomics as well. This, however, leads to a complex interpretation problem, where we need to annotate measured peaks with their respective generating protein, the number of charges, and the a priori unknown number of TMT-groups attached to this protein. In this work, we give an algorithm for the efficient enumeration of all valid annotations that fulfill available experimental constraints. Applying the algorithm to real-world data, we show that the annotation problem can indeed be efficiently solved. However, our experiments also demonstrate that reliable annotation in complex mixtures requires at least partial sequence information and high mass accuracy and resolution to go beyond the proof-of-concept stage.
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Anna Katharina Hildebrandt, Ernst Althaus, Hans-Peter Lenhof, Chien-Wen Hung, Andreas Tholey, and Andreas Hildebrandt. Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 56-67, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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@InProceedings{hildebrandt_et_al:OASIcs.GCB.2013.56,
  author =	{Hildebrandt, Anna Katharina and Althaus, Ernst and Lenhof, Hans-Peter and Hung, Chien-Wen and Tholey, Andreas and Hildebrandt, Andreas},
  title =	{{Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics}},
  booktitle =	{German Conference on Bioinformatics 2013},
  pages =	{56--67},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-59-0},
  ISSN =	{2190-6807},
  year =	{2013},
  volume =	{34},
  editor =	{Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.56},
  URN =		{urn:nbn:de:0030-drops-42304},
  doi =		{10.4230/OASIcs.GCB.2013.56},
  annote =	{Keywords: Mass spectrometry, TMT labeling, Top-down Proteomics}
}
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