Gas‐phase fragmentation reactions of protonated benzofuran‐ and dihydrobenzofuran‐type neolignans investigated by accurate‐mass electrospray ionization tandem mass spectrometry

We have investigated gas‐phase fragmentation reactions of protonated benzofuran neolignans (BNs) and dihydrobenzofuran neolignans (DBNs) by accurate‐mass electrospray ionization tandem and multiple‐stage (MSⁿ) mass spectrometry combined with thermochemical data estimated by Computational Chemistry. Most of the protonated compounds fragment into product ions B ([M + H–MeOH]⁺), C ([ B –MeOH]⁺), D ([ C –CO]⁺), and E ([ D –CO]⁺) upon collision‐induced dissociation (CID). However, we identified a series of diagnostic ions and associated them with specific structural features. In the case of compounds displaying an acetoxy group at C‐4, product ion C produces diagnostic ions K ([ C –C₂H₂O]⁺), L ([ K –CO]⁺), and P ([ L –CO]⁺). Formation of product ions H ([ D –H₂O]⁺) and M ([ H –CO]⁺) is associated with the hydroxyl group at C‐3 and C‐3′, whereas product ions N ([ D –MeOH]⁺) and O ([ N –MeOH]⁺) indicate a methoxyl group at the same positions. Finally, product ions F ([ A –C₂H₂O]⁺), Q ([ A –C₃H₆O₂]⁺), I ([ A –C₆H₆O]⁺), and J ([ I –MeOH]⁺) for DBNs and product ion G ([ B –C₂H₂O]⁺) for BNs diagnose a saturated bond between C‐7′ and C‐8′. We used these structure‐fragmentation relationships in combination with deuterium exchange experiments, MSⁿ data, and Computational Chemistry to elucidate the gas‐phase fragmentation pathways of these compounds. These results could help to elucidate DBN and BN metabolites in in vivo and in vitro studies on the basis of electrospray ionization ESI‐CID‐MS/MS data only.     

The unusual fragmentation of long‐chain feruloyl esters under negative ion electrospray conditions

Long‐chain ferulic acid esters, such as eicosyl ferulate ( 1 ), show a complex and analytically valuable fragmentation behavior under negative ion electrospay collision‐induced dissociation ((?)‐ESI‐CID) mass spectrometry, as studied by use of a high‐resolution (Orbitrap) mass spectrometer. In a strong contrast to the very simple fragmentation of the [M + H]⁺ ion, which is discussed briefly, the deprotonated molecule, [M – H]^?, exhibits a rich secondary fragmentation chemistry. It first loses a methyl radical (MS²) and the ortho‐quinoid [M – H – Me]^‐? radical anion thus formed then dissociates by loss of an extended series of neutral radicals, C_nH_2n + 1^? (n = 0–16) from the long alkyl chain, in competition with the expulsion of CO and CO₂ (MS³). The further fragmentation (MS⁴) of the [M – H – Me – C₃H₇]^? ion, discussed as an example, and the highly specific losses of alkyl radicals from the [M – H – Me – CO]^‐? and [M – H – Me – CO₂]^‐? ions provide some mechanistic and structural insights.     

A comparison of three experimental techniques for ion structure studies via collision-induced reactions: The [C5H8]+˙ example

Structure differentiation between [C₅H₈]⁺˙ ions, formed by electron ionization of various precursors, has been used as a test case for comparison of three experimental techniques involving collision-induced dissociation (CID). Low-energy CID in an rf-only quadrupole collision cell has been studied in the range 1–150 eV laboratory collision energy. These data have been compared with those obtained using mass-analyzed ion kinetic energy spectroscopy at 8 keV energy, and with results from dissociative charge-stripping (DCS) coupled with a second electron capture collision (EC) in order to remove intense interferences (DCS/EC). The greatest degree of structure differentiation was possible using the DCS/EC technique. The other two methods were comparable in this regard, although effects of pre-collision internal energy was apparent for collision energies much below 30 eV. Day-to-day reproducibility of spectra was most difficult to obtain for the low-energy CID technique. Of the [C₅H₈]⁺˙ ions thus tested, the isoprene molecular ion was clearly the best match to the fragment ion formed from limonene.     

