High Throughput Screening of High-Affinity Ligands for Proteins with Anion-Binding Sites using Desorption Electrospray Ionization (DESI) Mass Spectrometry

A high throughput screening system involving a linear ion trap (LTQ) analyzer, a house-made platform and a desorption electrospray ionization (DESI) source was established to screen ligands with a high affinity for proteins with anion-binding sites. The complexes were analyzed after incubation, ultrafiltration, washing, and displacement. A new anionic region inhibited dissociation (ARID) mechanism that was suitable for a protein with anion-binding site was proposed. We utilized the differences in detectable dissociation of protein–ligand complexes, combined with displacement experiments, to distinguish free ligands displaced from anion-binding sites from liberated ligands dissociated from nonspecific interactions. The method was validated by α₁-acid glycoprotein (AGP) and (R), (S)-amlodipine. Site-specific enantioselectivity shown in our experiments was consistent with earlier studies. Obtaining all of the qualitative information of 15*3 samples in 2.3 min indicates that the analysis process is no longer the time-limiting step in the initial stage of drug discovery. Quantitative information verified that our method was at least a semiquantitative method.

The Effective Temperature of Ions Stored in a Linear Quadrupole Ion Trap Mass Spectrometer

The extent of internal energy deposition into ions upon storage, radial ejection, and detection using a linear quadrupole ion trap mass spectrometer is investigated as a function of ion size (m/z 59 to 810) using seven ion-molecule thermometer reactions that have well characterized reaction entropies and enthalpies. The average effective temperatures of the reactants and products of the ion-molecule reactions, which were obtained from ion-molecule equilibrium measurements, range from 295 to 350 K and do not depend significantly on the number of trapped ions, m/z value, ion trap q _z value, reaction enthalpy/entropy, or the number of vibrational degrees of freedom for the seven reactions investigated. The average of the effective temperature values obtained for all seven thermometer reactions is 318?±?23 K, which indicates that linear quadrupole ion trap mass spectrometers can be used to study the structure(s) and reactivity of ions at near ambient temperature.

Bacterial Spores Survive Electrospray Charging and Desolvation

The survivability of Bacillus subtilis spores and vegetative Escherichia coli cells after electrospray from aqueous suspension was tested using mobility experiments at atmospheric pressure. E. coli did not survive electrospray charging and desolvation, but B. subtilis did. Experimental conditions ensured that any surviving bacteria were de-agglomerated, desolvated, and electrically charged. Based on mobility measurements, B. subtilis spores survived even with 2,000–20,000 positive charges. B. subtilis was also found to survive introduction into vacuum after either positive or negative electrospray. Attempts to measure the charge distribution of viable B. subtilis spores using electrostatic deflection in vacuum were inconclusive; however, viable spores with low charge states (less than 42 positive or less than 26 negative charges) were observed.

ESI Mass Spectrometric Exploration of Selective Recognition of G-Quadruplex in c-myb Oncogene Promoter Using a Novel Flexible Cyclic Polyamide

In this research, electrospray ionization mass spectrometry (ESI-MS) was used to probe the binding selectivity of a flexible cyclic polyamide (cβ) to G-quadruplexes from the long G-rich sequences in the c-myb oncogene promoter. The results show that three G-rich sequences, including d[(GGA)₃GGTCAC(GGA)₄], d[(GGA)₄GAA(GGA)₄], and d[(GGA)₃GGTCAC(GGA)₄GAA(GGA)₄] species in the c-myb promoter can form parallel G-quadruplexes, and cβ selectively binds towards these G-quadruplexes over both several other G-quadruplexes and the duplex DNA. These properties of cβ have profound implications on future studies of the regulation of c-myb oncogene expression.

