Charge location directs electron capture dissociation of peptide dications

The effect of peptide dication charge location on electron capture dissociation (ECD) fragmentation pattern is investigated. ECD fragmentation patterns are compared for peptides with amide and free acid C-terminal groups. ECD of free acid compared with C-terminally amidated peptides with basic residues near the N-terminus demonstrates increased formation of a-type ions. Similarly, ECD of free acid compared with C-terminally amidated peptides with basic residues near the C-terminus exhibits increased formation of y-type ions. Alteration of the peptide sequence to inhibit the formation of charged side chains (i.e., amino acid substitution and acetylation) provides further evidence for charge location effect on ECD. We propose that formation of zwitterionic peptide structures increases the likelihood of amide nitrogen protonation (versus basic side chains), which is responsible for the increase in a- and y-type ion formation.     

Combined infrared multiphoton dissociation and electron capture dissociation with a hollow electron beam in Fourier transform ion cyclotron resonance mass spectrometry

An electron injection system based on an indirectly heated ring-shaped dispenser cathode has been developed and installed in a 7 Tesla Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. This new hardware design allows high-rate electron capture dissociation (ECD) to be carried out by a hollow electron beam coaxial with the ion cyclotron resonance (ICR) trap. Infrared multiphoton dissociation (IRMPD) can also be performed with an on-axis IR-laser beam passing through a hole at the centre of the dispenser cathode. Electron and photon irradiation times of the order of 100 ms are required for efficient ECD and IRMPD, respectively. As ECD and IRMPD generate fragments of different types (mostly c, z and b, y, respectively), complementary structural information that improves the characterization of peptides and proteins by FTICR mass spectrometry can be obtained. The developed technique enables the consecutive or simultaneous use of the ECD and IRMPD methods within a single FTICR experimental sequence and on the same ensemble of trapped ions in multistage tandem (MS/MS/MS or MS(n)) mass spectrometry. Flexible changing between ECD and IRMPD should present advantages for the analysis of protein digests separated by liquid chromatography prior to FTICRMS. Furthermore, ion activation by either electron or laser irradiation prior to, as well as after, dissociation by IRMPD or ECD increases the efficiency of ion fragmentation, including the w-type fragment ion formation, and improves sequencing of peptides with multiple disulfide bridges. The developed instrumental configuration is essential for combined ECD and IRMPD on FTICR mass spectrometers with limited access into the ICR trap.     

Isotopically selective infrared multiphoton dissociation of 2,3-dihydropyran

Oxygen isotopic selectivity on infrared multiphoton dissociation of 2,3-dihydropyran has been studied by the examination of the effects of excitation frequency, laser fluence, and gas pressure on the dissociation probability of 2,3-dihydropyran and isotopic composition of products. Oxygen-18 was enriched in a dissociation product: 2-propenal. The enrichment factor of 18O and the dissociation probability were measured at a laser frequency between 1033.5 and 1057.3 cm-1, the laser fluence of 2.2-2.3 J/cm2, and the 2,3-dihydropyran pressure of 0.27 kPa. The dissociation probability decreases as the laser frequency being detuned from the absorption peak of 2,3-dihydropyran around 1081 cm-1. On the other hand, the enrichment factor increases with detuning the frequency. The enrichment factor of 18O increases with increasing the 2,3-dihydropyran pressure at the laser fluence of 2.7 J/cm2 or less and the laser frequency of 1033.5 cm-1, whereas the yield of 2-propenal decreases with increasing the pressure. A very high enrichment factor of 751 was obtained by the irradiation of 0.53 kPa of 2,3-dihydropyran at 2.1 J/cm2. Collisional effect of vibrationally excited molecules with ambient molecules on isotopic selectivity is discussed on the basis of a rate equation model including a collisional vibrational de-excitation process.     

Comparison of quantal and classical calculations of infrared multiphoton dissociation

A model for the dissociation of a triatomic molecule in a laser field is solved both quantally and classically. Calculations were made of the energy absorbed with a single laser frequency and with two laser frequencies. Good agreement between the classical and quantum calculation was found.     

Structural characterization of the GM1 ganglioside by infrared multiphoton dissociation, electron capture dissociation, and electron detachment dissociation electrospray ionization FT-ICR MS/MS

Gangliosides play important biological roles and structural characterization of both the carbohydrate and the lipid moieties is important. The FT-ICR MS/MS techniques of electron capture dissociation (ECD), electron detachment dissociation (EDD), and infrared multiphoton dissociation (IRMPD) provide extensive fragmentation of the protonated and deprotonated GM1 ganglioside. ECD provides extensive structural information, including identification of both halves of the ceramide and cleavage of the acetyl moiety of the N-acetylated sugars. IRMPD provides similar glycan fragmentation but no cleavage of the acetyl moiety. Cleavage between the fatty acid and the long-chain base of the ceramide moiety is seen in negative-ion IRMPD but not in positive-ion IRMPD of GM1. Furthermore, this extent of fragmentation requires a range of laser powers, whereas all information is available from a single ECD experiment. However, stepwise fragmentation by IRMPD may be used to map the relative labilities for a series of cleavages. EDD provides the alternative of electron-induced fragmentation for negative ions with extensive fragmentation, but suffers from low efficiency as well as complication of data analysis by frequent loss of hydrogen atoms. We also show that analysis of MS/MS data for glycolipids is greatly simplified by classification of product ion masses to specific regions of the ganglioside based solely on mass defect graphical analysis.     

