Table I Accuracy and average length of PEAKS, PepNovo+, and MS-Dictionary for the Standard data set

PEAKS (online 2.0), PepNovo+ (released July 24, 2008), and MS-Dictionary (released November 7, 2007) were run with parent mass and fragment mass tolerances of 0.5 Da, fixed modification of Cys + 57, no optional modifications, and without any enzyme preference. In contrast to PEAKS and MS-Dictionary, PepNovo+ allows gaps at the start/end of peptides thus giving PepNovo+ significant leverage when it comes to the reported accuracy of reconstruction. Although MS-Dictionary is designed for generating spectral dictionaries (rather than ensuring that the correct reconstruction has the top score), it can be used in de novo mode as well (it has slightly higher accuracy than PEAKS while generating slightly longer peptides). PEAKS and MS-Dictionary have a tendency to output de novo reconstructions that are longer than the correct peptides (e.g. for peptides of length 11–12, the average length of PEAKS and MS-Dictionary reconstructions is 12.1 and 12.2, respectively). Accuracy of each tool is defined as the percentage of the error-free reconstructions among all reconstructions for the Standard data set.

Peptide lengthPEAKSPepNovo+MS-Dictionary
AccuracyLengthAccuracyLengthAccuracyLength
7–80.598.10.657.80.547.8
9–100.3310.00.549.30.409.9
11–120.2712.10.4710.40.3112.2
13–140.1214.10.3612.00.1414.2
15–160.1016.00.3413.20.1216.1
17–180.0716.90.2914.10.0218.3
19–200.0519.00.3814.00.0420.8
Total0.2612.60.4611.00.2812.8