Electrospray low energy CID and MALDI PSD fragmentations of protonated sulfinamide cross-linked peptides

Murine S100A8 (A8) is a major cytoplasmic neutrophil protein and is converted to novel oxidation products containing Cys-epsilon amino-Lys sulfinamide cross-links and Met-sulfoxide by the neutrophil oxidant HOCl. Seven products were separated using RP-HPLC, with electrospray ionization mass spectrometry (ESI-MS) masses after deconvolution of 10,354, 10,388, +/- 1, and 20,707, +/- 3 Da, and all were resistant to reduction by dithiothreitol. The major products with masses of 10,354 Da contained Cys41-Lys34/35 intramolecular cross-links. Additional isomeric products with identical masses (10,354 Da) were isolated and peptide mapping and ESI/MS indicated that Cys41 forms covalent sulfinamide cross-links with either Lys6, Lys76, Lys83, or Lys87 present in A8. Electrospray low energy collisionally induced (CID) spectra of multiply-charged AspN digest peptides with sulfinamide cross-links contained characteristic fragmentations that corresponded to simple cleavage of the nitrogen-sulfur bond with charge retention on either of the fragment ions, allowing conformation of cross-linked peptides. Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) post source decay spectra of [M + H] + ions of the same sulfinamide-containing cross-linked peptides fragment similarly, but additional facile fragmentation reactions corresponding to formation of a protonated peptide containing de-hydroalanine were attributed to cleavage of the carbon-sulfur bond. In addition, lose of methanesulfenic acid from Met-sulfoxide was observed. A sulfinamide-containing adduct was isolated after incubation of the A8/HOCl reaction mixture with Lys or alpha N-acetyl Lys with masses of 10,500 or 10,542 Da. ESI/MS/MS and MALDI/post decay source (PSD) analysis of A8(32)-(57)-sulfinamide showed the same characteristic fragmentations as those in the sulfinamide cross-linked peptides, confirming the Cys41-Lys sulfinamide cross-link and suggesting that peptide-peptide sulfinamides may all fragment similarly, allowing ready identification of these cross-links in proteins from more complex biological materials.     

Spontaneous fragmentations of protonated benzaldimines mediated by intermediate ion-neutral complexes

4-Methoxymethylbenzaldimmonium ions (a) and the corresponding N-methylated ions (b) and N,N-dimethylated ions (c) were easily generated in the ion source by electron impact-induced dissociation from 1-(4-methoxymethylphenyl)ethylamine and its N-methylated derivatives. The spontaneous fragmentations of metastable ions a-c and of specifically deuterated derivatives in the second field-free region of a VG ZAB-2F mass spectrometer were studied by mass-analysed ion kinetic energy Spectrometry. The formation of an amino-p-quinodimethane radical cation by loss of the methoxy group is observed for all ions. In the case of a and b carrying at least one proton at the immonium group, competing fragmentations are the loss of CH₂O and CH₃OH, respectively, and the formation of ions CH₃OCH₂ ⁺, m/z 45, and C₇H₇ ⁺, m/z 91. Deuterium-labelling experiments indicated the migration of a proton from the protonated imino group of a and b to the aromatic ring followed by the loss of methanol from the methoxymethyl side-chain or protolysis of the bond to either side-chain to form ion-neutral complexes, in close analogy with the reactions of the corresponding protonated benzaldehydes. The intermediate ion-neutral complexes dissociate eventually by internal ion-neutral reactions resulting in the loss of CH₂ O and the formation of C₇H₇ ⁺, respectively.     

Secondary hydrogen-deuterium isotope effects on electron impact induced fragmentations

Secondary hydrogen-deuterium isotope effects have been observed in the mass spectra of cis-4-t-butylcyclohexyl iodide, 5-iodononane and 2-iodopropane. Under conditions which suppress competing and second generation fragmentations, β-deuterium substitution decreases the intensity ratio \documentclass{article}\pagestyle{empty}\begin{document}$ ([{\rm M} - {\rm I]}^{\rm + } /[{\rm M]}^{\mathop + \limits_ \cdot } ) $\end{document}, a result analogous to a normal isotope effect. The decrease is larger in the spectrum of cis-4-t-butylcyclohexyl iodide-trans-2-d than in the spectrum of the cis-2-d derivative. Since these effects parallel those in the better understood solvolysis reaction, both effects may have a common origin. In contrast, deuteration of more remote positions in cis-4-t-butylcyclohexyl iodide and 5-iodononane increases the indicated intensity ratio, an apparent inverse isotope effect. Although similar effects have been observed in solvolysis reactions, the mass spectral effect may be attributable to an increase in the nonfixed energy available for fragmentation. These results suggest that secondary isotope effects can be readily measured in certain cases, and that they may eventually become useful probes into the mechanisms of mass spectral fragmentations.     

