Probing Conformational Changes of Ubiquitin by Host–Guest Chemistry Using Electrospray Ionization Mass Spectrometry

We report mechanistic studies of structural changes of ubiquitin (Ub) by host–guest chemistry with cucurbit[6]uril (CB[6]) using electrospray ionization mass spectrometry (ESI-MS) combined with circular dichroism spectroscopy and molecular dynamics (MD) simulation. CB[6] binds selectively to lysine (Lys) residues of proteins. Low energy collision-induced dissociation (CID) of the protein-CB[6] complex reveals CB[6] binding sites. We previously reported (Anal. Chem. 2011, 83, 7916–7923) shifts in major charge states along with Ub-CB[6] complexes in the ESI-MS spectrum with addition of CB[6] to Ub from water. We also reported that CB[6] is present only at Lys₆ or Lys₁₁ in high charge state (+13) complex. In this study, we provide additional information to explain unique conformational change mechanisms of Ub by host–guest chemistry with CB[6] compared with solvent-driven conformational change of Ub. Additional CID study reveals that CB[6] is bound only to Lys₄₈ and Lys₆₃ in low charge state (+7) complex. MD simulation studies reveal that the high charge state complexes are attributed to the CB[6] bound to Lys₁₁. The complexation prohibits salt bridge formation between Lys₁₁ and Glu₃₄ and induces conformational change of Ub. This results in formation of high charge state complexes in the gas phase. Then, by utilizing stronger host–guest chemistry of CB[6] with pentamethylenediamine, refolding of Ub via detaching CB[6] from the protein is performed. Overall, this study gives an insight into the mechanism of denatured Ub ion formation via host-guest interactions with CB[6]. Furthermore, this provides a direction for designing function-controllable supramolecular system comprising proteins and synthetic host molecules.      

Novel Rearrangement of Small Peptides in Electrospray Ionization Tandem Mass Spectrometry

Electrospray ionization mass spectrometry (ESI-MS) is a powerful method for sequencing peptides. A novel fragmentation pattern with the loss of a neutral fragment of 45 Da was observed with the dipeptides, tripeptides,tetrapeptides and pentapeptides containing phenylalanine or histidine residues. A novel rearrangement reaction with the extrusion of a formamide piece was studied and the rearrangement mechanism was proposed and confirmed by deuterium labeling experiments with ESI-MS^n and high-resolution mass spectrometry. These findings are potentially helpful in identifying the specific sequence pattern in the peptide sequencing.     

Dissociation Kinetics of the Streptavidin–Biotin Interaction Measured Using Direct Electrospray Ionization Mass Spectrometry Analysis

Dissociation rate constants (k _off ) for the model high affinity interaction between biotin (B) and the homotetramer of natural core streptavidin (S₄) were measured at pH 7 and temperatures ranging from 15 to 45 °C using electrospray ionization mass spectrometry (ESI-MS). Two different approaches to data analysis were employed, one based on the initial rate of dissociation of the (S₄? + ?4B) complex, the other involving nonlinear fitting of the time-dependent relative abundances of the (S₄? + ?iB) species. The two methods were found to yield k _off values that are in good agreement, within a factor of two. The Arrhenius parameters for the dissociation of the biotin–streptavidin interaction in solution were established from the k _off values determined by ESI-MS and compared with values measured using a radiolabeled biotin assay. Importantly, the dissociation activation energies determined by ESI-MS agree, within 1 kcal?mol^–1, with the reported value. In addition to providing a quantitative measure of k _off , the results of the ESI-MS measurements revealed that the apparent cooperative distribution of (S₄? + ?iB) species observed at short reaction times is of kinetic origin and that sequential binding of B to S₄ occurs in a noncooperative fashion with the four ligand binding sites being kinetically and thermodynamically equivalent and independent.      

Qualitative Gas Chromatography–Mass Spectrometry Analyses Using Amines as Chemical Ionization Reagent Gases

Ammonia is a very useful chemical ionization (CI) reagent gas for the qualitative analyses of compounds by positive ion gas chromatography–mass spectrometry (GCMS). The gas is readily available, inexpensive, and leaves no carbon contamination in the MS source. Compounds of interest to our laboratory typically yield abundant protonated or ammoniated species, which are indicative of a compound’s molecular weight. Nevertheless, some labile compounds fragment extensively by substitution and elimination reactions and yield no molecular weight information. In these cases, a CI reagent gas mixture of methylamine in methane prepared dynamically was found to be very useful in obtaining molecular weight data. Likewise, deuterated ammonia and deuterated methylamine are useful CI reagent gases for determining the exchangeable protons in organic compounds. Deuterated methylamine CI reagent gas is conveniently prepared by dynamically mixing small amounts of methylamine with excess deuterated ammonia.

