Exhaustive computational analysis of peptides for the fragmentation in low-energy dissociation mass spectrometry

COMP 227

Kazuhiko Fukui, k-fukui@aist.go.jp and Yutaka Akiyama, akiyama-yutaka@aist.go.jp. Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-41-6 Aomi, Koto-ku, Tokyo, 135-0064, Japan
In recent years, there has been significant interest in the fragmentation analysis of polypeptides and proteins using a variety of mass spectrometric techniques that utilize collisions with gaseous atoms, surfaces, electrons, and photons. Of these methods, the widely used dissociation methods are performed in a low collision induced dissociation (CID) and multiphoton dissociation (IRMPD). It is known that protonated peptides/proteins under low-energy conditions dissociate mainly by charge-directed fragmentation along their backbone, leading to fragmentation into bn/yn ion series. We modeled all di-peptides (20x20 amino acids) to analyze the structure, energetics, binding energy (cleaved at C'-N bond) and proton affinity using ab initio molecular orbital calculations on a linux super cluster system. The calculated results were compared with the mass spectra obtained by FTICR MS for the analysis of fragmentation pattern and mechanism. The database based on the calculations is also built to predict the fragment ions in the low-energy dissociation.