Mapping a Noncovalent Protein–Peptide Interface by Top-Down FTICR Mass Spectrometry Using Electron Capture Dissociation

Noncovalent protein–ligand and protein–protein complexes are readily detected using electrospray ionization mass spectrometry (ESI MS). Furthermore, recent reports have demonstrated that careful use of electron capture dissociation (ECD) fragmentation allows covalent backbone bonds of protein complexes to be dissociated without disruption of noncovalent protein–ligand interactions. In this way the site of protein–ligand interfaces can be identified. To date, protein–ligand complexes, which have proven tractable to this technique, have been mediated by ionic electrostatic interactions, i.e., ion pair interactions or salt bridging. Here we extend this methodology by applying ECD to study a protein–peptide complex that contains no electrostatics interactions. We analyzed the complex between the 21 kDa p53-inhibitor protein anterior gradient-2 and its hexapeptide binding ligand (PTTIYY). ECD fragmentation of the 1:1 complex occurs with retention of protein–peptide binding and analysis of the resulting fragments allows the binding interface to be localized to a C-terminal region between residues 109 and 175. These finding are supported by a solution-phase competition assay, which implicates the region between residues 108 and 122 within AGR2 as the PTTIYY binding interface. Our study expands previous findings by demonstrating that top-down ECD mass spectrometry can be used to determine directly the sites of peptide–protein interfaces. This highlights the growing potential of using ECD and related top-down fragmentation techniques for interrogation of protein–protein interfaces.     

Gas-Phase Binding of Noncovalent Complexes Between α-cyclodextrin and Amino Acids Investigated by Mass Spectrometry

Noncovalent complexes between cyclodextrins and small molecules have been extensively studied recently because of their widespread application in the pharmaceutical industry for chiral and molecular recognition. To date, gas phase noncovalent binding affinities between α-cyclodextrin and amino acids have not been widely investigated. In this study, gas-phase binding of noncovalent complexes between α-CD and amino acids was investigated by electrospray ionization mass spectrometry (ESI-MS), demonstrating the formation of 1:1 stoichiometric noncovalent complexes. The binding of the complexes were further confirmed by collision-induced dissociation by tandem mass spectrometry. Mass spectrometric titrations between α-cyclodextrin and phenylalanine, glutamic acid, and arginine were performed to provide binding constants (lgK_a) as references for competitive ESI-MS. Calibration curves for the complexes of α-cyclodextrin with phenylalanine, glutamic acid, and arginine were plotted. Through competitive ESI-MS, the lgK_a for the complexes of α-CD with aspartic acid, lysine, proline, glycine, alanine, asparagine, cystine, glutamine, histidine, leucine, isoleucine, methionine, serine, threonine, and valine were measured directly. By comparison, it is seen that the measured binding constants for the complexes of α-cyclodextrin with basic amino acids such as arginine and lysine are lower than those for most complexes of neutral amino acids. The chiral selectivity of α-cyclodextrin for L- and D-isomers of methionine, threonine, asparagine, and phenylalanine determined by ESI-MS revealed its application as a chiral selector.     

Ion Mobility Measurements of Nondenatured 12–150 kDa Proteins and Protein Multimers by Tandem Differential Mobility Analysis–Mass Spectrometry (DMA-MS)

The mobilities of electrosprayed proteins and protein multimers with molecular weights ranging from 12.4 kDa (cytochrome C monomers) to 154 kDa (nonspecific concanavalin A hexamers) were measured in dry air by a planar differential mobility analyzer (DMA) coupled to a time-of-flight mass spectrometer (TOF-MS). The DMA determines true mobility at atmospheric pressure, without perturbing ion structure from that delivered by the electrospray. A nondenaturing aqueous 20 mM triethylammonium formate buffer yields compact ions with low charge states, moderating polarization effects on ion mobility. Conversion of mobilities into cross-sections involves a reduction factor ξ for the actual mobility relative to that associated with elastic specular collisions with smooth surfaces. ξ is known to be 1.36 in air from Millikan’s oil drop experiments. A similar enhancement effect ascribed to atomic-scale surface roughness has been found in numerical simulations. Adopting Millikan’s value ξ = 1.36 and assuming a spherical geometry yields a gas-phase protein density ρ _p = 0.949 ± 0.053 g cm⁻³ for all our protein data. This is substantially higher than the 0.67 g cm⁻³ found in recent low-resolution DMA measurements of singly charged proteins. DMA-MS can distinguish nonspecific protein aggregates formed during the electrospray process from those formed preferentially in solution. The observed charge versus diameter relation is compatible with a protein charge reduction mechanism based on the evaporation of triethylammonium ions from electrosprayed drops.     