Electrospray Ionization Mass Spectrometry of Hexanitrohexaazaisowurtzitane (CL‐20)

Abstract

Hexanitrohexaazaisowurzitane (CL‐20) is a newly developed propellant and has been examined using negative ion electrospray mass spectrometry. The primary ions observed included adduct ions (M+Cl)^– and (M+ONO₂)^?.     

Analysis of the Aconitine Alkaloids in Chuanwu by Electrospray Ionization ／ Tandem Mass Spectrometry

An electrospray ionization / tandem mass spectrometric (ESUMS/MS) method was developed for the simultaneous identification and analysis of three aconitine alkaloids [mesacontine (MA), hypaconitine (HA), and aconitine (A)] as intact molecules at low nanogram level in Chinese traditional medicine Chuanwu decoction as well as in human whole blood extract without chromatographic separation.     

New Fragmentation Pathways for Cephalosporins by Electrospray Ionization Quadrupole Time-of-flight Mass Spectrometry

Introduction Cephalosporins are antibiotics of β-lactam family. They have a broad spectrum of antibiotic activity due to their ability to inhibit bacterial cell wall synthesis of different Gram-positive and Gram-negative bacteria. Cephalosporins are used orally or parenterally to treat a wide variety of infections throughout the body and are often prescribed to fight penicillin resistant microorganisms.     

Sequence pattern Correlation of Amino Acid in Collision—induced Dissociation Electrospray Ionization Mass Spectrometry

A novel approach of seuqence pattern correlation has been applied to predict an expected amino acid sequence from CID ESI-MS spectra.The proposed approach deduces sequence patterns with no help form known protein database such that it is useful to identify an unknown petide or new protein.The algorithm applies a cross-correlation to match an experimental CID spectrum with predicted sequence pattern generated form fragmentation information.The fragmentation knowledge of both y-series and other non y-series are utilized to generate the predicted sequence patterns.In contrast to the normal de novo approach,the proposed approach is insensitive to mass tolerance and non-sussceptive to spectral integrality with no need for selection of a starting point.     

High Pressure (>1 atm) Electrospray Ionization Mass Spectrometry

High pressure electrospray ionization mass spectrometry has been performed by pressurizing a custom made ion source chamber with compressed air to a pressure higher than the atmospheric pressure. The ion source was coupled to a commercial time-of-flight mass spectrometer using a nozzle-skimmer arrangement. The onset voltage for the electrospray of aqueous solution was found to be independent on the operating pressure. The onset voltage for the corona discharge, however, increased with the rise of pressure following the Paschen’s law. Thus, besides having more working gas for the desolvation process, gaseous breakdown could also be avoided by pressurizing the ESI ion source with air to an appropriate level. Stable electrospray ionization has been achieved for the sample solution with high surface tension such as pure water in both positive and negative ion modes. Fragmentation of labile compounds during the ionization process could also be reduced by optimizing the operating pressure of the ion source.     

Protein–Protein Binding Affinities in Solution Determined by Electrospray Mass Spectrometry

Electrospray ionization (ESI) allows the transfer of multi-protein complexes into the gas phase, thereby providing a simple approach for monitoring the stoichiometry of these noncovalent assemblies by mass spectrometry (MS). It remains unclear, however, whether the measured ion abundance ratios of free and bound species are suitable for determining solution-phase binding affinities (K _d values). Many types of mass spectrometers employ rf-only quadrupoles as ion guides. This work demonstrates that the settings used for these devices are a key factor for ensuring uniform transmission behavior, which is a prerequisite for meaningful affinity measurements. Using bovine β-lactoglobulin and hemoglobin as model systems, it is demonstrated that under carefully adjusted conditions the “direct” ESI-MS approach is capable of providing K _d values that are in good agreement with previously published solution-phase data. Of the several ion sources tested, a regular ESI emitter operated with pressure-driven flow at 1 μL min^–1 provided the most favorable results. Potential problems in these experiments include conformationally-induced differences in ionization efficiencies, inadvertent collision-induced dissociation, and ESI-induced clustering artifacts. A number of simple tests can be conducted to assess whether or not these factors are prevalent under the conditions used. In addition, the fidelity of the method can be scrutinized by performing measurements over a wide concentration range. Overall, this work supports the viability of the direct ESI-MS approach for determining binding affinities of protein–protein complexes in solution.     

