Oxidation of Methionine Residues in Polypeptide Ions Via Gas-Phase Ion/Ion Chemistry

The gas-phase oxidation of methionine residues is demonstrated here using ion/ion reactions with periodate anions. Periodate anions are observed to attach in varying degrees to all polypeptide ions irrespective of amino acid composition. Direct proton transfer yielding a charge-reduced peptide ion is also observed. In the case of methionine and, to a much lesser degree, tryptophan-containing peptide ions, collisional activation of the complex ion generated by periodate attachment yields an oxidized peptide product (i.e., [M?+?H?+?O]⁺), in addition to periodic acid detachment. Detachment of periodic acid takes place exclusively for peptides that do not contain either a methionine or tryptophan side chain. In the case of methionine-containing peptides, the [M?+?H?+?O]⁺ product is observed at a much greater abundance than the proton transfer product (viz., [M?+?H]⁺). Collisional activation of oxidized Met-containing peptides yields a signature loss of 64 Da from the precursor and/or product ions. This unique loss corresponds to the ejection of methanesulfenic acid from the oxidized methionine side chain and is commonly used in solution-phase proteomics studies to determine the presence of oxidized methionine residues. The present work shows that periodate anions can be used to ‘label’ methionine residues in polypeptides in the gas phase. The selectivity of the periodate anion for the methionine side chain suggests several applications including identification and location of methionine residues in sequencing applications.

Top-down MS for rapid methionine oxidation site assignment in filgrastim

Protein therapeutics have emerged as a major new class of pharmaceuticals. One important shelf-life-limiting factor of biopharmaceuticals is methionine oxidation, and therefore, it is important that analytical methods are able to thoroughly characterize all possible oxidized variants. Here, we present a fast and sensitive method to perform online methionine oxidation site assignment using granulocyte colony-stimulating factor (filgrastim) as a model. The method is based on top-down MS using the all-ion fragmentation mode of the Exactive benchtop mass spectrometer. Conditions that provide information on the intact mass of the protein as well as on fragment ions that allow unambiguous site assignment of methionine oxidation in filgrastim variants as low as 0.12 % of total peak area in a chromatographic time scale were identified. Using this method, we performed methionine oxidation site assignment in H₂O₂-stressed filgrastim and in filgrastim which was stored at intended conditions, respectively. We show that the relative abundance of oxidation species observed in filgrastim stored under intended conditions differs strikingly from the oxidized species observed after H₂O₂ stress. Additionally, we report an oxidized filgrastim variant that has not been previously described in the literature.

A novel functional imidazole fluorescent ionic liquid: simple and efficient fluorescent probes for superoxide anion radicals

Novel imidazole fluorescent ionic liquids with anthracene groups (ImS-FILA) were synthesized for the first time to act as fluorescent probes. They were developed for the determination of superoxide anion radicals (O₂ ^?-) in an aqueous system. O₂ ^?- was produced by pyrogallol autoxidation. The fluorescence of ImS-FILA was quenched by superoxide anion radicals. The π-bond structure of the fluorescent molecules was oxidized and damaged. This method is very simple and sensitive. The linear range of sensitivity was 1–70 μM ImS-FILA, and the detection limit for reactive oxygen species was 0.1 μM. This method was used to detect superoxide radicals in papaya and garlic, with satisfactory results. Further work is needed to demonstrate the utility of this method in detecting reactive oxygen species in a biological aqueous system.

Synthesis and properties of multifunctional poly(amic acid) with oligoaniline and fluorene groups

A novel multifunctional poly(amic acid) bearing oligoaniline, fluorene groups (PAAOF) has been prepared through the one-step synthetic route. The structure of PAAOF was confirmed via nuclear magnetic resonance (NMR), Fourier-transform infrared spectra (FTIR), and gel permeation chromatography (GPC). Moreover, the electrochemical measurement results revealed that PAAOF material have an expected electrochemical activity, and good electrochromic properties with high contrast value and satisfactory coloration efficiency. The photophysical properties of the as-synthesized PAAOF at various oxidation states were studied. The results indicated that the fluorescence of PAAOF could be tuned by modulating the oxidation states of oligoaniline segments. In the fluorescence tuning, the fluorene groups are fluorophore, and the oligoaniline segments are used as regulatory unit.

