Collision-induced Dissociation Mass Research Articles

Incorporating measurement variability when comparing sets of high-resolution mass spectra

Mass spectra are an important signature by which compounds can be identified. We recently formulated a mathematical approach for incorporating measurement variability when comparing sets of high-resolution mass spectra. Leveraging replicate mass spectra, we construct high-dimensional consensus mass spectra—representing each of the compared analytes—and compute the similarity between these data structures. In this paper, we present this approach and discuss its applications and limitations when trying to discriminate methamphetamine and phentermine using in-source collision induced dissociation mass spectra collected with direct analysis in real time mass spectrometry.

Isolation, Identification and Characterization of Two Kinds of Deep-Sea Bacterial Lipopeptides Against Foodborne Pathogens.

Under multiple stresses of deep sea, many microorganisms have evolved potentials to produce different metabolites to cope with the stresses they face. In this study, we isolated a bacterial strain Bacillus sp. YJ17 from the deep-sea cold seep. Compared with commercial food preservative nisin, it showed broad and strong antibacterial activities against foodborne pathogens, including multiple resistant bacteria Pseudomonas aeruginosa PAO1 and methicillin-resistant Staphylococcus aureus (MRSA). The active agents were purified by reversed-phase high performance liquid chromatography (RP-HPLC). Analysis of high-energy collision induced dissociation mass spectrometry (HCD-MS) showed that the two active agents belong to family of fengycin and surfactin, and based on results of tandem mass spectrometry (HCD-MS/MS), the amino acid sequence of purified fengycin and surfactin might be Glu-Orn-Tyr-Thr-Glu-Val-Pro-Gln-Tyr-Ile and Glu-Leu/Ile-Leu/Ile-Leu/Ile-Val-Asp-Leu/Ile, respectively. Since the purified fengycin and surfactin exhibited strong inhibition against P. aeruginosa PAO1 and MRSA respectively, the inhibition mechanisms of fengycin against P. aeruginosa PAO1 and surfactin against MRSA were investigated by electron microscopy. After treatment with purified fengycin, the morphology of P. aeruginosa PAO1 became abnormal and aggregated together, and obvious cytoplasmic leakage was observed. After treatment with purified surfactin, the MRSA cells clustered together, and cell surface became rough and jagged. Further study showed that reactive oxygen species (ROS) accumulation and cell membrane damage occurred in P. aeruginosa PAO1 and MRSA after treated with fengycin and surfactin, respectively. Furthermore, typical ROS scavenging enzymes catalase (CAT) and superoxide dismutase (SOD) were also significantly reduced in P. aeruginosa PAO1 and MRSA after treated with fengycin and surfactin, respectively. Therefore, the inhibition mechanisms of fengycin against P. aeruginosa PAO1 and surfactin against MRSA are closely related with accumulation of ROS, which might be due to the decreased activity of CAT and SOD after treated with fengycin and surfactin, respectively. Overall, our study provides good candidates from the deep-sea environment to deal with foodborne pathogens, especially multidrug-resistant bacteria.

In Silico Tandem Mass Spectrometer: an Analytical and Fundamental Tool

AbstractIn this article, we summarize some aspects of the recently developed computational approach to model and predict collision induced dissociation mass spectra. In particular, we describe how initial conditions can be set to model fragmentation conditions and then obtain different results from the analysis of an ensemble of reactive trajectories. This approach was studied and validated on different systems, from small organic molecules to large biomolecules. Recently an iterative procedure was proposed to increase the fragmentation sampling, reducing computational time and providing a more comprehensive fragmentation pattern. All these fundamental developments are at the basis of the application of this approach to analytical problems. One important and possible outcome will be in creating an in silico data base which will be an useful complement to the experimental ones. This is discussed within other possible future outlooks.

