Electrospray mass and tandem mass spectrometry identification of ozone oxidation products of amino acids and small peptides

Comprehensive Glycomic and Glycoproteomic Analyses of Human Programmed Cell Death Protein 1 Extracellular Domain

Human programmed cell death protein 1 (hPD-1) is an essential receptor in the immune checkpoint pathway. It has played an important role in cancer therapy. However, not all patients respond positively to the PD-1 antibody treatment, and the underlying mechanism remains unknown. PD-1 is a transmembrane glycoprotein, and its extracellular domain (ECD) is reported to be responsible for interactions and signal transduction. This domain contains 4 N-glycosylation sites and 25 potential O-glycosylation sites, which implicates the importance of glycosylation. The structure of hPD-1 has been intensively studied, but the glycosylation of this protein, especially the glycan on each glycosylation site, has not been comprehensively illustrated. In this study, hPD-1 ECD expressed by human embryonic kidney 293 (HEK 293) and Chinese hamster ovary (CHO) cells was analyzed; not only N- and O-glycosylation sites but also the glycans on these sites were comprehensively analyzed using mass spectrometry. In addition, hPD-1 ECD binding to different anti-hPD-1 antibodies was tested, and N-glycans were found functioned differently. All of this glycan information will be beneficial for future PD-1 studies.

Mechanism of the Low-Temperature Organic Removal from Imidazolium-Containing Zeolites by Ozone Treatment: Fluoride Retention in Double-4-Rings

For zeolites synthesized using imidazolium cations, the organic matter can be extracted at very low temperatures (100 °C) using ozone. This is possible for zeolites with 12-ring or larger pores but requires higher temperatures in medium-pore zeolites. The first chemical events in this process occur fast, even at room temperature, and imply the loss of aromaticity likely by the formation of an adduct between ozone and the imidazole ring through carbons C4 and C5. Subsequent rupture of the imidazole ring provides smaller and more flexible fragments that can desorb more readily. This process has been studied experimentally, mainly through infrared spectroscopy, and theoretically by density functional theory. Amazingly, fluoride anions occluded in the small double-four-ring units (d4r) during the synthesis remain inside the cage throughout the whole process when the temperature is not too high (≤150 °C). However, fluoride in larger cages in MFI ends up bonded to silicon in penta or hexacoordinated units, likely out of the cages, after ozone treatment at 150 °C. For several germanosilicate zeolites, the process allows their subsequent degermanation to yield stable high-silica zeolites. Quaternary ammonium cations require harsher conditions that eventually also extract fluoride from zeolite cages, including the d4r unit.

Oxidation Products of Tryptophan and Proline in Adipokinetic Hormones-Artifacts or Post-Translational Modifications?

BACKGROUND

Adipokinetic hormones (AKHs) regulate important physiological processes in insects. AKHs are short peptides with blocked termini and Trp in position 8. Often, proline occupies position 6. Few post-translational modifications have been found, including hydroxyproline ([Hyp6]) and kynurenine. Our recent data suggest that the Hyp- and Kyn-containing AKHs occur more often than originally thought and we here investigate if they are natural or artifactual.

METHODS

From crude extracts of the corpora cardiaca (CC) of various insect species, AKHs were analyzed using liquid chromatography coupled to high-resolution mass spectrometry (LC-MS). Synthetic [Hyp6]-AKHs were tested in an in vivo metabolic assay. Freshly dissected Periplaneta americana and Blaberus atropos CCs (with precautions taken against oxidation) were analyzed. B. atropos CC were placed into a depolarizing saline and the released AKHs were measured.

RESULTS

Hyp was detected in several decapeptides from cockroaches. The modified form accompanied the AKH at concentrations below 7%. The [Hyp6]-AKHs of B. atropos were present in fresh CC preparations and were shown to be releasable from the CC ex vivo. Synthetic [Hyp6]-containing peptides tested positively in a hypertrehalosemic bioassay. Hydroxyprolination was also detected for Manto-CC from the termite Kalotermes flavicollis and for Tetsu-AKH of the grasshopper, Tetrix subulata. Oxidized Trp-containing forms of Nicve-AKH were found in species of the burying beetle genus Nicrophorus.

CONCLUSIONS

Trp oxidation is known to occur easily during sample handling and is likely the reason for the present findings. For hydroxyprolination, however, the experimental evidence suggests endogenous processes.

