Universal and Confident Phosphorylation Site Localization Using phosphoRS
| Autor: | Thomas Taus, Carmen Paschke, Christoph Henrich, Andreas Schmidt, Karl Mechtler, Thomas Köcher, Peter Pichler |
|---|---|
| Rok vydání: | 2011 |
| Předmět: |
Phosphopeptides
Proteomics Phosphorylation sites Applied probability Analytical chemistry Chemical Fractionation Tandem mass spectrometry Mass spectrometry Biochemistry Tandem mass spectrum 03 medical and health sciences Fragmentation (mass spectrometry) Tandem Mass Spectrometry Humans Protein Isoforms Cutoff Phosphorylation 030304 developmental biology 0303 health sciences Binding Sites Chemistry 030302 biochemistry & molecular biology Reproducibility of Results Experimental data General Chemistry Biological system Algorithms Software HeLa Cells |
| Zdroj: | Journal of Proteome Research |
| ISSN: | 1535-3907 1535-3893 |
| DOI: | 10.1021/pr200611n |
| Popis: | An algorithm for the assignment of phosphorylation sites in peptides is described. The program uses tandem mass spectrometry data in conjunction with the respective peptide sequences to calculate site probabilities for all potential phosphorylation sites. Tandem mass spectra from synthetic phosphopeptides were used for optimization of the scoring parameters employing all commonly used fragmentation techniques. Calculation of probabilities was adapted to the different fragmentation methods and to the maximum mass deviation of the analysis. The software includes a novel approach to peak extraction, required for matching experimental data to the theoretical values of all isoforms, by defining individual peak depths for the different regions of the tandem mass spectrum. Mixtures of synthetic phosphopeptides were used to validate the program by calculation of its false localization rate versus site probability cutoff characteristic. Notably, the empirical obtained precision was higher than indicated by the applied probability cutoff. In addition, the performance of the algorithm was compared to existing approaches to site localization such as Ascore. In order to assess the practical applicability of the algorithm to large data sets, phosphopeptides from a biological sample were analyzed, localizing more than 3000 nonredundant phosphorylation sites. Finally, the results obtained for the different fragmentation methods and localization tools were compared and discussed. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|