Notes 2016.03.09

Here's a Thermo Q Exactive datafile, human target + decoy database search (HeLa cells), searched with both the high-high and high-low parameter settings. This plot compares the high res versus low res fragment ion settings above. FDR/q-values are calculated based on Comet's E-value scores. This plot demonstrates the advantages of high res search settings for high res MS/MS data.