MS/MS Fragmentation Behavior Study of meso-Phenylporphyrinoids Containing Nonpyrrolic Heterocycles and meso-Thienyl-Substituted Porphyrins

Free base and cobalt(II) complexes of six meso-tetraphenylporphyrinoids containing nonpyrrolic heterocycles and of three meso-thienylporphyrins were investigated using electrospray ionization tandem mass spectrometry (ESI-MS/MS). Their fragmentation was studied in a quadrupole ion trap as a function of the porphyrinoid macrocycle structure and compared with the fragmentation behavior of the benchmark compound meso-tetraphenylporphyrin. In situ oxidation of the neutral cobalt(II) complexes under ESI conditions produced singly charged cobalt(III) porphyrinoid ions; the free bases were ionized by protonation. For the porphyrinoids with an intact porphyrin core, the major fragmentation pathways observed were the losses of the meso-substituent (for meso-phenyl groups) and characteristic fragmentations of one or more meso-substituents (for the meso-thienyl group). Complex fragmentation pathways were observed for porphyrinoids with modifications to the porphyrin core but chemically reasonable structures could be assigned to most fragments, thus delineating general patterns for the behavior of pyrrole-modified porphyrins under CID conditions.

Mass spectrometric profiling of Bacillus cereus strains and quantitation of the emetic toxin cereulide by means of stable isotope dilution analysis and HEp-2 bioassay

A fast and robust high-throughput ultra-performance liquid chromatography/time-of-flight mass spectrometry (UPLC–TOF MS) profiling method was developed and successfully applied to discriminate a total of 78 Bacillus cereus strains into no/low, medium and high producers of the emetic toxin cereulide. The data obtained by UPLC–TOF MS profiling were confirmed by absolute quantitation of cereulide in selected samples by means of high-performance liquid chromatography with tandem mass spectrometry (HPLC–MS/MS) and stable isotope dilution assay (SIDA). Interestingly, the B. cereus strains isolated from four vomit samples and five faeces samples from patients showing symptoms of intoxication were among the group of medium or high producers. Comparison of HEp-2 bioassay data with those determined by means of mass spectrometry showed differences, most likely because the HEp-2 bioassay is based on the toxic action of cereulide towards mitochondria of eukaryotic cells rather than on a direct measurement of the toxin. In conclusion, the UPLC–electrospray ionization (ESI)–TOF MS and the HPLC–ESI–MS/MS–SIDA analyses seem to be promising tools for the robust high-throughput analysis of cereulide in B. cereus cultures, foods and other biological samples.

Negative ion tandem mass spectrometry of prenylated fungal metabolites and their derivatives

Liquid chromatography negative ion electrospray ionisation tandem mass spectrometry has been used for characterisation of naturally occurring prenylated fungal metabolites and synthetic derivatives. The fragmentation studies allow an elucidation of the decomposition pathways for these compounds. It could be shown, that the prenyl side chain is degraded by successive radical losses of C₅ units. Both the benzoquinones and the phenolic derivatives display significant key ions comprising the aromatic ring. In some cases, the formation of significant oxygen-free key ions could be evidenced by high-resolution MS/MS measurements. Furthermore, the different types of basic skeletons, benzoquinones and phenol type as well as cyclic prenylated compounds, can be differentiated by their MS/MS behaviour.

Traveling Wave Ion Mobility Mass Spectrometry and Ab Initio Calculations of Phosphoric Acid Clusters

Positive and negative ion electrospray mass spectra obtained from 50 mM phosphoric acid solutions presented a large number of phosphoric acid clusters: [(H₃PO₄)_n?+?zH] ^z+ or [(H₃PO₄)_n – zH] ^z– , with n up to 200 and z up to 4 for positively charged clusters, and n up to 270 and z up to 7 for negatively charged cluster ions. Ion mobility experiments allowed very explicit separation of the different charge states. Because of the increased pressures involved in ion mobility experiments, dissociation to smaller clusters was observed both in the trap and transfer areas. Voltages along the ion path could be optimized so as to minimize this effect, which can be directly associated with the cleavage of hydrogen bonds. Having excluded the ion mobility times that resulted from dissociated ions, each cluster ion appeared at a single drift time. These drift times showed a linear progression with the number of phosphoric atoms for cluster ions of the same charge state. Cross section calculations were carried out with MOBCAL on DFT optimized geometries with different hydrogen locations and with three types of atomic charges. DFT geometry optimizations yielded roughly spherical structures. Our results for nitrogen gas interaction cross sections showed that values were dependent on the atomic charges definition used in the MOBCAL calculation. This pinpointed the necessity to define a clear theoretical framework before any comparative interpretations can be attempted with uncharacterized compounds.

