. Author manuscript; available in PMC: 2008 Sep 17.

Published in final edited form as: J Proteome Res. 2007 Jan;6(1):114–123. doi: 10.1021/pr060271u

Table 3.

Correctness of De novo paths and number of generated peptides. The highest scoring de novo paths were generated for 376 mass spectra of doubly charged tryptic peptides, de novo path were generated. The table contains the percentage of spectra for which at least one of the k highest scoring paths (k = 1, 5, 10) is correct along with the number of unique peptides that were generated from those paths for the database lookup. The statistics are given for paths derived from spectrum graphs without PTMs, and for graphs containing 10 types of PTMs with the paths allowed to include only 1 or 2 PTM instances.

# De Novo Paths Used	No PTMs		10 PTMs / 1 allowed		10 PTMs / 2 allowed

	% Correct	# Peptides	% Correct	# Peptides	% Correct	# Peptides
1	90.4	4.4	86.2	7.9	85.9	10.7
5	97.3	33.7	96.0	58.0	96.0	76.9
10	98.4	74.4	97.1	119.9	97.1	162.2