Mass spectral fragmentation pathways in nitramines. A collision-induced dissociation study

A collision-induced dissociation (CID) study of five synthesized nitramines was carried out using a hybrid EBQQ mass spectrometer. CID spectra were obtained in two modes: B/E linked-scan mode and MS/MS mode using the EB sector combination as the first mass spectrometer and the QQ as collision cell and second mass spectrometer, respectively. Fragmentation pathways of the compounds were determined in the electron-impact mode. It was found that dominant fragmentation pathways included the loss of OH, NO₂ and HNO₂ in addition to the loss of CH₂NNO and CH₂NNO₂.     

Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides

We have broadened the utility of the SEQUEST computer algorithms to permit correlation of uninterpreted high-energy collision-induced dissociation spectra of peptides with all sequences in a database. SEQUEST now allows for the additional fragment ion types observed under high-energy conditions. We analyzed spectra from peptides isolated following trypsin digestion of 13 proteins. SEQUEST ranked the correct sequence first for 90% (18/20) of the spectra in searches of the OWL database, without constraint by enzyme cleavage specificity or species of origin. All false-positives were flagged by the scoring system. SEQUEST searches databases for sequences that correspond to the precursor ion mass ±0.5 u. Preliminary ranking of the top 500 candidates is done by calculation of fragment ion masses for each sequence, and comparison to the measured ion masses on the basis of ion series continuity, summed ion intensity, and immonium ion presence. Final ranking is done by construction of model spectra for the 500 candidates and constructing/performing of a cross-correlation analysis with the actual spectrum. Given the need to relate mounting genome sequence information with corresponding suites of proteins that comprise the cellular molecular machinery, tandem mass spectrometry appears destined to play the leading role in accelerating protein identification on the large scale required.     

Low-mass ions produced from peptides by high-energy collision-induced dissociation in tandem mass spectrometry

High-energy collision-induced dissociation (CID) mass spectrometry provides a rapid and sensitive means for determining the primary sequence of peptides. The low-mass region (below mass 300) of a large number of tandem CID spectra of peptides has been analyzed. This mass region contains several types of informative fragment ions, including dipeptide ions, immonium ions, and other related ions. Useful low-mass ions are also present in negative-ion CID spectra. Immonium ions (general structure [H₂N=CH-R]⁺, where R is the amino acid side chain) and related ions characteristic of specific amino acid residues give information as to the presence or absence of these residues in the peptide being analyzed. Tables of observed immonium and reiated ions for the 20 standard amino acids and for a number of modified amino acids are presented. A database consisting of 228 high-energy CID spectra of peptides has been established, and the frequency of occurrence of various ions indicative of specific ammo acid residues has been determined. Two model computer-aided schemes for analysis of the ammo-acid content of unknown peptides have been developed and tested against the database.     

Charge-remote fragmentation of taurine-conjugated bile acids

Taurine-conjugated bile acids are an important group of biological metabolites. When investigated by negative-ion fast-atom bombardment collision-induced dissociation mass spectroscopy they show charge-remote fragmentations of the [M-H]- pseudomolecular ion. These fragmentations provide information on the positions of ring substituents remote from the charge site. In the present work we have compared the negative-ion fast-atom bombardment collision-induced dissociation spectra of six different conjugated bile acids.     

Peptide sequence determination from high-energy collision-induced dissociation spectra using artificial neural networks

This paper reports a newly developed technique that uses artificial neural networks to aid in the automated interpretation of peptide sequence from high-energy collision-induced dissociation (CID) tandem mass spectra of peptides. Two artificial neural networks classify fragment ions before the commencement of an iterative sequencing algorithm. The first neural network provides an estimation of whether fragment ions belong to 1 of 11 specific categories, whereas the second network attempts to determine to which category each ion belongs. Based upon numerical results from the two networks, the program generates an idealized spectrum that contains only a single ion type. From this simplified spectrum, the program’s sequencing module, which incorporates a small rule base of fragmentation knowledge, directly generates sequences in a stepwise fashion through a high-speed iterative process. The results with this prototype algorithm, in which the neural networks were trained on a set of reference spectra, suggest that this method is a viable approach to rapid computer interpretation of peptide CID spectra.     