Effect of mobile phase on resolution of the isomers and homologues of tocopherols on a triacontyl stationary phase

Reversed-phase liquid chromatographic (RPLC) separation of isomers and homologues of similar polarity is challenging. Tocopherol isomers and homologues are one such example. α, β, γ, and δ-tocopherols have been successfully separated by RPLC on triacontyl (C₃₀) stationary phase. System suitability was tested by using four mobile phases, and observed chromatographic separations of β and γ-tocopherols were compared. Comparison indicated that methanol–tert-butyl methyl ether (TBME) 95:5 (v/v) at a flow rate of 0.75 mL min^?1 was the best mobile phase. Detection systems were also evaluated on the basis of limit of quantification; it was concluded that fluorescence detection was best. The method was validated by analysis of two homologues and two isomers of tocopherol in sesame, maize, and soybean samples. MS coupled with an ESI interface in negative-ion mode [M ? H]^? was used for identification of individual components. It was concluded that addition of TBME to methanol was required to enhance the separation of β and γ-tocopherols, although methanol alone provided similar results. The applicability of the method to cereal, pulse, and oilseed samples was confirmed. The reproducibility of the procedure was good, with relative standard deviations in the range 1.7–3.9 %. Recovery of tocopherols added to sesame samples ranged from 91 to 99 %.

Unblocking the Sink: Improved CID-Based Analysis of Phosphorylated Peptides by Enzymatic Removal of the Basic C-Terminal Residue

A one-step enzymatic reaction for improving the collision-induced dissociation (CID)-based tandem mass spectrometry (MS/MS) analysis of phosphorylated peptides in an ion trap is presented. Carboxypeptidase-B (CBP-B) was used to selectively remove C-terminal arginine or lysine residues from phosphorylated tryptic/Lys-C peptides prior to their MS/MS analysis by CID with a Paul-type ion trap. Removal of this basic C-terminal residue served to limit the extent of gas-phase neutral loss of phosphoric acid (H₃PO₄), favoring the formation of diagnostic b and y ions as determined by an increase in both the number and relative intensities of the sequence-specific product ions. Such differential fragmentation is particularly valuable when the H₃PO₄ elimination is so predominant that localizing the phosphorylation site on the peptide sequence is hindered. Improvement in the quality of tandem mass spectral data generated by CID upon CBP-B treatment resulted in greater confidence both in assignment of the phosphopeptide primary sequence and for pinpointing the site of phosphorylation. Higher Mascot ion scores were also generated, combined with lower expectation values and higher delta scores for improved confidence in site assignment; Ascore values also improved. These results are rationalized in accordance with the accepted mechanisms for the elimination of H₃PO₄ upon low energy CID and insights into the factors dictating the observed dissociation pathways are presented. We anticipate this approach will be of utility in the MS analysis of phosphorylated peptides, especially when alternative electron-driven fragmentation techniques are not available.

Non-enzymatic amperometric sensor for hydrogen peroxide based on a biocomposite made from chitosan, hemoglobin, and silver nanoparticles

We report on a novel non-enzymatic sensor for hydrogen peroxide (HP) that is based on a biocomposite made up from chitosan (CS), hemoglobin (Hb), and silver nanoparticles (AgNPs). The AgNPs were prepared in the presence of CS and glucose in an ultrasonic bath, and CS is found to act as a stabilizing agent. They were then combined with Hb and CS to construct a carbon paste biosensor. The resulting electrode gave a well-defined redox couple for Hb, with a formal potential of about ?0.17?V (vs. SCE) at pH?6.86 and exhibited a remarkable electrocatalytic activity for the reduction of HP. The sensor was used to detect HP by flow injection analysis, and a linear response is obtained in the 0.08 to 250?μM concentration range. The detection limit is 0.05?μM (at S/N?=?3). These characteristics, along with its long-term stability make the sensor highly promising for the amperometric determination of HP.

