High-energy Collision-induced Dissociation Research Articles

Automated interpretation of MS/MS spectra of oligosaccharides

The emerging glycomics and glycoproteomics projects aim to characterize all forms of glycoproteins in different tissues and organisms. Tandem mass spectrometry (MS/MS) is the key experimental methodology for high-throughput glycan identification and characterization. Fragmentation of glycans from high energy collision-induced dissociation generates ions from glycosidic as well as internal cleavages. The cross-ring ions resulting from internal cleavages provide additional information that is important to reveal the type of linkage between monosaccharides. This information, however, is not incorporated into the current programs for analyzing glycan mass spectra. As a result, they can rarely distinguish from the mass spectra isomeric oligosaccharides, which have the same saccharide composition but different types of sequences, branches or linkages. In this paper, we describe a novel algorithm for glycan characterization using MS/MS. This algorithm consists of three steps. First, we develop a scoring scheme to identify potential bond linkages between monosaccharides, based on the appearance pattern of cross-ring ions. Next, we use a dynamic programming algorithm to determine the most probable oligosaccharide structures from the mass spectrum. Finally, we re-evaluate these oligosaccharide structures, taking into account the double fragmentation ions. We also show the preliminary results of testing our algorithm on several MS/MS spectra of oligosaccharides. The program GLYCH is available upon request from the authors.

Laser-Induced Dissociation/High-Energy Collision-Induced Dissociation Fragmentation Using MALDI-TOF/TOF-MS Instrumentation for the Analysis of Neutral and Acidic Oligosaccharides

Producing detailed mass spectrometric fragmentation data of native oligosaccharides for the purpose of basic structure elucidation has become a readily accessible tool since the availability of enhanced technical equipment. In this report, high-energy collision-induced dissociation (heCID) in combination with MALDI-TOF/TOF technology for analysis of native neutral and acidic oligosaccharides is described. By providing complementary data, heCID-MALDI-TOF/TOF adds a variety of valuable cross-ring fragmentation information to the information of glycosidic fragmentation obtained preferably by laser-induced dissociation (LID). We examined parameters influencing fragmentation behavior of both-acidic and neutral-compounds. Results show a dependency of the fragmentation pattern for the employed matrix as well as the laser intensity provided for the ionization of the analytes and the complexity of the analytes. Due to instrument-specific settings, protonated glycosidic ion series within spectra of sodiated compounds could also be identified. Furthermore, acquired spectra could be readily used to identify compounds by comparison to existing glycan databases such as GlycoSuiteDB and GlycosciencesDB. The results show a better scoring of heCID data sets in comparison to LID-derived data. heCID-MALDI-TOF/TOF analysis in combination with database search algorithms is demonstrated to be suitable for an initial identification/classification of carbohydrates.

Structural characterization of fatty acids cationized with copper by electrospray ionization mass spectrometry under low‐energy collision‐induced dissociation

Fatty acids have for many years been characterized by mass spectrometry using electron ionization after chemical derivatization. When fatty acids are ionized using desorption/ionization methods such as electrospray ionization or fast atom bombardment, structural information is usually obtained through high-energy collision-induced dissociation (CID) using sector instruments. It has been shown that copper displays very interesting properties in the gas phase during CID. In this study, the reactivity of saturated and unsaturated fatty acid-copper [M-H+Cu(II)]+ complex and the role of the copper ion in promoting fragmentations were investigated under low-energy collisional activation conditions. The decomposition of these species in an ion trap instrument led to diagnostic ion series that reflect C--C bond cleavage, which involves Cu(II) reduction followed by the release of an alkyl radical. It was demonstrated that in this way the localization of one or two homoconjugated double bonds is possible using low-energy CID. Moreover, the distinction of cis and trans isomers is possible through characteristic product ions related to a specific loss of CO2. When these experiments are repeated using a triple-quadrupole instrument with argon as collision gas, a different behavior is observed as in this case, in addition to the product ion distributions observed in the ion trap, other distributions are observed that reflect the influence of the different kinetic shifts and the occurrence of consecutive decompositions. Different examples are presented with various saturated and unsaturated fatty acid chains. Mechanisms are proposed in order to rationalize the experimental observations.