Reagent Cluster Anions for Multiple Gas-Phase Covalent Modifications of Peptide and Protein Cations

Multiple gas phase ion/ion covalent modifications of peptide and protein ions are demonstrated using cluster-type reagent anions of N-hydroxysulfosuccinimide acetate (sulfo-NHS acetate) and 2-formyl-benzenesulfonic acid (FBMSA). These reagents are used to selectively modify unprotonated primary amine functionalities of peptides and proteins. Multiple reactive reagent molecules can be present in a single cluster ion, which allows for multiple covalent modifications to be achieved in a single ion/ion encounter and at the ‘cost’ of only a single analyte charge. Multiple derivatizations are demonstrated when the number of available reactive sites on the analyte cation exceeds the number of reagent molecules in the anionic cluster (e.g., data shown here for reactions between the polypeptide [K₁₀ + 3H]³⁺ and the reagent cluster [5R_5Na – Na]^–). This type of gas-phase ion chemistry is also applicable to whole protein ions. Here, ubiquitin was successfully modified using an FBMSA cluster anion which, upon collisional activation, produced fragment ions with various numbers of modifications. Data for the pentamer cluster are included as illustrative of the results obtained for the clusters comprised of two to six reagent molecules.

Optical choline sensor based on a water-soluble fluorescent conjugated polymer and an enzyme-coupled assay

We report on a simple and sensitive water-soluble fluorescent conjugated polymer for use in a choline biosensor. Choline is oxidized by the enzyme choline oxidase (ChOx), and the hydrogen peroxide (H₂O₂) formed is used to oxidize catechol via catalysis by horseradish peroxidase. The product of oxidation acts as a quencher of the photoluminescence of a fluorescent conjugated polymer. The ratio of the fluorescence intensity of the system in the presence and absence of the choline, respectively, serves as the analytical information. It is proportional to the concentration of choline in the 0.1 μM to 20 μM concentration range. The detection limit for choline is 50 nM. The biosensor was successfully applied to the determination of choline in milk samples with satisfactory reproducibility and accuracy. This is the first biosensor where a ChOx/HRP enzyme-coupled assay is used in combination with a water-soluble conjugated polymer for the fluorescent detection of choline. In our opinion, it provides a common platform for further development of enzymatic biosensors based on fluorescent conjugated polymers.

Fragmentation of Electrospray-Produced Deprotonated Ions of Oligodeoxyribonucleotides Containing an Alkylated or Oxidized Thymidine

Alkylation and oxidation constitute major routes of DNA damage induced by endogenous and exogenous genotoxic agents. Understanding the biological consequences of DNA lesions often necessitates the availability of oligodeoxyribonucleotide (ODN) substrates harboring these lesions, and sensitive and robust methods for validating the identities of these ODNs. Tandem mass spectrometry is well suited for meeting these latter analytical needs. In the present study, we evaluated how the incorporation of an ethyl group to different positions (i.e., O ², N3, and O ⁴) of thymine and the oxidation of its 5-methyl carbon impact collisionally activated dissociation (CAD) pathways of electrospray-produced deprotonated ions of ODNs harboring these thymine modifications. Unlike an unmodified thymine, which often manifests poor cleavage of the C3′–O3′ bond, the incorporation of an alkyl group to the O ² position and, to a much lesser extent, the O ⁴ position, but not the N3 position of thymine, led to facile cleavage of the C3′–O3′ bond on the 3′ side of the modified thymine. Similar efficient chain cleavage was observed when thymine was oxidized to 5-formyluracil or 5-carboxyluracil, but not 5-hydroxymethyluracil. Additionally, with the support of computational modeling, we revealed that proton affinity and acidity of the modified nucleobases govern the fragmentation of ODNs containing the alkylated and oxidized thymidine derivatives, respectively. These results provided important insights into the effects of thymine modifications on ODN fragmentation.

