Structural elucidation of the ceramide moiety of starfish gangliosides by collision-induced dissociation of the sodium ion complex.

Collision-induced dissociation (CID) spectra of sodium ion complexes ([M+Na]+ ions), produced by FAB-MS of methyl ester derivatives of ganglioside, indicate the length of the fatty acyl chain of the ceramide moieties without chemical degradation. In the case of a genuine ganglioside, only the fission of the glycosyl linkage of sialic acid was prominently observed.     

The determination of glycopeptides by liquid chromatography/mass spectrometry with collision-induced dissociation

Glycopeptides derived from ribonuclease B and ovomucoid have been subjected to collision-induced dissociation (CID) in the second quadrupole of a triple quadrupole mass spectrometer. Doubly charged parent ions gave predictable fragmentation that yielded partial sequence information of the attached oligosaccharide as Hex and HexNAc units. Common oxonium ions are observed in the product ion mass spectra of the glycopeptides that correspond to HexNAc⁺ (m/z 204) and HexHexNAc⁺ (m/z 366). A strategy for locating the glycopeptides in the proteolytic digest mixtures of glycoproteins by ions spray liquid chromatography mass spectrometry (LC/MS) is described by utilizing CID in the declustering region of the atmospheric pressure ionization mass spectrometer to produce these characteristic oxonium ions. This LC/CID/MS approach is used to identify glycopeptides in proteolytic digest mixtures of ovomucoid, asialofetuin, and fetuin. LC/CID/MS in the selected ion monitoring mode may be used to identify putative glycopeptides from the proteolytic digest of fetuin.     

Comparison of charged derivatives for high energy collision-induced dissociation tandem mass spectrometry

Fixed-charge derivatives have been used to direct the fragmentation pattern of high energy collision-induced dissociation tandem mass spectra for several years. It has been noted that a fixed-charge placed at a terminus of a peptide will simplify the pattern of fragment ions that are produced in collision-induced dissociation. Trimethylammoniumacetyl, dimethyloctylammoniumacetyl, and triphenylphosphoniumethyl derivatives have been cited in the literature for this purpose and many other structures are possible. This work compares the cited derivatives as well as some new structures. The criteria used include the ease of synthesis and purification of the derivatized peptide and the effects of the derivative on the peptide sequence fragment ion yield and ionization efficiency. The trimethylammoniumacetyl derivative is concluded to be the most practical for general use, whereas the dimethyloctylammoniumacetyl derivative is found to be desirable for use with hydrophilic peptides.     

Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra

A new strategy is reported for extracting complete and partial sequence information from collision-induced dissociation (CID) spectra of peptides, CID spectra are obtained from high energy CID of peptide molecular ions on a four-sector tandem mass spectrometer with an electro-optically coupled microchannel array detector, A peak detection routine reduces the spectrum to a list of peak masses and peak heights, which is then used for sequencing, The sequencing algorithm was designed to use spectral data to generate sequence fits directly rather than to use data to test the fit of series of sequence guesses. The peptide sequencing algorithm uses a pattern based on the polymeric nature of peptides to classify spectral peaks into sets that are related in a sequence-independent manner, It then establishes sequence relationships among these sets, Peak detection from raw data takes 10–20 s, with sequence generation requiring an additional 10–60 s on a Sun 3/60 workstation, The program is written in the C language to run on a Unix platform. The principal advantages of our method are in the speed of analysis and the potential for identifying modified or rare amino acids. The algorithm was designed to permit real-time sequencing but awaits hardware modifications to allow real-time access to CID spectra.     