Probing the Gaseous Structure of a β-Hairpin Peptide with H/D Exchange and Electron Capture Dissociation

An improved understanding of the extent to which native protein structure is retained upon transfer to the gas phase promises to enhance biological mass spectrometry, potentially streamlining workflows and providing fundamental insights into hydration effects. Here, we investigate the gaseous conformation of a model β-hairpin peptide using gas-phase hydrogen–deuterium (H/D) exchange with subsequent electron capture dissociation (ECD). Global gas-phase H/D exchange levels, and residue-specific exchange levels derived from ECD data, are compared among the wild type 16-residue peptide GB1p and several variants. High protection from H/D exchange observed for GB1p, but not for a truncated version, is consistent with the retention of secondary structure of GB1p in the gas phase or its refolding into some other compact structure. Four alanine mutants that destabilize the hairpin in solution show levels of protection similar to that of GB1p, suggesting collapse or (re)folding of these peptides upon transfer to the gas phase. These results offer a starting point from which to understand how a key secondary structural element, the β-hairpin, is affected by transfer to the gas phase. This work also demonstrates the utility of a much-needed addition to the tool set that is currently available for the investigation of the gaseous conformation of biomolecules, which can be employed in the future to better characterize gaseous proteins and protein complexes.

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Structural Characterization and Disulfide Assignment of Spider Peptide Phα1β by Mass Spectrometry

Native Phα1β is a peptide purified from the venom of the armed spider Phoneutria nigriventer that has been shown to have an extensive analgesic effect with fewer side effects than ω-conotoxin MVIIA. Recombinant Phα1β mimics the effects of the native Phα1β. Because of this, it has been suggested that Phα1β may have potential to be used as a therapeutic for controlling persistent pathological pain. The amino acid sequence of Phα1β is known; however, the exact structure and disulfide arrangement has yet to be determined. Determination of the disulfide linkages and exact structure could greatly assist in pharmacological analysis and determination of why this peptide is such an effective analgesic. Here, we used biochemical and mass spectrometry approaches to determine the disulfide linkages present in the recombinant Phα1β peptide. Using a combination of MALDI-MS, direct infusion ESI-MS, and nanoLC-MS/MS analysis of the undigested recombinant Phα1β peptide and digested with AspN, trypsin, or AspN/trypsin, we were able to identify and confirm all six disulfide linkages present in the peptide as Cys1-2, Cys3-4, Cys5-6, Cys7-8, Cys9-10, and Cys11-12. These results were also partially confirmed in the native Phα1β peptide. These experiments provide essential structural information about Phα1β and may assist in providing insight into the peptide’s analgesic effect with very low side effects.

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Direct Infusion Electrospray Ionization – Ion Mobility – High Resolution Mass Spectrometry (DIESI-IM-HRMS) for Rapid Characterization of Potential Bioprocess Streams

Direct infusion electrospray ionization?-?ion mobility?-?high resolution mass spectrometry (DIESI-IM-HRMS) has been utilized as a rapid technique for the characterization of total molecular composition in "whole-sample" biomass hydrolysates and extracts. IM-HRMS data reveal a broad molecular weight distribution of sample components (up to 1100 m/z) and provide trendline isolation of feedstock components from those introduced "in process." Chemical formulas were obtained from HRMS exact mass measurements (with typical mass error less than 5 ppm) and were consistent with structural carbohydrates and other lignocellulosic degradation products. Analyte assignments are supported via IM-MS collision-cross-section measurements and trendline analysis (e.g., all carbohydrate oligomers identified in a corn stover hydrolysate were found to fall within 6% of an average trendline). These data represent the first report of collision cross sections for several negatively charged carbohydrates and other acidic species occurring natively in biomass hydrolysates.     

