ETD Spectra Processing and Database Searching - Performance Evaluation of a new MS/MS Search Algorithm

0.3 - 0.4 0.4 - 0.5 0.5 - 0.6 0.6 -0.7 0.7 - 0.8 0.8 - 0.9 the 0.5 to 0.9 range. Compared to MASCOT, the new algorithm had more peptides with a deltaCn in the range of 0.5 - 0.6 and 0.7 - 0.9, while MASCOT had more peptides with a deltaCn from 0.3 - 0.5 and 0.6 - 0.7. The average deltaCn scores for the new algorithm, SEQUEST and MASCOT are 0.69, 0.43 and 0.61 respectively. This result indicates that this newly developed ETD scoring algorithm has a higher discriminatory power on average than either MASCOT or SEQUEST.