License: Creative Commons Attribution 3.0 Unported license (CC BY 3.0)
When quoting this document, please refer to the following
DOI: 10.4230/LIPIcs.WABI.2018.25
URN: urn:nbn:de:0030-drops-93270
URL: http://dagstuhl.sunsite.rwth-aachen.de/volltexte/2018/9327/
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Majewski, Szymon ; Ciach, Michal Aleksander ; Startek, Michal ; Niemyska, Wanda ; Miasojedow, Blazej ; Gambin, Anna

The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution

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Abstract

We propose a new approach for the comparison of mass spectra using a metric known in the computer science under the name of Earth Mover's Distance and in mathematics as the Wasserstein distance. We argue that this approach allows for natural and robust solutions to various problems in the analysis of mass spectra. In particular, we show an application to the problem of deconvolution, in which we infer proportions of several overlapping isotopic envelopes of similar compounds. Combined with the previously proposed generator of isotopic envelopes, IsoSpec, our approach works for a wide range of masses and charges in the presence of several types of measurement inaccuracies. To reduce the computational complexity of the solution, we derive an effective implementation of the Interior Point Method as the optimization procedure. The software for mass spectral comparison and deconvolution based on Wasserstein distance is available at https://github.com/mciach/wassersteinms.

BibTeX - Entry

@InProceedings{majewski_et_al:LIPIcs:2018:9327,
  author =	{Szymon Majewski and Michal Aleksander Ciach and Michal Startek and Wanda Niemyska and Blazej Miasojedow and Anna Gambin},
  title =	{{The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution}},
  booktitle =	{18th International Workshop on Algorithms in  Bioinformatics (WABI 2018)},
  pages =	{25:1--25:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Laxmi Parida and Esko Ukkonen},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2018/9327},
  URN =		{urn:nbn:de:0030-drops-93270},
  doi =		{10.4230/LIPIcs.WABI.2018.25},
  annote =	{Keywords: Mass spectrometry, Tandem mass spectrometry, Wasserstein distance, Earth mover's distance, Similarity measure, Jaccard score, Tanimoto similarity}
}

Keywords: Mass spectrometry, Tandem mass spectrometry, Wasserstein distance, Earth mover's distance, Similarity measure, Jaccard score, Tanimoto similarity
Collection: 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Issue Date: 2018
Date of publication: 02.08.2018

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