Dehydration of peptide [M + H]+ ions in the gas phase

The loss of water from protonated peptides was studied using [¹⁸O]-labeling of the C-terminal carboxyl group. The structures (including the location of the isotopic label) of first-generation product ions were examined by sequential product ion scanning (MS³ and MS⁴) using a hybrid sector/quadrupole mass spectrometer. Water loss may involve carboxylic acid groups, side-chain hydroxyls, or peptide backbone oxygens. Although one of these three pathways often predominates, more than one dehydration route can be operative for a single peptide structure. When peptide backbone oxygen is lost, the dehydration can occur at one or two primary sites along the backbone, with the location of the site(s) varying among peptides. When water loss involves the C-terminal carboxyl group, the resulting ion may undergo extensive intraionic oxygen isotope exchange. This evidence for complex intraionic interactions further emphasizes the significance of gas-phase conformation in determining the fragmentations of peptide ions.     

Criteria for distinguishing between [M]+· and [M+H]+ ions in field desorption mass spectra

Ten criteria are introduced to distinguish between molecular ions and protonated parent molecules in field desorption mass spectrometry.     

Electrospray ionization mass spectrometric analysis of microcystins, cyclic heptapeptide hepatotoxins: modulation of charge states and [M+H]+ to [M+Na]+ ratio

Electrospray ionization mass spectrometry was used to develop a rapid, sensitive, and accurate method for determination and identification of hepatotoxic microcystins, cyanobacterial cyclic heptapeptides. To optimize the electrospray ionization conditions, factors affecting charge state distribution, such as amino acid components of sample, proton affinity of the additives, and additive concentration, were investigated in detail and a method for controlling charge states was developed to provide molecular-related ions for assignment of molecular weight and reasonably abundant precursor ions for MS/MS analysis. A procedure for identification of microcystins consisting of known amino acids was proposed: for microcystins giving abundant [M + 2H]2+ ions, the addition of nitrogen-containing bases to the aqueous sample solution is effective to obtain an increased intensity of [M + H]+ ions, whereas the addition of Lewis acids containing nitrogen can produce increased abundances of [M + 2H]2+ ions for microcystins giving weak [M + 2H]2+ ions. Microcystins possessing no arginine residue always give sodium adduct ions [M + Na]+ as the base peak, and these are difficult to fragment via low energy collision-induced dissociation to yield structurally informative products; the addition of oxalic acid increases [M + H]+ ion abundances, and these fragment readily.     

Comparison of intensities between doubly charged ions [M + 2H]2+ and singly charged ions [M + H]+ of gramicidin S by electrospray mass spectrometry.

The reason why the intensity of doubly charged ions [M + 2H]2+ of gramicidin S is higher than that of singly charged ions [M + H]+ in electrospray is investigated by ion evaporation theory. As a result of comparison between the total free energies of extracting [M + 2H]2+ and [M + H]+ from a charged droplet to infinity, it is found that the total free energy of [M + 2H]2+ is estimated to be lower than that of [M + H]+. This clearly supports the experimental result. In addition, the importance of the electrostatic contribution in electrospray is demonstrated by showing the result that the total free energy of [M + 2H]2+ without electrostatic contribution is higher than that of [M + H]+.     

Fragmentation chemistry of [M + Cu]+ peptide ions containing an N-terminal arginine

[M + Cu]+ peptide ions formed by matrix-assisted laser desorption/ionization from direct desorption off a copper sample stage have sufficient internal energy to undergo metastable ion dissociation in a time-of-flight mass spectrometer. On the basis of fragmentation chemistry of peptides containing an N-terminal arginine, we propose the primary Cu+ ion binding site is the N-terminal arginine with Cu+ binding to the guanidine group of arginine and the N-terminal amine. The principal decay products of [M + Cu]+ peptide ions containing an N-terminal arginine are [a(n) + Cu - H]+ and [b(n) + Cu - H]+ fragments. We show evidence to suggest that [a(n) + Cu - H]+ fragment ions are formed by elimination of CO from [b(n) + Cu - H]+ ions and by direct backbone cleavage. We conclude that Cu+ ionizes the peptide by attaching to the N-terminal arginine residue; however, fragmentation occurs remote from the Cu+ ion attachment site involving metal ion promoted deprotonation to generate a new site of protonation. That is, the fragmentation reactions of [M + Cu]+ ions can be described in terms of a "mobile proton" model. Furthermore, proline residues that are adjacent to the N-terminal arginine do not inhibit formation of [b(n) + Cu - H]+ ion, whereas proline residues that are distant to the charge carrying arginine inhibit formation of [b(n) + Cu - H]+ ions. An unusual fragment ion, [c(n) + Cu + H]+, is also observed for peptides containing lysine, glutamine, or asparagine in close proximity to the Cu+ carrying N-terminal arginine. Mechanisms for formation of this fragment ion are also proposed.     