Rearrangements in the electron impact induced fragmentations of sulfonyl chlorides

The major fragmentation pattern obsrved in the mass spectra of simple alkane- and arylsulfonyl chlorides may be rationalized by loss of a chlorine atom from the molecular ion, followed by loss of SO₂ with concomitant carbocation formation. The mass spectra of α-mesyl sulfonyl chlorides and napthalenesulfonyl chlorides exhibit ions resulting from chlorine atom migration to the α-carbon atom with concomitant loss of SO₂. The mass spectra of α-mesyl sulfonyl chlorides also show ions which involve chlorine atom migration to the β-sulfonyl group.     

Theoretical studies of damage to 3'-uridine monophosphate induced by electron attachment

Low-energy electrons (LEE) are well known to induce nucleic acid damage. However, the damage mechanisms related to charge state and structural features remain to be explored in detail. In the present work, we have investigated the N1-glycosidic and C3'-O(P) bond ruptures of 3'-UMP (UMP=uridine monophosphate) and the protonated form 3'-UMPH with -1 and zero charge, respectively, based on hybrid density functional theory (DFT) B3 LYP together with the 6-31+G(d,p) basis set. The glycosidic bond breakage reactions of the 3'UMP and 3'UMPH electron adducts are exothermic in both cases, with barrier heights of 19-20 kcal mol(-1) upon inclusion of bulk solvation. The effects of the charge state on the phosphate group are marginal, but the C2'-OH group destabilizes the transition structure of glycosidic bond rupture of 3'-UMPH in the gas phase by approximately 5.0 kcal mol(-1). This is in contrast with the C3'-O(P) bond ruptures induced by LEE in which the charge state on the phosphate influences the barrier heights and reaction energies considerably. The barrier towards C3'-O(P) bond dissociation in the 3'UMP electron adduct is higher in the gas phase than the one corresponding to glycosidic bond rupture and is dramatically influenced by the C2'-OH group and bulk salvation, which decreases the barrier to 14.7 kcal mol(-1). For the C3'-O(P) bond rupture of the 3'UMPH electron adduct, the reaction is exothermic and the barrier is even lower, 8.2 kcal mol(-1), which is in agreement with recent results for 3'-dTMPH and 5'-dTMPH (dTMPH=deoxythymidine monophosphate). Both the Mulliken atomic charges and unpaired-spin distribution play significant roles in the reactions.     

Barrier-free intermolecular proton transfer induced by excess electron attachment to the complex of alanine with uracil

The photoelectron spectrum of the uracil-alanine anionic complex (UA)(-) has been recorded with 2.540 eV photons. This spectrum reveals a broad feature with a maximum between 1.6 and 2.1 eV. The vertical electron detachment energy is too large to be attributed to an (UA)(-) anionic complex in which an intact uracil anion is solvated by alanine, or vice versa. The neutral and anionic complexes of uracil and alanine were studied at the B3LYP and second-order M?ller-Plesset level of theory with 6-31++G(*) (*) basis sets. The neutral complexes form cyclic hydrogen bonds and the three most stable neutral complexes are bound by 0.72, 0.61, and 0.57 eV. The electron hole in complexes of uracil with alanine is localized on uracil, but the formation of a complex with alanine strongly modulates the vertical ionization energy of uracil. The theoretical results indicate that the excess electron in (UA)(-) occupies a pi(*) orbital localized on uracil. The excess electron attachment to the complex can induce a barrier-free proton transfer (BFPT) from the carboxylic group of alanine to the O8 atom of uracil. As a result, the four most stable structures of the uracil-alanine anionic complex can be characterized as a neutral radical of hydrogenated uracil solvated by a deprotonated alanine. Our current results for the anionic complex of uracil with alanine are similar to our previous results for the anion of uracil with glycine, and together they indicate that the BFPT process is not very sensitive to the nature of the amino acid's hydrophobic residual group. The BFPT to the O8 atom of uracil may be relevant to the damage suffered by nucleic acid bases due to exposure to low energy electrons.     

