pNOVO+ is a new de novo sequencing algorithm that makes use of the complementary fragmentation that we available from HCD and ETD fragmentation. The authors, Hao Chi et. al., test their system on peptides derived from a number of different enzymes and demonstrate a staggering level of efficiency.
The paper is available here.
More importantly, as of right now, the link for downloading the program isn't accessible, but it is supposed to be here. Hopefully it will be up soon! I can not wait to try it!