Direct structural assignment of neutral and sialylated N-glycans of glycopeptides using collision-induced dissociation MSn spectral matching

Mass spectrometric analyses of various N-glycans binding to proteins and peptides are highly desirable for elucidating their biological roles. An approach based on collision-induced dissociation (CID) MS(n) spectra acquired by electrospray ionization linear ion trap time-of-flight mass spectrometry (ESI-LIT-TOFMS) in the positive- and negative-ion modes has been proposed as a direct method of assigning N-glycans without releasing them from N-glycopeptides. In the positive-ion mode of this approach, the MS(2) spectrum of N-glycopeptide was acquired so that a glycoside-bond cleavage occurs in the chitobiose residue (i.e., GlcNAcbeta1-4GlcNAc, GlcNAc: N-acetylglucosamine) attached to asparagine (N), and two charges on the [M+H+Na](2+) precursor ion are shared with both of the resulting fragments. These fragments are sodiated B(n)-type fragment ions of oligosaccharide (N-glycan) and a protonated peptide ion retaining one GlcNAc residue on the asparagine (N) residue. The structure of N-glycan was assigned by comparing MS(3) spectra derived from both the sodiated B(n)-type fragment ions of N-glycopeptide and the PA (2-aminopyridine) N-glycan standard (i.e., MS(n) spectral matching). In a similar manner, the structural assignment of sialylated N-glycan was performed by employing the negative-ion CID MS(n) spectra of deprotonated B(n)-type fragment ions of N-glycopeptide and the PA N-glycan standard. The efficacy of this approach was tested with chicken egg yolk glycopeptides with a neutral and a sialylated N-glycan, and human serum IgG glycopeptides with neutral N-glycan isomers. These results suggest that the approach based on MS(n) spectral matching is useful for the direct and simple structural assignment of neutral and sialylated N-glycans of glycopeptides.     

Characteristics of high energy collision-induced dissociation tandem Mass Spectra of Polycyclic aromatic Hydrocarbon diolepoxide adducted peptides

Polycyclic aromatic hydrocarbon (PAH) diolepoxides are known to covalently modify serum albumin and hemoglobin. Mass spectrometric techniques have proven quite useful in the characterization of the site of adduction on these proteins. To facilitate the study of PAH diolepoxide adducted peptides, model peptide adducts of benzo[a]pyrene-trans-7,8-dihydrodiol-epoxide [anti-BaP(9,10)DE] and benzo[a]anthracene-trans-8,9-dihydrodiol-10,11-epoxide [anti-BaA(10,11)DE] have been synthesized for the purpose of studying their high energy collision-induced dissociation tandem mass spectra. These spectra are dominated by ions produced from cleavage of the peptide-adduct bond with charge retention by the adducting moiety. Such ions allow for the facile identification of adducted peptides in a mixture by use of neutral loss scans. The peptide sequence can still be deduced from the data in most cases, and the site of adduction can be determined. For those peptide-adducts in which this is not possible, a charged derivative placed at the N-terminus simplifies the peptide fragmentation pattern and makes the spectrum more interpretable.     

Large translational energy loss and scattering in collision-induced dissociation processes

Large translational energy losses (TEL) of between 10 and 35 eV have been observed and studied in the collision-induced decomposition (CID) of some CsI clusters, Cs₃I₂⁺, Cs₅I₄⁺ and Cs₁₄I₁₃⁺. The TEL was found to depend strongly on the collision energy. In some cases the TEL was greater than the centre of mass collision energy, showing that recoil energy of the target is undoubtedly important. The results suggest further that, at least for projectiles consisting of heavy atoms, most of the TEL is due to a scattering process. From the TEL and CID peak shapes approximate collision angle distributions were also determined.     

Structural confirmation of ostreocin-D by application of negative-ion fast-atom bombardment collision-induced dissociation tandem mass spectrometric methods

Negative-ion fast-atom bombardment collision-induced dissociation tandem mass spectrometric (FAB-CID-MS/MS) methodology was successfully applied to verify the highly complex structure of ostreocin-D (MW 2633), a new palytoxin analog isolated from the marine dinoflagellate Ostreopsis siamensis and proposed to be 42-hydroxy-3,26-didemethyl-19,44-dideoxypalytoxin based on NMR data. The charge-remote fragmentations were facilitated by a negative charge introduced to a terminal amino group or to a hydroxyl group at the other terminus by a reaction with 2-sulfobenzoic acid cyclic anhydride. Product ions generated from the [M - H](-) ions provided information on the structural details of ostreocin-D. Comparisons between the spectral data for ostreocin-D and palytoxin also provided a rational basis for the assignments of product ions.     