Determination of the glycosylation site in flavonoid mono‐O‐glycosides by collision‐induced dissociation of electrospray‐generated deprotonated and sodiated molecules

The influence of the glycosylation site on the fragmentation behavior of 18 flavonoid glycoside standards was studied using positive and negative electrospray ionization mass spectrometry in combination with collision-induced dissociation and tandem mass spectrometry. The glycosylation position is shown to affect the relative abundance of the radical aglycone ions that can be observed in the [M-H]- collision-induced dissociation spectra. In particular, the radical aglycone ions are very abundant for deprotonated flavonol 3-O-glycosides. Collisional activation of the radical aglycone ions produced from positional isomers revealed minor differences: m,nB0- product ions are pronounced for 7-O-glycosides, whereas m,nA0- product ions are relatively more abundant for 4'-O-glycosides. In addition, the ratio between the radical aglycone and the regular aglycone ions in the [M+Na]+ high-energy collision-induced dissociation spectra gives an indication about the glycosylation site. This ion ratio allows the differentiation between flavonoid 3-O- and 7-O-glycosides or can be useful in the comparison of unknown compounds with standards. Unambiguous differentiation between O-glycosylation at the common positions of flavonoid O-glycosides, i.e. the 3-, 4'- and 7-positions, is achieved by collisional activation of sodiated molecules at high collision energy. The presence of a B-ring product ion containing the sugar residue indicates 4'-O-glycosylation, whereas the loss of the B-ring part from the aglycone product ion is characteristic of 3-O-glycosylation and the loss of the B-ring part from both the [M+Na]+ precursor ion and the aglycone product ion points to 7-O-glycosylation.

Very high critical energy fragmentations observed in CID

High energy CID fragmentations of triatomic alkali halide cluster ions were examined to estimate the energy transfer during the CID process. A detailed CID study using keV collisions revealed that M 2X + clusters yield not only the expected M + ions but practically all possible combinations of mono- and biatomic ions. In the case of Cs 2I +, for example Cs +, Cs 2 +, CsI +, and even I + fragment ions are observed. The results suggest that collisional energy transfer in keV collisions has a monotonously decreasing shape (full width at half height is ∼2 eV) and has a long high energy tail extending well over 10 eV (with at least 5% probability), the average collisional energy transfer being about 5 eV.

A new charge-associated mechanism to account for the production of fragment ions in the high-energy CID spectra of fatty acids

A new mechanism, termed a charge-assisted process, is proposed as an additional mechanism to the charge-remote process to account for ions of the [M - CnH2n+2] series found in the positive and negative high energy CID spectra of fatty acids and related compounds when ionized as closed-shell ([M - H]- or [M + X]+) species. The new mechanism is based on that commonly invoked to account for similar ions in the electron-impact spectra of derivatized fatty acids whereby the positive charge on the derivative abstracts a hydrogen atom from various positions of the alkyl chain to leave a radical that initiates a radical-induced cleavage of the chain. It is proposed that in the high energy CID spectra of closed-shell ions, similar hydrogen migrations occur but unpairing of electrons is avoided by charge transfer to the alkyl chain. This charge then initiates a concerted cleavage of the chain to give an allylic carbonium (positive ion spectrum) or carbanion (negative ion spectrum). The mechanism avoids the need to involve radicals or loss of hydrogen atoms from even-electron (closed shell) ions and provides a driving force for the reaction, namely, the formation of ions with a stabilized charge. An extension of the mechanism is also proposed to account for the formation of odd-electron ions from these compounds. The charge-assisted mechanism does not rule out the occurrence of other mechanisms that have been accepted for many years but provides an alternative process that can account for some spectral features which were difficult to explain earlier.