Comprehensive profiling of semi\u2010polar phytochemicals in whole wheat grains (Triticum aestivum) using liquid chromatography coupled with electrospray ionization quadrupole time\u2010of\u2010flight mass spectrometry

IntroductionWheat (Triticum aestivum) it is one of the most important staple food crops worldwide and represents an important resource for human nutrition. Besides starch, proteins and micronutrients wheat grains accumulate a highly diverse set of phytochemicals.ObjectivesThis work aimed at the development and validation of an analytical workflow for comprehensive profiling of semi-polar phytochemicals in whole wheat grains.MethodReversed-phase ultra-high performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry (UHPLC/ESI-QTOFMS) was used as analytical platform. For annotation of metabolites accurate mass collision-induced dissociation mass spectra were acquired and interpreted in conjunction with literature data, database queries and analyses of reference compounds.ResultsBased on reversed-phase UHPLC/ESI-QTOFMS an analytical workflow for comprehensive profiling of semi-polar phytochemicals in whole wheat grains was developed. For method development the extraction procedure and the chromatographic separation were optimized. Using whole grains of eight wheat cultivars a total of 248 metabolites were annotated and characterized by chromatographic and tandem mass spectral data. Annotated metabolites comprise hydroquinones, hydroxycinnamic acid amides, flavonoids, benzoxazinoids, lignans and other phenolics as well as numerous primary metabolites such as nucleosides, amino acids and derivatives, organic acids, saccharides and B vitamin derivatives. For method validation, recovery rates and matrix effects were determined for ten exogenous model compounds. Repeatability and linearity were assessed for 39 representative endogenous metabolites. In addition, the accuracy of relative quantification was evaluated for six exogenous model compounds.ConclusionsIn conjunction with non-targeted and targeted data analysis strategies the developed analytical workflow was successfully applied to discern differences in the profiles of semi-polar phytochemicals accumulating in whole grains of eight wheat cultivars.

Seed treatment with prodigiosin controls damping-off of cucumber caused by Pythium ultimum

Ethanol extract of cell mass of Serratia marcescens strain N4-5, when applied as a treatment to cucumber seed, has been shown to provide control of the oomycete soil-borne plant pathogen Pythium ultimum equivalent to that provided by a seed-treatment chemical pesticide in some soils. Two dominant compounds in this extract, prodigiosin and the serratamolide serrawetin W1, were identified based on mass and collision induced dissociation mass fragmentation spectra. An additional four compounds with M+H+ masses (487, 541, 543, and 571) consistent with serratamolides reported in the literature were also detected. Several other compounds with M+H+ masses of 488, 536, 684, 834, 906, and 908 m/z were detected in this ethanol extract inconsistently over multiple liquid chromatography coupled with tandem mass spectrometry (LC/MS–MS) runs. A purified preparation of prodigiosin provided control of damping-off of cucumber caused by P. ultimum when applied as a seed treatment while ethanol extract of cell mass of strain Tn246, a transposon-mutant-derivative of strain N4-5, did not. Strain Tn246 contained a mini-Tn5 Km insertion in a prodigiosin biosynthetic gene and was deficient in production of prodigiosin. All other compounds detected in N4-5 extract were detected in the Tn246 extract. This is the first report demonstrating that prodigiosin can control a plant disease. Other compounds in ethanol extract of strain N4-5 may contribute to disease control.

A green analytical method for estimation of letermovir in degradation studies

The present established analytical method depicts identification of degradation products of letermovir with the aid of U.P.L.C-M.S/M.S. Letermovir was subjected to hydrolysis, oxidation, photolysis and thermal pressure, according to with I.C.H conditions. The analyte shows degradation in oxidative and photolysis stress conditions. The analyte elution was finished on an intersil ODS column (150 × 4.6 m.m; 5 μ.m) with polar eluent contains water and methanol (20:80%, v/v) in an isocratic elution mode at a flow rate of 0.6m.L/min. The eluents have been monitored through the use of a U.P.L.C-M.S/M.S and linearity range was obtained from 50-500 ng./m.L. The method was found to be stable and precision study was expressed in %R.S.D, ranged from 0.43 to 1.69. The developed method was validated as per I.C.H guidelines. No prior approach became made concerning degradation behavior of letermovir. The multiple reaction monitoring transitions were set at and for Letermovir and Tenofovir disoproxil respectively. The calibration curve was linear over the range of 50-550.00ng/ml with lower limit of quantification validated at 50ng/mL. The inter and intra-day accuracy values were below 15% at all quality control levels. The within run and between run precisions were within 15%, while accuracy ranged from 97.07 to 101.98. The degradation products were characterized by comparing their collision induced dissociation mass spectral data with that of Letermovir and the most possible degradation and fragmentation pathways were identified.