Metastable decomposition of peptide [M + H]+ ions via rearrangement involving loss of the C-terminal amino acid residue

A novel fragmentation of metastable peptide [M + H]⁺ ions is described. Loss of the C-terminal amino acid residue is accomqanied by retention of one of the carboxyl oxygens, as judged by ¹⁸O-labeling. The retained ⁸O label is located at the new C-terminus. Sequential mass spectrometric analyses indicate that the structure of the first-generation product ion is indistinguishable from that of the [M + H]⁺ ion of the peptide with one fewer amino acid residues. Thus, for example, the metastable decompositions of ions of m/z 904 are similar whether they correspond to des-Arg⁹-bradykinin [M + H]⁺ ions or to fragments derived from bradykinin [M + H]⁺ ions. No corresponding rearrangements have been observed for peptides with C-terminal amide or ester functions. The mechanism of this fragmentation may be considered to be analogous to that previously suggested for fragmentations of [M + alkali metal cation]⁺ ions. For the examples of bradykinin and related peptides, the rearrangement is strongly promoted when arginine is the amino acid residue lost. The same fragmentation is also favored by the presence of an arginine residue at or near the N-terminus. The strong influence of peptide amino acid composition, including residues remote from the C-terminus, on the prevalence of this fragmentation suggests mechanistic complexities that require further elucidation.

     

A combined ab initio and photoionization mass spectrometric study of polyynes in fuel-rich flames

Polyynic structures in fuel-rich low-pressure flames are observed using VUV photoionization molecular-beam mass spectrometry. High-level ab initio calculations of ionization energies for C2nH2 (n=1-5) and partially hydrogenated CnH4 (n=7-8) polyynes are compared with photoionization efficiency measurements in flames fuelled by allene, propyne, and cyclopentene. C2nH2 (n=1-5) intermediates are unambiguously identified, while HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH=C=CH2, HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH=CH2 (vinyltriacetylene) and HC[triple bond, length as m-dash]C-C[triple bond, length as m-dash]C-CH[double bond, length as m-dash]CH-C[triple bond, length as m-dash]CH are likely to contribute to the C7H4 and C8H4 signals. Mole fraction profiles as a function of distance from the burner are presented. C7H4 and C8H4 isomers are likely to be formed by reactions of C2H and C4H radicals but other plausible formation pathways are also discussed. Heats of formation and ionization energies of several combustion intermediates have been determined for the first time.     

Collisional activation spectra of [M + Li]+, [M + Na]+ and [M + K]+ ions formed by field desorption of some monosaccharides

The collisional activation spectra of monosaccharide ions formed by [Li]⁺, [Na]⁺ and [K]⁺ ion attachment under field desorption conditions are reported. It is shown that the elimination of the alkali ions is determined by the alkali ion affinities of the molecules (M) and competes with a fragmentation of M which is almost independent of the alkali ion attached. Correspondingly the alkali ion is predominantly retained in the fragment ions. The usefulness of this method for the differentiation of underivatized isomers is demonstrated.     

Electrospray ionization ion trap multiple-stage mass spectrometric fragmentation pathways of leucine and isoleucine: an ab initio computational study

We recently demonstrated the possibility to distinguish between leucine and isoleucine in several tryptic peptides by means of consecutive tandem mass steps (Armirotti et al. J. Am. Soc. Mass Spectrom. 2007; 18: 57), exploiting a gas-phase rearrangement of the immonium ion of Ile. In the present paper we explore the tandem mass spectrometric behaviour of the two amino acids. We propose a plausible structure for the diagnostic m/z 69 ion of Ile, that was reported for the first time in 1996 (Hulst and Kientz J. Mass. Spectrom. 1996; 31: 1188), and we explain why its formation is favoured with respect to Leu. Our conclusions are supported by ab initio quantum chemistry calcultations and isotope-labelled standards experiments.     

