On 2014 Feb 03, David Simpson commented:

This is an interesting approach, but I would have liked to see some attempt made to calculate false discovery rates. Something along the lines of the method reported by Qian et al. (J. Proteome Res. 2005, 4, 53–62) would have been great. Requiring a minimum Sequest XCorr score of 1.5 for identification acceptance is very permissive. A high false discovery rate would be a good explanation for the limited overlap reported in Figure 3.

On 2014 Feb 03, David Simpson commented:

This is an interesting approach, but I would have liked to see some attempt made to calculate false discovery rates. Something along the lines of the method reported by Qian et al. (J. Proteome Res. 2005, 4, 53–62) would have been great. Requiring a minimum Sequest XCorr score of 1.5 for identification acceptance is very permissive. A high false discovery rate would be a good explanation for the limited overlap reported in Figure 3.