PTMSearch: a greedy tree traversal algorithm for finding protein post-translational modifications in tandem mass spectra

  • Authors:

  • Attila Kertész-Farkas;Beáta Reiz;Michael P. Myers;Sándor Pongor

  • Affiliations:

  • International Centre for Genetic Engineering and Biotechnology, Trieste, Italy;Biological Research Centre, Hungarian Academy of Sciences and Institute of Informatics, University of Szeged, Szeged, Hungary;International Centre for Genetic Engineering and Biotechnology, Trieste, Italy;International Centre for Genetic Engineering and Biotechnology, Trieste, Italy and Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary

  • Venue:
  • ECML PKDD'11 Proceedings of the 2011 European conference on Machine learning and knowledge discovery in databases - Volume Part II
  • Year:
  • 2011

Quantified Score

Hi-index 0.01

Visualization

Abstract

Peptide identification by tandem mass spectrometry (MS/MS) and database searching is becoming the standard high-throughput technology in many areas of the life sciences. The analysis of post-translational modifications (PTMs) is a major source of complications in this area, which calls for efficient computational approaches. In this paper we describe PTMSearch, a novel algorithm in which the PTM search space is represented by a tree structure, and a greedy traversal algorithm is used to identify a path within the tree that corresponds to the PTMs that best fit the input data. Tests on simulated and real (experimental) PTMs show that the algorithm performs well in terms of speed and accuracy. Estimates are given for the error caused by the greedy heuristics, for the size of the search space and a scheme is presented for the calculation of statistical significance.