DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs

BMC Bioinformatics

Research Article

Tilman Schell¹  Markus Pfenninger²  Jörg Rahnenführer³  Vera Rieder³  Marleen Stuhr⁴  Achim Meyer⁴  Hildegard Westphal⁴  Bernhard Blank-Landeshammer⁵  Karsten Biß⁵  Laxmikanth Kollipara⁵  Albert Sickmann⁶ 

[1] Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany;Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Frankfurt, Germany;Faculty of Biological Science, Institute for Ecology, Evolution and Diversity, Department of Molecular Ecology, Goethe University, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany;Department of Statistics, TU Dortmund University, Dortmund, Germany;Leibniz Center for Tropical Marine Ecology (ZMT), Bremen, Germany;Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany;Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany;Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom;Medizinische Fakultät, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany;

关键词: Proteomics;    LC-MS/MS;    Mass spectrometry;    Comparison of MS/MS spectra;    Peptide identification;    Distance of LC-MS/MS runs;   

DOI  :  10.1186/s12859-017-1514-2

 received in 2016-10-08, accepted in 2017-01-31,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe classification of samples on a molecular level has manifold applications, from patient classification regarding cancer treatment to phylogenetics for identifying evolutionary relationships between species. Modern methods employ the alignment of DNA or amino acid sequences, mostly not genome-wide but only on selected parts of the genome. Recently proteomics-based approaches have become popular. An established method for the identification of peptides and proteins is liquid chromatography-tandem mass spectrometry (LC-MS/MS). First, protein sequences from MS/MS spectra are identified by means of database searches, given samples with known genome-wide sequence information, then sequence based methods are applied. Alternatively, de novo peptide sequencing algorithms annotate MS/MS spectra and deduce peptide/protein information without a database. A newer approach independent of additional information is to directly compare unidentified tandem mass spectra. The challenge then is to compute the distance between pairwise MS/MS runs consisting of thousands of spectra.MethodsWe present DISMS2, a new algorithm to calculate proteome-wide distances directly from MS/MS data, extending the algorithm compareMS2, an approach that also uses a spectral comparison pipeline.ResultsOur new more flexible algorithm, DISMS2, allows for the choice of the spectrum distance measure and includes different spectra preprocessing and filtering steps that can be tailored to specific situations by parameter optimization.ConclusionsDISMS2 performs well for samples from species with and without database annotation and thus has clear advantages over methods that are purely based on database search.

【 授权许可】

CC BY   
© The Author(s) 2017

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