Comparison of infrared multiphoton dissociation and collision-induced dissociation of supercharged peptides in ion traps

The number and types of diagnostic ions obtained by infrared multiphoton dissociation (IRMPD) and collision-induced dissociation (CID) were evaluated for supercharged peptide ions created by electrospray ionization of solutions spiked with m-nitrobenzyl alcohol. IRMPD of supercharged peptide ions increased the sequence coverage compared with that obtained by CID for all charge states investigated. The number of diagnostic ions increased with the charge state for IRMPD; however, this trend was not consistent for CID because the supercharged ions did not always yield the greatest number of diagnostic ions. Significantly different fragmentation pathways were observed for the different charge states upon CID or IRMPD with the latter yielding far more immonium ions and often fewer uninformative ammonia, water, and phosphoric acid neutral losses. Pulsed-Q dissociation resulted in an increase in the number of internal product ions, a decrease in sequence-informative ions, and reduced overall ion abundances. The enhanced sequence coverage afforded by IRMPD of supercharged ions was demonstrated for a variety of model peptides, as well as for a tryptic digest of cytochrome c.     

Improved infrared multiphoton dissociation of peptides through N-terminal phosphonite derivatization

A strategy for improving the sequencing of peptides by infrared multiphoton dissociation (IRMPD) in a linear ion trap mass spectrometer is described. We have developed an N-terminal derivatization reagent, 4-methylphosphonophenylisothiocyanate (PPITC), which allows the attachment of an IR-chromogenic phosphonite group to the N-terminus of peptides, thus enhancing their IRMPD efficiencies. After the facile derivatization process, the PPITC-modified peptides require shorter irradiation times for efficient IRMPD and yield extensive series of y ions, including those of low m/z that are not detected upon traditional CID. The resulting IRMPD mass spectra afford more complete sequence coverage for both model peptides and tryptic peptides from cytochrome c. We compare the effectiveness of this derivatization/IRMPD approach to that of a common N-terminal sulfonation reaction that utilizes 4-sulfophenylisothiocyanate (SPITC) in conjunction with CID and IRMPD.     

Electron capture dissociation of singly and multiply phosphorylated peptides

Analysis of phosphotyrosine and phosphoserine containing peptides by nano-electrospray Fourier transform ion cyclotron resonance (FTICR) mass spectrometry established electron capture dissociation (ECD) as a viable method for phosphopeptide sequencing. In general, ECD spectra of synthetic and native phosphopeptides appeared less complex than conventional collision activated dissociation (CAD) mass spectra of these species. ECD of multiply protonated phosphopeptide ions generated mainly c- and z(.)-type peptide fragment ion series. No loss of water, phosphate groups or phosphoric acid from intact phosphopeptide ions nor from the c and z(.) fragment ion products was observed in the ECD spectra. ECD enabled complete or near-complete amino acid sequencing of phosphopeptides for the assignment of up to four phosphorylation sites in peptides in the mass range 1400 to 3500 Da. Nano-scale Fe(III)-affinity chromatography combined with nano-electrospray FTMS/ECD facilitated phosphopeptide analysis and amino acid sequencing from crude proteolytic peptide mixtures.     

Real-time multiphoton ionization detection of iodine atoms produced by infrared multiphoton dissociation of perfluoroalkyl iodides

We report the direct detection of iodine atoms following infrared multiphoton dissociation of perfluoroalkyl iodides. The technique, three-photon resonant two-photon ionization, shows great promise as an actinometer for primary dissociation yield in IRMPD.     

Electron capture versus energetic dissociation of protein ions

The identity of neighboring amino acids has little influence on the dissociation of multiply protonated proteins by electron capture dissociation. As exceptions, no cleavage occurs on the N-terminal side of Pro, and little on either side of Cys, whereas the C-terminal side of Trp is heavily favored. The neighboring amino acids have a far greater effect on energetic dissociation, making the combined methods promising for the de novo sequencing of proteins.     

Electron capture dissociation mass spectrometry of metallo-supramolecular complexes

The electron capture dissociation (ECD) of metallo-supramolecular dinuclear triple-stranded helicate Fe₂L₃⁴⁺ ions was determined by Fourier transform ion cyclotron resonance mass spectrometry. Initial electron capture by the di-iron(II) triple helicate ions produces dinuclear double-stranded complexes analogous to those seen in solution with the monocationic metal centers Cu^I or Ag^I. The gas-phase fragmentation behavior [ECD, collision-induced dissociation (CID), and infrared multiphoton dissociation (IRMPD)] of the di-iron double-stranded complexes, (i.e., MS³ of the ECD product) was compared with the ECD, CID, and IRMPD of the Cu^I and Ag^I complexes generated from solution. The results suggest that iron-bound dimers may be of the form Fe₂^IL₂²⁺ and that ECD by metallo-complexes allows access, in the gas phase, to oxidation states and coordination chemistry that cannot be accessed in solution.     