FiD: a software for ab initio structural identification of product ions from tandem mass spectrometric data

We present FiD (Fragment iDentificator), a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. Tandem mass spectrometry (MS/MS) has proven to be an indispensable tool in modern, cell-wide metabolomics and fluxomics studies. In such studies, the structural information of the MS(n) product ions is usually needed in the downstream analysis of the measurement data. The manual identification of the structures of MS(n) product ions is, however, a nontrivial task requiring expertise, and calls for computer assistance. Commercial software tools, such as Mass Frontier and ACD/MS Fragmenter, rely on fragmentation rule databases for the identification of MS(n) product ions. FiD, on the other hand, conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well-known fragmentation mechanisms are processed. FiD software implements two fragmentation models, the single-step model that ignores intermediate fragmentation states and the multi-step model, which allows for complex fragmentation pathways. The software works for MS/MS data produced both in positive- and negative-ion modes. The software has an easy-to-use graphical interface with built-in visualization capabilities for structures of product ions and fragmentation pathways. In our experiments involving amino acids and sugar-phosphates, often found, e.g., in the central carbon metabolism of yeasts, FiD software correctly predicted the structures of product ions on average in 85% of the cases. The FiD software is free for academic use and is available for download from www.cs.helsinki.fi/group/sysfys/software/fragid. Copyright (c) 2008 John Wiley & Sons, Ltd.     

Competitive formation of M+˙ and [M + H]+ ions under fast atom bombardment conditions

The competitive formation of molecular ions M^+˙ and protonated molecules [M + H]⁺ under fast atom bombardment (FAB) conditions was examined using various kinds of organic compounds. The use of protic/hydrophilic matrices such as thioglycerol and glycerol resulted in relatively large values of the peak intensity ratio I([M + H]⁺)/I(M^+˙) compared with the use of relatively aprotic/hydrophobic matrices such as m-nitrobenzyl alcohol and o-nitrophenyl octyl ether. The change of matrix from thiol-containing such as thioglycerol and dithiothreitol to alcoholic such as glycerol and pentamethylene glycol increased the I([M + H]⁺)/I(M^+˙) ratio. Furthermore, the change of matrix increased the peak intensity ratio of the doubly charged ion [M + 2H]²⁺ to [M + H]⁺ in the FAB mass spectra of angiotensin I and gramicidin S. The addition of acids to the matrix solution increased the I([M + H]⁺)/I(M^+˙) ratio, although such an effect did not always occur. The acetylation of simple aniline compounds markedly increased the I([M + H]⁺)/I(M^+˙) ratio. It was concluded from these results that the hydrogen bonding interaction between hydroxyl groups(s) of the matrix and basic site(s) of analyte molecules in solution acts advantageously as a quasi-preformed state for [M + H]⁺ formation, and that the presence of significant proton acceptor(s) such as carbonyl group in analytes hinder the M^+˙ formation which may generally occur under FAB conditions. The formation of M^+˙ and [M + H]⁺ ions seemed to occur competitively, reflecting or according to the interaction or solvation states between the analyte and matrix molecules in solution and the structural characteristics of the analytes.     

Collisional activation mass spectra of [C6H8]+ ions

Collisional activation spectra and isotopic labeling indicate that for [C₆H₈]⁺ ions at least six stable isomers can be formed from a variety of precursors.     

Competing pathways in the [2 + 2] cycloadditions of cyclopentyne and benzyne. A DFT and ab initio study

The [2 + 2] cycloadditions of cyclopentyne and benzyne to ethylene are explored at the B3LYP and CASSCF levels, supplemented by CCSD(T) and CAS-MP2 calculations at the stationary points. The biradical path in the benzyne system is computed to be about 4.1 kcal/mol lower than the concerted path, consistent with the experimentally observed loss of original stereochemistry in this cycloaddition. However, computations fail to confirm the 99% stereoretention in the corresponding reaction of cyclopentyne. The concerted and biradical paths in the latter reaction are found to involve nearly isoenergetic barriers, thus predicting only about 75% stereoretention. More sophisticated theoretical methods seem to be needed to resolve the issue in the cyclopentyne system.     

