Figure 7

Utility and optimization of de novo assembly for LC-MS/MS shotgun proteomics database searching. A. Representative base peak chromatogram (blue) of trypsin digested A. leptorhynchus central nervous tissue protein extract across a 4 hour gradient (magenta). B-D. Enhancement of IDs by database by peptide ID, Mascot-assigned protein families, and individual protein at multiple false discovery rate thresholds (1% = blue bar, 2% = orange bar, 5% = grey bar).