A case study of de novo sequence analysis of N-sulfonated peptides by MALDI TOF/TOF mass spectrometry

The simplicity and sensitivity of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry have increased its application in recent years. The most common method of "peptide mass fingerprint" analysis often does not provide robust identification. Additional sequence information, obtained by post-source decay or collision induced dissociation, provides additional constraints for database searches. However, de novo sequencing by mass spectrometry is not yet common practice, most likely because of the difficulties associated with the interpretation of high and low energy CID spectra. Success with this type of sequencing requires full sequence coverage and demands better quality spectra than those typically used for data base searching. In this report we show that full-length de novo sequencing is possible using MALDI TOF/TOF analysis. The interpretation of MS/MS data is facilitated by N-terminal sulfonation after protection of lysine side chains (Keough et al., Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7131-7136). Reliable de novo sequence analysis has been obtained using sub-picomol quantities of peptides and peptide sequences of up to 16 amino acid residues in length have been determined. The simple, predictable fragmentation pattern allows routine de novo interpretation, either manually or using software. Characterization of the complete primary structure of a peptide is often hindered because of differences in fragmentation efficiencies and in specific fragmentation patterns for different peptides. These differences are controlled by various structural parameters including the nature of the residues present. The influence of the presence of internal Pro, acidic and basic residues on the TOF/TOF fragmentation pattern will be discussed, both for underivatized and guanidinated/sulfonated peptides.

The N‐linked oligosaccharides of aminopeptidase N from Manduca sexta

Mass spectrometric studies on the N-linked glycans of aminopeptidase 1 from Manduca sexta have revealed unusual structures not previously observed on any insect glycoprotein. Structure elucidation of these oligosaccharides was carried out by high-energy collision-induced dissociation (CID) using a matrix-assisted laser desorption/ionization time-of-flight/time-of-flight (MALDI-TOF/TOF) tandem mass spectrometer. These key experiments revealed that three out of the four N-linked glycosylation sites in this protein (Asn295, Asn623 and Asn752) are occupied with highly fucosylated N-glycans that possess unusual difucosylated cores. Cross-ring fragment ions and 'internal' fragment ions observed in the CID spectra, showed that these fucoses are found at the 3-position of proximal GlcNAc and at the 3-position of distal GlcNAc in the chitobiose unit. The latter substitution has only been previously observed in nematodes. In addition, these core structures can be decorated with novel fucosylated antennae composed of Fucalpha(1-3)GlcNAc. Key fragment ions revealed that these antennae are predominantly found on the upper 6-arm of the core mannose. The paucimannosidic N-glycan (Man(3)GlcNAc(2)), commonly found on other insect glycoproteins, is the predominant oligosaccharide found at the remaining N-glycosylation site (Asn609).

High-energy collision-induced dissociation of oxosteroids derivatised to Girard hydrazones.

Neutral oxosteroids have been derivatised with Girard T and P hydrazine reagents to give the corresponding Girard hydrazone quaternary ammonium salts. Both Girard T (GT) and Girard P (GP) hydrazones of oxosteroids give very intense [M](+) ion signals in electrospray (ES) mass spectra and fragment within the ES interface and collision cell to give characteristic fragment ions. GT and GP derivatives give informative high-energy collision-induced dissociation spectra, from which the structure of the precursor oxosteroid can be determined. Both charge-remote and charge-mediated mechanisms are responsible for the formation of the fragment ions at high collision-energy.

Characterization of epoxy carotenoids by fast atom bombardment collision-induced dissociation MS/MS.