Sequential hydration of small protonated peptides

The sequential addition of water molecules to a series of small protonated peptides was studied by equilibrium experiments using electrospray ionization combined with drift cell techniques. The experimental data were compared to theoretical structures of selected hydrated species obtained by molecular mechanics simulations. The sequential water binding energies were measured to be of the order of 7-15 kcal/mol, with the largest values for the first water molecule adding to either a small nonarginine containing peptide (e.g., protonated dialanine) or to a larger peptide in a high charge state (e.g., triply protonated neurotensin). General trends are (a) that the first water molecules are more strongly bound than the following water molecules, (b) that very small peptides (2-3 residues) bind the first few water molecules more strongly than larger peptides, (c) that the first few water molecules bind more strongly to higher charge states than to lower charge states, and (d) that water binds less strongly to a protonated guanidino group (arginine containing peptides) than to a protonated amino group. Experimental differential entropies of hydration were found to be of the order of -20 cal/mol/K although values vary from system to system. At constant experimental conditions the number of water molecules adding to any peptide ion is strongly dependent on the peptide charge state (with higher charge states adding proportionally more water molecules) and only weakly dependent on the choice of peptide. For small peptides molecular mechanics calculations indicate that the first few water molecules add preferentially to the site of protonation until a complete solvation shell is formed around the charge. Subsequent water molecules add either to water molecules of the first solvation shell or add to charge remote functional groups of the peptide. In larger peptides, charge remote sites generally compete more effectively with charge proximate sites even for the first few water molecules.     

Collision-induced reporter fragmentations for identification of covalently modified peptides

Collision-induced reporter fragmentations of the currently most important covalent peptide modifications as detected by tandem mass spectrometry are summarized. These fragmentations comprise the formation of reporter ions, which are preferentially immonium ions, immonium ion-derived fragments or side chain fragments. In addition, the reporter neutral loss reactions for covalently modified amino acid residues are summarized. For each individual covalent modification which can be recognized by a reporter fragmentation, the accurate mass shift and the gross formula shift of the modified amino acid residue are given. The same set of data is provided for the reporter fragmentations. Finally, an extensive accurate mass and gross formula list is presented as supplementary material, describing mostly regular and modified y₁ and dipeptide a and b ions, which are helpful for identification of the peptide ends of covalently modified peptides. Figure When modified peptides are fragmented by collision-induced dissociation in a tandem mass spectrometer, the modification is either lost as part of a charged fragment, so that a reporter ion for the modification is generated or it is lost as part of a neutral fragment, so that a modification-specific reporter neutral loss is observed in the fragment ion spectrum. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Chien-Wen Hung and Andreas Schlosser contributed equally to this work.     

Dissociative electron attachment to triflates

Gas phase studies of dissociative electron attachment to simple alkyl (CF(3)SO(3)CH(3)) and aryl (C(6)H(5)SO(3)CF(3) and CF(3)SO(3)C(6)H(4)CH(3)) triflates, model molecules of nonionic photoacid generators for modern lithographic applications, were performed. The fragmentation pathways under electron impact below 10 eV were identified by means of crossed electron-molecular beam mass spectrometry. Major dissociation channels involved C-O, S-O, or C-S bond scissions in the triflate moiety leading to the formation of triflate (OTf(-)), triflyl (Tf(-)), or sulfonate (RSO(3)(-)) anions, respectively. A resonance leading to C-O bond breakage and OTf(-) formation in alkyl triflates occurred at electron energies about 0.5 eV lower than the corresponding resonance in aryl triflates. A resonance leading to S-O bond breakage and Tf(-) formation in aryl triflates occurred surprisingly at the same electron energies as C-O bond breakage. In case of alkyl triflates S-O bond breakage required 1.4 eV higher electron energies to occur and proceeded with substantially lower yields than in aryl triflates. C-S bond scission occurred for all presently studied triflates at energies close to 3 eV.     