Solution to collision induced dissociation mass spectrometry challenge

Solution to collision induced dissociation mass spectrometry challenge

Theoretical study of perbenzoate anion decomposition pathways in the gas phase

Perbenzoic acid (a weak organic acid) and its conjugate base (perbenzoate anion, C6H5C(O)O2−) are important organic reagents used extensively in synthetic chemistry. A few studies are available in the literature on the structure and reactivity of the perbenzoate anion. Gas phase dissociation of the perbenzoate anion and its substituted analogues by collision induced dissociation mass spectrometry experiments revealed carbon dioxide (CO2) loss as the major dissociation pathway. CO2 loss was proposed to occur via intramolecular nucleophilic attack by the negatively charged oxygen atom at the ipso or ortho position of the benzene ring. In the present work, we investigated decomposition pathways of perbenzoate anion in the gas phase via classical direct chemical dynamics simulations to establish the atomic level reaction mechanisms. Classical trajectories were integrated on-the-fly using the density functional B3LYP/6-31+G* level of electronic structure theory. Removal of CO3, CO2 from the perbenzoate anion and isomerization to an oxydioxirane intermediate were the primary reaction pathways observed in the simulations. In a major fraction of the trajectories, elimination of CO2 happened via initial CO3 loss from the perbenzoate anion followed by removal of O atom from the unstable neutral CO3 molecule.

Quantitative correlations between collision induced dissociation mass spectrometry coupled with electrospray ionization or atmospheric pressure chemical ionization mass spectrometry – Experiment and theory

The problematic that we consider in this paper treats the quantitative correlation model equations between experimental kinetic and thermodynamic parameters of coupled electrospray ionization (ESI) mass spectrometry (MS) or atmospheric pressure chemical ionization (APCI) mass spectrometry with collision induced dissociation mass spectrometry, accounting for the fact that the physical phenomena and mechanisms of ESI– and APCI–ion formation are completely different. There are described forty two fragment reactions of three analytes under independent ESI– and APCI–measurements. The developed new quantitative models allow us to study correlatively the reaction kinetics and thermodynamics using the methods of mass spectrometry, which complementary application with the methods of the quantum chemistry provide 3D structural information of the analytes. Both static and dynamic quantum chemical computations are carried out. The object of analyses are [2,3-dimethyl-4-(4-methyl-benzoyl)-2,3-di-p-tolyl-cyclobutyl]-p-tolyl-methanone (1) and the polycyclic aromatic hydrocarbons derivatives of dibenzoperylen (2) and tetrabenzo [a,c,fg,op]naphthacene (3), respectively. As far as (1) is known to be a product of [2π+2π] cycloaddition reactions of chalcone (1,3-di-p-tolyl-propenone), however producing cyclic derivatives with different stereo selectivity, so that the study provide crucial data about the capability of mass spectrometry to provide determine the stereo selectivity of the analytes. This work also first provides quantitative treatment of the relations ‘3D molecular/electronic structures’–‘quantum chemical diffusion coefficient’–‘mass spectrometric diffusion coefficient’, thus extending the capability of the mass spectrometry for determination of the exact 3D structure of the analytes using independent measurements and computations of the diffusion coefficients. The determination of the experimental diffusion parameters is carried out within the ‘current monitoring method’ evaluating the translation diffusion of charged analytes, while the theoretical modelling of MS ions and computations of theoretical diffusion coefficients are based on the Arrhenius type behavior of the charged species under ESI– and APCI–conditions. Although the study provide certain sound considerations for the quantitative relations between the reaction kinetic–thermodynamics and 3D structure of the analytes together with correlations between 3D molecular/electronic structures–quantum chemical diffusion coefficient–mass spectrometric diffusion coefficient, which contribute significantly to the structural analytical chemistry, the results have importance to other areas such as organic synthesis and catalysis as well.

