Taste like a Chicken
You may have heard that dinosaurs are related to birds. A study on the soft tissue of a T.rex fossil pioneered the theory but there has been enough heated debate that several other teams have re-analyzed the data. See Dinosaur Study Backs Controversial Find in Science.
Suffice to say that PARC's Bioinformatic team entered the fray with ByOnic, a peptide identification program. And, indeed, T.rex is related to birds.
Beyond looking at a pre-historic top of the food chain animal, the technical advantage of ByOnic over the traditional peptide identification tools is in its ability to do "smart scoring". In other words, it has a more accurate way of matching observed spectra to "theoretical" spectra predicted from protein sequence.
For easy searches, a smart scorer like ByOnic beats the standard scorers by a margin of, say, 30%. However, as the complexity of the searches increase, such as the number of proteins, chemical modifications, mutations, spectra with more than one peptide, etc., the total advantage of smart scorer goes up significantly. In other words, a very smart scorer system should be just as good as manual analysis - without the manual work.
We believe ByOnic is almost there.
There are also other crowd pleasers features such as the ability to trade off speed and sensitivity to do large searches and "wild-card" modification to catch peptides with unanticipated modifications.
Work with ByOnic and PARC's Bioinformatic team
Please contact me if you are interested in trying out ByOnic for your peptide analysis. The PARC research team thinks that the T.rex analysis was "easy", say a 3 on a scale of 1 to 10. If you have searches in the difficult range of 8, 9, or 10, we would love to talk with you.