Electron impact mass spectrometry of [C7H8N]+ and [C6H7]+ and [C6H7]+ fragment ions produced from o-toluidine and N-methylaniline

An energetic study of the production of [C₇H₈N]⁺ and [C₆H₇]⁺ fragment ions from o-toluidine and N-methylaniline is reported. The mechanisms for the formation of the ions are suggested. Metastable peaks associated with the formation and fragmentation of reactive [C₇H₈N]⁺ and [C₆H₇]⁺ ions were detected and kinetic energy released were determined. The results indicate that the [C₇H₈N]⁺ ion is formed at threshold from o-toluidine with an aminotropylium structure whereas for N-methylaniline the ion is formed with anN-phenylmethaniminium structure. [C₆H₇]⁺ ions are believed to be formed at threshold from the two precursors with a protonated benzene structure.     

A photoionization study of [C4H7]+ ions in the gas phase

The ionization and [C₄H₇]⁺ appearance energies for a series of C₄H₇CI and C₄H₇Br isomers have been measured by dissociative photoionization mass spectrometry. Cationic heats of formation, based on the stationary electron convention, are derived. No threshold ion is observed with a heat of formation corresponding to the trans-1-methylallyl cation, although there is evidence for formation of the less stable cis isomer. A 298 K heat of formation of 871 kJ mol^?1 is obtained for the cyclopropylcarbinyl cation, with the cyclobutyl cation having a higher value of 886 kJ mol^?1. At the HF/6-31G^** level, ab initio molecular orbital calculations show the 2-butenyl, isobutenyl and homoallyl cations to be stable forms of [C₄H₇]⁺, being less stable than the trans-1-methylallyl cation by 101 kJ mol^?1, 159 kJ mol^?1 and 164 kJ mol^?1, respectively. However, threshold formation is not observed for any of these ions, the fragmentation of appropriate precursor molecules producing [C₄H₇]⁺ ions with lower energy structures.     

A mass spectrometry/mass spectrometry investigation of the nature of [C10H10]+˙, [C9H7]+ and [C10H8]+˙ gas phase ions

Additional evidence for the rearrangement of the 1- and 3-phenylcyclobutene radical cations, their corresponding ring-opened 1,3-butadiene ions and 1,2-dihydronaphthalene radical cations to methylindenetype ions has been obtained for the decomposing ions by mass analysed ion kinetic energy spectroscopy (MIKES). The nature of the [C₉H₇]⁺ and [C₁₀H₈]^+˙ daughter ions arising from the electron ionization induced fragmentation of these [C₁₀H₁₀]^+˙ precursors has been investigated by collisionally activated dissociation (CAD), collisional ionization and ion kinetic energy spectroscopy. The [C₉H₇]⁺ produced from the various C₁₀H₁₀ hydrocarbons are of identical structure or an identical mixture of interconverting structures. These ions are similar in nature to the [C₉H₇]⁺ generated from indene by low energy electron ionization. The [C₁₀H₈]^+˙ ions also possess a common structure, which is presumably that of the maphthalene radical cation.     

SOS: A simple interactive program for ab initio oligonucleotide sequencing by mass spectrometry

Mass spectra of oligonucleotides derived from collision-induced dissociation following electrospray ionization provide an effective means of sequence determination, at the 20-mer level and below. An interactive, stand-alone computer program, Simple Oligonucleotide Sequencer (SOS) has been developed for rapid oligonucleotide sequencing from mass spectra, under user control on a residue by residue basis. Modifications can be defined in any combination for the base, sugar or backbone. Sequence ladders can be independently constructed in both the 5' --> 3' directions and 3' --> 5' directions, and graphically compared for homology and overlap. A particular advantage of this method is the ability to easily erase and rebuild alternate subsequences. The program can be used for ab initio sequencing of modified or unmodified oligonucleotides, for rapid verification of sequence, and in studies of fragmentation processes of model oligonucleotide derivatives.