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ABSTRACT: Middle-sized b ( n ) (n ≥ 5) fragments of protonated peptides undergo selective complex formation with ammonia under experimental conditions typically used to probe hydrogen-deuterium exchange in Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Other usual peptide fragments like y, a, a*, etc., and small b ( n ) (n ≤ 4) fragments do not form stable ammonia adducts. We propose that complex formation of b ( n ) ions with ammonia is characteristic to macrocyclic isomers of these fragments. Experiments on a protonated cyclic peptide and N-terminal acetylated peptides fully support this hypothesis; the protonated cyclic peptide does form ammonia adducts while linear b ( n ) ions of acetylated peptides do not undergo complexation. Density functional theory (DFT) calculations on the proton-bound dimers of all-Ala b ( 4 ), b ( 5 ), and b ( 7 ) ions and ammonia indicate that the ionizing proton initially located on the peptide fragment transfers to ammonia upon adduct formation. The ammonium ion is then solvated by N(+)-H…O H-bonds; this stabilization is much stronger for macrocyclic b ( n ) isomers due to the stable cage-like structure formed and entropy effects. The present study demonstrates that gas-phase guest-host chemistry can be used to selectively probe structural features (i.e., macrocyclic or linear) of fragments of protonated peptides. Stable ammonia adducts of b ( 9 ), b ( 9 ) -A, and b ( 9 ) -2A of A(8)YA, and b ( 13 ) of A(20)YVFL are observed indicating that even these large b-type ions form macrocyclic structures.
Journal of the American Society for Mass Spectrometry 09/2012; · 4.00 Impact Factor
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Alex G Harrison
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ABSTRACT: The doubly-protonated peptides Ala-Ala-Xaa-Ala-Ala-Ala-Arg show extensive loss of H(2)O when Xaa = Ser or Thr. Using quasi-MS(3) techniques the fragmentation reactions of the [M + 2H - H(2)O](+2) ions have been studied in detail. For both Ser and Thr, the [M + 2H - H(2)O](+2) ions show three primary fragmentation reactions, elimination of CH(3)CH=NH, elimination of one Ala residue, and elimination of two Ala residues, in all cases forming doubly-charged products. From a study of the further fragmentation of these products, it is concluded that elimination of two Ala residues results in formation of a three-membered aziridine ring by interaction with the adjacent amide function as H(2)O is lost. The elimination of one Ala residue results in formation of a five-membered oxazoline ring through interaction with the N-terminal adjacent carbonyl function as H(2)O is lost. The elimination of CH(3)CH=NH appears to involve formation of an eight-membered ring by interaction with the remote N-terminal carbonyl function as H(2)O is lost. However, this initial structure undergoes rearrangement through interaction with the adjacent C-terminal carbonyl function prior to further fragmentation. The [MH - H(2)O](+) ion of Ala-Ala-Ser-Ala-Ala-Ala also shows elimination of CH(3)CH=NH, one Ala residue and two Ala residues.
Journal of the American Society for Mass Spectrometry 11/2011; 23(1):116-23. · 4.00 Impact Factor
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Alex G Harrison
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ABSTRACT: A detailed study has been made of the b(5) and a(5) ions derived from the amides H-Ala-Ala-Ala-Ala-Pro-NH(2), H-Ala-Ala-Ala-Pro-Ala-NH(2), and H-Ala-Ala-Pro-Ala-Ala-NH(2). From quasi-MS(3) experiments it is shown that the product ion mass spectra of the three b(5) ions are essentially identical, indicating macrocyclization/reopening to produce a common mixture of intermediates prior to fragmentation. This is in agreement with numerous recent studies of sequence scrambling in b ions. By contrast, the product ion mass spectra for the a(5) ions show substantial differences, indicating significant differences in the mixture of structures undergoing fragmentation for these three species. The results are interpreted in terms of a mixture of classical substituted iminium ions as well as protonated C-terminal amides formed by cyclization/rearrangement as reported recently for a(4) ions (Bythell, Maître , Paizs, J . Am. Chem. Soc. 2010, 132, 14761-14779). Novel fragment ions observed upon fragmentation of the a(5) ions are protonated H-Pro-NH(2) and H-Pro-Ala-NH(2) which arise by fragmentation of the amides. The observation of these products provides strong experimental evidence for the cyclization/rearrangement reaction to form amides and shows that it also applies to a(5) ions.
