Customized software for peptide identification by tandem mass spectrometry

There are a number of different programs for identifying peptides by tandem mass spectrometry (MS/MS), including Mascot, SEQUEST, X!Tandem, Spectrum Mill, Phenyx, and Paragon. A couple years ago, I made the beginner's mistake of writing another such program, ByOnic. But now that I've got the program and can quickly customize it for new types of data, I am finding that this enables some interesting collaborations. I will talk about three such projects: data-independent MS/MS, alcohol-induced carbonylation, and oxidative surface mapping using laser-induced oxidation.