Structural characterization of flavonol di-O-glycosides from Farsetia aegyptia by electrospray ionization and collision-induced dissociation mass spectrometry

This study reports the application of mass spectrometric methods to characterize unknown flavonoids of the herb Farsetia aegyptia Turra (Crucifereae). High-performance liquid chromatography was performed in combination with UV-photodiode array detection (LC/UV-DAD) and electrospray ionization mass spectrometry (LC/ESI-MS) in both positive and negative ion modes. Collision-induced dissociation (CID) mass spectral data were obtained off-line by nanospray (nano-ESI) analysis, which provided a wealth of information and led to the structural proposal of the flavonol di-O-glycosides present in the herb extract. In addition to the mass spectral data, we also report NMR data for the major compound which allowed the completion of its structural elucidation. The Farsetia aegyptia Turra herb extract was found to contain three flavonol di-O-glycosides containing a monosaccharidic residue linked to the 3-O position and a disaccharidic residue linked to the 7-O position; the major compound was characterized as the new flavonoid, isorhamnetin 3-O-alpha-L-arabinoside 7-O-[beta-D-glucosyl-1 --> 2]-alpha(L)rhamnoside. Different types of CID spectra, i.e., low-energy [M+H]+, [M+Na]+ and [M--H]- spectra as well as high-energy [M+Na]+ spectra, were evaluated with respect to their utility to locate the O-linked saccharidic residues in flavonol di-O-glycosides and to determine the sequence in the disaccharidic part. In agreement with previously published data, the 3-O-glycosyl residue was more readily lost from the protonated molecule than the 7-O-glycosyl residue. The opposite behavior was noted for the fragmentation of the deprotonated and sodiated molecules. Radical ions were observed in the high-energy [M+Na]+ CID spectra which provided supporting information on the glycosylation positions.     

Structural determination of saponins extracted from starfish by fast atom bombardment collision-induced dissociation mass spectrometry.

Three saponins were extracted and isolated from starfish by reversed-phase high performance liquid chromatography (HPLC), and analyzed by fast atom bombardment mass spectrometry (FAB-MS). Their molecular weight information could be obtained by the presence of abundant [M+Na]+ ions and weak [M+H]+ ions in FAB-MS spectra. Moreover, high resolution mass measurements of their [M+Na]+ ions were performed at the resolution of 10000 to elucidate the element composition of extracted saponins. The collision-induced dissociation (CID) of sodium-adducted molecules [M+Na]+ yielded diverse product ions via dissociated processes. In the collision-induced dissociation (CID)-MS/MS analysis of [M+Na]+ ion, the sulfate-containing saponins produced characteristic ions such as SO4Na+, [NaHSO4+Na]+, [M+Na-sugar]+ and [M+Na-2sugar]+ ions, whereas the sulfate-free compound showed characteristic ions produced by cleavage of sugar moiety and side chain of aglycone. The fragmentation patterns could provide information on the linkage position of sugar groups in aglycone and sulfate groups.     

