High-energy collisional dissociation (HCD) is an efficient peptide fragmentation method that is widely used in Orbitrap mass spectrometers. A greater understanding of HCD fragmentation patterns would benefit the development of proteomic data analysis algorithms. In this study, b and y ion fragmentation patterns and residue-specific cleavage effects in HCD mode were statistically characterized on a LTQ Orbitrap Velos mass spectrometer. We compared HCD and CID spectra collected in an Orbitrap for the same doubly and triply charged tryptic peptides. Our analytical results revealed novel statistical features of HCD spectra. The intensity of y ions reached a maximum in the 60-70% and 40-50% relative mass bins of HCD spectra from doubly and triply charged peptides, respectively. The HCD mode showed a slight preference for generating y ions with lower charges than did CID mode. Singly charged fragment ions dominated the five fragment ions with the highest intensity in HCD spectra. Hydrophobic residues for b ions were the primary differences in cleavage selectivity between the two modes, while residues for y ions showed a similar cleavage preference. These results will assist with the development of database search engines and the design of proper transitions for targeted proteomic analysis. Biological significance Orbitrap mass spectrometry is becoming the popular instrument for proteomic analysis, and HCD mode is becoming the main analysis mode for its high resolution and high sensitivity. This study characterizes the features of HCD spectrum by comparing with CID mode on LTQ Velos Orbitrap. The patterns of b and y ions in HCD and CID modes were systematically compared for the first time, including the charge state, ion frequency and intensity and cleavage selectivity. These results will help develop database search engines and design proper transitions for targeted proteomic analysis in the future. (C) 2014 Elsevier B.V. All rights reserved.