Journal of the American Society for Mass Spectrometry 09/2011; 23(4):594-601. · 4.00 Impact Factor
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ABSTRACT: The product ion spectra of proline-containing peptides are commonly dominated by y(n) ions generated by cleavage at the N-terminal side of proline residues. This proline effect is investigated in the current work by collision-induced dissociation (CID) of protonated Ala-Ala-Xxx-Pro-Ala (Xxx includes Ala, Ser, Leu, Val, Phe, and Trp) in an electrospray/quadrupole/time-of-flight (QqTOF) mass spectrometer and by quantum chemical calculations on protonated Ala-Ala-Ala-Pro-Ala. The CID spectra of all investigated peptides show a dominant y(2) ion (Pro-Ala sequence). Our computational results show that the proline effect mainly arises from the particularly low threshold energy for the amide bond cleavage N-terminal to the proline residue, and from the high proton affinity of the proline-containing C-terminal fragment produced by this cleavage. These theoretical results are qualitatively supported by the experimentally observed y(2)/b(3) abundance ratios for protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp). In the post-cleavage phase of fragmentation the N-terminal oxazolone fragment with the Ala-Ala-Xxx sequence and Pro-Ala compete for the ionizing proton for these peptides. As the proton affinity of the oxazolone fragment increases, the y(2)/b(3) abundance ratio decreases.
Journal of the American Society for Mass Spectrometry 06/2011; 22(6):1032-9. · 4.00 Impact Factor
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Alex G Harrison
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ABSTRACT: The product ion mass spectra resulting from collisional activation of doubly-protonated tryptic-type peptides Ala-Ala-Xaa-Ala-Ala-Ala-Arg have been determined for Xaa = Ala(A), Ser(S), Val(V), Thr(T), Ile(I), Phe(F), Tyr(Y), Sar, Met(M), Trp(W), Pro(P), and Gln(Q). The major fragmentation reaction involves cleavage of the second amide bond (counting from the N-terminus) except for Xaa = Ser and Thr where elimination of H(2)O from the [M + 2H](+2) ion forms the base peak. In general, the extent of cleavage of the second amide bond shows little dependence on the identity of Xaa and little dependence on whether the bond cleavage involves symmetrical bond cleavage to form a y(5)/b(2) ion pair or asymmetrically to form y (5) (+2) and a neutral b(2) species. Notable exceptions to this generalization occur for Xaa equal to Pro or Sar. For Xaa = Pro only cleavage of the second amide bond is observed, consistent with a pronounced proline effect, i.e., cleavage N-terminal to Pro. When Xaa = Sar considerably enhanced cleavage of the second amide bond also is observed, suggesting that at least part of the proline effect relates to the tertiary nature of the amide nitrogen. In the competition between symmetric and asymmetric bond cleavage an attempt to establish a linear free energy correlation in relating ln(y(5)(+2)/y(5)) to PA(H-Xaa-OH) did not lead to a reasonable correlation although the trend of increasing y(5)(+2)/y(5) ratio with increasing proton affinity of H-Xaa-OH was clear. Proline showed a unique behavior in giving a much higher y(5)(+2)/y(5) ratio than any of the other residues studied.
Journal of the American Society for Mass Spectrometry 05/2011; 22(5):906-11. · 4.00 Impact Factor
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ABSTRACT: The MS(n) spectra of the [M + H](+) and b(5) peaks derived from the peptides HAAAAA, AHAAAA, AAHAAA, AAAHAA, and AAAAHA have been measured, as have the spectra of the b(4) ions derived from the first four peptides. The MS(2) spectra of the [M + H](+) ions show a substantial series of b(n) ions with enhanced cleavage at the amide bond C-terminal to His and substantial cleavage at the amide bond N-terminal to His (when there are at least two residues N-terminal to the His residue). There is compelling experimental and theoretical evidence for formation of nondirect sequence ions via cyclization/reopening chemistry in the CID spectra of the b ions when the His residue is near the C-terminus. The experimental evidence is less clear for ions when the His residue is near the N-terminus, although this may be due to the use of multiple alanine residues in the peptide making identifying scrambled peaks more difficult. The product ion mass spectra of the b(4) and b(5) ions from these isomeric peptides with cyclically permuted amino acid sequences are similar, but also show clear differences. This indicates less active cyclization/reopening followed by fragmentation of common structures for b(n) ions containing His than for sequences of solely aliphatic residues. Despite more energetically favorable cyclization barriers for the b(5) structures, the b(4) ions experimental data show more clear evidence of cyclization and sequence scrambling before fragmentation. For both b(4) and b(5) the energetically most favored structure is a macrocyclic isomer protonated at the His side chain.
