Examination of Ortho effects in the collisionally activated dissociation of closed-shell aromatic ions

The collisionally activated dissociation of a variety of isomeric disubstituted aromatic ions formed by ion–molecule reactions were examined in order to characterize ortho effects in closed-shell systems. Closed-shell ions of methoxyacetophenone, hydroxyacetophenone, methoxyphenol, anisaldehyde and hydroxybenzaldehyde were formed by proton transfer, methyl addition or methyne addition by using dimethyl ether or ethylene oxide as chemical ionization reagents, and then the structures of these adducts were studied by deuterium-labelling methods and by collisionally activated dissociation techniques in a triple quadrupole mass spectrometer or a quadrupole ion trap. Typically, the meta and para isomers have qualitatively similar dissociation spectra which reflect the types of dissociation reactions observed for the corresponding monosubstituted aromatic ions. The predominant dissociation pathways of the [M + H]⁺ and [M + 15]⁺ ions are directed by the electron-withdrawing substituents, whereas the major dissociation pathways of the [M + 13]⁺ ions are related to the electron-releasing substituent. In contrast, the dissociation routes of the corresponding ortho isomers are dramatically different. This is attributed to the opportunity for functional group interactions of the ortho isomers which facilitate alternative pathways.     

The unimolecular and collisionally activated decompositions of fluorine-substituted tetraphenyltetrahedrane ions on the microsecond time-scale

Unimolecular and collision-induced decomposition products of [C₄(C₆H₅)₂(C₆H₄F)₂]⁺˙ generated from four unsymmetrical sources include [C₁₄H₁₀]⁺˙ and [C₁₄H₈F₂]⁺˙ and so provide evidence for a tetrahedral intermediate. Other decompositions show substantial influence of the position of the ρ-fluorophenyl ring on ion energy distributions. This influence may be related to the reported absence of peaks diagnostic for the tetrahedral intermediate from the spectrum of the equivalent ion from the appropriate ¹³C-labeled analog. Alternatively the difference in spectra can be correlated with lifetimes of ions.     

Minimizing base loss and internal fragmentation in collisionally activated dissociation of multiply deprotonated RNA

In recent years, new classes of nonprotein-coding ribonucleic acids (ncRNAs) with important cellular functions have been discovered. Of particular interest for biomolecular research and pharmaceutical developments are small ncRNAs that are involved in gene regulation, such as small interfering RNAs (21–28 nt), pre-microRNAs (70–80 nt), or riboswitches (34–200 nt). De novo sequencing of RNA by top-down mass spectrometry has so far been limited to RNA consisting of up to ∼20 nt. We report here complete sequence coverage for 34 nt RNA (10.9 kDa), along with 30 out of 32 possible complementary ion pairs from collisionally activated dissociation (CAD) experiments. The key to minimizing undesired base loss and internal fragmentation is to minimize the internal energy of fragment ions from primary backbone cleavage. This can be achieved by collisional cooling of primary fragment ions and selection of precursor ions of relatively low negative net charge (about −0.2/nt).     

Cyclization reaction of peptide fragment ions during multistage collisionally activated decomposition: An inducement to lose internal amino-acid residues

During characterization of some peptides (linear precursors of the cyclic peptides showing potential to be anticancer drugs) in an ion trap, it was noted that many internal amino acid residues could be lost from singly charged b ions. The phenomenon was not obvious at the first stage of collisionally activated decomposition (CAD), but was apparent at multiple stages of CAD. The unique fragmentation consisting of multiple steps is induced by a cyclization reaction of b ions, the mechanism of which has been probed by experiments of N-acetylation, MS(n), rearranged-ion design, and activation-time adjustment. The fragmentation of synthetic cyclic peptides demonstrates that a cyclic peptide intermediate (CPI) formed by b ion cyclization exhibits the same fragmentation pattern as a protonated cyclic peptide. Although no rules for the cyclization reaction were discerned in the experiments of peptide modification, the fragmentations of a number of b ions indicate that the "Pro and Asn/Gln effects" can influence ring openings of CPIs. In addition, large-scale losses of internal residues from different positions of a-type ions have been observed when pure helium was used as collision gas. The fragmentation is initiated by a cyclization reaction forming an a-type ion CPI. This CPI with a fixed-charge structure cannot be influenced by the "Pro effect", causing a selective ring opening at the amide bond Pro-Xxx rather than Xxx-Pro. With the knowledge of the unique fragmentations leading to internal residue losses, the misidentification of fragments and sequences of peptides may be avoided.     