Elucidation of O-Phosphoryl and N-Phosphoryl Amino Acids by Electrospray Ionization Tandem Mass Spectrometry

Mass spectroscopic characteristics of phosphoryl amino acids were studied in detail by positive and negative electrospray ionization mass spectrometry (ESI-MS) in conjunction with tandem mass spectrometry (MS/MS). Besides N-diisopropyloxyphosphoryl amino acids (N-DIPP-AA), O-phospho- and O-diisopropyloxyphosphoryl amino acids (O-DIPP-AA) were studied and compared to N-DIPP-AA. The fragmentation pathways of [M H]^ ,[M Na]^ and [M-H]^- ions of phosphoryl amino acids were summarized. In addition to several similar patterns, each of them showed its characteristic fragmention.     

Determination of Phenylethanoid Glycosides in Lagotis brevituba Maxim. by High-Performance Liquid Chromatography–Electrospray Ionization Tandem Mass Spectrometry

High performance liquid chromatography coupled with electrospray ionization quadrupole-time-of-flight tandem mass spectrometry was used to profile the phenylethanoid glycosides in Lagotis brevituba. A total of twenty-three phenylethanoid glycosides were characterized by comparing the retention time and fragmentation with standards, accurate mass measurements, and fragmentation at low and high collision energies. Most phenylethanoid glycosides were reported in L. brevituba for the first time. This established method may be employed for comprehensive quality control of L. brevituba.     

Improved Accuracy of Low Affinity Protein–Ligand Equilibrium Dissociation Constants Directly Determined by Electrospray Ionization Mass Spectrometry

There is continued interest in the determination by ESI-MS of equilibrium dissociation constants (K_D) that accurately reflect the affinity of a protein–ligand complex in solution. Issues in the measurement of K_D are compounded in the case of low affinity complexes. Here we present a K_D measurement method and corresponding mathematical model dealing with both gas-phase dissociation (GPD) and aggregation. To this end, a rational mathematical correction of GPD (f_sat) is combined with the development of an experimental protocol to deal with gas-phase aggregation. A guide to apply the method to noncovalent protein–ligand systems according to their kinetic behavior is provided. The approach is validated by comparing the K_D values determined by this method with in-solution K_D literature values. The influence of the type of molecular interactions and instrumental setup on f_sat is examined as a first step towards a fine dissection of factors affecting GPD. The method can be reliably applied to a wide array of low affinity systems without the need for a reference ligand or protein.     

Solution or Gas Phase? Oxidation and Radical Formation in Electrospray Ionization Mass Spectrometry (ESI MS)

The relationship between one‐electron (e^?) oxidation processes and the formation of radical cations of endogenous and exogenous compounds in vivo is of considerable interest. This paper reports on the experiments that allow FTICR mass spectrometric (MS) detection of ion signals that are consistent with the formation of radical cations of caffeine (CA) and theophylline (TP) during electrospray ionization (ESI) in ESI FTICR MS and in on‐line electrochemistry (EC)/ESI FTICR MS in positive mode. Significantly, the signals of the radicals of CA^?+ and TP^?+can be enhanced by simple modifications of the operating conditions in ESI MS, facilitating investigations of radical formation and related reactions.     

Determination of n-Alkanes in Jet Fuel by Cold-electron Ionization Gas Chromatography–Mass Spectrometry

A rapid, easy, and reliable method was developed for the characterization of jet fuel with minimal sample preparation. A standard solution of 13 aliphatic n-alkanes in hexane was used to evaluate and validate the separation using cold-electron ionization gas chromatography–mass spectrometry. The method was evaluated and validated by the linearity, accuracy, and precision for all analytes. The limits of detection and quantification for each n-alkane were also evaluated. Nine major n-alkanes from n-octane to n-hexadecane were positively identified and quantified in jet fuel due to the enhanced molecular ion in the mass spectra. Major n-alkanes and their corresponding isomers in jet fuel were also identified from the extracted ion chromatograms. n-Undecane, n-dodecane, n-tridecane, and n-tetradecane were present at the highest concentrations in jet fuel at approximately 7% (v/v). The total concentrations of total straight chain alkanes were 34–37% in jet fuel that was comparable with the standard value of 32%.     