A new label-free approach for the determination of reaction rates in oxidative footprinting experiments

Hydroxyl radical-mediated oxidative footprinting coupled to mass spectrometric analysis is an attractive technique for protein surface mapping, conformational changes monitoring, and protein–ligand interfaces mapping in solution. In this technique, a protein is oxidized by in situ-generated hydroxy radicals and the site and rate of oxidation can be determined by proteolysis followed by mass spectrometric analysis. Changes in peptide oxidation rate can then be correlated to the changes in solvent exposure, and information about conformational changes or interaction domains can be obtained. The method relies, therefore, on the accurate measurements of peptide oxidation rate. Here, we describe a new label-free method to determine the oxidation rate of peptides that is based on the consumption of the unoxidized peptide instead of measuring the formation of oxidized peptides. The reaction rate thus obtained presents a better linearity and lower variation when compared to the traditional method. The label-free method is also simpler to implement and automation can be achieved through label-free quantitation software.

Insights into the Binding Sites of Organometallic Ruthenium Anticancer Compounds on Peptides Using Ultra-High Resolution Mass Spectrometry

The binding sites of two ruthenium(II) organometallic complexes of the form [(η⁶-arene)Ru(N,N)Cl]⁺, where arene/N,N = biphenyl (bip)/bipyridine (bipy) for complex AH076, and biphenyl (bip)/o-phenylenediamine (o-pda) for complex AH078, on the peptides angiotensin and bombesin have been investigated using Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. Fragmentation was performed using collisionally activated dissociation (CAD), with, in some cases, additional data being provided by electron capture dissociation (ECD). The primary binding sites were identified as methionine and histidine, with further coordination to phenylalanine, potentially through a π-stacking interaction, which has been observed here for the first time. This initial peptide study was expanded to investigate protein binding through reaction with insulin, on which the binding sites proposed are histidine, glutamic acid, and tyrosine. Further reaction of the ruthenium complexes with the oxidized B chain of insulin, in which two cysteine residues are oxidized to cysteine sulfonic acid (Cys-SO₃H), and glutathione, which had been oxidized with hydrogen peroxide to convert the cysteine to cysteine sulfonic acid, provided further support for histidine and glutamic acid binding, respectively.

Nonenzymatic glucose sensor based on glassy carbon electrode modified with a nanocomposite composed of nickel hydroxide and graphene

We report on a nonenzymatic glucose sensor based on a glassy carbon electrode that was electrochemically modified with a nanocomposite prepared from nickel hydroxide and graphene. Scanning electron microscopy revealed that the nickel hydroxide in the nanocomposite was present in the form of a nanostructure of three-dimensional spheres that were assembled by many densely arranged nanosheets. The electrocatalytic activity of the electrode toward the oxidation of glucose was investigated by chronoamperometry. The current response was linearly related to the glucose concentration in the range from 1 to 10?μM, with a sensitivity of 494?μA?mM^–1?cm^–2 and a correlation coefficient of 0.9990, and a second range (from 10 to 1000?μM with a sensitivity of 328?μA?mM^–1?cm^–2 and a correlation coefficient of 0.9990). The detection limit was 0.6?μM at a signal-to-noise ratio of 3, and the response time was as short as 2?s.

Electrochemical synthesis of a novel platinum nanostructure on a glassy carbon electrode, and its application to the electrooxidation of methanol

We show that the addition of white dextrin during the electrochemical deposition of platinum nanostructures (nano-Pt) on a glassy carbon electrode (GCE) results in an electrochemically active surface that is much larger than that of platinum microparticles prepared by the same procedure but in the absence of dextrin. The nano-Pt deposits are characterized by scanning electron microscopy (SEM), energy dispersive spectroscopy, and electrochemical methods. The SEM images reveal deposits composed of mainly nanoparticles and short nanorods. The GCE was applied as a novel and cost-effective catalyst for methanol oxidation. The use of nano-Pt improves the electrocatalytic activity and the stability of the electrodes.