Characterization of flavonoids by aluminum complexation and collisionally activated dissociation

Aluminum complexes of the type [Al(III) (flavonoid-H)2]+ are generated by electrospray ionization in order to allow differentiation of isomeric flavonoids by tandem mass spectrometry. The dominant species observed from the aluminum complexation reaction has a 1:2 aluminum(III):flavonoid stoichiometry. Differentiation of 18 flavonoids constituting seven isomeric series was achieved based on the collisionally activated dissociation patterns of the aluminum complexes. Characteristic fragmentation pathways allow identification of the site of glycosylation, the type of saccharide (rutinose versus neohesperidose) and the type of bond between the C-2 and C-3 atoms (thus distinguishing flavanones from flavonols and flavones). Two stable coordination geometries of the aluminum complex of apigenin were identified. The non-planar structure with a plane-angle of nearly 90 degrees is 25.3 kcal mol-1 more favorable than the planar structure. The conformations of the complexes, which involve multiple interactions between the aglycone and disaccharide portions of the flavonoid with the metal ion, are significantly different for the isomeric flavonoids.     

Fragmentation of collisionally activated hydroxyphenoxide anions in the gas phase

Low-energy collisionally activated dissociation of O-deprotonated dihydroxybenzenes (catechol, resorcinol, hydroquinone) in the gas phase causes both fragmentation to form [C₆H₄O₂]^– ions by loss of the remaining oxygen-bound hydrogen atom and intramolecular hydrogen atom migration from O to C. The rearranged anions then undergo ring-cleavage reactions which are different in each case. Both catechol and hydroquinone produce fragments which are the result of the loss of two carbon atoms and both oxygen atoms but the proposed mechanisms are different. Resorcinol also produces a fragment which derives from the loss of carbon dioxide. For this process a mechanism is proposed which involves a 6-methylpyranone anion intermediate.     

Electron transfer dissociation versus collisionally activated dissociation of cationized biodegradable polyesters

Biodegradable polyesters were ionized by electrospray ionization and characterized by tandem mass spectrometry using collisionally activated dissociation (CAD) and electron transfer dissociation (ETD) as activation methods. The compounds studied include one homopolymer, polylactide and two copolymers, poly(ethylene adipate) and poly(butylene adipate). CAD of [M+2Na]²⁺ ions from these polyesters proceeds via charge‐remote 1,5‐H rearrangements over the ester groups, leading to cleavages at the (CO)O–alkyl bonds. ETD of the same precursor ions creates a radical anion at the site of electron attachment, which fragments by radical‐induced cleavage of the (CO)O–alkyl bonds and by intramolecular nucleophilic substitution at the (CO)–O bonds. In contrast to CAD, ETD produces fragments in one charge state only and does not cause consecutive fragmentations, which simplifies spectral interpretation and permits conclusive identification of the correct end groups. The radical‐site reactions occurring during ETD are very similar with those reported for ETD of protonated peptides. Unlike multiply protonated species, multiply sodiated precursors form ion pairs (salt bridges) after electron transfer, thereby promoting dissociations via nucleophilic displacement in addition to the radical‐site dissociations typical in ETD. Copyright © 2012 John Wiley & Sons, Ltd.     

Reactivity of collisionally activated dichlorocarbene dications studied by tandem mass spectrometry

The dissociation mechanisms of dichlorocarbene dications following collisional activation have been investigated via tandem mass spectrometric techniques and semi-empirical calculations. Three channels appear to be significant: {fx1019-1} The second channel becomes dominant at high internal energy. Production of ground state fragments (channel 1) involves a transition driven by spin—orbit coupling from the CCl ₂ ²⁺ $CCl_2^2 \tilde X^1 \Sigma _g^ + $ state to the CCl ₂ ^2? ā³Σ _u ^? state en route to the fragments. The dissociation barrier for the production of ground state fragments from the ground electronic state of CCl ₂ ²⁺ via the spin—orbit-induced transition is equal to 420 kJ mol^?1. The dissociation pathway that corresponds to channel 3 includes a first isomerization step from the linear Cl-C-Cl²⁺ structure to a bent Cl-Cl-C²⁺ connectivity. The calculated isomerization barrier amounts to 550 kJ mol^?1. The calculated reverse activation barriers are compatible with the measured kinetic energy released on the fragments.     