The electron impact induced fragmentations of some 7-alkyl-3-oxabicyclo[3.3.1]nonanes

The mass spectra of a series of 7-alkyl substituted 3-oxabicyclo[3.3.1]nonanes are recorded. The fragmentation has been studied by the use of the metastable DADI and defocussing techniques. The character of the alkyl group is found to influence the fragmentation pattern. Stereoselective fragmentations for the 7-t-butyl derivatives are observed. In the endo-isomer, in contrast to the exo-isomer, a transannular hydrogen transfer plays a role.     

Remote fragmentations of protonated aromatic carbonyl compounds via internal reactions in intermediary ion-neutral complexes

Protonated aromatic aldehydes and methyl ketones 1a–10a, carrying initially the proton at the carbonyl group, are prepared by electron impact-induced loss of a methyl radical from 1?arylethanols and 2?aryl?2?propanols, respectively. The aryl moiety of the ions corresponds to a benzene group, a naphthalene group, a phenanthrene group, a biphenyl group, and a terphenyl group. respectively, each substituted by a CH₃OCH₂ side-chain as remote from the acyl substituent as possible. The characteristic reactions of the metastable ions, studied by mass-analyzed ion kinetic energy spectrometry, are the elimination of methanol, the formation of CH₃OCH ₂ ⁺ ions, and the elimination of an ester RCOOCH₃ (R = H and CH₃) . The mechanisms of these fragmentations were studied by using D-labeled derivatives. Confirming earlier results, it is shown that the ester elimination, at least from the protonated aryl methyl ketones, has to proceed by an intermediate [acyl cation/arylmethyl methyl ether]-complex. The relative abundances of the elimination of methanol and of the ester decrease and increase, respectively, with the size of the aromatic system. Clearly, the fragmentation via intermediate ion-neutral complexes is favored for the larger ions. Furthermore, the acyl cation of these complexes can move unrestricted over quite large molecular distances to react with the remote CH₃OCH₂-side-chain, contrasting the restricted migration of a proton by 1,2-shifts (“ring walk”) in these systems.     

Dissociative electron attachment to gas-phase formamide

Dissociative electron attachment (DEA) to gaseous formamide, HCONH(2), has been investigated in the energy range between 0 eV and 18 eV using a crossed electron/molecule beam technique. The negative ion fragments have been comprehensively monitored and assigned to molecular structures by comparison with the results for two differently deuterated derivatives, namely 1D-formamide, DCONH(2), and N,N,D-formamide, HCOND(2). The following products were observed: HCONH(-), CONH(2)(-), HCON(-), OCN(-), HCNH(-), CN(-), NH(2)(-)/O(-), NH(-), and H(-). NH(2)(-) was also separated from O(-) by using high-resolution negative ion mass spectrometry. Four resonant dissociation channels can be resolved, the strongest ones being located between 2.0 and 2.7 eV and between 6.0 and 7.0 eV. CN(-) as the most abundant fragment and HCONH(-) are the dominant products of the first of these two resonances. The most important products of the latter resonance are NH(2)(-), CN(-), H(-), CONH(2)(-), and OCN(-). It is thus found that the loss of neutral H is a site-selective process, dissociation from the N site taking place between 2.0 and 2.7 eV while dissociation from the C site occurs between 6.0 and 7.0 eV. The suitability of these reactions and thus of formamide as an agent for electron-induced surface functionalisation is discussed.     

Dissociative electron attachment to NO probed by velocity map imaging

An experimental and theoretical investigation of the dissociative electron attachment process in nitric oxide is presented. Measurements using the recently developed ion momentum imaging conclusively show the presence of two resonance features in the O(-) channel. These are found to dissociate to give N atoms in the (2)D and (2)P excited states respectively, thus settling the controversies regarding the possible dissociation limits of this process. Though the angular distribution of O(-) shows the resonances contributing to these dissociations are of Π symmetry and a mixture of Π and Σ or Δ symmetry respectively, our calculations using R-matrix theory show no direct electron attachment channel leading to O(-) through these resonances, as all the allowed resonances below 10 eV decay to either O + N(-) or O(-) + N((4)S) channels. We propose that indirect mechanisms through curve crossings lead to the experimentally observed results.     