A comparative study on the behaviour of 1,3-diheterocyclopentanes (X = O,O; S,S; O,S) under electron impact. The formation of thioacetyl and thiiranyl cations

The electron-impact-induced mass spectra of 1,3-dioxolane (la), 1,3-dithiolane (2a) and 1,3-oxatbiolane (3a) and their 2-methyl (1b–3b) and 2,2-dimethyl [(CH₃)₂: 1c–3c or (CD₃)₂: 1d–3d] derivatives have been studied in detail to gain further insight into their ion structures and competing reaction pathways with low-resolution, high-resolution, metastable and collision-induced dissociation (CID) techniques. For compounds 1a–1d the most significant reaction is loss of H^˙ and CH₃^˙ by α-cleavage and a subsequent formation of CHO⁺ and C₂H₃O⁺ ions. The [M ? H]⁺ ions from 1a and 1b give a C₂H₃O⁺ ion which does not have the acyl cation structure as shown by their CID spectra. In compounds 3a–3d the sulphur-containing ions predominate, the C₂H₃O⁺ now having the acyl cation structure. 1,3-Dithiolanes (2a–2d) exhibit the most complicated fragmentation patterns. Furthermore the [M ? H]⁺ ion from 2a and [M ? CH₃]⁺ ion from 2b have different structures as well as the [M ? H]⁺ ion from 2b and [M ? CH₃]⁺ ion from 2c, as shown by their CID spectra. This can be utilized to explain why 3a–3c and 2a give principally a thiiranyl cation, whereas 2b gives a mixture of this and the thioacyl cation and 2c practically only the open-chain thioacetyl cation.     

Comparison of collisional activation spectra of some positive ions produced both by charge reversal of negative ions and by decomposition of positive ions

The charge reversal collision induced decomposition mass analyzed ion kinetic energy spectrum of allyl anion has been compared with the collision induced dissociation mass analyzed ion kinetic energy spectrum of allyl cation and found to be identical except for the presence of +2 ions formed by charge stripping in the spectrum of the [C₃H₅]⁺ ion. Likewise, the collision induced dissociation mass analyzed ion kinetic energy charge reversal spectrum of [CH₃Se]^? has been compared with the collision induced dissociation mass analyzed ion kinetic energy spectrum of [CH₃Se]⁺ and found to be identical. A study of the pressure dependence of the collision induced dissociation mass analyzed ion kinetic energy spectrum of [C₃H₅]⁺ and [C₃H₅]^? showed increasing fragmentation with increasing collision gas pressure, and suggests that a greater mean number of collisions converts more energy to internal modes in the collision induced dissociation mass analyzed ion kinetic energy experiment even at low pressures.     

Molecular formula analysis of fragment ions by isotope‐selective collision‐induced dissociation tandem mass spectrometry of pharmacologically active compounds

The purpose of this work is to explore the mass fragment characterization of commonly used drugs through a novel approach, which involves isotope‐selective tandem mass spectrometry (MS/MS). Collision‐induced dissociation (CID) was performed with a low‐resolution linear ion trap mass spectrometer in positive electrospray ionization. Three pharmacologically active ingredients, i.e. omeprazole, meloxicam and brinzolamide, selected as model compounds in their own formulation, were investigated as a sodiated adduct [C₁₇H₁₉N₃O₃S + Na]⁺ (omeprazole) and as protonated adducts, [C₁₄H₁₃N₃O₄S₂ + H]⁺ and [C₁₂H₂₁N₃O₅S₃ + H]⁺, meloxicam and brinzolamide, respectively. Selecting a narrow window of ±0.5 m/z units, precursor ion fragmentation by CID‐MS/MS of isotopologues A + 0, A + 1 and A + 2 was found very useful to confirm the chemical formula of product ions, thus aiding the establishment of characteristic fragmentation pathways of all three examined compounds. The correctness of putative molecular formula of product ions was easily demonstrated by exploiting the isotope peak abundance ratios (i.e. I_F+0/I_F+1 and I_F+0/I_F+2) as simple constraints in low‐resolution MS instrumentations. Copyright © 2014 John Wiley & Sons, Ltd.     