Analysis of Soil by Magnetic Field Assisted Calibration-Free Laser Induced Breakdown Spectroscopy (CF-LIBS) and Laser Ablation – Time-of-Flight Mass Spectrometry (LA-TOF-MS)

The qualitative and quantitative analysis of soil samples collected from Sialkot, Pakistan (which contains leather industrial plants), has been performed using laser-induced breakdown spectroscopy (LIBS) and laser ablation time of flight mass spectrometry (LA-TOF-MS). The focused beam of a Q-switched Nd: YAG laser (532?nm) was used to ablate the soil samples in air at atmospheric pressure. The optical emission spectra demonstrate the presence of the spectral lines of Si, Fe, Al, Ca, Ti, K, Cr, Mg, Na, Ba, and Li in all of the samples. The emission lines intensities, electron number densities, and excitation temperatures were significantly enhanced in the presence of an external 0.3 T magnetic field applied perpendicular to the plasma plume. A maximum enhancement factor of approximately 8 was observed in the emission intensity. The emergence of several additional lines has also been detected using the magnetic field-assisted LIBS approach. The elemental composition determined using calibration-free laser-induced breakdown spectroscopy (CF-LIBS), with and without magnetic field, reveals that the external magnetic field only adjusts the laser-generated plasma dynamics without affecting the quantitative analysis of the samples. Importantly, the toxic and heavy elements such as chromium and barium were detected and quantified in all of the soil samples by both of these techniques. The variations in the compositional analysis using CF-LIBS with and without the applied magnetic field and LA-TOF-MS were less than 10%.     

Determination of the Chemical Structure of Poly-β (-)-pinene by NMR Spectroscopy

This paper is dedicated to the memory of our friend and colleague Annalaura Segre.

The chemical structure of a series of β (-)-pinene polymers (PBP) obtained by radiation-induced polymerization, free radical initiation, cationic polymerization over a Friedel-Craft catalyst and by coordinative polymerization over a Ziegler-Natta catalyst has been fully elucidated by ¹H and ¹³C-NMR spectroscopy. 2D NMR techniques have been applied in order to assign all the NMR resonances to the structures of the PBP investigated. The NMR spectra show that the most regular PBP structure is obtained by radiation-induced polymerization followed by the free radical initiated polymerization. The most defective structure has been observed in the case of PBP prepared by cationic mechanism over a Friedel-Crafts catalyst. The discussion accounts for different types of defects and cross-links present in the PBPs investigated whose fundamental structure is based on the p-menthene repeating unit.

NMR self-diffusion measurements have been performed to evaluate the molecular weight of all the PBP investigated. The highest molecular weight (2600 Dalton) was found in the case of PBP prepared by Ziegler-Natta catalyst, while the lowest molecular weight was found in the case of PBP prepared by radiation-induced polymerization (about 1000 Dalton).     

Elemental Analysis of Cement by Calibration-Free Laser Induced Breakdown Spectroscopy (CF-LIBS) and Comparison with Laser Ablation – Time-of-Flight – Mass Spectrometry (LA-TOF-MS), Energy Dispersive X-Ray Spectrometry (EDX), X-Ray Fluorescence Spectroscopy (XRF), and Proton Induced X-Ray Emission Spectrometry (PIXE)

The purpose of the present study is to determine the elemental composition of Pakistani cement brands using calibration-free laser induced breakdown spectroscopy (CF-LIBS) and to compare the obtained results with the other analytical techniques such as, laser ablation – time-of-flight – mass spectrometry (LA-TOF-MS), energy dispersive X-ray spectrometry (EDX), X-ray fluorescence spectroscopy (XRF) and proton induced X-ray emission spectrometry (PIXE). Compositional results reveal that all the cement brands are mainly composed of calcium, silicon, iron, aluminum, magnesium, potassium, sodium, titanium, lithium and strontium with varying concentrations. The compositions obtained by LIBS and LA-TOF-MS are in good agreement with results obtained by the other standard techniques and demonstrate the potential use of LIBS for the online monitoring of industrial cement production.     

Mass Spectrometry Study of Multiply Negatively Charged, Gas-Phase NaAOT Micelles: How Does Charge State Affect Micellar Structure and Encapsulation?

