Rieder, Vera, Blank-Landeshammer, Bernhard, Stuhr, Marleen, Schell, Tilman, Biß, Karsten, Kollipara, Laxmikanth, Meyer, Achim, Pfenninger, Markus, Westphal, Hildegard, Sickmann, Albert and Rahnenführer, Jörg (2017) DISMS2: A flexible algorithm for direct proteome- wide distance calculation of LC-MS/MS runs. BMC Bioinformatics, 18 (1). DOI https://doi.org/10.1186/s12859-017-1514-2.

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Abstract

The 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.

Document Type: Article
Research affiliation: Affiliations > Not ZMT
Infrastructure > Biology Laboratory
Biogeochemistry and Geology > Geoecology & Carbonate Sedimentology
Refereed: Yes
Open Access Journal?: Yes
DOI etc.: https://doi.org/10.1186/s12859-017-1514-2
ISSN: 1471-2105
Date Deposited: 23 May 2019 10:59
Last Modified: 01 Oct 2020 12:58
URI: http://cris.leibniz-zmt.de/id/eprint/1913

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