Journal of the American Society for Mass Spectrometry 08/2010; 21(8):1352-63. · 4.00 Impact Factor
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Alex G Harrison
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ABSTRACT: The collision induced dissociation of doubly-protonated (Ala)(x)His (x = 5, 6, 7, 8, 10) peptides have been studied. The major fragmentation reactions observed are symmetrical amide bond cleavages to give the complementary b(m) and y(N-m) ions, where N is the total number of residues in the peptide. Minor asymmetric cleavage to give doubly-protonated y ions also is observed, involving cleavage near the N-terminus. The shorter peptides (x = 5, 6, 7) show major cleavage of the second amide bond to yield b2 and y(N-2) ions, while (Ala)10His shows major symmetrical cleavage at the fourth and fifth amide bonds. (Ala)8His appears to be a transitional peptide in showing substantial symmetrical cleavage at the second, fourth, and fifth amide bonds. The results are in general agreement with the bifurcating nature of charge separation noted by Zubarev (J. Am. Soc. Mass Spectrom.2008, 19, 1755-1763) from a statistical analysis of a large body of doubly-protonated tryptic peptide CID mass spectra. It is shown that the b2 ion derived from doubly-protonated (Ala)5His has a protonated oxazolone structure.
Journal of the American Society for Mass Spectrometry 08/2009; 20(10):1890-5. · 4.00 Impact Factor
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ABSTRACT: When ionized by electrospray from acidic solutions, the tripeptides Pro-His-Xaa (Xaa = Gly, Ala, Leu) form abundant doubly-protonated ions, [M + 2H]2+. Collision-induced dissociation (CID) of these doubly-protonated species results, in part, in formation of b(2)(2+) ions, which fragment further by loss of CO to form a(2)(2+) ions; the latter fragment by loss of CO to form the Pro and His iminium [immonium is commonly used in peptide MS work] ions. Although larger doubly-charged b ions are known, this represents the first detailed study of b(2)(2+) ions in CID of small doubly protonated peptides. The most abundant CID products of the studied doubly-protonated peptides arise mainly in charge separation involving two primary fragmentation channels, formation of the b2/y1 pair and formation of the a1/y2 pair. Combined molecular dynamics and density functional theory calculations are used to gain insight into the structures and fragmentation pathways of doubly-protonated Pro-His-Gly including the energetics of potential protonation sites, backbone cleavages, post-cleavage charge-separation reactions and the isomeric structures of b(2)(2+) ions. Three possible structures are considered for the b(2)(2+) ions: the oxazolone, diketopiperazine, and fused ring isomers. The last is formed by cleavage of the His-Gly amide bond on a pathway that is initiated by nucleophilic attack of one of the His side-chain imidazole nitrogens. Our calculations indicate the b(2)(2+) ion population is dominated by the oxazolone and/or fused ring isomers.
Journal of the American Society for Mass Spectrometry 08/2009; 20(11):2135-43. · 4.00 Impact Factor
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Alex G Harrison
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ABSTRACT: The product ion mass spectra obtained by CID of the b(9) ions derived by loss of neutral alanine from the MH+ ion of the peptides Tyr(Ala)9, (Ala)4Tyr(Ala)5, and (Ala)8TyrAla are essentially identical, indicative of full cyclization reaction to a common intermediate before fragmentation. This leads to abundant nondirect sequence ions in the product ion mass spectra of the b9 ions. The product ion mass spectra of the b8 ions from the first two peptides also are essentially identical. The fragmentation of the MH+ ions also leads to low intensity nondirect sequence ions in the product ion mass spectra. N-terminal acetylation blocks the cyclization and eliminates nondirect sequence fragment ions in the product ion mass spectra.
