Fragmentation of the pentapeptide leucine enkephalin (YGGFL) is accomplished via higher-order resonances combined with simultaneous analysis of low-mass product ions. Two methods of achieving excitation are explored: (1) 0.5 ms resonant excitation at the ω and at Ω-ω secular frequencies of ion motion (where Ω is the radio-frequency (rf) drive frequency) in a manner similar to both pulsed q collision-induced dissociation (PQD) and high amplitude short time excitation (HASTE), and (2) 0.5 ms pulse of the ω or at Ω-ω excitation frequencies when the secular frequency of the ions is quickly swept across resonance conditions (pulsed q dynamic CID, PqDCID). In both methods of excitation, the rf amplitude on the ring electrode is rapidly decreased after excitation, therefore enabling analysis of low-mass product ions. Maximum fragmentation efficiencies of ∼20% can be obtained with pulsed CID with both regular and high-order frequency excitation, while pulsed DCID offers maximum efficiencies of ∼12%. All the excitation methods studied offer increased internal energy depositions when compared to conventional CID, as measured by the a4/b4 product ion ratios of leucine enkephalin. These ratios were as high as 13:1 for pulsed CID and 8:1 for PqDCID. Successful mass analysis of the low-mass ions is observed with both pulsed CID and PqDCID. The combined benefit of high internal energy deposition and wider dynamic mass range offers the possibility of increased sequence coverage and the identification of unique internal fragments or high-energy product ions which may provide complementary information to biological applications of conventional CID. This is the first report on deliberate fragmentation of precursor ions at a higher-order component of the ion secular frequency combined with a successful mass analysis of the low-mass ions through pulsed CID and PqDCID. Copyright © 2008 John Wiley & Sons, Ltd.