Rapid sequencing of a peptide containing a single disulfide bond using high-energy collision-induced dissociation

A peptide containing a single disulfide bond was sequenced using high-energy collision-induced dissociation (HE-CID) in conjunction with a high mass resolution time-of-flight tandem mass spectrometer equipped with a matrix-assisted laser desorption/ionization source. This mass spectrometer, which has spiral ion trajectory, allowed both high mass resolution and high precursor ion selectivity. It is difficult to obtain sufficient product ions from peptides containing disulfide bonds using HE-CID due to the single collision in the gas phase. To compensate for insufficient dissociation, the disulfide bond was cleaved via an in-source reduction process using 1,5-diaminonaphthalene, a reducing matrix. After applying the reduction in the ionization, subsequent sequencing using HE-CID provided the detailed structural information of the peptide containing the single disulfide bond.     

Charge-remote and charge-proximate fragmentation processes in alkali-cationized fatty acid esters upon high-energy collisional activation. A new mechanistic proposal

The effect of the metal ion on the high-energy collision-induced dissociation (CID) of alkali metal-cationized n-butyl and methyl ester derivatives of palmitic and oleic acid was examined. The results show that the alkali metal ion has a pronounced effect and does not act as a mere ‘spectator’ ion with respect to the fragmentation process. While C–H cleavage is a dominant process for [M+Li]⁺ as well as [M+Na]⁺ precursor ions, C–C cleavage is also significant for the [M+Na]⁺ ions. Homolytic mechanisms involving the formation of a transient biradical cation are proposed which enable us to rationalize in a straightforward manner all product ions formed by both charge-remote and charge-proximate fragmentations. The mechanistic proposal is discussed in view of available knowledge on electron impact, CID and related processes. In order to predict how the alkali metal ion could affect the reactivity of the postulated biradical state formed following electronic excitation of the alkali metal-cationized molecules, quantum chemical calculations were performed on methyl and n-butyl acetate as model substances. The decreased spin density at the carbonyl oxygen atom in the biradical state may provide an explanation for the greater tendency towards C–C cleavage reactions of the sodium-cationized fatty acid esters relative to the corresponding lithium complexes. © 1988 John Wiley & Sons, Ltd.     

Bounday trajectories in collision-induced dissociation

The boundary trajectories separating non-reactive, reactive, and dissociative bands of trajectories in atom—diatom collision-induced dissociation are defined. Trajectory calculations are reported for the collinear H + H₂ reaction which demonstrate how the boundary trajectories can be used to obtained information on the non-reactive, reactive, and dissociative regions of the reagents phase space.     

Mass spectral fragmentation pathways in phthalate esters. A tandem mass spectrometric collision-induced dissociation study

A collision-induced dissociation study of a series of phthalate esters was carried out using a tandem BB mass spectrometer. Fragmentation pathways of the phthalates were determined in the electron impact mode. Two major daughter ions are formed, one by a McLafferty rearrangement and hydrogen transfer and the other by loss of an alkoxy radical Another major daughter ion, at m/z 149—which is the base peak in the electron impact mass spectra of most phthalate esters—is being formed through four alternate pathways.     

Studies on high-energy collision-induced dissociation of endogenous cannabinoids: 2-arachidonoylglycerol and n-arachidonoylethanolamide in FAB-mass spectrometry.