ToF‐SIMS and computation analysis: Fragmentation mechanisms of polystyrene,polystyrene‐d5, and polypentafluorostyrene

We studied the time‐of‐flight secondary ion mass spectrometry fragmentation mechanisms of polystyrenes—phenyl‐fluorinated polystyrene (5FPS), phenyl‐deuterated polystyrene (5DPS), and hydrogenated polystyrene (PS). From the positive ion spectra of 5FPS, we identified some characteristic molecular ion structures with isomeric geometries such as benzylic, benzocyclobutene, benzocyclopentene, cyclopentane, and tropylium systems. These structures were evaluated by the B3LYP‐D/jun‐cc‐pVDZ computation method. The intensities of the C₇H₂F₅⁺ (m/z = 181), CyPent‐C₉H₃F₄⁺ (m/z = 187), CyPent‐C₉H₄F₅⁺ (m/z = 207), and CyPent‐C₉H₂F₅⁺ (m/z = 205) ions were enhanced by resonance stabilization. The positive fluorinated ions from 5FPS tended to rearrange and produce fewer fluorine‐containing molecular ions through the loss of F (m/z = 19), CF (m/z = 31), and CF₂ (m/z = 50) ion fragments. Consequently, the fluorine‐containing polycyclic aromatic ions had much lower intensities than their hydrocarbon counterparts. We propose the fragmentation mechanisms for the formation of C₅H₅⁺, C₆H₅⁺, and C₇H₇⁺ ion fragments, substantiated with detailed analyses of the negative ion spectra. These ions were created through elimination of a pentafluoro‐phenyl anion (C₆F₅⁻) and H⁺, followed by a 1‐electron‐transfer process and then cyclization of the newly generated polyene with carbon‐carbon bond formation. The pendant groups with elements of different electronegativities exerted strong influences on the intensities and fragmentation processes of their corresponding ions.     

Sulfate migration in oligosaccharides induced by negative ion mode ion trap collision‐induced dissociation

Migration of sulfate groups between hydroxyl groups was identified after collision‐induced dissociation (CID) of sulfated oligosaccharides in an ion trap mass spectrometer in negative ion mode. Analysis of various sulfated oligosaccharides showed that this was a common phenomenon and was particularly prominent in sulfated oligosaccharides also containing sialic acid. It was also shown that the level of migration was increased when the sulfate was positioned on the flexible areas of the oligosaccharides not involved in the pyranose ring, such as the extra‐cyclic C‐6 carbon of hexoses or N‐acetylhexosamines, or on reduced oligosaccharide. This suggested that migration is dependent on the spatial availability of the sulfate in the ion trap during collision. It is proposed that the migration is initiated when the negatively charged ‐SO₃^– residue attached to the oligosaccharide precursor becomes protonated by a CID‐induced proton transfer. This is supported by the CID fragmentation of precursor ions depleted of acidic protons such as doubly charged [M – 2H]^2– ions or the sodiated [M + Na – 2H]^– ions of oligosaccharides containing one sulfate and one sialic acid in the same molecule. Compared to the CID fragmentation of their monocharged [M – H]^– ions, no migration was observed in CID of proton depleted precursors. Alternative fragmentation parameters to suppress migration of sulfated oligosaccharides also showed that it was not present when sulfated oligosaccharides were fragmented by HCD (High‐Energy C‐trap Dissociation) in an Orbitrap mass spectrometer. Copyright © 2011 John Wiley & Sons, Ltd.     

