Electron capture dissociation of polypeptides in a three-dimensional quadrupole ion trap: Implementation and first results

Quinn

J. Am. Soc. Mass Spectrom.

et al. 2008

Successful electron capture dissociation (ECD) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) applications to peptide and protein structural analysis have been enabled by constant progress in implementation of improved electron injection techniques. The rate of ECD product ion formation has been increased to match the liquid chromatography and capillary electrophoresis timescales, and ECD has been combined with infrared multiphoton dissociation in a single experimental configuration to provide simultaneous irradiation, fast switching between the two techniques, and good spatial overlap between ion, photon, and electron beams. Here we begin by describing advantages and disadvantages of the various existing electron injection techniques for ECD in FT-ICR MS. We next compare multiple-pass and single-pass ECD to provide better understanding of ECD efficiency at low and high negative cathode potentials. We introduce compressed hollow electron beam injection to optimize the overlap of ion, photon, and electron beams in the ICR ion trap. Finally, to overcome significant outgassing during operation of a powerful thermal cathode, we introduce nonthermal electron emitter-based electron injection. We describe the first results obtained with cold cathode ECD, and demonstrate a general way to obtain low-energy electrons in FT-ICR MS by use of multiple-pass ECD.

mentioning

confidence: 99%

Electron capture dissociation implementation progress in fourier transform ion cyclotron resonance mass spectrometry

Quinn

J. Am. Soc. Mass Spectrom.

et al. 2008

“…9 Unfortunately, ECD is largely limited to FT-ICR mass spectrometers, and other types of mass spectrometers are not well suited for the technique, although there have been some recent reports of efforts to adapt electrodynamic ion traps for ECD. 10,11 While the trapping of electrons and peptide/protein cations simultaneously is difficult in electrodynamic ion traps, cations and anions can be stored together readily, 12 and it has recently been reported that ion/ion reactions can provide a way to access ECD-like results in electrodynamic ion traps. Hunt and co-workers have reported results for some anionic reagents that react with peptide cations by electron transfer, producing ECD-like fragmentation to yield c-type and z-type sequence ions in a process termed electron-transfer dissociation (ETD).…”

mentioning

confidence: 99%

Electron-Transfer Ion/Ion Reactions of Doubly Protonated Peptides: Effect of Elevated Bath Gas Temperature

2005

In this study, the electron-transfer dissociation (ETD) behavior of cations derived from 27 different peptides (22 of which are tryptic peptides) has been studied in a 3D quadrupole ion trap mass spectrometer. Ion/ion reactions between peptide cations and nitrobenzene anions have been examined at both room temperature and in an elevated temperature bath gas environment to form ETD product ions. From the peptides studied, the ETD sequence coverage tends to be inversely related to peptide size. At room temperature, very high sequence coverage (~100%) was observed for small peptides (≤7 amino acids). For medium-sized peptides composed of 8-11 amino acids, the average sequence coverage was 46%. Larger peptides with 14 or more amino acids yielded an average sequence coverage of 23%. Elevated-temperature ETD provided increased sequence coverage over roomtemperature experiments for the peptides of greater than 7 residues, giving an average of 67% for medium-sized peptides and 63% for larger peptides. Percent ETD, a measure of the extent of electron transfer, has also been calculated for the peptides and also shows an inverse relation with peptide size. Bath gas temperature does not have a consistent effect on percent ETD, however. For the tryptic peptides, fragmentation is localized at the ends of the peptides suggesting that the distribution of charge within the peptide may play an important role in determining fragmentation sites. A triply protonated peptide has also been studied and shows behavior similar to the doubly charged peptides. These preliminary results suggest that for a given charge state there is a maximum size for which high sequence coverage is obtained and that increasing the bath gas temperature can increase this maximum.Mass spectrometric analysis of peptides produced by enzymatic digestion is common to most protein identification work currently being performed. Tandem mass spectrometry of enzymatically produced peptides, either via the generation of "sequence tags" 1 or via automated analysis of uninterpreted data, 2,3 is particularly important when protein mixtures are being analyzed. By far, the most common enzyme used for digestion is trypsin, which cleaves proteins at positions C-terminal of lysine and arginine residues. As a consequence of the basic nature of these two amino acids, and the typical size of the peptides produced, most tryptic peptides produce doubly charged ions when subjected to electrospray ionization (ESI). This makes the analysis of doubly charged peptides, and particularly tryptic peptides, important for most LC/MS/MS-based methods for protein identification because electrospray is the most common ionization method used in coupling on-line condensed-phase separations with mass spectrometry. The most prevalent MS/MS methods in use for peptide/protein identification involve the collision-induced dissociation (CID) of protonated peptide cations, which generally leads to cleavage of the peptide backbone amide (C 0 -N) bond to produce b-type and y-type sequence ions. Unf...

“…156,157 More recently, efforts have been made to develop a quadrupole ion trap capable of performing ECD experiments. 158,159 Since the first application of ECD to the characterization of peptides and proteins, 160 the combination of high resolving power FT-ICR with ECD and other activation methods has been successfully applied to de novo protein sequencing 148,154,161 -163 and the location of labile post-translational modifications in polypeptides and proteins. 153,164 -166 Fig.…”

mentioning

confidence: 99%

Charge permutation reactions in tandem mass spectrometry

McLuckey

2004

J. Mass Spectrom.

Central to the tandem mass spectrometry experiment is the process that gives rise to product ions, i.e. the reaction intermediate to stages of mass analysis. Changes in mass or charge of the parent ion (or both) are generally readily detected by all forms of tandem mass spectrometry. Charge changing, or charge permutation, reactions have a long history in mass spectrometry. However, with the advent of new ionization methods, such as electrospray ionization, and the expansion of tandem mass spectrometry instrumentation to include ion trapping instruments, the past decade has seen a major increase in the types of charge permutation reactions that can be studied. Most charge permutation reactions involve electrons or protons as the charge mediating agents. This report, therefore, provides an overview of charge permutation reactions involving protons or electrons. Particular emphasis is placed on processes that involve interactions of precursor ions with gaseous neutral species, electrons or oppositely charged ions. Charge permutation reactions involving electron gain/loss are described first according to a rough order of the energy required for the reaction beginning with the most endoergic reactions and ending with the most exoergic reactions. An analogous approach is then taken with charge permutation reactions involving proton gain/loss. Important charge permutation reactions discussed herein, among others, include those referred to as charge inversion, charge stripping, electron capture dissociation, collision-induced ionization and charge separation. These reaction types, and others described herein, are the subjects of active research and are also finding use in many current areas of application.