Maize kernel metabolome involved in resistance to fusarium ear rot and fumonisin contamination

Fusarium verticillioides poses a threat to worldwide maize production due to its ability to infect maize kernel and synthesize fumonisins that can be accumulated above safety levels for humans and animals. Maize breeding has been proposed as key tool to decrease kernel contamination with fumonisins, but metabolic studies complementary to genomic approaches are necessary to disclose the complexity of maize resistance. An untargeted metabolomic study was proposed using inbreds genetically related but with contrasting levels of resistance in order to uncover pathways implicated in resistance to Fusarium ear rot (FER) and fumonisin contamination in the maize kernel and to look for possible biomarkers. Metabolite determinations were performed in kernels collected at 3 and 10 days after inoculation with F. verticillioides (dat). Discriminant metabolites between resistant and susceptible RILs were rather found at 10 than 3 dat, although metabolite differences at later stages of colonization could be driven by subtle variations at earlier stages of infection. Within this context, differences for membrane lipid homeostasis, methionine metabolism, and indolacetic acid conjugation seemed highly relevant to distinguish between resistant and susceptible inbreds, confirming the polygenic nature of resistance to FER and fumonisin contamination in the maize kernels. Nevertheless, some specific metabolites such as the polyamine spermidine and/or the alkaloid isoquinoline seemed to be promising indirect selection traits to improve resistance to FER and reduce fumonisin accumulation. Therefore, in vitro and in vivo experiments will be necessary to validate the inhibitory effects of these compounds on fumonisins biosynthesis.

Tuning oxidative modification by a strong electric field using nanoESI of highly conductive solutions near the minimum flow rate

Oxidative modification is usually used in mass spectrometry (MS) for labeling and structural analysis. Here we report a highly tunable oxidation that can be performed in line with the nanoESI-MS analysis at the same ESI emitter without the use of oxidative reagents such as ozone and H₂O₂, and UV activation. The method is based on the high-pressure nanoESI of a highly conductive (conductivity >3.8 S m^-1) aqueous solution near the minimum flow rate. The ion source is operated under super-atmospheric pressure (0.5 MPa gauge pressure) to avoid the contribution of electric discharge. The analyte at the tip of the Taylor cone or in the emitter droplet can be locally oxidized in an on-demand manner by varying the nanoflow rate. With an offline nanoESI, the degree of oxidation, i.e., the average number of incorporated oxygen atoms, can be finely tuned by voltage modulation using spray current as the feedback signal. Oxidations of easily oxidized residues present in peptides/proteins and the double bonds of the unsaturated phosphatidylcholine occur at low flow rate operation (<5 nL min^-1) when the electric field at the tip of the Taylor cone and the initially produced charged droplet reaches approximately 1.3 V nm^-1. The oxidized ion signal responds instantaneously to changes in flow rate, indicating that the oxidation is highly localized. Using isotope labeling, it was found that the incorporated oxygen primarily originates from the gas phase, suggesting a direct oxidation pathway for the analyte enriched on the liquid surface via the reactive oxygen atoms formed by the strong electric field.

Beneficial Activities of Alisma orientale Extract in a Western Diet-Induced Murine Non-Alcoholic Steatohepatitis and Related Fibrosis Model via Regulation of the Hepatic Adiponectin and Farnesoid X Receptor Pathways

The hepatic adiponectin and farnesoid X receptor (FXR) signaling pathways play multiple roles in modulating lipid and glucose metabolism, reducing hepatic inflammation and fibrosis, and altering various metabolic targets for the management of non-alcoholic fatty liver disease (NAFLD). Alisma orientale (AO, Ze xie in Chinese and Taeksa in Korean) is an herbal plant whose tubers are enriched with triterpenoids, which have been reported to exhibit various bioactive properties associated with NAFLD. Here, the present study provides a preclinical evaluation of the biological functions and related signaling pathways of AO extract for the treatment of NAFLD in a Western diet (WD)-induced mouse model. The findings showed that AO extract significantly reversed serum markers (liver function, lipid profile, and glucose) and improved histological features in the liver sections of mice fed WD for 52 weeks. In addition, it also reduced hepatic expression of fibrogenic markers in liver tissue and decreased the extent of collagen-positive areas, as well as inhibited F4/80 macrophage aggregation and inflammatory cytokine secretion. The activation of adiponectin and FXR expression in hepatic tissue may be a major mechanistic signaling cascade supporting the promising role of AO in NAFLD pharmacotherapy. Collectively, our results demonstrated that AO extract improves non-alcoholic steatohepatitis (NASH) resolution, particularly with respect to NASH-related fibrosis, along with the regulation of liver enzymes, postprandial hyperglycemia, hyperlipidemia, and weight loss, probably through the modulation of the hepatic adiponectin and FXR pathways.

Proteomic profiling and oxidation site analysis of gaseous ozone oxidized myosin from silver carp (Hypophthalmichthys molitrix) with different oxidation degrees

Ozone is used to in surimi production and affects the conformation of myosin and gelling properties. Amino acid analysis, SDS-PAGE, in-gel trypsin hydrolysis and LC-MS/MS were used to investigate the effect of the ozone treatment time on the oxidation principle of amino acids to identify the oxidation site and oxidation mechanism of myosin with different oxidation degrees. The results showed that the order of ozonation of amino acids from easy to difficult was tyrosine > cysteine > histidine > proline. The protein structure near the SH1-SH2 region initially changed when the ozone treatment time was 50 s. Prolonging the oxidation to 80 s leads to an irregular distribution of oxidation sites. Ten min of ozone treatment resulted in the aggregation from the SH1 helical region and myosin rod. This study helped to clarify the mechanism of ozone oxidation, thus providing a theoretical basis for producing surimi products of improved quality.