Analysis of triacylglycerol hydroperoxides in human lipoproteins by Orbitrap mass spectrometer

Herein, we represent a simple method for the detection and characterization of molecular species of triacylglycerol monohydroperoxides (TGOOH) in biological samples by use of reversed-phase liquid chromatography with a LTQ Orbitrap XL mass spectrometer (LC/LTQ Orbitrap) via an electrospray ionization source. Data were acquired using high-resolution, high-mass accuracy in Fourier-transform mode. Platform performance, related to the identification of TGOOH in human lipoproteins and plasma, was estimated using extracted ion chromatograms with mass tolerance windows of 5 ppm. Native low-density lipoproteins (nLDL) and native high-density lipoproteins (nHDL) from a healthy donor were oxidized by CuSO₄ to generate oxidized LDL (oxLDL) and oxidized HDL (oxHDL). No TGOOH molecular species were detected in the nLDL and nHDL, whereas 11 species of TGOOH molecules were detected in the oxLDL and oxHDL. In positive-ion mode, TGOOH was found as [M + NH₄]⁺. In negative-ion mode, TGOOH was observed as [M + CH₃COO]^–. TGOOH was more easily ionized in positive-ion mode than in negative-ion mode. The LC/LTQ Orbitrap method was applied to human plasma and three molecular species of TGOOH were detected. The limit of detection is 0.1 pmol (S/N?=?10:1) for each synthesized TGOOH.

Isolation and sequence analysis of peptides from the skin secretion of the Middle East tree frog Hyla savignyi

Novel peptides were identified in the skin secretion of the tree frog Hyla savignyi. Skin secretions were collected by mild electrical stimulation. Peptides were separated by reversed-phase high-performance liquid chromatography. Mass spectra were acquired by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS), and fragment ion spectra were obtained after collision-induced dissociation and electron capture dissociation. Peptides were analyzed by manual de novo sequencing and composition-based sequencing (CBS). Sequence analyses of three so far undescribed, structurally unrelated peptides are presented in this paper, having the sequences DDSEEEEVE-OH, P*EEVEEERJK-OH, and GJJDPJTGJVGGJJ-NH₂. The glutamate-rich sequences are assumed to be acidic spacer peptides of the prepropeptide. One of these peptides contains the modified amino acid hydroxyproline, as identified and localized by high-accuracy FTICR-MS. Combination of CBS and of experience-based manual sequence analysis as complementary and database-independent sequencing strategies resulted in peptide identification with high reliability.

Radical polymerization of methyl methacrylate with 2,2,3-triphenylpropanoic acid as an initiator

An unsymmetrical compound, 2,2,3-triphenylpropanoic acid (TPPA), was successfully prepared from phenyllithium, 1,1-diphenylethylene (DPE), gas carbon dioxide (CO₂), and aqueous standard solution of hydrochloric acid with LiCl deprivation. Characterization of the compound was performed by ¹H and ¹³C nuclear magnetic resonance (NMR) spectroscopy. The polymerization of methyl methacrylate (MMA) was performed in the presence of TPPA at 95 °C. The free radicals obtained were characterized by ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS). Gel permeation chromatography (GPC) traces of the average molecular weight of poly(MMA) (PMMA) showed a series of translations with increasing time. The average molecular weight of PMMA indicated narrow polydispersity, and an approximately linear relationship was found between ln ([M]₀/[M]) and polymerization time.

Soft Ionization of Saturated Hydrocarbons, Alcohols and Nonpolar Compounds by Negative-Ion Direct Analysis in Real-Time Mass Spectrometry

Large polarizable n-alkanes (approximately C18 and larger), alcohols, and other nonpolar compounds can be detected as negative ions when sample solutions are injected directly into the sampling orifice of the atmospheric pressure interface of the time-of-flight mass spectrometer with the direct analysis in real time (DART) ion source operating in negative-ion mode. The mass spectra are dominated by peaks corresponding to [M + O₂]￣^?. No fragmentation is observed, making this a very soft ionization technique for samples that are otherwise difficult to analyze by DART. Detection limits for cholesterol were determined to be in the low nanogram range.

Analytical Properties of Solid-substrate Electrospray Ionization Mass Spectrometry

Conventional electrospray ionization mass spectrometry (ESI-MS) uses a capillary for sample loading and ionization. Along with the development of ambient ionization techniques, ESI-MS using noncapillary emitters has attracted more interest in recent years. Following our recent report on ESI-MS using wooden tips (Anal. Chem. 83, 8201–8207 (2011)), the technique was further investigated and extended in this study. Our results revealed that the wooden tips could serve as a chromatographic column for separation of sample components. Sequential and exhaustive ionization was observed for proteins and salts on wooden tips with salts ionized sooner and proteins later. Nonconductive materials that contain microchannels/pores could be used as tips for ESI-MS analysis with sample solutions loaded to the sharp-ends only, since rapid diffusion of sample solutions by capillary action would enable the tips to become conductive. Tips of inert materials such as bamboo, fabrics, and sponge could be used for sample loading and ionization, while samples such as tissue, mushroom, and bone could form tips to induce ionization for direct analysis with application of a high voltage.