The characterization and structure of epoxy carotenoids possessing 5,6-epoxy, 5,8-epoxy and 3,6-epoxy end groups conjugated to the polyene chain were investigated using high-energy fast atom bombardment collision-induced dissociation MS/MS methods. In addition to [M - 80](+*), a characteristic fragment ion of an epoxy carotenoid, product ions resulting from the cleavage of C-C bonds in the polyene chain from the epoxy end group, such as m/z 181 (b ion) and 121 (c ion), were detected. On the other hand, diagnostic ions of m/z 286 (e-H ion) and 312 (f-H ion) were observed, not in the 5,6-epoxy or 5,8-epoxy carotenoid but in the 3,6-epoxy carotenoid. These fragmentation patterns can be used to distinguish 3,6-epoxy carotenoids from 5,6-epoxy or 5,8-epoxy carotenoids. The structure of an epoxy carotenoid, 3,6-epoxy-5,6-dihydro-7',8'-didehydro-beta,beta-carotene-5,3'-diol (8), isolated from oyster, was characterized using FAB CID-MS/MS by comparing fragmentation patterns with those of related known compounds.

High energy collision-induced dissociation (CID) product ion spectra of isomeric polyhydroxy sugars

High energy (4 keV) collision-induced dissociation (CID) product ion spectra have been obtained for a series of isomeric sugar molecules of close structural similarity. The reproducibility of the approach has been established and the spectra shown to have significant differences. These differences have been rationalised in terms of conventional mass spectrometric fragmentation rules. The data have also been subjected to analysis using chemometric methods, which require no specialist mass spectrometric input. The resulting classification of the data shows good agreement with the conventional interpretation approach.

Entropy evaluation using the kinetic method: is it feasible?

The kinetic method is one of the most widely used experimental techniques for the measurement of thermochemical parameters by mass spectrometry. Recently it has been realized that it can also be used to determine reaction entropies, but the validity of this approach has not been established. This Perspective evaluates kinetic method plots in cases where there is a significant entropy difference between the competing fragmentation channels (i.e. between sample and reference compounds in the dissociating cluster ion). The concept underlying this study is to calculate mass spectra theoretically, based on known thermochemical parameters and as a function of experimental conditions. This can be done accurately using the RRKM-based MassKinetics software. The resulting mass spectra are then interpreted by the kinetic method, yielding DeltaH and DeltaS values. These values are, in turn, compared with the true values used to generate the calculated mass spectra. The results show that the reaction entropy difference between sample and reference has a very large influence on kinetic method plots. This should always be considered when studying energy-dependent mass spectra (using metastable ions or low- or high-energy collision-induced dissociation (CID)), even if only DeltaH is to be determined. Kinetic method plots are not strictly linear and this becomes a serious issue in the case of small molecules showing a large entropy effect. In such cases, results obtained at a low degree of excitation are more accurate. Energy and entropy effects can be evaluated in a relatively straightforward manner: first, the apparent Gibbs energy (DeltaG(app)) and effective temperature (T(eff)) are determined from kinetic method plots (intercept and slope, respectively), obtained from experiments using various degrees of excitation. Second, the resulting DeltaG(app) is plotted against T(eff), the slope yielding DeltaS while the intercept (extrapolation to zero temperature) yields DeltaH. This data evaluation yields more accurate results than alternative methods used in the literature. The resulting DeltaH values are fairly accurate, with errors, in most cases, <4 kJ mol(-1). On the other hand, DeltaS is systematically underestimated by 20-40%. Empirically scaling DeltaS values determined by the kinetic method by 1.35 results in a DeltaS value within 20% (or 10 J mol(-1) K(-1)) of the theoretical value.

Tandem mass spectrometric characterization of branched peptides derived from photoaffinity labeling