Analysis of 2-arachidonoylglycerol (2-AG) and N-arachidonoylethanolamide (anandamide) via alkali or alkaline earth metal-adduct high-energy collision-induced dissociation (CID) in fast-atom bombardment (FAB) ionization-mass spectrometry (MS) is described. The CID-MS/MS of the [2-AG+Li](+) or [2-AG+Na](+) ion undergoes charge-remote fragmentation (CRF), which is useful for the determination of the double-bond positions in the hydrocarbon chain, while the CID-MS/MS of the [2-AG-H+Cat](+) (Cat = Mg(2+), Ca(2+), Ba(2+)) ion provides an abundant fragment ion of the cationized arachidonic acid species, which is derived from cleaving the ester bond via a McLafferty-type rearrangement in addition to structurally informative CRF ions in small amounts. On the other hand, the CID-MS/MS spectra of anandamide cationized with both alkali metal (Li(+) or Na(+)) and alkaline earth metal (Mg(2+), Ca(2+), or Ba(2+)) show CRF patterns: the spectra obtained in lithium or sodium adduct are more clearly visible than those in magnesium, calcium, or barium adduct. The McLafferty rearrangement is not observed with metal-adduct anandamide. The characteristics in each mass spectrum are useful for the detection of these endogenous ligands. m-Nitrobenzyl alcohol (m-NBA) is the most suitable matrix. A lithium-adduct [2-AG+Li](+) or [anandamide+Li](+) ion is observed to be the most abundant in each mass spectrum, since the affinity of lithium for m-NBA is lower than that for other matrices examined.     

Energy-dependent collision-induced dissociation of lithiated polytetrahydrofuran: Effect of the size on the fragmentation properties

The fragmentation properties of singly and doubly lithiated polytetrahydrofuran (PTHF) were studied using energy-dependent collision-induced dissociation. The product ion spectrum of [PTHF + Li]⁺ showed the formation of three different series corresponding to product ions with hydroxyl, aldehyde and vinyl end-groups. Interestingly, besides these series, two additional, non-lithiated product ions C₄H₉O⁺ and C₄H ₇ ⁺ were identified in the MS/MS spectra. The MS/MS of the doubly lithiated PTHF ([PTHF + 2Li]²⁺) with a number of repeat units ranging from 8 to 27 showed the formation of product ions similar to those of the singly lithiated series, however, doubly lithiated product ions and product ions formed by the loss of one Li⁺-ion from the precursor ion also appeared with significant abundances. Analysis of the breakdown curves for the singly and doubly charged PTHF indicated that the series A ions are formed most probably together with the series B ions, while members of the series C ions appeared at significantly higher collision energies. The fragmentation properties of [PTHF + Li]⁺ and [PTHF + 2Li]²⁺ were also interpreted using the survival yield method. It was found that the collision energy/voltage necessary to obtain 50% fragmentation (CV₅₀) was dependent linearly on the number of the repeat units, i.e., on the size, or the number of degrees of freedom (DOF).     

Mass spectral fragmentation pathways in some dinitroaromatic compounds studied by collision-induced dissociation and tandem mass spectrometry

A collision-induced dissociation study of a series of dinitroaromatic compounds was carried out using a tandem BB mass spectrometer. Fragmentation pathways were determined in the electron impact mode. Loss of NO₂˙ from the molecular ion was observed In most of the investigated compounds. In some compounds loss of NO₂˙ occurred only after loss of OH˙. In other compounds it was not observed at all because of competitive processes, such as loss of NO˙, CO₂, CH₂O, C₂H₄ or H₂O. Loss of NO˙ was a major decomposition pathway, forming ‘dished peaks’ in some of the compounds having a nitro group ortho to a phenyl group, indicating a release of kinetic energy associated with the decomposition. Loss of OH˙ due to an ‘ortho effect’ occurred in compounds where a nitro group was ortho to a group containing a labile hydrogen, but was not observed when competitive processes such as loss of NO˙, NO₂˙ or H₂O occurred. ‘Nitro to nitrite’ isomerization was suggested to explain the decarboxylation process in 2,4- and 2,5-dinitrobenzoic acid and the loss of COH₂ in 2,4-dinitroanisole.     

Letter: collision-induced dissociation of peptide thioesters: influence of the peptide length on the fragmentation

Five peptide thioesters of increasing length were fragmented under two processes, in-source and in- collision cell fragmentation, using an electrospray source coupled to a triple quadrupole. Comparison of their fragmentations was made in regard to the length. The two fragmentation conditions show that the peptide length has no influence on structural information and that the fragmentation efficiency is higher for the smallest peptides than for the longest. The particularity of these peptide thioesters consists on the neutral loss of ethanethiol. The absence of the a3 fragment ion and the presence of the (a3-17) ion on the CID mass spectra are noted.     

