Fig. 2.

New scoring methods show improved discrimination over Mascot and dot product scores. The UPS1 standard protein dataset was searched against the NIST reference spectral library to evaluate search discrimination for (A) DP and SIM, (B) RDP and RSIM, and (C) SHP and MHP. Performance of the Mascot ions score (black line) is shown using a peptide sequence database corresponding to those peptides represented in the NIST reference library. The correct hits are MS/MS spectra whose assignments match the peptides for protein in the Sigma UPS1 protein mixture (see Experimental Procedures).