We report the formation and characterization of multiply negatively charged sodium bis(2-ethylhexyl) sulfosuccinate (NaAOT) aggregates in the gas phase, by electrospray ionization of methanol/water solution of NaAOT followed by detection using a guided-ion-beam tandem mass spectrometer. Singly and doubly charged aggregates dominate the mass spectra with the compositions of [Na_n-zAOT_n]^z– (n?=?1–18 and z?=?1–2). Solvation by water was detected only for small aggregates [Na_n-1AOT_nH₂O]^– of n?=?3–9. Incorporation of glycine and tryptophan into [Na_n-zAOT_n]^z– aggregates was achieved, aimed at identifying effects of guest molecule hydrophobicity on micellar solubilization. Only one glycine molecule could be incorporated into each [Na_n-zAOT_n]^z– of n?≥?7, and at most two glycine molecules could be hosted in that of n?≥?13. In contrast to glycine, up to four tryptophan molecules could be accommodated within single aggregates of n?≥?6. However, deprotonation of tryptophan significantly decrease its affinity towards aggregates. Collision-induced dissociation (CID) was carried out for mass-selected aggregate ions, including measurements of product ion mass spectra for both empty and amino acid-containing aggregates. CID results provide a probe for aggregate structures, surfactant-solute interactions, and incorporation sites of amino acids. The present data was compared with mass spectrometry results of positively charged [Na_n+zAOT_n]^z+ aggregates. Contrary to their positive analogues, which form reverse micelles, negatively charged aggregates may adopt a direct micelle-like structure with AOT polar heads exposed and amino acids being adsorbed near the micellar outer surface.      

Structure of AcMet-Gly and Its Interaction with Palladium(II) Tetraaqua Complex Studied by Electrospray Mass Spectrometry and Density Functional Theory

Introduction Palladium(II) complexes, as a promising artificial metallopeptidase, have been extensively studied for se-lective cleavage of methionine and histidine-containing dipeptides,1-11 oligopeptides12-16 and proteins.16-20 Dipeptides AcMet-aa and AcHis-aa, in which the amino-terminus is protected by acetylation and aa is an amino acid residue, are usually cleaved at the Met-aa and His-aa bond with a modest but significant turn-over.6,7,9 In oligopeptides which contain Met or His or b…     

Discrimination of Chili Powder Origin Using Inductively Coupled Plasma–Mass Spectrometry (ICP-MS), Inductively Coupled Plasma–Optical Emission Spectroscopy (ICP-OES), and Near Infrared (NIR) Spectroscopy

This study investigated the content of macronutrients (Ca, K, Mg, Na, P, and S), trace elements (Ba, Be, Co, Cr, Cu, Fe, Ga, Li, Mn, Ni, Rb, Se, Sr, V, and Zn), and trace toxic elements (As, Cd, In, Pb, and Tl) in chili powder from Korea, China, and Vietnam. For the analyses, inductively coupled plasma mass spectrometry (ICP-MS) and inductively coupled plasma-optical emission spectroscopy (ICP-OES) were used. In addition, near-infrared (NIR) spectroscopy was used to differentiate functional groups based on the chemical constituents. For the validation of the applied analytical methods, good linearity (coefficients of determination, 0.9443–0.99997), and relative standard deviations below 4% were obtained. The contents of the toxic elements were below the provisional tolerable weekly intake values. Linear discriminant analysis using elemental contents and NIR data was performed to establish and authenticate the geographical origin of chili powder, which confirmed the reliability of the obtained results.     

Structure and Energy Studies of β-Diketonates. X. Molecular Structure of Sc(aa)3 According to Gas-Phase Electron Diffraction Data

Synchronous electron diffraction and mass spectrometric investigation of the saturated vapor of scandium tris-acetylacetonate was carried out. It was stated that at 155(5)°C the vapor contains only monomeric Sc(aa)₃ molecules, whose structural parameters r _a , r _g , and r were determined. The internuclear distances in the chelate ring were found to be r (Sc–O) = 2.076(4) , r (O–C) = 1.271(3) , r (C–C_r) = 1.386(4) . The coordination polyhedron ScO₆ has a nearly antiprism structure of D ₃ symmetry. The angle of rotation of the O–O–O trigonal faces relative to their position in a regular prism is 26.8(1.1)°.     