Journal of the American Society for Mass Spectrometry 08/2009; 20(12):2248-53. · 4.00 Impact Factor
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Alex G Harrison
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ABSTRACT: The fragmentation reactions of b3 ions of nominal structure AAAoxa, YAAoxa, AYAoxa and AAYoxa have been studied as a function of collision energy, allowing the construction of breakdown graphs expressing in a qualitative way the energy dependence of the fragmentation reactions. The primary fragmentation reactions of the AAAoxa b3 ion involve formation of the a3* (a3-NH3) ion and the b2 ion, with the latter becoming the dominant product at higher internal energies. For both YAAoxa and AYAoxa b3 ions the pathway to a3* is relatively minor with formation of b2 the dominant primary fragmentation reaction. For the AAYoxa b3 ion, in addition to a3*, abundant formation of the tyrosine (Y) iminium ion is observed with only minor formation of the b2 ion. The results support and expand upon the detailed mechanism of fragmentation of b3 ions proposed by Cooper et al. (J. Am. Soc. Mass Spectrom. 2006; 17: 1654).
Rapid Communications in Mass Spectrometry 04/2009; 23(9):1298-302. · 2.79 Impact Factor
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Alex G Harrison
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ABSTRACT: Modern soft ionization techniques readily produce protonated or multiply protonated peptides. Collision-induced dissociation (CID) of these protonated species is often used as a method to obtain sequence information. In many cases fragmentation occurs at amide bonds. When the charge resides on the C-terminal fragment so-called y ions are produced which are known to be protonated amino acids or truncated peptides. When the charge resides on the N-terminal fragment so-called b ions are produced. Often the sequence of y and b ions are essential for peptide sequencing. The b ions have many possible structures, a knowledge of which is useful in this sequencing. The structures of b ions are reviewed in the following with particular emphasis on the variation of structure with the number of amino acid residues in the b ion and the effect of peptide side chain on b ion structure. The recent discovery of full cyclization of larger b ions results in challenges in peptide sequencing. This aspect is discussed in detail.
Mass Spectrometry Reviews 04/2009; 28(4):640-54. · 10.46 Impact Factor
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ABSTRACT: The gas-phase structures and fragmentation pathways of the N-terminal b and a fragments of YAGFL-NH(2), AGLFY-NH(2), GFLYA-NH(2), FLYAG-NH(2), and LYAGF-NH(2) were investigated using collision-induced dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. Our combined experimental and theoretical approach allows probing of the scrambling and rearrangement reactions that take place in CID of b and a ions. It is shown that low-energy CID of the b(5) fragments of the above peptides produces nearly the same dissociation patterns. Furthermore, CID of protonated cyclo-(YAGFL) generates the same fragments with nearly identical ion abundances when similar experimental conditions are applied. This suggests that rapid cyclization of the primarily linear b(5) ions takes place and that the CID spectrum is indeed determined by the fragmentation behavior of the cyclic isomer. This can open up at various amide bonds, and its fragmentation behavior can be understood only by assuming a multitude of fragmenting linear structures. Our computational results fully support this cyclization-reopening mechanism by showing that protonated cyclo-(YAGFL) is energetically favored over the linear b(5) isomers. Furthermore, the cyclization-reopening transition structures are energetically less demanding than those of conventional bond-breaking reactions, allowing fast interconversion among the cyclic and linear isomers. This chemistry can lead in principle to complete loss of sequence information upon CID, as documented for the b(5) ion of FLYAG-NH(2). CID of the a(5) ions of the above peptides produces fragment ion distributions that can be explained by assuming b-type scrambling of their parent population and a --> a*-type rearrangement pathways ( Vachet , R. W. , Bishop , B. M. , Erickson , B. W. , and Glish , G. L. J. Am. Chem. Soc. 1997, 119, 5481 ). While a ions easily undergo cyclization, the resulting macrocycle predominantly reopens to regenerate the original linear structure. Computational data indicate that the a --> a*-type rearrangement pathways of the linear a isomers involve post-cleavage proton-bound dimer intermediates in which the fragments reassociate and the originally C-terminal fragment is transferred to the N-terminus.
