Figure 5.

Error plot. The accuracy of predictions of relative intensities of y ions in MSMS spectra of the doubly charged GAVLK peptide. The best performing conformational space sampling method (DFT EHC; DFT energies with enthalpic corrections) and the worst performing method (DFT GEEC; DFT Gibbs free energy of single equilibrium conformer for each isomer) are presented in comparison to averaged experimental data. The Log Relative Errors were calculated as log10 (predicted relative intensity/measured relative intensity) for each ion. To demonstrate that our best predictions were within the experimental variation of the measurements, the differences between the most extreme experimental values and the averaged values are also presented. The intensity of the y3 ion was predicted as the highest according to the experiment, in which the y3 was chosen to have a reference value of 1.0, and consequently its logErr values are zero.

Pechan and Gwaltney BMC Bioinformatics 2012 13(Suppl 15):S13   doi:10.1186/1471-2105-13-S15-S13