Kinetic Studies of Peptide Fragmentation in

Tandem Mass Spectrometry

Tandem mass spectrometry (MS/MS) is a valuable tool used in protein sequencing prediction in the field of proteomics. Considerable efforts have been spent to compile MS/MS spectral databases for rapid peptide identification. Modest efforts, however, have been spent toward understanding of the fundamental processes affecting peptide fragmentation pathways. We are using electronic structure methods to generate potential energy surfaces (PES) in order to understand kinetic influences on peptide fragmentation pathways. Given the large number of degrees of freedom for large polypeptides, transition state searching via intuitive methods can be inefficient or incorrect. We have developed algorithms for elucidating low energy exit channels from a well on a PES without previous knowledge of the products by the researcher. Current efforts are geared toward parallel implementation of these algorithms to obtain greater efficiency for transition state and product searching.

Author Information

            Name:                          John K. Merle

            Mentor’s name:            Karl K. Irikura

            Division:                       Physical and Chemical Properties, 838

            Laboratory:                  CSTL

            Room/Building: B346/221

            Mail Stop:                    8380

            Telephone #:                 301-975-4417

            Fax #:                           301-869-4020

            Email:                           john.merle@nist.gov

            Sigma Xi:                      not a member

            Category:                     Chemistry