Journal of the American Chemical Society 01/2009; 130(52):17774-89. · 9.91 Impact Factor
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Alex G Harrison
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ABSTRACT: The CID mass spectra of the MH(+) ions and the b(5) ions derived therefrom have been determined for the hexapeptides YAAAAA, AYAAAA, AAYAAA, AAAYAA, and AAAAYA. The CID mass spectra for the b(5) ions derived from the five isomers are essentially identical and show abundant ion signals for nonsequence b ions. This result is consistent with cyclization of the b(5) ions to a cyclic pentapeptide before fragmentation; this cyclic peptide can open at various positions, leading to losses of amino acid residues that are not characteristic of the original amino acid sequence. These nonsequence b ions are also observed in the fragmentation of the MH(+) ions and increase substantially in importance with increasing collision energy. A comparison of the fragmentation of AAAYAA and Ac-AAAYAA indicates that N-acetylation eliminates the cyclization of b(5) ions and, thus, eliminates the nonsequence ions in the CID mass spectra of both b(5) and MH(+) ions.
Journal of the American Society for Mass Spectrometry 12/2008; 19(12):1776-80. · 4.00 Impact Factor
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ABSTRACT: The fragmentation reactions of the protonated dipeptides Gly-Arg and Arg-Gly have been studied using collision-induced dissociation (CID) in a quadrupole ion trap, by in-source CID in a single-quadrupole mass spectrometer and by CID in the quadrupole cell of a QqTOF mass spectrometer. In agreement with earlier quadrupole ion trap studies (Farrugia, J. M.; O'Hair, R. A. J., Int. J. Mass Spectrom., 2003, 222, 229), the CID mass spectra obtained with the ion trap for the MH(+) ions and major fragment ions are very similar for the two isomers indicating rearrangement to a common structure before fragmentation. In contrast, in-source CID of the MH(+) ions and QqTOF CID of the MH(+), [MH - NH(3)](+) and [MH <23 HN = C(NH(2))(2)](+) ions provide distinctly different spectra for the isomeric dipeptides, indicating that rearrangement to a common structure has not occurred to a significant extent under these conditions even near the threshold for fragmentation in the QqTOF instrument. Clearly, under normal operating conditions significantly different fragmentation behavior is observed in the ion trap and beam-type experiments. This different behavior probably can be attributed to the shorter observation times and concomitant higher excitation energies in the in-source and QqTOF experiments compared to the long observation times and lower excitation energies relevant to the ion trap experiments. Based largely on elemental compositions derived from accurate mass measurements in QqTOF studies fragmentation schemes are proposed for the MH(+), [MH - NH(3)](+), and [MH - (HN = C(NH(2))(2))](+) ions.
Journal of the American Society for Mass Spectrometry 11/2007; 18(11):1959-66. · 4.00 Impact Factor
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ABSTRACT: Collision-induced dissociation (CID) of protonated YAGFL-NH2 leads to nondirect sequence fragment ions that cannot directly be derived from the primary peptide structure. Experimental and theoretical evidence indicate that primary fragmentation of the intact peptide leads to the linear YAGFLoxa b5 ion with a C-terminal oxazolone ring that is attacked by the N-terminal amino group to induce formation of a cyclic peptide b5 isomer. The latter can undergo various proton transfer reactions and opens up to form something other than the YAGFLoxa linear b5 isomer, leading to scrambling of sequence information in the CID of protonated YAGFL-NH2.
Journal of the American Chemical Society 09/2006; 128(32):10364-5. · 9.91 Impact Factor
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Rapid Communications in Mass Spectrometry 02/2006; 20(10):1483-5. · 2.79 Impact Factor
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ABSTRACT: The collision-induced dissociation (CID) fragmentation reactions of a variety of deprotonated peptides containing proline have been studied in detail using MS(2) and MS(3) experiments, deuterium labelling and accurate mass measurements when necessary. The [M--H--CO(2)](-) (a(2)) ion derived from H-Pro-Xxx-OH dipeptides shows an unusual fragmentation involving loss of C(2)H(4); this fragmentation reaction is not observed for larger peptides. The primary fragmentation reactions of deprotonated tripeptides with an N-terminal proline are formation of a(3) and y(1) ions. When proline is in the central position of tripeptides, a(3), y(2) and y(1) ions are the primary fragmentation products of [M--H](-), while when the proline is in the C-terminal position, a(3)and y(1) ions are the major primary products. In the latter case, the a(3) ion fragments primarily to the ''b(2) ion; further evidence is presented that the ''b(2) ions have a deprotonated oxazolone structure. Larger deprotonated peptides having at least two amino acid residues N-terminal to proline show a distinct preference for cleavage of the amide bond N-terminal to proline to form, mainly, the appropriate y ion. This proline effect is compared and contrasted with the similar proline effect observed in the fragmentation of protonated peptides containing proline.