Gas-phase fragmentation studies of biotinylated oligomannuronopyranosides under conditions of collisionally activated dissociation

Russian Chemical Bulletin - High-resolution electrospray ionization mass spectra (MS and MS/MS) of a series of glycoconjugates containing biotin and oligomannuronopyranosyl residues linked via a...     

High- and low-energy collisionally activated decompositions of octaethylporphyrin and its metal complexes

High-energy (HE) and low-energy (LE) collisionally activated decompositions of octaethylporphyrin (OEP) and its metal complexes (ZnOEP and CuOEP) depend on whether the precursor is produced by electrospray ionization as protonated molecules or by fast atom bombardment as radical cations or protonated molecules. LE activation leads to such simple product-ion spectra that a complete picture of fragmentation emerges only after nine stages of tandem mass spectrometry (MS⁹). HE activation, on the other hand, gives product-ion spectra that afford an integrated view of all the decomposition channels in a single MS/MS experiment. These results are the basis of a recommendation that OEP is an appropriate model compound for investigating energy effects in the collisional activation of organic and bioorganic molecule ions.     

Interference to linear superposability of collisionally activated decomposition spectra at high resolution

A new factor causing the superposability of collisionally activated decomposition spectra of ions to fail has been established for isobaric ions. If the two isobaric ion beams are not transmitted in their entirety simultaneously to the collision cell, the resulting spectrum is not a linear combination of the two spectra of the individually transmitted complete ion beams. Apparently the energy content of collimated ions varies across the ion beam, so that transmission of different portions of the ion beam produces samples of ions with different energy contents.     

Structural characterization of flavonoid glycosides by collisionally activated dissociation of metal complexes

Collisionally activated dissociation is used for structural characterization of a series of flavonoid glycosides. Dissociation of transition metal/flavonoid binary complexes of the type [MII(L - H+)]+ and transition metal/2,2'-bipyridine/flavonoid ternary complexes of the type [MII(L - H+)bpy]+ give fragmentation patterns that are complementary and more diagnostic than those of the protonated, deprotonated, or sodium-cationized flavonoids. Analysis of fragmentation patterns of the [MII(L - H+)bpy]- complexes permits determination of the disaccharide as a rutinose or neohesperidose and the relative placement of the disaccharide (i.e., 3 vs. 7 positions).     

Observations on the detection of b‐ and y‐type ions in the collisionally activated decomposition spectra of protonated peptides

Tandem mass spectrometric data from peptides are routinely used in an unsupervised manner to infer product ion sequence and hence the identity of their parent protein. However, significant variability in relative signal intensity of product ions within peptide tandem mass spectra is commonly observed. Furthermore, instrument‐specific patterns of fragmentation are observed, even where a common mechanism of ion heating is responsible for generation of the product ions. This information is currently not fully exploited within database searching strategies; this motivated the present study to examine a large dataset of tandem mass spectra derived from multiple instrumental platforms. Here, we report marked global differences in the product ion spectra of protonated tryptic peptides generated from two of the most common proteomic platforms, namely tandem quadrupole‐time‐of‐flight and quadrupole ion trap instruments. Specifically, quadrupole‐time‐of‐flight tandem mass spectra show a significant under‐representation of N‐terminal b‐type fragments in comparison to quadrupole ion trap product ion spectra. Energy‐resolved mass spectrometry experiments conducted upon test tryptic peptides clarify this disparity; b‐type ions are significantly less stable than their y‐type N‐terminal counterparts, which contain strongly basic residues. Secondary fragmentation processes which occur within the tandem quadrupole‐time‐of‐flight device account for the observed differences, whereas this secondary product ion generation does not occur to a significant extent from resonant excitation performed within the quadrupole ion trap. We suggest that incorporation of this stability information in database searching strategies has the potential to significantly improve the veracity of peptide ion identifications as made by conventional database searching strategies. Copyright © 2009 John Wiley & Sons, Ltd.     