Cetyltrimethylammonium-coated magnetic nanoparticles for the extraction of bromate,followed by its spectrophotometric determination

We report on a combination of magnetic solid-phase extraction and spectrophotometric determination of bromate. Cetyltrimethylammonium ion was adsorbed on the surface of phenyl-functionalized silica-coated Fe₃O₄ nanoparticles (Ph-SiO₂@Fe₃O₄), and these materials served as the sorbent. The effects of surfactant and amount of sorbent, the composition of the desorption solution, the extraction time and temperature were optimized. Under optimized conditions, an enrichment factor of 12 was achieved, and the relative standard deviation is 2.9 % (for n?=?5). The calibration plot covers the 1–50 ng mL^?1 range with reasonable linearity (r ²?>?0.998); and the limit of detection is 0.5 ng mL^?1. The method is not interfered by ionic compounds commonly found in environmental water samples. It was successfully applied to the determination of bromate in spiked water samples.

Determination of nitrotyrosine in Arabidopsis thaliana cell cultures with a mixed-mode solid-phase extraction cleanup followed by liquid chromatography time-of-flight mass spectrometry

In this work, a method for the determination of trace nitrotyrosine (NO₂Tyr) and tyrosine (Tyr) in Arabidopsis thaliana cell cultures is proposed. Due to the complexity of the resulting extracts after protein precipitation and enzymatic digestion and the strong electrospray signal suppression displayed in the detection of both Tyr and NO₂Tyr from raw A. thaliana cell culture extracts, a straightforward sample cleanup step was proposed. It was based on the use of mixed-mode solid-phase extraction (SPE) using MCX-type cartridges (Strata?-X-C), prior to identification and quantitation using fast liquid chromatography–electrospray time-of-flight mass spectrometry. Unambiguous confirmation of both amino acids was accomplished with accurate mass measurements (with errors lower than 2 ppm) of each protonated molecule along with a characteristic fragment ion for each species. Recovery studies were accomplished to evaluate the performance of the SPE sample preparation step obtaining average recoveries in the range 92–101 %. Limit of quantitation obtained for NO₂Tyr in A. thaliana extracts was 3 nmol L^?1. Finally, the proposed method was applied to evaluate stress conditions of the plant upon different concentrations of peroxynitrite, a protein-nitrating compound, which induces the nitration of Tyr at the nanomolar range. Detection and confirmation of the compounds demonstrated the usefulness of the proposed approach.

Protein-mediated synthesis of antibacterial silver nanoparticles deposited on titanium dioxide nanotube arrays

We report on an effective route to decorate titanium nanotube arrays (TiNT) with silver nanoparticles (AgNPs). In this method, surface-adsorbed antibody molecules serve as templates to bind silver ions by electrostatic interaction. The photocatalytic activity of the TiNT under UV irradiation causes the photoreduction of AgNPs to occur, and the biological template is decomposed simultaneously. This route also was successfuly applied to gold nanoparticles (starting from negatively charged metallic precursor ions). Compared to undecorated samples, the AgNPs/TiNT samples under visible light display a much higher antibacterial activity against Escherichia coli.

NADH oxidation using modified electrodes based on lactate and glucose dehydrogenase entrapped between an electrocatalyst film and redox catalyst-modified polymers

We have developed a simple and efficient method for the enhanced loading of silver nanoparticles onto carbon nanospheres, and how this method can be used to design an electrochemical sensor for hydrogen peroxide (HP). A glassy carbon electrode was modified with hemoglobin, carbon nanospheres, and by enhanced loading of silver nanoparticles onto the carbon nanospheres via spontaneous polymerization of dopamine. The hemoglobin exhibits a remarkable electrocatalytic activity for the reduction of HP. The electrochemical response to HP is linear range in the 1.0–147.0?μM concentration range, with a detection limit of 0.3?μM at a signal-to-noise ratio of 3.