Collision induced dissociation in a flowing afterglow-tandem mass spectrometer for the selective detection of C5 unsaturated alcohols and isoprene

A flowing afterglow-tandem mass spectrometer (FA-TMS) was used to study a series of C₅ unsaturated alcohols and isoprene. The analytical procedure was validated through collision induced dissociation (CID) experiments on proton hydrates. In the FA, reagent H₃O⁺ ions were used to chemically ionize the alcohols under study and isoprene. Chemical ionization (CI) by H₃O⁺ is widely used, especially in PTR-MS instruments, and produces a main peak at m/z 69 for all studied compounds, implying the impossibility to distinguish them by a simple quadrupole mass filter. The CID of these ions at m/z 69 resulted in daughter ions with the same masses but with different intensities depending on the organic compound, the collision energy and the Ar target gas pressure in the collision cell. From these observations, pentenols were easily distinguished from methylbutenols and 3-methyl-3-buten-1-ol from the other compounds. CID experiments were also performed on the protonated alcohol, which is only a stable ion for 1-penten-3-ol, 2-methyl-3-buten-2-ol and 3-methyl-3-buten-1-ol, showing different CID patterns as a function of the collision energy. The coupling between a FA reactor and a TMS has proven to be a valuable approach to identify C₅ unsaturated alcohols and isoprene.     

The origins of the base peak in the electron impact spectrum of limonene

The origins and nature of the [C₅H₈]⁺? ions which form the base peak in the electron impact spectrum of limonene, at nominal electron energies greater than 11 eV, have been investigated. Linked scan techniques were used to study unimolecular and collision induced fragmentation reactions. No fragmentation pathway leading to [C₅H₈]⁺? could be found. Measurement of ionization efficiency curves indicated that the threshold for formation of C₅H₈[⁺?] lies above the range of internal energies deposited in incident ions by collisional activation. By a combination of comparisons of collisionally activated spectra and energetic considerations, the [C₅H₈]⁺? ions formed from limonene were shown to resemble those of the molecular ion of isoprene, while the neutral fragment is most likely isoprene also. Deuterium labelling experiments yielded evidence of extensive scrambling prior to fragmentation. The most probable mechanism of formation of [C₅H₈]⁺? appears to involve a retro Diels–Alder reaction of a structurally intact molecular ion of limonene.     

Positive chemical ionization triple‐quadrupole mass spectrometry and ab initio computational studies of the multi‐pathway fragmentation of phthalates

We report the first positive chemical ionization (PCI) fragmentation mechanisms of phthalates using triple‐quadrupole mass spectrometry and ab initio computational studies using density functional theories (DFT). Methane PCI spectra showed abundant [M + H]⁺, together with [M + C₂H₅]⁺ and [M + C₃H₅]⁺. Fragmentation of [M + H]⁺, [M + C₂H₅]⁺ and [M + C₃H₅]⁺ involved characteristic ions at m/z 149, 177 and 189, assigned as protonated phthalic anhydride and an adduct of phthalic anhydride with C₂H₅⁺ and C₃H₅⁺, respectively. Fragmentation of these ions provided more structural information from the PCI spectra. A multi‐pathway fragmentation was proposed for these ions leading to the protonated phthalic anhydride. DFT methods were used to calculate relative free energies and to determine structures of intermediate ions for these pathways. The first step of the fragmentation of [M + C₂H₅]⁺ and [M + C₃H₅]⁺ is the elimination of [R? H] from an ester group. The second ester group undergoes either a McLafferty rearrangement route or a neutral loss elimination of ROH. DFT calculations (B3LYP, B3PW91 and BPW91) using 6‐311G(d,p) basis sets showed that McLafferty rearrangement of dibutyl, di(‐n‐octyl) and di(2‐ethyl‐n‐hexyl) phthalates is an energetically more favorable pathway than loss of an alcohol moiety. Prominent ions in these pathways were confirmed with deuterium labeled phthalates. Copyright © 2010 John Wiley & Sons, Ltd.     