Determination of Electron and Hole Mobility of Regioregular Poly(3‐hexylthiophene) by the Time of Flight Method

Time of flight method (TOF) is used to measure the electron and hole mobility of a spin coated regioregular poly(3‐hexylthiophene) (P3HT) film. We find that both electron and hole have the same mobility (about 3.8～3.9×10^?4 cm²/Vs) at an applied field of 120 kV/cm. It is demonstrated in this paper that the electron‐hole recombination process may prevent the electron transport in the material due to the fact that the carrier recombination time is much shorter than the transit time.     

Changes of the Molecular Mobility of Poly(ε-caprolactone) upon Drawing,Studied by Dielectric Relaxation Spectroscopy

Dielectric relaxation spectroscopy(DRS) of poly(ε-caprolactone) with different draw ratios showed that the mobility of polymer chains in the amorphous part decreases as the draw ratio increases. The activation energy of the α process, which corresponds to the dynamic glass transition, increases upon drawing. The enlarged gap between the activation energies of the α process and the β process results in a change of continuity at the crossover between the high temperature a process and the α and β processes. At low drawing ratios the a process connects with the β process, while at the highest drawing ratio in our measurements, the a process is continuous with the αprocess. This is consistent with X-ray diffraction results that indicate that upon drawing the polymer chains in the amorphous part align and densify upon drawing. As the draw ratio increases, the α relaxation broadens and decreases its intensity, indicating an increasing heterogeneity. We observed slope changes in the α traces, when the temperature decreases below that at which τα≈ 1 s. This may indicate the glass transition from the ‘rubbery' state to the non-equilibrium glassy state.     

Formation of Peptide Radical Cations (M<Superscript>+·</Superscript>) in Electron Capture Dissociation of Peptides Adducted with Group IIB Metal Ions

Peptides adducted with different divalent Group IIB metal ions (Zn²⁺, Cd²⁺, and Hg²⁺) were found to give very different ECD mass spectra. ECD of Zn²⁺ adducted peptides gave series of c-/z-type fragment ions with and without metal ions. ECD of Cd²⁺ and Hg²⁺ adducted model peptides gave mostly a-type fragment ions with M^+• and fragment ions corresponding to losses of neutral side chain from M^+•. No detectable a-ions could be observed in ECD spectra of Zn²⁺ adducted peptides. We rationalized the present findings by invoking both proton-electron recombination and metal-ion reduction processes. As previously postulated, divalent metal-ions adducted peptides could adopt several forms, including (a) [M + Cat]²⁺, (b) [(M + Cat – H) + H]²⁺, and (c) [(M + Cat – 2H) + 2H]²⁺. The relative population of these precursor ions depends largely on the acidity of the metal–ion peptide complexes. Peptides adducted with divalent metal-ions of small ionic radii (i.e., Zn²⁺) would form predominantly species (b) and (c); whereas peptides adducted with metal ions of larger ionic radii (i.e., Hg²⁺) would adopt predominantly species (a). Species (b) and (c) are believed to be essential for proton-electron recombination process to give c-/z-type fragments via the labile ketylamino radical intermediates. Species (c) is particularly important for the formation of non-metalated c-/z-type fragments. Without any mobile protons, species (a) are believed to undergo metal ion reduction and subsequently induce spontaneous electron transfer from the peptide moiety to the charge-reduced metal ions. Depending on the exothermicity of the electron transfer reaction, the peptide radical cations might be formed with substantial internal energy and might undergo further dissociation to give structural related fragment ions.     