Observation of self-ion-molecule reactions during collisionally activated dissociation in an ion-trap mass spectrometer

This paper describes the formation of protonated molecules ([M + H]+) and adduct ions by self-ion-molecule reactions (SIMR) during collisionally activated decomposition (CAD) of methyne addition ions ([M + CH]+) produced from chemical ionization (CI) or SIMR in both an external and internal source ion-trap mass spectrometer (ITMS). The CAD results for the methyne addition ions of dopamine produced from both SIMR and dimethyl ether CI undertaken in the external and internal source ITMS were compared in order to prove the occurrence of SIMR during CAD processes. Compared with the external source ITMS, the internal source ITMS is much more easily applicable to this type of reaction owing to the large population of neutral analytes present in the trap.     

Electron capture and collisionally activated dissociation mass spectrometry of doubly charged hyperbranched polyesteramides

Electron capture dissociation (ECD) of doubly protonated hyperbranched polyesteramide oligomers (1100-1900 Da) was examined and compared with the structural information obtained by low energy collisionally activated dissociation (CAD). Both the ester and amide bonds of the protonated species were cleaved easily upon ECD with the formation of odd electron (OE(.+)) or even electron (EE(+)) fragment ions. Several mechanistic schemes are proposed that describe the complex ECD fragmentation behavior of the multiply charged oligomers. In contrast to studies of biomolecules, the present results indicate that consecutive cleavages induced by intramolecular H-shifts are significant for ECD and of less importance for low energy CAD. The capture of an electron by the ionized species results in fragmentation associated with a redistribution of the excess internal energy over the products and the subsequent bond cleavage. Low energy, multiple collision CAD is found to be a more selective dissociation method than ECD in view of the observation that only amide bonds are cleaved for most of the hyperbranched polymers examined with CAD in this study. ECD appears not to provide complementary structural information compared to CAD in the study of hyperbranched polymers, even though a significantly more complex ECD fragmentation behavior is observed. ECD is shown to be of use for the structural characterization of large oligomers that may not dissociate upon low energy CAD. This is a direct result of the fact that ECD produces ionized hyperbranched oligomers with a relatively high internal energy.     

A relation between ion structures and experimental overall cross-sections for collisionally activated decomposition

Collisionally activated dissociation (CAD) mass spectra sometimes appear to be identical in spite of the fact that the precursor ion structures are known to differ. It is shown that determination of the experimental overall cross-section for collisionally activated decomposition yields valuable extra information. After applying it to examples of known structure, [C₄H₅N]^+·, [C₅H₅N]^+· and [C₅H₅O]⁺, it is used to study a more complex problem, that of [C₆H₆]^+· ions from four isomeric precursors.     

Alkane elimination from ionized alkanols

The energetics, metastable characteristics and daughter ion structures for the loss of small alkane molecules from ionized 2-propanol, 2-butanol and 3-pentanol have been examined in detail. [2-Propanol]^+˙ ions lose CH₄ to generate the keto and enol forms of [C₂H₄O]^+˙ and the same daughter ions are produced by loss of C₂H₆ from [2-butanol]^+˙. Ionized 3-pentanol does not lose CH₄ but readily eliminates C₂H₆ to produce the enol ion [CH₃CH?CHOH]^+˙. The last reaction was shown to proceed by a simple 1,2 elimination mechanism in the μs time-frame; isotope effects are also discussed.     

A field ionization and collisionally activated dissociation/charge stripping study of some [C9H10]+˙ ions

The extent of isomerization of [C₉H₁₀]^+˙ ions, with lifetimes of approximately 10^?11 and 10^?6 s has been investigated using field ionization, collisionally activated dissociation and charge stripping techniques. The [C₉H₁₀]^+˙ ions which were investigated included the molecular ions of α-methylstyrene, β-methylstyrene, o-methylstyrene, m-methylstyrene, p-methylstyrene, indan, cyclopropylbenzene, allylbenzene and the product of water loss from 3-phenylpropanol. The field ionization spectra of all the C₉H₁₀ hydrocarbons were different indicating that isomerization to a common ion structure had not occurred to a measurable extent for ions with lifetimes of approximately 10^?11 s. Collisionally activated dissociation and charge stripping results indicated that most of the [C₉H₁₀]^+˙ ions continued to maintain unique ion structures (or mixtures of structures) at ion lifetimes of 10^?6 s. Possible exceptions are the [C₉H₁₀]^+˙ ions from allylbenzene and cyclopropylbenzene which gave indistinguishable collisionally activated dissociation and charge stripping spectra.