Structural determination of cerebrosides isolated from Asterias amurensis starfish eggs using high-energy collision-induced dissociation of sodium-adducted molecules

Six cerebrosides were isolated from the eggs of the starfish Asterias amurensis using solvent extraction, silica gel column chromatography, and reversed‐phase high‐performance liquid chromatography. This study demonstrated that the structures of cerebrosides could be completely characterized, based on their sodium‐adducted molecules, using fast atom bombardment (FAB) tandem mass spectrometry. The high‐energy collision‐induced dissociation of the sodium‐adducted molecule, [M + Na]⁺, of each cerebroside molecular species generated abundant ions, providing information on the compositions of the 2‐hydroxy fatty acids and long‐chain sphingoid bases, as well as the sugar moiety polar head group. Each homologous ion series along the fatty acid and aliphatic chain of the sphingoid base was useful for locating the double‐bond positions of both chains and the methyl branching position of the long‐chain base. The N‐fatty acyl portions were primarily long‐chain saturated or monoenoic acids (C16 to C24) with an α‐hydroxy group. The sphingoid long‐chain base portions were aliphatic chains (C18 or C22) with two or three degrees of unsaturation and with or without methyl branching. Copyright © 2011 John Wiley & Sons, Ltd.     

Mass spectral fragmentation pathways in some glycoluril-type explosives. A study by collision-induced dissociation and isotope labeling

Electron impact (EI), chemical ionization and negative-ion chemical ionization (NCI) mass spectra of 1,4-dinitroglycoluril (DINGU), its ¹⁵N- and ²H-labeled analogues and the dimethyl-substituted derivatives were recorded. Tandem mass spectrometry with collision induced dissociation was used to study the fragmentation pathways of these compounds. It was found that the main EI fragmentation processes of DINGU are due to the cleavage of C? N bonds and some rearrangement reactions.     

Improving fragmentation of poorly fragmenting peptides and phosphopeptides during collision-induced dissociation by malondialdehyde modification of arginine residues

Despite significant technological and methodological advancements in peptide sequencing by mass spectrometry, analyzing peptides that exhibit only poor fragmentation upon collision-induced dissociation (CID) remains a challenge. A major cause for unfavorable fragmentation is insufficient proton 'mobility' due to charge localization at strongly basic sites, in particular, the guanidine group of arginine. We have recently demonstrated that the conversion of the guanidine group of the arginine side chain by malondialdehyde (MDA) is a convenient tool to reduce the basicity of arginine residues and can have beneficial effects for peptide fragmentation. In the present work, we have focused on peptides that typically yield incomplete sequence information in CID-MS/MS experiments. Energy-resolved tandem MS experiments were carried out on angiotensins and arginine-containing phosphopeptides to study in detail the influence of the modification step on the fragmentation process. MDA modification dramatically improved the fragmentation behavior of peptides that exhibited only one or two dominant cleavages in their unmodified form. Neutral loss of phosphoric acid from phosphopeptides carrying phosphoserine and threonine residues was significantly reduced in favor of a higher abundance of fragment ions. Complementary experiments were carried out on three different instrumental platforms (triple-quadrupole, 3D ion trap, quadrupole-linear ion trap hybrid) to ascertain that the observation is a general effect.     

APCI low energy collision-induced dissociation fragmentation of protonated ortho silicates: mclafferty or ion-neutral complex rearrangement?

The fragmentation mechanism of tetraethyl ortho silicate and tetrapropyl ortho silicate was studied to determine if the consecutive alkene losses observed in their MS/MS daughter ion spectra were produced via a McLafferty rearrangement or by ion-neutral rearrangement mechanisms. The experiments were carried out using atmospheric pressure chemical ionization and low energy collision-induced dissociation. Deuterium labeling of the γ-position provided evidence mat the rearrangement mechanism of the successive alkene losses proceeds predominantly via the ion-neutral complex mechanism. Because the energies imparted to the ions in this experiment are of the same order of magnitude as solution phase reactions, this mechanism may shed light on the formation of silica gels (e.g., aerogels) in that similar structures have been proposed as reaction intermediates in the polymerization of SiO₂.     