Heavy Metal Determination by Inductively Coupled Plasma – Mass Spectrometry (ICP-MS) and Direct Mercury Analysis (DMA) and Arsenic Mapping by Femtosecond (fs) – Laser Ablation (LA) ICP-MS in Cereals

A study of the lead (Pb), cadmium (Cd), arsenic (As), and mercury (Hg) contents in popular cereals was conducted using inductively coupled plasma – mass spectrometry (ICP-MS), direct mercury analysis (DMA), and femtosecond laser ablation – inductively coupled plasma – mass spectrometry (fs-LA-ICP-MS). For Pb, Cd, and As determination, the samples were prepared using microwave digestion, while for Hg, the samples were homogenized and measured by DMA without additional pretreatment. Satisfactory values for all of the quality parameters that include the SD, limit of detection (LOD), limit of quantitation (LOQ), accuracy, and recovery were obtained, clearly validating the analytical techniques used in the current study. Recovery and accuracy measurements were done using rice flour CRM 108-01-002 from Korea Research Institute of Standards and Science (KRISS). All measured concentrations for these elements were lower than the national regulatory guideline values provided by the CODEX Alimentarius and Ministry of Food and Drug Safety. A sample from each group was also selected for an As distribution study within a grain using fs-LA-ICP-MS. As is classified as a first-class carcinogen by the International Agency for Research on Cancer (IARC). For adlay, oats, and barley, As was determined to be primarily distributed in the area where the grain splits, while for foxtail millet, sorghum and corn, As was concentrated in the grain embryo. Also, it was confirmed that the exposure of heavy metals in the diet was negligible due to the low metal concentrations consumed daily in these foods.     

Intermediates of N-Heterocyclic Carbene (NHC) Dimerization Probed in the Gas Phase by Ion Mobility Mass Spectrometry: C−H⋅⋅⋅:C Hydrogen Bonding Versus Covalent Dimer Formation

N-Heterocyclic carbenes (NHCs, :C ) can interact with azolium salts ( C−H⁺ ) by either forming a hydrogen-bonded aggregate ( CHC⁺ ) or a covalent C−C bond ( CCH⁺ ). In this study, the intramolecular NHC–azolium salt interactions of aromatic imidazolin-2-ylidenes and saturated imidazolidin-2-ylidenes have been investigated in the gas phase by traveling wave ion mobility mass spectrometry (TW IMS) and DFT calculations. The TW IMS experiments provided evidence for the formation of these important intermediates in the gas phase, and they identified the predominant aggregation mode (hydrogen bond vs. covalent C−C) as a function of the nature of the interacting carbene–azolium pairs.     

Rapid Determination of Adenine Arabinoside Monophosphate in Pharmaceutical Injections by Droplet Spray Ionization – Tandem Mass Spectrometry (DSI-MS/MS)

Abstract

Rapid analysis of pharmaceutical preparations is of great interest in clinical studies with benefits for identifying counterfeit drugs. In this study, droplet spray ionization tandem mass spectrometry (DSI-MS/MS) was developed for the rapid determination of adenine arabinoside monophosphate in pharmaceutical injections without complex sample pretreatment. The sample solution was loaded on the slip corner placed in front of the inlet of a mass spectrometer, and high voltage was applied to the solution to create a charged spray from the corner for MS analysis. The sample was loaded for analysis without additional sample preparation protocols, which greatly simplifies the operation. The limit of detection and limit of quantification were determined to be 2.7 and 9.1?ng/mL, respectively. The recoveries were in the range from 96% to 112%, and the calculated relative standard deviations were less than 7% for the DSI-MS/MS method. Three adenine arabinoside monophosphate pharmaceutical injection samples and a degraded sample obtained by acid treatment at 40?°C were successfully analyzed by directly dissolving and diluting the sample. Moreover, the sample-loading step required only 2?s. Together these capabilities indicate that the DSI-MS/MS is a simple and robust method and has promising applications in pharmacology studies without complicated sample pretreatment.     

Analysis of Codeine in Urine and Opiate Sample by Solid-Phase Microextraction (SPME) and Gas Chromatography——Mass Spectrometry (GC/MS)

The growth of the illegal heroin use has stimulated widespread testing for its abuse. However, since the heroin metabolizes quickly in the human body and not reliably detected in urine,its metabolites are by necessity the analytical targets for the detection of its intake. Of the metabolites of street heroin,codeine is important one. Thus,the analysis of codeine in urine also become an important application for the detection of street heroin intake. There are extensive literature on the determination of codeine in biological samples using gas chromatography/mass spectrometry(GC/MS). In those methods,the analytes were isolated by liquid-liquid or solid-phase extraction from the urine. Such procedure suffers from the requirement of high purity solvent and time consuming.