Dissociation of Gas Phase Ions of Atomically Precise Silver Clusters Reflects Their Solution Phase Stability

We report an attempt to probe into the energy demand of the fragmentation of atomically precise silver clusters using collision induced dissociation mass spectrometry. Energy resolved collisions of several gas phase ions of clusters, Ag29(S2R)12, Ag25(SR)18, and Ag44(SR)30, reveal distinct fragmentation kinetics involving charge separation. The fragmentation pattern of [Ag25(SR)18]− is found to be different from its structural analog, [Au25(SR)18]−. Survival yield analysis has been used to establish a direct comparison between the stability of the ions of these clusters, which reveals that [Ag29(S2R)12]3– is the most stable cluster ion, followed by [Ag25(SR)18]− and [Ag44(SR)30]4–. Gas phase stabilities reflect their solution phase stabilities, indicating that the molecular nature of the clusters is retained in the gas phase, too. We further report that fragmentation occurs in a stepwise fashion, conserving the closed shell electronic stability of the parent ion at each step. Such studies are important in...

Differences in collision-induced dissociation of the protonated molecules of isomeric alkyl phenols

It is shown that isomeric ortho- and para-substituted alkyl phenols are characterized by significant differences in the collision-induced dissociation (CID) mass spectra of their protonated molecules formed at chemical ionization using methane as a reagent gas. Mass spectra of p-substituted isomers contain intensive peaks of characteristic ions [M + H − H2O]+, which are absent from the spectra of o-isomers. Such principal differences in CID mass spectra permit us to distinguish ortho-alkyl phenols from other isomers without using the MS reference data and/or chromatographic retention parameters.

Application of LC/MS systems to structural characterization of flavonoid glycoconjugates

Mass spectrometry is currently one of the most versatile and sensitive instrumental methods applied to structural characterization of plant secondary metabolite mixtures isolated from biological material. Plant tissues contain thousands of natural products fulfilling different roles in plant physiology and biochemistry. These natural products have various biological activities in respect to plants synthesizing them, in their responses to different environmental stresses and are also active principles of food supplements and pharmaceuticals of plant origin. Flavonoids constitute a large group of phenolic secondary metabolites and are probably produced by all terrestrial plant species. More than 9000 glycoconjugates of flavonoids are presently known in the plant kingdom and more than 50 of them may be present in a single plant. For this reason methods of identification and analysis of this group of compounds are particularly demanded. Due to a high number of metabolites present in plant extracts, the isolation and purification of most compounds in amounts suitable for unambiguous characterization with NMR methods is often impossible. For these reasons elaboration of strategies for sufficiently precise structural characterization of compounds present in mixture samples is currently a primary task. Mass spectrometry, thanks to application of different physical phenomena for ionization, separation and detection of analyzed molecules, became the method of choice among analytical methods applied for identification, structural characterization and quantitative analysis of the natural products. Methods of analysis of differently substituted flavonoids (O- and C-glycosides, differentiation of various oligosaccharidic substituents, detection of acylated compounds) are presented in the paper. A proper application of mass spectrometric methods in well-defined and strictly controlled technical parameters of analysis permits obtaining important structural information. Among others, recording collision induced dissociation mass spectra allows identification of compounds after comparison of the registered MS spectra with these present in the existing databases.

Dissociation of the anthracene radical cation: a comparative look at iPEPICO and collision-induced dissociation mass spectrometry results.

The dissociation of the anthracene radical cation has been studied using two different methods: imaging photoelectron photoion coincidence spectrometry (iPEPCO) and atmospheric pressure chemical ionization-collision induced dissociation mass spectrometry (APCI-CID). Four reactions were investigated: (R1) C14H10(+•) → C14H9(+) + H, (R2) C14H9(+) → C14H8(+•) + H, (R3) C14H10(+•) → C12H8(+•) + C2H2 and (R4) C14H10(+•) → C10H8(+•) + C4H2. An attempt was made to assign structures to each fragment ion, and although there is still room for debate whether for the C12H8(+•) fragment ion is a cyclobuta[b]naphthalene or a biphenylene cation, our modeling results and calculations appear to suggest the more likely structure is cyclobuta[b]naphthalene. The results from the iPEPICO fitting of the dissociation of ionized anthracene are E0 = 4.28 ± 0.30 eV (R1), 2.71 ± 0.20 eV (R2), and 4.20 ± 0.30 eV (average of reaction R3) whereas the Δ(‡)S values (in J K(-1) mol(-1)) are 12 ± 15 (R1), 0 ± 15 (R2), and either 7 ± 10 (using cyclobuta[b]naphthalene ion fragment in reaction R3) or 22 ± 10 (using the biphenylene ion fragment in reaction R3). Modeling of the APCI-CID breakdown diagrams required an estimate of the postcollision internal energy distribution, which was arbitrarily assumed to correspond to a Boltzmann distribution in this study. One goal of this work was to determine if this assumption yields satisfactory energetics in agreement with the more constrained and theoretically vetted iPEPICO results. In the end, it did, with the APCI-CID results being similar.