Covalent photoadducts were obtained by photoaffinity labeling of the corticotropin-releasing factor (CRF) binding protein (CRFBP) with three photoreactive benzophenone-derivatized CRF analogs that differed in the position of the photophore. Enzymatic digestion of these photoadducts resulted in branched peptides that were analyzed by tandem mass spectrometry (MS/MS) under the conditions of high-energy collision-induced dissociation. Thereby, the branching site and, thus, the site of photoincorporation into CRFBP was identified. Comparison of the MS/MS spectra of the single linear peptide components with that of the branched peptide is presented as an analytical approach to facilitate its structural characterization. The major fragmentation pathways of the linear peptides were used to assist the assignment of the fragments derived from backbone fragmentation of the branched peptide. In addition, the low-mass fragment ions that are indicative for the presence of certain amino acid residues were analyzed to assign the modified amino acid residue. By using photoaffinity labeling in combination with mass spectrometry, three arginine residues in position 23, 36, and 111 of rat CRFBP were identified as the sites of photoincorporation of the three different photoreactive CRF analogs. Thereby, three contact sites between CRF and CRFBP could be assigned. These results in future will be helpful to further elucidate the conformation of the ligand-binding site of CRFBP.

Internal residue loss produced by rearrangement of a novel cationic glycosphingolipid, glyceroplasmalopsychosine, in collision-induced dissociation.

A novel plasmal conjugate of galactosylsphingosine (psychosine), Gro1(3)-O-plasmal-O-6Galbeta-sphingosine (glyceroplasmalopsychosine), was analyzed by electrospray ionization and liquid secondary ion mass spectrometry with low- or high-energy collision-induced dissociation (CID). In the product ion spectra of the [M + H](+) ions, [M + H - glycerol](+) ions arising from the loss of a glycerol were predominant. Unexpectedly, CID of the [M + H - glycerol](+) ion produced an outstanding ion, [(M + H - glycerol) - Hex](+), which required the loss of the galactose from inside the molecule. This ion was greatly reduced in the spectra of N,N-dimethyl derivatives, indicating that the [(M + H - glycerol) - Hex](+) ion is formed from an intramolecular rearrangement with migration of the plasmal residue to the free amino group of sphingosine. It would be expected that the rearrangement occurs simultaneously with the elimination of glycerol or a rearranged [M + H](+) ion leads to the elimination of glycerol, to form a Schiff base-type [M + H - glycerol](+) ion, from which the terminal galactose could be removed by the normal mechanism of glycosidic cleavage. On the other hand, the [M + Na - glycerol](+) ion derived from the sodiated molecule did not produce an ion corresponding to the rearrangement reaction, possibly owing to a higher stability of the sodiated ions against conformational changes.

Retrograde labeling of single neurons in conjunction with MALDI high-energy collision-induced dissociation MS/MS analysis for peptide profiling and structural characterization.

To reveal the peptide contents of the visually nonidentifiable neurons from a neuronal circuit of interest, we combined retrograde labeling of neurons with mass spectrometric single cell analysis. We used the neuronal circuit involved in the copulation behavior of a freshwater snail, Lymnaea stagnalis, as a model. Central neurons that control this behavior are known to send their axons to the penis nerve and innervate the penis complex. By retrograde filling from the penis nerve with nickel-lysine, these neurons were selectively labeled darkish blue. Matrix-assisted laser desorption/ionization (MALDI) time-of-flight mass spectrometric analyses of single stained neurons in the parietal ganglion from different animals reveal consistently the presence of several molecular ion species in the range of 800-1200 Da. From a single neuron, six molecular ion species were further characterized with MALDI time-of-flight/time-of-flight mass spectrometry, which demonstrates that the peptides are derived from a previously reported -FLRFamide precursor.

Distinguishing of Ile/Leu amino acid residues in the PP3 protein by (hot) electron capture dissociation in Fourier transform ion cyclotron resonance mass spectrometry.