Direct glycan structure determination of intact N-linked glycopeptides by low-energy collision-induced dissociation tandem mass spectrometry and predicted spectral library searching

Intact glycopeptide MS analysis to reveal site-specific protein glycosylation is an important frontier of proteomics. However, computational tools for analyzing MS/MS spectra of intact glycopeptides are still limited and not well-integrated into existing workflows. In this work, a new computational tool which combines the spectral library building/searching tool, SpectraST (Lam et al. Nat. Methods2008, 5, 873–875), and the glycopeptide fragmentation prediction tool, MassAnalyzer (Zhang et al. Anal. Chem.2010, 82, 10194–10202) for intact glycopeptide analysis has been developed. Specifically, this tool enables the determination of the glycan structure directly from low-energy collision-induced dissociation (CID) spectra of intact glycopeptides. Given a list of possible glycopeptide sequences as input, a sample-specific spectral library of MassAnalyzer-predicted spectra is built using SpectraST. Glycan identification from CID spectra is achieved by spectral library searching against this library, in which both m/z and intensity information of the possible fragmentation ions are taken into consideration for improved accuracy. We validated our method using a standard glycoprotein, human transferrin, and evaluated its potential to be used in site-specific glycosylation profiling of glycoprotein datasets from LC-MS/MS. In addition, we further applied our method to reveal, for the first time, the site-specific N-glycosylation profile of recombinant human acetylcholinesterase expressed in HEK293 cells. For maximum usability, SpectraST is developed as part of the Trans-Proteomic Pipeline (TPP), a freely available and open-source software suite for MS data analysis.     

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.     

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.     

Vibrational relaxation and collision-induced dissociation of xenon fluoride by neon

Rate coefficients were calculated for vibrational relaxation and collision-induced dissociation of ground state xenon fluoride in neon at temperatures between 300 and 1000 K for each of nine vibrational levels. These coefficients were calculated using a pairwise additive potential energy surface, which consists of a Morse function for the XeF interaction and Lennard–Jones functions for the NeXe and NeF interactions. Rate coefficients are provided for both temperature and v- dependences. The vibrational relaxation and dissociation processes occur by multiquanta transitions. Dissociation can take place from all v-levels provided that the internal energy of the XeF molecule is close to the rotationless dissociation limit. The order of increase effectiveness of the various forms of energy in promoting dissociation in XeF was found to be translation–rotation-vibration. At room temperature, neon atoms were found to be more efficient than helium atoms in the dissociation processes; helium atoms were found to be more efficient than neon atoms in the vibrational relaxation of XeF. Strong vibration–rotation coupling in both vibrational relaxation and in the dissociation processes is demonstrated.     

a compact high pressure ion source for high and low energy collision-induced dissociation studies of cluster ions on a VG analytical ZAB-2FQ

A compact, field-free high pressure ion source designed to replace, with minimum disruption, the electron impact/chemical ionization ion source of a VG Analytical ZAB-2FQ hybrid BEqQ mass spectrometer is described. This ion source may be operated at temperatures from ≈40 to 250 °C and at pressures up to 4–5 torr and, thus, is capable of producing proton-bound cluster ions up to hexamers in good yields. Examples of high energy collision-induced dissociation, low energy collision-induced dissociation, and neutralization-reionization studies of proton-bound cluster ions produced in this source are presented.     

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.     

High-energy collision-induced dissociation of multiply charged polypeptides produced by electrospray

The recent commercial implementation of an electrospray source on a four-sector mass spectrometer has allowed the study of high-energy collisional activation of multiply charged cations. With this configuration, higher mass-to-charge ratios can be accommodated in both precursor ion selection and fragment ion detection. Good mass accuracy facilitates analysis of fragment ions and allows more reliable mechanistic correlation of these fragments. A convenient scheme was devised to permit the use of kilovolt potentials in both MS-I and MS-II, with precursors of varying charge states. Algorithms were devised to assign masses of different types of multiply charged fragment ions. Nine polypeptides were studied in the mass range 2000–5000 Da. Through this entire mass range, fragment ions were observed to be amply formed by cleavages in both the backbone and side chains, analogous to high-energy collisional activation of singly charged ions. This stands in sharp contrast to the patterns reported with low-energy, multiple collisions. Abundances of sequence ion series are influenced by the positions of basic residues. Analysis of charge distributions in fragment ions also indicates that the charges tend to be spread out across the peptides.     

