PTMTreeSearch

PTMTreeSearch is a new algorithm using an extensive database of known PTMs to identify PTMs from MS/MS data rapidly. It builds a computational tree with each path labeled with the amino acids of a peptide sequence and branches representing PTMs. Pruning rules narrow the search by eliminating biologically unlikely solutions, allowing it to identify a smaller set of high-confidence PTM types quickly. A second stage then performs a more exhaustive search on this set, using relaxed parameter settings.

Topic

Proteomics experiment;Protein expression

Detail

  • Operation: Post-translation modification site prediction

  • Software interface: Web user interface

  • Language: C++

  • License: -

  • Cost: Free

  • Version name: -

  • Credit: Arturo Falaschi Fellowship program, Informatics PhD Program of the University of Szeged, Hungary, Hungarian National Research Foundation.

  • Input: -

  • Output: -

  • Contact: contact@thegpm.org

  • Collection: -

  • Maturity: -

Publications

  • PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra.
  • Kertész-Farkas A, et al. PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. 2014; 30:234-41. doi: 10.1093/bioinformatics/btt642
  • https://doi.org/10.1093/BIOINFORMATICS/BTT642
  • PMID: 24215026
  • PMC: -

Download and documentation

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