Figure 2

Simulated data mimicking experimental distributions. a) The error to signal ratio (ε/S-ratio) displayed shows that 85% of the experimentally observed spectra (red line) matched the theoretical reconstruction well, with less than 10% of the total spectral intensity assigned to the error term (dotted line). 50% of the spectra were matched very well with less than 5% error (dashed line). Noise was introduced into the simulated spectra in order to reflect a similar ε/S-ratio distribution (blue line). b) The labelling efficiency was found to vary considerably between experimental spectra (red bars). One peptide was not labelled at all, while another was completely absent in the treated sample, which produced the three spectra with a labelling efficiency of zero observed. The simulated spectra were generated to reflect this long tailed and high variability distribution (blue bars).