Alternative approaches to infrared multiphoton dissociation in an external ion reservoir

In this work we present variations on in-hexapole infrared multiphoton dissociation (IRMPD) for the characterization of modified oligonucleotides using an ESI-FTICR spectrometer. We demonstrate that IRMPD in the external ion reservoir provides a comprehensive series of fragments allowing thorough characterization of a wide range of oligonucleotides containing alternative backbones and 2′ substitutions. An alternative pulse sequence is presented that allows alternating MS and IRMPD MS/MS spectra to be acquired on a chromatographic timescale without loss in ionization duty cycle. Ions are excited to a larger cyclotron radius such that they “dodge” the IR laser beam that travels through the center of the trapped ion cell and impinges on the external ion reservoir creating IRMPD fragments that will be detected in the next scan. An alternative approach for directing IR radiation into the external ion reservoir using a hollow fiber waveguide as a photon conduit is presented. This approach offers a simple and robust alternative to the previously utilized on-axis scheme and may allow effective implementation with lower power lasers owing to the inherent increase in power density achieved by focusing the nascent laser beam into the hollow fiber waveguide.     

Electron capture dissociation of weakly bound polypeptide polycationic complexes

We have previously reported that, in electron capture dissociation (ECD), rupture of strong intramolecular bonds in weakly bound supramolecular aggregates can proceed without dissociation of weak intermolecular bonds. This is now illustrated on a series of non-specific peptide-peptide dimers as well as specific complexes of modified glycopeptide antibiotics with their target peptide. The weak nature of bonding is substantiated by blackbody infrared dissociation, low-energy collisional excitation and force-field simulations. The results are consistent with a non-ergodic ECD cleavage mechanism.     

Electron capture dissociation mass spectrometry of tyrosine nitrated peptides

In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification. Here, we have investigated the electron capture dissociation (ECD) and collision-induced dissociation (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains.     

Characterization of erythromycin analogs by collisional activated dissociation and infrared multiphoton dissociation in a quadrupole ion trap

The effectiveness of two activation techniques, collision activated dissociation (CAD) and infrared multiphoton dissociation (IRMPD), is compared for structural characterization of protonated and lithium-cationized macrolides and a series of synthetic precursors in a quadrupole ion trap (QIT). Generally, cleavage of the glycosidic linkages attaching the sugars to the macrolide ring and water losses constitute the major fragmentation pathways for most of the protonated compounds. In the IRMPD spectra, a diagnostic fragment ion assigned as the desosamine ion is a dominant ion that is not observed in the CAD spectra because of the higher m/z limit of the storage range required during collisional activation. Activation of the lithium-cationized species results in new diagnostic fragmentation pathways that are particularly useful for confirming the identities of the protecting groups in the synthetic precursors. Multi-step IRMPD allows mapping of the fragmentation genealogies in greater detail and supports the proposed structures of the fragment ions.     

A kinetic study of the infrared multiphoton dissociation of s-trioxane

The IR multiple photon dissociation of s-trioxane is reported. The molecule is dissociated with high efficiency at low fluences (i.e. 6 J cm^?2) At high s-trioxane pressures, the dissociation is enhanced via V-V processes. Addition of He results in V-T deactivation of the energized molecule. The dissociation is well described by RRKM theory.     

Chloroform infrared multiphoton dissociation in the presence of O2 and NO2

The infrared multiphoton dissociation (IRMPD) of CDCl3 in the presence of O2 and NO2 as acceptor gases has been studied. We have worked with both pure CDCl3 and mixtures with CHCl3. The reaction mechanism following IRMPD of CDCl3 is discussed in detail. CCl2O, CCl4 and DCl were found to be the main products. With added O2, the observed CDCl3 dissociation was larger than with nonoxygenated acceptor gases. The reaction mechanism probably involves a catalytic cycle initiated by the oxidation of CCl3. With the aim of discriminating the different CDCl3 dissociation mechanisms, the IRMPD of CDCl3 in the presence of NO2 was first studied. In order to make evident the CDCl3 dissociation produced by the catalytic cycle, we then studied the IRMPD of CDCl3 in mixtures with CHCl3 with O2 as the acceptor gas. In this case, the dissociation mechanism subsequent to IRMPD is evidenced in the competence between the two isotopic species.     

Electron capture dissociation initiates a free radical reaction cascade

For small cyclic peptides, one electron capture by the [M + 2H](2+) ion generates numerous fragments corresponding to amino acid losses, side-chain losses, and losses of some low molecular weight species such as H(2)O, CH(3)(*), C(3)H(6), and (*)CONH(2). As predicted, the side-chain cleavages are amplified relative to linear peptides of similar size, but the amino acid losses were unexpected because they require that one electron capture cause more than one backbone cleavage, a phenomenon which necessitates further refinement or reinterpretation of current ECD mechanisms. A modified mechanism is postulated in which nonergodic electron capture fragmentation generates an alpha-carbon radical species that then propagates along the protein backbone. This radical migration initiates multiple free radical rearrangements, which cause both multiple backbone cleavages and additional side-chain cleavages.