Identification of Antifungal Peptides from Bacillus subtilis BS-918

Bacillus subtilis BS-918 shows strong activity against a broad spectrum of plant and postharvest pathogenic fungi. Antifungal compounds produced by BS-918 were isolated by extraction and gel chromatography, and structural identification was performed by electrospray ionization coupled with collision induced dissociation mass spectrometry. Two kinds of precursor ions belonging to iturin and fengycin were revealed. The first precursor ion at m/z 1071.7 was analyzed by collision induced dissociation mass spectrometry and was identified to be iturin A with a C16 β-amino fatty acid chain. Collision induced dissociation mass spectrometry of the second precursor showed the presence of two fengycins. Ions at m/z 1449.5 and m/z 1463.9 were identified to homologs of fengycin A with C15 and C16 β-hydroxy fatty acid chains, whereas ions at m/z 1477.8 and m/z 1491.9 were homologs of fengycin B with C15 and C16 fatty acid chains.

LC-MS/MS characterization of forced degradation products of ambrisentan: development and validation of a stability-indicating RP-HPLC method

The current study reports the characterization of degradation products of ambrisentan by liquid chromatography-tandem mass spectrometry, and development and validation of a stability-indicating reversed phase high performance liquid chromatographic method for determination of ambrisentan in the presence of its process related impurities in bulk drugs. The drug was subjected to various stress conditions such as hydrolysis, oxidation, photo- and thermal degradations to investigate the stability-indicating ability of the method. Significant degradation was observed during acidic and oxidative stresses. Ambrisentan was well resolved from its process related impurities and degradation products formed under stress conditions. The chromatographic separation was accomplished on an Agilent XDB C18 column (150 × 4.6 mm; 5 μm) with the mobile phase consisting of 10 mM NH4OAc (pH = 5.2) and CH3CN in a gradient elution mode at a flow rate of 1.0 ml min−1. The eluents were monitored by a photodiode array detector at 215 nm and quantitation limits were obtained in the range of 0.07–0.25 μg ml−1 for ambrisentan and all its process related impurities. The developed liquid chromatographic method was validated with respect to accuracy, precision, linearity, robustness and limits of detection and quantitation. The degradation products were characterized by comparing their collision induced dissociation mass spectral data with that of ambrisentan and the most possible degradation and fragmentation pathways were proposed.

Cyanide–Arene Meisenheimer Complex Generated in Electrospray Ionization Mass Spectrometry Using Acetonitrile as a Solvent

The C - C bond formation activated under negative electrospray ionization of an acetonitrile solution of 1,3,5-trinitrobenzene is reported. The solvent function is to provide a source of cyanide ion, a highly problematic reagent, which is found to attack the electron-deficient aromatic ring to form a covalently bound anionic complex (Meisenheimer complex). The structure of the complex is elucidated by means of collision induced dissociation mass spectrometry and IR multiple photon dissociation spectroscopy in the 'fingerprint' region.