Gas‐phase fragmentation of γ‐lactone derivatives by electrospray ionization tandem mass spectrometry

Fragmentation reactions of β‐hydroxymethyl‐, β‐acetoxymethyl‐ and β‐benzyloxymethyl‐butenolides and the corresponding γ‐butyrolactones were investigated by electrospray ionization tandem mass spectrometry (ESI‐MS/MS) using collision‐induced dissociation (CID). This study revealed that loss of H₂O [M + H ?18]⁺ is the main fragmentation process for β‐hydroxymethylbutenolide (1) and β‐hydroxymethyl‐γ‐butyrolactone (2). Loss of ketene ([M + H ?42]⁺) is the major fragmentation process for protonated β‐acetoxymethyl‐γ‐butyrolactone (4), but not for β‐acetoxymethylbutenolide (3). The benzyl cation (m/z 91) is the major ion in the ESI‐MS/MS spectra of β‐benzyloxymethylbutenolide (5) and β‐benzyloxymethyl‐γ‐butyrolactone (6). The different side chain at the β‐position and the double bond presence afforded some product ions that can be important for the structural identification of each compound. The energetic aspects involved in the protonation and gas‐phase fragmentation processes were interpreted on the basis of thermochemical data obtained by computational quantum chemistry. Copyright © 2009 John Wiley & Sons, Ltd.     

Photofragmentation of 2‐Deoxy‐D‐Ribose Molecules in the Gas Phase

We have measured the synchrotron‐induced photofragmentation of isolated 2‐deoxy‐D ‐ribose molecules (C₅H₁₀O₄) at four photon energies, namely, 23.0, 15.7, 14.6, and 13.8 eV. At all photon energies above the molecule′s ionization threshold we observe the formation of a large variety of molecular cation fragments, including CH₃⁺, OH⁺, H₃O⁺, C₂H₃⁺, C₂H₄⁺, CH_xO⁺ (x=1,2,3), C₂H_xO⁺ (x=1–5), C₃H_xO⁺ (x=3–5), C₂H₄O₂⁺, C₃H_xO₂⁺ (x=1,2,4–6), C₄H₅O₂⁺, C₄H_xO₃⁺ (x=6,7), C₅H₇O₃⁺, and C₅H₈O₃⁺. The formation of these fragments shows a strong propensity of the DNA sugar to dissociate upon absorption of vacuum ultraviolet photons. The yields of particular fragments at various excitation photon energies in the range between 10 and 28 eV are also measured and their appearance thresholds determined. At all photon energies, the most intense relative yield is recorded for the m/q=57 fragment (C₃H₅O⁺), whereas a general intensity decrease is observed for all other fragments— relative to the m/q=57 fragment—with decreasing excitation energy. Thus, bond cleavage depends on the photon energy deposited in the molecule. All fragments up to m/q=75 are observed at all photon energies above their respective threshold values. Most notably, several fragmentation products, for example, CH₃⁺, H₃O⁺, C₂H₄⁺, CH₃O⁺, and C₂H₅O⁺, involve significant bond rearrangements and nuclear motion during the dissociation time. Multibond fragmentation of the sugar moiety in the sugar–phosphate backbone of DNA results in complex strand lesions and, most likely, in subsequent reactions of the neutral or charged fragments with the surrounding DNA molecules.     

Unimolecular and collision-induced dissociation reactions of peracetylated methyl glucopyranoside

The mechanism of the collision-induced fragmentation of peracetylated methyl-α-D-glucopyranoside was investigated using deuterium-labelled acetates and sequential mass spectrometry. Loss of the substituent at C(1), the anomeric carbon, yields an ion of m/z 331, [C₁₄H₁₉O₉]⁺. This ion further dissociates via two pathways, the first including m/z 271, [C₁₂H₁₅O₇]⁺, 169, [C₈H₉O₄]⁺ and 109, [C₆H₅O₂]⁺, and the second including m/z 211, [C₁₀H₁₁O₅]⁺, 169, [C₈H₉O₄]⁺ and 127 [C₆H₇O₃]⁺. The first path proceeds via loss of acetate at C(3), followed by a single-step concerted loss of acetates from C(2) and C(4), and ending with loss of acetate from C(6). The second path proceeds predominantly via loss of acetates from C(3) and C(4), elimination of ketene from the C(2)-acetate and finally loss of ketene from the acetate at C(6). This path is also characterized by an ill-defined series of parallel decomposition reactions involving acetates from other sites on the molecule. At low collision energy, and in the absence of collision gas (unimolecular reaction conditions), the former pathway predominates; m/z 331 dissociates via loss of acetate at C(3), followed by a single-step concerted loss of acetates from C(2) and C(4).     