A mass spectrometry-based workflow for the proteomic analysis of in vitro cultured cell subsets isolated by means of laser capture microdissection

This paper describes a microproteomic workflow that is useful for simultaneously identifying and quantifying proteins from a minimal number of morphotypically heterogeneous cultured adherent cells. The analytical strategy makes use of laser capture microdissection, an effective means of harvesting pure cell populations, and label-free mass spectrometry. We optimised the workflow with particular reference to cell fixation which is crucial for successful laser-based microdissection and also downstream molecular studies. In addition, we defined the minimum number of cells to be isolated and analysed for satisfactory proteome coverage. To set up this workflow, we choose human monocyte-derived macrophages spontaneously differentiated in vitro. These cells, under our culture conditions, show distinct morphotypes, reminiscent of the heterogeneity observed in tissues in various homeostatic and pathological states, e.g. atherosclerosis. This optimised workflow may provide new insights into biology and pathology of heterogeneous cell in culture, particularly when other cell selection approaches are not suitable.

Biocatalytic reactors based on ribonuclease A immobilized on macroporous monolithic supports

Immobilized enzyme reactors (IMERs) produced by the covalent attachment of ribonuclease A to macroporous methacrylate-based monolithic supports using different experimental approaches are discussed and compared. Enzyme immobilization was carried out by direct covalent binding, as well as through attachment via a polymer spacer. The kinetic properties of an IMER operating in either recirculation mode or zonal elution mode were studied. Additionally, the effect of flow rate on the bioconversion efficiency of each IMER sample was examined.

Electrochemical detection of in situ DNA damage induced by enzyme-catalyzed Fenton reaction. Part II in hydrophobic room temperature ionic liquid

A hydrophobic room temperature ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF₆]), was applied as nonaqueous solvent for the generation of hydroxy radical (?OH) through glucose oxidase-catalyzed Fenton reaction. The enzyme catalyzes the oxidation of glucose, and the produced H₂O₂ further reacts with transition metal ions, generating hydroxyl radicals. They attacked DNA and led its damage. This was detected by square wave voltammetry (SWV) of the electroactive indicator Co(bpy) ₃ ³⁺ . It bound more strongly to intact DNA, and the SWV peak currents decreased at the potential of 0.064?V when DNA was damaged. The experimental results testified that the antioxidants, ascorbic acid, aloe-emodin and rutin, inhibited oxidative DNA damage by hydroxyl radicals. The method is promising for rapid, sensitive, and inexpensive detection of DNA damage.

Stereospecific electrophoretically mediated microanalysis assay for methionine sulfoxide reductase enzymes

An electrophoretically mediated microanalysis assay (EMMA) for the determination of the stereoselective reduction of l-methionine sulfoxide diastereomers by methionine sulfoxide reductase enzymes was developed using fluorenylmethyloxycarbonyl (Fmoc)-l-methionine sulfoxide as substrate. The separation of the diastereomers of Fmoc-l-methionine sulfoxide and the product Fmoc-l-methionine was achieved in a successive multiple ionic-polymer layer-coated capillary using a 50 mM Tris buffer, pH 8.0, containing 30 mM sodium dodecyl sulfate as background electrolyte and an applied voltage of 25 kV. 4-Aminobenzoic acid was employed as internal standard. An injection sequence of incubation buffer, enzyme, substrate, enzyme, and incubation buffer was selected. The assay was optimized with regard to mixing time and mixing voltage and subsequently applied for the analysis of stereoselective reduction of Fmoc-l-methionine-(S)-sulfoxide by human methionine sulfoxide reductase A and of the Fmoc-l-methionine-(R)-sulfoxide by human methionine sulfoxide reductase B. The Michaelis–Menten constant, K _m, and the maximum velocity, v _max, were determined. Essentially identical data were determined by the electrophoretically mediated microanalysis assay and the analysis of the samples by CE upon offline incubation. Furthermore, it was shown for the first time that Fmoc-methionine-(R)-sulfoxide is a substrate of human methionine sulfoxide reductase B.

Nonenzymatic sensor for glucose based on a glassy carbon electrode modified with Ni(OH)2 nanoparticles grown on a film of molybdenum sulfide

A glassy carbon electrode (GCE) was modified with nickel(II) hydroxide nanoparticles and a film of molybdenum sulfide. The nanocomposite was prepared by two-step electrodeposition. Scanning electron microscopy reveals that the nanoparticles are uniformly deposited on the film. Cyclic voltammetry and chronoamperometry indicate that this modified GCE displays a remarkable electrocatalytic activity towards nonenzymatic oxidation of glucose. Response is linear in the 10–1,300 μM concentration range (R ² ?=?0.9987), the detection limit is very low (5.8 μM), response is rapid (< 2 s), and selectivity over ascorbic acid, dopamine, uric acid, fructose and galactose is very good.