Electrospray Ionization and Collision Induced Dissociation Mass Spectrometry of Primary Fatty Acid Amides

Primary fatty acid amides are a group of bioactive lipids that have been linked with a variety of biological processes such as sleep regulation and modulation of monoaminergic systems. As novel forms of these molecules continue to be discovered, more emphasis will be placed on selective, trace detection. Currently, there is no published experimental determination of collision induced dissociation of PFAMs. A select group of PFAM standards, 12 to 22 length carbon chains, were directly infused into an electrospray ionization source Quadrupole Time of Flight Mass Spectrometer. All standards were monitored in positive mode using the [M + H](+) peak. Mass Hunter Qualitative Analysis software was used to calculate empirical formulas of the product ions. All PFAMs showed losses of 14 m/z indicative of an acyl chain, while the monounsaturated group displayed neutral losses corresponding to H(2)O and NH(3). The resulting spectra were used to propose fragmentation mechanisms. Isotopically labeled PFAMs were used to validate the proposed mechanisms. Patterns of saturated versus unsaturated standards were distinctive, allowing for simple differentiation. This determination will allow for fast, qualitative identification of PFAMs. Additionally, it will provide a method development tool for selection of unique product ions when analyzed in multiple reaction monitoring mode.

Binding motifs of silver in prion octarepeat model peptides: a joint ion mobility, IR and UV spectroscopies, and theoretical approach

Transition metal-ion complexation is essential to the function and structural stability of many proteins. We studied silver complexation with the octarepeat motif ProHisGlyGlyGlyTrpGlyGln of the prion protein, which shows competitive sites for metal chelation including amide, indole and imidazole groups. This octapeptide is known as a favourable transition metal binding site in prion protein. We used ion mobility spectrometry (IMS), infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory calculations (DFT) to identify the binding motifs of a silver cation on HisGlyGlyGlyTrp peptide as well as on peptide subsequences. Ultra-violet photodissociation (UVPD) and collision induced dissociation mass spectrometry together with the time-dependent density functional method was then exploited to study the influence of binding sites on optical properties and on the ground and excited states reactivity of the peptide. We show that the metal cation is bound to the π-system of the indole group and a nitrogen atom of the imidazole group and that charge transfers from the indole group to the silver cation occur in excited electronic states.

Identification of Outer Membrane Proteins from an Antarctic Bacterium Pseudomonas syringae Lz4W

Subcellular fractionation of proteins is a preferred method of choice for detection and identification of proteins from complex mixtures such as bacterial cells. To characterize the membrane proteins of the Antarctic bacterium Pseudomonas syringae Lz4W, the membrane fractions were prepared using three different methods, namely Triton X-100 solubilization, sucrose density gradient, and carbonate extraction methods. The proteins were separated on one-dimensional polyacrylamide gels and analyzed using a combination of liquid chromatography-coupled electrospray ionization-MS. The membrane proteins that were prepared by carbonate extraction were separated on two-dimensional PAGE in different pI ranges using the detergent 2% amidosulfobetaine (ASB). The proteins were then subjected to matrix-assisted laser desorption ionization-time-of-flight/time-of-flight for analysis and identification. Because the genome sequence of P. syringae Lz4W is not known, the proteins were identified by using the relevant sequence databases of the Pseudomonas sp available at National Centre for Biotechnology Information (NCBI). The sequence identification of some tryptic peptides were validated by de novo sequencing and others by chemical modification and mass spectrometry. The peptide sequences of P. syringae Lz4W were then matched with the sequences of the peptides from different Pseudomonas sp. by similarity search of the proteins from different species using clustal W2 program. Thus by using a combination of the methods, we have been able to identify large number of proteins of this bacterial strain, which include most of the outer membrane proteins.

Use of collision induced dissociation mass spectrometry as a rapid technique for the identification of pharmacologically active peptides in pharmacopoeial testing

The applicability of collision induced dissociation mass spectrometry (CID-MS) for the pharmacopoeial identification of pharmacologically active peptides was examined. Two different classes of related peptides were selected, i.e. four synthetic gonadotropin releasing hormone analogues (gonadorelin, goserelin, buserelin and leuprorelin) being either nona- or decapeptides, and human insulin and 2 insulin analogues (insulin lispro and insulin aspart). For all these substances the pharmacopoeial identification currently requires a combination of several partly rather laborious tests using sophisticated equipment. In contrast, CID-MS as a stand alone test can provide increased reassurance about the identity and is rapid and efficient. Moreover, the substance consumption for testing is significantly lower, which is a non-negligible factor for very expensive substances.