Fast atom bombardment and collision-induced dissociation of prostaglandins and thromboxanes: Some examples of charge remote fragmentation

The mass spectra of products found by collisional activation of selected prostaglandins and thromboxanes were studied by tandem mass spectrometry as barium carboxylate salts and as carboxylate anions. Collision-induced dissociation (CID) of these closed shell ions generated by fast atom bombardment mass spectrometry reveals a wealth of structural information for these hydroxy acids. Decomposition reactions were found to be dependent upon the eicosanoid ring structure and the type of ion being studied, either positive or negative ion. The bariated carboxylate salts undergo reactions by processes that are similar to those previously characterized as charge remote mechanisms in which neutral species are lost as in thermal and photolytic decompositions. The most abundant ion is formed by loss of water from each of the hydroxyl groups present on the prostaglandin or thromboxane structure. For these multifunctionalized eicosanoids, typical patterns of decomposition emerge as characteristic of the oxygen substituents present along the carbon chain of the eicosanoid structure. The structural information obtained from the barium salts along with those from the carboxylate anions is substantially different, yet the structural information from each process is complementary. The CIDs of positive ions (metalated salts) provide structural information concerning the substituents between the carboxyl group and C₁₂ of the eicosanoid structure, whereas the decompositions of the carboxylate anions (negative ion mode) provide data concerning structure alterations of the eicosanoid structure between C₁₅ and C₂₀     

Influence of a 4-aminomethylbenzoic acid residue on competitive fragmentation pathways during collision-induced dissociation of metal-cationized peptides

Formation of [bn+17+cat]+ is a prominent collision-induced dissociation (CID) pathway for Li+- and Na+-cationized peptides. Dissociation of protonated and Ag+-cationized peptides instead favors formation of the rival bn+/[bn-1+cat]+ species. In this study the influence of a 4-aminomethylbenzoic acid (4AMBz) residue on the relative intensities of [b(3)-1+cat]+ and [b(3)+17+cat]+ fragment ions was investigated using several model tetrapeptides including those with the general formula A(4AMBz)AX and A(4AMBz)GX (where X=G, A, V). For Li+- and Na+-cationized versions of the peptides there was a significant increase in the intensity of [b(3)-1+cat]+ for the peptides that contain the 4AMBz residue, and in some cases the complete elimination of the [b(3)+17+cat]+ pathway. The influence of the 4AMBz residue may be attributed to the fact that [b(3)-1+cat]+ would be a highly conjugated species containing an aromatic ring substituent. Comparison of CID profiles generated from Na+-cationized AAGV and A(4AMBz)GV suggests an apparent decrease in the critical energy for generation of [b(3)-1+Na]+ relative to that of [b(3)+17+Na]+ when the aromatic amino acid occupies a position such that it leads to the formation of the highly conjugated oxazolinone, thus leading to an increase in formation rate for the former compared to the latter.     

Statistical modeling of sequential collision-induced dissociation thresholds

Thermochemistry determined from careful analysis of the energy dependence of cross sections for collision-induced dissociation (CID) reactions has primarily come from the primary dissociation channel. Higher order dissociations generally have thresholds measured to be higher than the thermodynamic limit because of the unknown internal and kinetic energy distributions of the primary products. A model that utilizes statistical theories for energy-dependent unimolecular decomposition to estimate these energy distributions is proposed in this paper. This permits a straightforward modeling of the cross sections for both primary and secondary dissociation channels. The model developed here is used to analyze data for K+(NH3)x, x=2-5, complexes, chosen because the thermochemistry previously determined by threshold CID studies agrees well with values from theory and equilibrium high pressure mass spectrometry. The model is found to reproduce the cross sections with high fidelity and the threshold values for secondary processes are found to be in excellent agreement with literature values. Furthermore, relative thresholds for higher order dissociation processes appear to provide accurate thermodynamic information as well.