Fig. 2: Mass calibration and parameter optimization.
From: Identification of modified peptides using localization-aware open search
a Precursor mass error before and after mass calibration, where color indicates point density. Precursor mass error is shown against m/z (upper panel) and retention time (lower panel). The smoothed moving average line is shown in dark gray. b Same as a, for fragment mass calibration. c Parameter optimization performance of MSFragger. Each heatmap shows the number of identified PSMs as a function of the fragment mass tolerance (rows) and the number of peaks used for matching (columns). The color of each cell indicates total PSMs (at 1% FDR) compared with the benchmark search result, where parameter combinations performing better than the benchmark are colored red and those with fewer PSMs are colored blue. The optimal parameters selected by the automatic procedure are marked with a black box.