In hot electron capture dissociation (HECD), multiply protonated polypeptides fragment upon capturing approximately 11-eV electrons. The excess of energy upon the primary c, z* cleavage induces secondary fragmentation in z* fragments. The resultant w ions allow one to distinguish between the isomeric Ile and Leu residues. The analytical utility of HECD is evaluated using tryptic peptides from the bovine milk protein PP3 containing totally 135 amino acid residues. Using a formal procedure for Ile/Leu (Xle) residue assignment, the identities of 20 out of 25 Xle residues (80%) were determined. The identity of an additional two residues could be correctly guessed from the absence of the alternative w ions, and only two residues, for which neither expected nor alternative w ions were observed, remained unassigned. Reinspection of conventional ECD spectra also revealed the presence of Xle w ions, although at lower abundances, with 44% of all Xle residues distinguished. Using a dispenser cathode as an electron source, identification of four out of five Xle residues in a 2.7-kDa peptide was possible with one acquisition 2 s long, with identification of all five residues by averaging of five such acquisitions. Unlike the case of high-energy collision-induced dissociation, no d ions were observed in the HECD of tryptic peptides.

Internal energy deposition in chemical ionization/tandem mass spectrometry

The efficiency of the collision-induced dissociation (CID) process as a function of the internal energy deposited into the ion during the ionization event was evaluated. (M + H) + ions of pyrrole, pyrrolidine, pyridine and piperidine (five and six-membered ring heterocyclics) were generated by chemical ionization (CI). The internal energy of the ions was varied by using different reagent gases. Both high-energy (keV) and low-energy (eV) CID were performed on these ions. The experiments showed that the (M + H) + ions of the five-membered ring compounds, pyrrole and pyrrolidine, have higher fragmentation efficiencies than the six-membered ring compounds, pyridine and piperidine. Fragmentation efficiencies in high-energy CID clearly correlate with the internal energy deposited by the ionization technique. Experiments showed that the low-energy CID process is more sensitive than high-energy CID to changes in internal energy.

Collision-induced dissociation of the phenylsilane molecular ion.

The high-energy collision-induced dissociation of the phenylsilane molecular ion generated by electron ionization has been investigated using tandem mass spectrometry (MS/MS). It was observed that the dissociation of the molecular ion (M(+*)) occurs mainly via [M-H](+), [M-2H](+*), and [M-3H](+), followed by two consecutive losses of C(2)H(2). The structures of the precursors for the [M-CH(3)](+), [M-SiH](+), and [M-SiH(2)](+*) ions are proposed. The data suggest that the molecular ion undergoes rearrangements to several isomers prior to dissociation, including the ion containing a five-membered carbon ring. Reaction mechanisms are proposed for the dissociations via the isomeric molecular ions.

Tandem time-of-flight mass spectrometer (TOF-TOF) with a quadratic-field ion mirror

A tandem time-of-flight (TOF-TOF) mass spectrometer comprised of two ion mirrors is described. The first ion mirror, which is a linear-field, single-stage mirror (MS1) with an intermediate collision cell, has been designed to provide the temporal focus necessary for the second, quadratic-field ion mirror (MS2) to function effectively. Due to the wide energy-range focusing capabilities of the quadratic field employed in the second ion mirror all the fragment ions can be collected in one spectrum without the need to step the reflecting working voltage of the MS2. The size of the active area of the microchannel plate detector used in the preliminary experiments was the limiting factor governing the collection efficiently of fragment ions. The use of the first ion mirror to provide temporal focusing of the precursor ion packet at the first focal point of the quadratic mirror used as the MS2 requires no alteration of the focusing conditions for different masses, in contrast to delayed extraction or postsource pulsed focusing. Precursor ions formed by matrix-assisted laser desorption/ionization were mass-selected with an ion gate located before the collision cell and the fragment ions were mass analyzed using the quadratic-field ion mirror. Experimental results demonstrating effective high-energy collision-induced dissociation of polymer and fullerene molecule-ions are presented.

Confirmation of the Connectivity of 4,8,12,16,20-Pentamethylpentacosylphoshoryl β-d-Mannopyranoside, an Unusual β-Mannosyl Phosphoisoprenoid from Mycobacterium avium, through Synthesis

The synthesis of the title glycolipid is reported. Comparison of the electrospray and high-energy collision-induced dissociation mass spectra of the synthetic material with those reported for the isolate confirm the structure of this unusual antigenic substance with its modified isoprenoid chain.