Journal of Mass Spectrometry 10/2005; 40(9):1173-86. · 3.27 Impact Factor
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ABSTRACT: The high-energy collision-induced dissociation (CID) mass spectra of C, C, C, C and C are reported. In all cases, fragmentation occurs by loss of an even number of carbon atoms, in agreement with photodissociation studies of C and C. No charge-separation reactions are observed for the multiply charged ions. Collision-induced dissociation of C leads to a slight preference for formation of C, while dissociation of C and C shows a more pronounced preferenced for formation of C and C, respecstively. Under electron-capture Chemical-ionization conditions the fullerenes readily capture an electron to form the molecular anions. Collision-induced dissociation of C and C leads to elimination of 1, 2 and 4 carbon atoms; the elimination of one carbon is unique among larger carbon cluster ions. Charges inversion of the molecular anions leads to formation of the respective molecular cations and fragementation of these cations by loss of an even number of carbon atoms. Formation of C is slightly preferred in the C case, while C is the most abundant ion in the charge inversion mass spectrum of C.
Rapid Communications in Mass Spectrometry 04/2005; 5(5):226 - 229. · 2.79 Impact Factor
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ABSTRACT: The energy dependence of the fragmentation of a selection of ester enolate ions has been studied by variable, low-energy collision-induced dissociation experiments in the quadrupole collision cell of a hybrid BEQQ mass spectrometer. The dominant fragmentation reactions observed are where ΔH1 − ΔH2=PA([RCCO]−) − PA([ŔO]−) (PA=proton affinity). The anion of lowest proton affinity is formed preferentially at low internal energies with the yield of the anion of higher proton affinity increasing with increasing internal energy. The [CH3OCOCOCH2]− anion derived from methyl pyruvate forms [CH3OCO]− by reaction (2); this anion readily fragments to [CH3G]−+ CO consistent with a structure represented by a dipole-stabilized cluster of [CH3O]− and CO.Comparison of the 8-keV with the 50-eV collision-induced dissociation mass spectra indicated that the average internal energy of the fragmenting ions is considerably lower in the high-energy collisional experiments than it is in the low-energy collisional experiments.
Biological Mass Spectrometry 04/2005; 22(9):622 - 626. · 3.41 Impact Factor
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ABSTRACT: The O−˙ chemical ionization (CI) mass spectra of the mono- to pentafluorobenzenes, fluorotoluenes and fluoroanisoles were measured. For comparison, the O−˙ CI mass spectra of toluene (including deuterium-labelled variants) and anisole were also measured. The major reaction channels of O−˙ with fluorobenzene involve H-atom displacement and H abstraction. With increasing fluoring substitution H+ abstraction increases in importance. For the tri- and tetrafluorobenzenes H abstractions is important only when there are two hydrogen ortho to each other. Reaction channels which are unique to the fluoroaromatic molecules involve the formation of [M + O – HF]−˙, which, for polyfluoro compounds, fragments further by elimination of HF or CO. For the fluoroanisoles, formation of FC6H4O− and elimination of CH2O from [M – H]− and [M – 2H]−˙ are important reaction channels. The formation of [M + O – H]− by reaction of O−. with toluene is shown to involve specific displacement of a ring hydrogen, whereas the formation of [M – H]− involves primarily abstraction of a proton from the methyl group. By contrast, H abstraction is non-specific and proceeds by three pathways: (i) abstraction of two hydrogens from the aromatic ring, (ii) abstraction of two hydrogens from the methyl group and (iii) abstraction of one hydrogen from each position; however, the resuls are not in accord with a random selection of hydrogens.
Biological Mass Spectrometry 04/2005; 28(10):1124 - 1128. · 3.41 Impact Factor