Analysis of Norditerpenoid Alkaloids. Extracted from Aconitum sinomantanum Nakai by Electrospray Ionization Tandem Mass Spectrometry

Introduction AconitumsinomantanumNakai(GaowutouinChi nese)isdistributedinthenorthwesternareaofChina,anditsroots(RAS)areexternallyusedasakindof folkmedicineinChina.Themainactiveconstituentsof RASarenorditerpenoidalkaloids.Themajoralkaloid,lappaconitine,was…     

Gas-Phase Fragmentation Studies of Biotinylated,Hexaethylene Glycol–Spacered Oligosaccharides—Molecular Probes—Using Electrospray Mass Spectrometry on a Hybrid High-Resolution Mass Spectrometer

The electrospray ionization high-resolution mass spectra of biotinylated hexaethylene glycol–spacered molecular probes bearing biologically relevant carbohydrate moieties in positive and negative modes were recorded and interpreted. Collisionally induced decay mass spectra (positive mode) revealed different patterns depending on the charge of the parent ion, attached cations (or ions), the composition, and the sequence of carbohydrate fragments. The most intense peaks (two series) originated from the sequential cleavage of glycoside bonds resulting in charge location on the reducing end (Y series observed for all of the test compounds) or nonreducing end (B series). Hexaethylene glycol chain fragmentation giving rise to the cleavage of the C–O bond remote from the biotin moiety was observed. Other fragment ions lighter than the above by a difference of (C₂H₄O) _n were absent or much smaller. Similar fragmentation was found for all of the nonsulfated biotinylated glycosides with the hexaethylene glycol spacer thus demonstrating that this type of fragmentation was characteristic of such molecular probes. Similar cleavages along with biotin moiety decay via the elimination of H₂S and H₂CS were observed for negative ions in the collisionally induced decay mass spectra of sulfated and neutral molecular probes.     

Rapid Determination of Coumatetralyl in Human Serum by High‐Performance Liquid Chromatography Coupled with Electrospray Ionization Tandem Mass Spectrometry

Abstract

A rapid, sensitive, and selective high‐performance liquid chromatography‐tandem mass spectrometric method (HPLC‐MS‐MS) for the determination of coumatetralyl in human serum using warfarin as an internal standard has been developed and validated. Coumatetralyl and the internal standard were extracted from the human serum samples by liquid‐liquid extraction with ethyl acetate, followed by separation on a XDB C₁₈ reversed‐phase column (150 mm×2.1 mm i.d., 5 µm) using a mobile phase consisting of acetic acid‐ammonium acetate (5 mmol/L, pH=4.5)/methanol (20:80, v/v) at a constant flow rate of 0.40 mL/min. Coumatetralyl and the internal standard were ionized by negative ion pneumatically assisted electrospray and detected in the multiple‐reaction monitoring mode using precursor→product ion combinations at m/z 291→247 and 307→161, respectively. The calibration curve was linear (r²=0.9945) in the concentration range of 0.5～100.0 ng/mL, with a lower limit of quantification of 0.5 ng/mL in human serum. Intra‐ and inter‐day relative standard deviations were less than 6.3 and 11.0%, respectively. The mean extraction recovery was 87.9% for coumatetralyl and 90.1% for the internal standard. This method is found to be able to determine trace coumatetralyl in human serum and can be used for the diagnosis of poisoned human beings.     

Atmospheric Pressure Photo Ionization Hydrogen/Deuterium Exchange Mass Spectrometry—a Method to Differentiate Isomers by Mass Spectrometry

In this report, a method for in-source hydrogen/deuterium (H/D) exchange at atmospheric pressure is reported. The method was named atmospheric pressure photo ionization hydrogen/deuterium exchange mass spectrometry (APPI HDX MS). H/D exchange was performed by mixing samples dissolved in toluene with CH₃OD solvent and analyzing the mixture using atmospheric pressure photo ionization mass spectrometry (APPI-MS). The APPI HDX spectra obtained with contact times between the analyte solution and methanol-OD (CH₃OD) of?<?0.5 s or 1 h showed the same pattern of H/D exchange. Therefore, it was concluded that APPI HDX occurred in the source but not in the solution. The proposed method does not require a specific type of mass spectrometer and can be performed at atmospheric pressure. H/D exchange can be performed in any laboratory with a mass spectrometer and a commercial APPI source. Using this method, multiple H/D exchanges of aromatic hydrogen and/or H/D exchange of active hydrogen were observed. These results demonstrated that H/D exchange can be used to distinguish between isomers containing primary, secondary, and tertiary amines, as well as pyridine and pyrrole functional groups.