Characterization of microcystins using in-source collision-induced dissociation

The efficiency of the in-source collision-induced dissociation (in-source CID) technique for the structural characterization of microcystins (MCYSTs) was evaluated. Microcystins that did not contain arginine underwent facile fragmentation to produce characteristic product ions at relatively low cone voltage and could be fully characterized based on their mass spectra. On the other hand, cyclic peptides possessing arginine residues, such as MCYST-RR, -LR, -YR and nodularin, were considerably more stable under in-source CID conditions and required higher cone voltage to induce fragmentation. This behaviour is explained in terms of the mobile proton model for peptide fragmentation that can be used as an indication for the presence of arginine when unknown microcystins are analyzed. In-source CID was applied to the characterization of microcystins released into water from a Microcystis aeruginosa culture (UTCC299) (UTCC: University of Toronto Culture Collection of Algae and Cyanobacteria). Six microcystins were detected in extracts from UTCC299: I, [D-Asp(3)]MCYST-LR; II, MCYST-LR; III, isomer of MCYST-LR; IV, isomer of methyl MCYST-LR; V, [D-Asp(3), Glu(OCH(3))(6)]MCYST-LR; and VI, [D-Glu(OCH(3))(6)]MCYST-LR. In-source CID provided mass spectral patterns similar to those obtained by CID in the collision cell of the mass spectrometer but was more sensitive for the analysis of microcystins.     

Enkephalin-based drug design: conformational analysis of O-linked glycopeptides by NMR and molecular modeling

Glycosylation provides an effective means of enhancing penetration of the blood–brain barrier by pharmacologically active peptides. Glycosylated enkephalin analogues demonstrate much greater analgesic effects than their unglycosylated counterparts when administered peripherally. The solution conformations of glycopeptide enkephalin analogues with the sequences H-Tyr-c-[d-Cys-Gly-Phe-d-Cys]-Ser(β-O-Glcp)-Gly-NH₂, 2, and H-Tyr-c-[d-Cys-Gly-Phe-d-Cys]-Ser(α-O-Glcp)-Gly-NH₂, 3, have been determined by NMR and molecular modeling, and were compared to the unglycosylated peptide H-Tyr-c-[d-Cys-Gly-Phe-d-Cys]-Ser-Gly-NH₂, 1, to determine the impact of glycosylation on peptide conformation. The only observed conformational effects were on the residue of attachment, Ser⁶, and on the adjacent Gly⁷-amide. This has important implications in peptide-based drug design in that strategically placed glycosylation can improve transport without destruction of the receptor selectivity of a pre-existing non-glycosylated peptide pharmacophore.     

Detection and characterization of methionine oxidation in peptides by collision-induced dissociation and electron capture dissociation

Electron capture dissociation (ECD) and collision-induced dissociation (CID), the two complementary fragmentation techniques, are demonstrated to be effective in the detection and localization of the methionine sulfoxide [Met(O)] residues in peptides using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. The presence of Met(O) can be easily recognized in the low-energy CID spectrum showing the characteristic loss of methanesulfenic acid (CH(3)SOH, 64 Da) from the side chain of Met(O). The position of Met(O) can then be localized by ECD which is capable of providing extensive peptide backbone fragmentation without detaching the labile Met(O) side chain. We studied CID and ECD of several Met(O)-containing peptides that included the 44-residue human growth hormone-releasing factor (GRF) and the human atrial natriuretic peptide (ANP). The distinction and complementarity of the two fragmentation techniques were particularly remarkable in their effects on ANP, a disulfide bond-containing peptide. While the predominant fragmentation pathway in CID of ANP was the loss of CH(3)SOH (64 Da) from the molecular ion, ECD of ANP resulted in many sequence-informative products, including those from cleavages within the disulfide-bonded cyclic structure, to allow for the direct localization of Met(O) without the typical procedures for disulfide bond reduction followed by [bond]SH alkylation.