Selective detection of the tolyl cation among other [C7H7]+ isomers by ion/molecule reaction with dimethyl ether

The ion/molecule reaction of the tolyl cation with dimethyl ether has been investigated using triple quadrupole mass spectrometry. Three isomers with [C₇H₇]⁺ composition, the 3-tolyl, benzyl, and tropylium cations, were individually selected and reacted with dimethyl ether at a pressure of 1 mtorr in the second quadrupole (Q₂) collision cell. Only the tolyl ion reacted to yield a methoxylated product ion peak at m/z 122. This reaction product having m/z 122 is postulated to be identical in structure with the molecular ion of 3-methyl anisole, as supported by thermochemical data and the similarity of the collision induced dissociation (CID) daughter ion mass spectra of the product ion and the molecular ion of authentic 3-methyl anisole. The daughter ion mass spectra of the three [C₇H₇]⁺ isomers during CID, by using a triple quadrupole mass spectrometer, are nearly identical; on the other hand, the analytical approach based on the ion/molecule reaction with dimethyl ether clearly exhibits distinct gas-phase chemistry reflecting structural differences among the isomers. Sot     

Generation of gas‐phase sodiated arenes such as [(Na3(C6H4)+] from benzene dicarboxylate salts

Upon collision‐induced activation, gaseous sodium adducts generated by electrospray ionization of disodium salts of 1,2‐ 1,3‐, and 1,4‐benzene dicarboxylic acids (m/z 233) undergo an unprecedented expulsion of CO₂ by a rearrangement process to produce an ion of m/z 189 in which all three sodium atoms are retained. When isolated in a collision cell of a tandem‐in‐space mass spectrometer, and subjected to collision‐induced dissociation (CID), only the m/z 189 ions derived from the meta and para isomers underwent a further CO₂ loss to produce a peak at m/z 145 for a sodiated arene of formula (Na₃C₆H₄)⁺. This previously unreported m/z 145 ion, which is useful to differentiate meta and para benzene dicarboxylates from their ortho isomer, is in fact the sodium adduct of phenelenedisodium. Moreover, the m/z 189 ion from all three isomers readily expelled a sodium radical to produce a peak at m/z 166 for a radical cation [(^?C₆H₄CO₂Na₂)⁺], which then eliminated CO₂ to produce a peak at m/z 122 for the distonic cation (^?C₆H₄Na₂)⁺. Copyright © 2009 John Wiley & Sons, Ltd.     

Characterization of five [C4H7O]+ Ion structures. Fragmentation of the 2-pentanone molecular ion

The [C₄H₇0]⁺ ions [CH₂?CH? C(?OH)CH₃]⁺ (1), [CH₃CH?CH? C(?OH)H]⁺ (2), [CH₂?C(CH₃)C(?OH)H]⁺ (3), [Ch₃CH₂CH₂C?O]⁺ (4) and [(CH₃)₂CHC?O]⁺ (5) have been characterized by their collision-induced dissociation (CID) mass spectra and charge stripping mass spectra. The ions 1–3 were prepared by gas phase protonation of the relevant carbonyl compounds while 4 and 5 were prepared by dissociative electron impact ionization of the appropriate carbonyl compounds. Only 2 and 3 give similar spectra and are difficult to distinguish from each other; the remaining ions can be readily characterized by either their CID mass spectra or their charge stripping mass spectra. The 2-pentanone molecular ion fragments by loss of the C(1) methyl and the C(5) methyl in the ratio 60:40 for metastable ions; at higher internal energies loss of the C(1) methyl becomes more favoured. Metastable ion characteristics, CID mass spectra and charge stripping mass spectra all show that loss of the C(1) methyl leads to formation of the acyl ion 4, while loss of the C(5) methyl leads to formation of protonated vinyl methyl ketone (1). These results are in agreement with the previously proposed potential energy diagram for the [C₅H₁₀O]⁺˙ system.     

