Dear Sir, Electron transfer dissociation coupled to an Orbitrap analyzer may promise a straightforward and accurate sequencing of disulfide-bridged cyclic peptides: a case study Cyclic peptides constitute a large group of compounds that possess potent biological and pharmacological activities, and thus have attracted ever-growing attentions in areas such as drug development and biomedical research [1]. Therefore, the ability to analyze cyclic peptides by high-throughput methods such as the tandem mass spectrometry (MS) will be of high interest [2]. Nevertheless, sequencing of these peptides by conventional MS techniques, which typically employ collision induced dissociation (CID) to obtain sequence-informative fragments, represents a daunting challenge. Cyclic peptides maintain a highly rigid conformation due to a circular backbone, which often accounts for their high receptor selectivity, metabolic stability, and potency [1]. Circular backbones present several challenges when sequencing by CID. First, the largely random initial ring scissions of the backbone often result in a perplexing mixture of different sets of b/y ions and neutral loss/ internal fragments [3], rendering the CID spectra very complex [2,4]. Second, the CID fragmentation of cyclic peptides often produces many fragments that are not typical for the cleavage of a linear peptide (such as sequence scrambling product ions), and thus are difficult to interpret [4,5]. Third, the cyclic backbone of a majority of therapeutic cyclic peptides is held together by a disulfide bond that cannot be cleaved efficiently utilizing the CID mechanism [6]. Consequently, the application of CID for the structure elucidation of cyclic peptides is severely limited.Electron transfer dissociation (ETD), which is an analogue of the electron capture dissociation (ECD) technique, converts multiple-charged peptide cations into radicals and cleaves the N-C α bonds, providing a fragmentation mechanism orthogonal to that by CID [7,8]. The resulting fragment ions that contain the N-and C-termini of the peptides are termed c and z ions, respectively. It has been demonstrated that the electron-initiated dissociation during an ETD process is less discriminated by the amino acid residues and side-chain chemistry compared with CID [7]. As a result, in most cases ETD provides more complete peptide backbone cleavage, and shows particular strength in the identification of [7,8]. Another advantage of ETD over CID is that it provides efficient cleavage of disulfide bonds (cf. the discussion), which may enable the localization of disulfide linkages in peptides or intact proteins under non-reducing conditions. Therefore, it is possible to utilize the ETD technique to achieve a favorable sequencing of the disulfide-bridged cyclic peptides, which account for most of the cyclic peptides.So far only a few studies have been conducted on the fragmentation of cyclic peptides by ETD or ECD [9,10]. As a result, a detailed investigation of the ETD behaviors of cyclic peptides, as well as an evaluat...