Silicon-hybrid carbon dots strongly enhance the chemiluminescence of luminol

We report on a 4-min microwave pyrolytic method for the preparation of fluorescent and water-soluble silicon-hybrid carbon dots (C-dots) with high fluorescent quantum yield. The material is prepared by preheating aminopropyltriethoxysilane and ethylene diamine tetraacetic acid for 1 min, then adding a mixture of poly(ethylene glycol) and glycerin to the solution and heating for another 3 min. It is found that the hybrid carbon dots strongly enhance the chemiluminescence (CL) of the luminol/N-bromosuccinimide system. A study on the enhancement mechanism via CL, fluorescence and electron paramagnetic resonance spectroscopy showed that the effect most probably is due to electrostatic interaction between the C-dots and the luminol anion which facilitates electron transfer from luminol anion to the N-bromosuccinimide oxidant. CL intensity is linearly related to the concentration of the C-dots in the range between 1.25 and 20 μg mL^?1. The detection limit is 0.6 μg mL^?1 (at an S/N of 3).

Mass spectrometry and inflammation—MS methods to study oxidation and enzyme-induced changes of phospholipids

Many diseases such as arthritis or atherosclerosis are accompanied by inflammatory processes. Inflammation is characterized by the infiltration of cells such as neutrophilic granulocytes and (a) the release of phospholipases [particularly phospholipase A₂ (PLA₂)] and (b) the generation of reactive oxygen as well as nitrogen species (ROS and RNS). While PLA₂ leads to defined lyso products (lacking one acyl residue), lipid oxidation is characterized by much more complex product patterns, including lipid peroxides, aldehydes (by double bond cleavage), and many others. Nevertheless, oxidation processes are highly important under in vivo conditions because molecules with regulatory functions are generated by the oxidation of lipids and/or free fatty acids. Therefore, lipid oxidation products as well as lysolipids are increasingly assumed to represent important disease (bio)markers. Consequently, there is also increasing interest in methods to characterize these products qualitatively and quantitatively. Mass spectrometry (MS) seems to be the method of choice to study (phospho)lipids changed under inflammatory conditions: nowadays, soft ionization MS methods are regularly used to study oxidative lipid modifications because of their high sensitivities and the tremendous mass resolutions that are achievable by using modern mass spectrometers. However, experimental care is required to be able to detect all relevant products. Although electrospray ionization (ESI) MS is so far most popular, applications of matrix-assisted laser desorption and ionization (MALDI) MS are continuously increasing. This review aims to summarize the so far available data on MS analyses of oxidized lipids as well as lysolipids. In addition to model systems, special attention will be paid to the monitoring of oxidized lipids and lysolipids under in vivo conditions. It is the aim of this review to provide a critical survey of the advantages and drawbacks of the different MS methods, with the focus on MALDI and ESI.

The detection of T-Nos,a genetic element present in GMOs,by cross-priming isothermal amplification with real-time fluorescence

An isothermal cross-priming amplification (CPA) assay for Agrobacterium tumefaciens nopaline synthase terminator (T-Nos) was established and investigated in this work. A set of six specific primers, recognizing eight distinct regions on the T-Nos sequence, was designed. The CPA assay was performed at a constant temperature, 63 °C, and detected by real-time fluorescence. The results indicated that real-time fluorescent CPA had high specificity, and the limit of detection was 1.06?×?10³ copies of rice genomic DNA, which could be detected in 40 min. Comparison of real-time fluorescent CPA and conventional polymerase chain reaction (PCR) was also performed. Results revealed that real-time fluorescent CPA had a comparable sensitivity to conventional real-time PCR and had taken a shorter time. In addition, different contents of genetically modified (GM)-contaminated rice seed powder samples were detected for practical application. The result showed real-time fluorescent CPA could detect 0.5 % GM-contaminated samples at least, and the whole reaction could be finished in 35 min. Real-time fluorescent CPA is sensitive enough to monitor labeling systems and provides an attractive method for the detection of GMO.