Fragmentation of the enolate ion of 2,3-butanedione. Characterization of the acetyl anion by charge inversion mass spectrometry

The unimolecular and collision-induced fragmentation reactions of the enolate ion of 2,3-butanedione, [CH₃COCOCH₂]^?, have been studied, Unimolecular fragmentation on the metastable ion time-scale forms [HCCO]^?, [C₂H₃O]^?, [C₃H₅O]^? and [CH₃CO₂]^?. Charge inversion mass spectrometry shows that the [C₂H₃O]^? ion is the acetyl anion while the [C₃H₅O]^? product is the acetone enolate ion; formation of the latter product involves a large release of kinetic energy (T _1/2 = 0.99 eV). The fragmentation reactions occurring following collisional activation have been determined for 8 keV collisions and over the range 1.5–30 eV center-of-mass collision energy. Formation of [HCCO]^? and [CH₃CO]^? are of the most important reactions following collisional activation and it is concluded that the two reactions have similar critical reaction energies even though formation of [HCCO]^? is favored thermochemically.     

Isomer differentiation via collision‐induced dissociation: The case of protonated α‐, β2‐ and β3‐phenylalanines and their derivatives

A combination of electrospray ionisation (ESI), multistage and high‐resolution mass spectrometry experiments is used to examine the gas‐phase fragmentation reactions of the three isomeric phenylalanine derivatives, α‐phenylalanine, β²‐phenylalanine and β³‐phenylalanine. Under collision‐induced dissociation (CID) conditions, each of the protonated phenylalanine isomers fragmented differently, allowing for differentiation. For example, protonated β³‐phenylalanine fragments almost exclusively via the loss of NH₃, only β²‐phenylalanine via the loss of H₂O, while α‐ and β²‐phenylalanine fragment mainly via the combined losses of H₂O + CO. Density functional theory (DFT) calculations were performed to examine the competition between NH₃ loss and the combined losses of H₂O and CO for each of the protonated phenylalanine isomers. Three potential NH₃ loss pathways were studied: (i) an aryl‐assisted neighbouring group; (ii) 1,2 hydride migration; and (iii) neighbouring group participation by the carboxyl group. Finally, we have shown that isomer differentiation is also possible when CID is performed on the protonated methyl ester and methyl amide derivatives of α‐, β²‐ and β³‐phenylalanines. Copyright © 2010 John Wiley & Sons, Ltd.     

Electrospray ionization collision induced dissociation of thiocarbocyanine and selenocarbocyanine dyes

The effect of the properties of sulphur and selenium atoms, the composition and location of substituents (―CH₃, ―OCH₃, ―C₂H₅, and ―C₃H₆―((N⁺Br^?)C₅H₅)), and the charge state on the collision induced dissociation (CID) behaviour of ions generated by electrospray ionization (ESI) of thiocarbocyanine and selenocarbocyanine dyes have been investigated. The results show that, for of all the examined singly charged ions, the main dissociation channel was related to the formation of distonic ions, generated as a result of cleavages within the dimethine bridge. In the case of doubly charged ions (with propyl‐pyridinium substituents), competition between fragmentation processes related to charges located at different nitrogen atoms has been observed. The S/Se replacement also has an impact on the CID behaviour of the examined carbocyanine dyes. On the basis of the performed CID MS/MS experiments, general rules for the CID of thiocarbocyanine and selenocarbocyanine dyes have been proposed.