ML Anthology

PTMSearch: A Greedy Tree Traversal Algorithm for Finding Protein Post-Translational Modifications in Tandem Mass Spectra

Attila Kertész-Farkas, Beáta Reiz, Michael P. Myers, Sándor Pongor
ECML-PKDD 2011 pp. 162-176
doi:10.1007/978-3-642-23783-6_11 /ecmlpkdd/2011/kerteszfarkas2011ecmlpkdd-ptmsearch/

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.

ECML-PKDD Semantic Scholar

Cite

Text

Kertész-Farkas et al. "PTMSearch: A Greedy Tree Traversal Algorithm for Finding Protein Post-Translational Modifications in Tandem Mass Spectra." European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases, 2011. doi:10.1007/978-3-642-23783-6_11

Markdown

[Kertész-Farkas et al. "PTMSearch: A Greedy Tree Traversal Algorithm for Finding Protein Post-Translational Modifications in Tandem Mass Spectra." European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases, 2011.](https://mlanthology.org/ecmlpkdd/2011/kerteszfarkas2011ecmlpkdd-ptmsearch/) doi:10.1007/978-3-642-23783-6_11

BibTeX

@inproceedings{kerteszfarkas2011ecmlpkdd-ptmsearch,
  title     = {{PTMSearch: A Greedy Tree Traversal Algorithm for Finding Protein Post-Translational Modifications in Tandem Mass Spectra}},
  author    = {Kertész-Farkas, Attila and Reiz, Beáta and Myers, Michael P. and Pongor, Sándor},
  booktitle = {European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases},
  year      = {2011},
  pages     = {162-176},
  doi       = {10.1007/978-3-642-23783-6_11},
  url       = {https://mlanthology.org/ecmlpkdd/2011/kerteszfarkas2011ecmlpkdd-ptmsearch/}
}