Dissociative electron attachment to gas-phase glycine

By using a high-resolution electron energy monochromator low-energy electron attachment to gas-phase glycine (H₂NCH₂COOH, or G) has been studied by means of mass spectrometric detection of the product anions. In the same way as for several other biologically relevant molecules no stable parent anion was formed by free electron attachment. The largest dissociative electron attachment (DEA) cross-section, approximately 5×10^–20 m², was observed for (G–H)^–+H at an electron energy of 1.25 eV. Glycine and formic acid (HCOOH) have several common features, because a precursor ion can be characterized by electron attachment to the unoccupied * orbital of the –COOH group. At higher incident electron energies several smaller fragment anions are formed. Except for H^–, which could not be observed in this study, there was good agreement with an earlier investigation by Gohlke et al.     

Dissociative electron attachment to abasic DNA

Thin films of the short single DNA strand, GCAT, in which one of the bases has been removed were bombarded with 3 to 15 eV electrons. The yield functions of the H(-), O(-) and OH(-) ions desorbed from these films exhibit a broad peak near 9 eV, which is attributed to dissociative electron attachment to the basic molecules. Whereas removal of any one of the bases considerably decreases N-glycosidic and backbone C-O bond scission, the creation of basic sites does not appreciably modify bond rupture leading to anion electron stimulated desorption. These seemingly contradictory results make it possible to propose a detailed mechanism leading to the transfer of electrons in the range 5-13 eV within DNA.     

Dissociate electron attachment to monohalogenated benzenes

Formation of halogen negative ions by dissociative electron attachment on the halobenzenes C₆H₅Br, C₆H₅Cl and C₆H₅F is studied as a function of incident electron energy up to 7.5 eV by mass spectrometry. The threshold energies for Cl⁻ and Br⁻ provide a determination of the first electron affinities for C₆H₅Cl and C₆H₅Br. The absolute cross section for Ci⁻ formation from C₆H₅Cl was also measured.     

The fragmentations of substituted cinnamic acids after electron impact

The fragmentations of a number of cinnamic acids substituted at the phenyl ring have been studied with the aid of 70 eV mass spectra and mass analysed ion kinetic energy spectra. Evidence is presented that the formation of [C₉H₇O₂]⁺ ions occurs by intramolecular aromatic substitution reactions. A mechanism is proposed for the energetically favourable loss of the substituents from meta and para positions of the phenyl ring. The analytical use of intramolecular aromatic substitution reactions is briefly discussed.     

Dissociation of the peptide bond in protonated peptides

The dissociation of the amide (peptide) bond in protonated peptides, [M + H](+), is discussed in terms of the structures and energetics of the resulting N-terminal b(n) and C-terminal y(n) sequence ions. The combined data provide strong evidence that dissociation proceeds with no reverse barriers through interconverting proton-bound complexes between the segments emerging upon cleavage of the protonated peptide bond. These complexes contain the C-terminal part as a smaller linear peptide (amino acid if one residue) and the N-terminal part either as an oxazolone or a cyclic peptide (cyclic amide if one residue). Owing to the higher thermodynamic stability but substantially lower gas-phase basicity of cyclic peptides vs isomeric oxazolones, the N-terminus is cleaved as a protonated oxazolone when ionic (b(n) series) but as a cyclic peptide when neutral (accompanying the C-terminal y(n) series). It is demonstrated that free energy correlations can be used to derive thermochemical data about sequence ions. In this context, the dependence of the logarithm of the abundance ratio log[y(1)/b(2)], from protonated GGX (G, glycine; X, varying amino acid) on the gas-phase basicity of X is used to obtain a first experimental estimate of the gas-phase basicity of the simplest b-type oxazolone, viz. 2-aminomethyl-5-oxazolone (b(2) ion with two glycyl residues).     

Length effects in VUV photofragmentation of protonated peptides

We have studied photoionization of protonated synthetic peptides YG(n)F (n = 0, 1, 3, 5, 10). Photon energies ranging from 8 to 30 eV were used. For YG(n)F peptides up to n = 5 small fragment ions related to the sidechains of the aromatic terminal amino acids Y and F dominate the fragmentation patterns. The associated yields scale with total photoabsorption cross section, demonstrating efficient hole migration towards the terminal amino acids upon photoionization of the peptide backbone. For n = 10 the side-chain loss channel is quenched and a series of large dications appear.