Ambivalent role of ascorbic acid in the metal-catalyzed oxidation of oligopeptides

The effect of ascorbic acid on the metal-catalyzed oxidation of a human prion protein model peptide has been studied. The complex formation of the peptide was clarified first. The studied model peptide contains a methionine and a histidine amino acids which are important both as binding sites for metal ions and sensitive parts of the protein for oxidation. pH-potentiometric, UV-Vis and circular dichroism spectroscopic techniques were applied to study the stoichiometry, stability and structure of the copper(II) complexes, while HPLC-MS and MS/MS were used for identifying the products of metal-catalyzed oxidation. 3N and 4N complexes with (N_im,N^-,N^-,S) and (N_im,N^-,N^-,N^-) coordination modes are formed at pH 7.4, where the oxidation was studied. Singly, doubly and triply oxidized products are formed in which the methionine and/or the histidine side chain is oxidized. The oxidation was carried out with hydrogen peroxide solution by the addition of metal ions, namely copper(II) and iron(III) and/or ascorbic acid.

Reactivity and degradation products of tryptophan in solution and proteins

Tryptophan is one of the essential mammalian amino acids and is thus a required component in human nutrition, animal feeds, and cell culture media. However, this aromatic amino acid is highly susceptible to oxidation and is known to degrade into multiple products during manufacturing, storage, and processing. Many physical and chemical processes contribute to the degradation of this compound, primarily via oxidation or cleavage of the highly reactive indole ring. The central contributing factors are reactive oxygen species, such as singlet oxygen, hydrogen peroxide, and hydroxyl radicals; light and photosensitizers; metals; and heat. In a multi-component mixture, tryptophan also commonly reacts with carbonyl-containing compounds, leading to a wide variety of products. The purpose of this review is to summarize the current state of knowledge regarding the degradation and interaction products of tryptophan in complex liquid solutions and in proteins. For the purposes of context, a brief summary of the key pathways in tryptophan metabolism will be included, along with common methods and issues in tryptophan manufacturing. The review will focus on the conditions that lead to tryptophan degradation, the products generated in these processes, their known biological effects, and methods which may be applied to stabilize the amino acid.

Two-step reaction mechanism reveals new antioxidant capability of cysteine disulfides against hydroxyl radical attack

Cysteine disulfides, which constitute an important component in biological redox buffer systems, are highly reactive toward the hydroxyl radical (^•OH). The mechanistic details of this reaction, however, remain unclear, largely due to the difficulty in characterizing unstable reaction products. Herein, we have developed a combined approach involving mass spectrometry (MS) and theoretical calculations to investigate reactions of ^•OH with cysteine disulfides (Cys-S-S-R) in the gas phase. Four types of first-generation products were identified: protonated ions of the cysteine thiyl radical (⁺Cys-S^•), cysteine (⁺Cys-SH), cysteine sulfinyl radical (⁺Cys-SO^•), and cysteine sulfenic acid (⁺Cys-SOH). The relative reaction rates and product branching ratios responded sensitively to the electronic property of the R group, providing key evidence to deriving a two-step reaction mechanism. The first step involved ^•OH conducting a back-side attack on one of the sulfur atoms, forming sulfenic acid (-SOH) and thiyl radical (-S^•) product pairs. A subsequent H transfer step within the product complex was favored for protonated systems, generating sulfinyl radical (-SO^•) and thiol (-SH) products. Because sulfenic acid is a potent scavenger of peroxyl radicals, our results implied that cysteine disulfide can form two lines of defense against reactive oxygen species, one using the cysteine disulfide itself and the other using the sulfenic acid product of the conversion of cysteine disulfide. This aspect suggested that, in a nonpolar environment, cysteine disulfides might play a more active role in the antioxidant network than previously appreciated.

Lung macrophages: current understanding of their roles in Ozone-induced lung diseases

Through the National Ambient Air Quality Standards (NAAQS), the Clean Air Act of the United States outlines acceptable levels of six different air pollutants considered harmful to humans and the environment. Included in this list is ozone (O₃), a highly reactive oxidant gas, respiratory health hazard, and common environmental air pollutant at ground level. The respiratory health effects due to O₃ exposure are often associated with molecular and cellular perturbations in the respiratory tract. Periodic review of NAAQS requires comprehensive scientific evaluation of the public health effects of these pollutants, which is formulated through integrated science assessment (ISA) of the most policy-relevant scientific literature. This review focuses on the protective and pathogenic effects of macrophages in the O₃-exposed respiratory tract, with emphasis on mouse model-based toxicological studies. Critical findings from 39 studies containing the words O₃, macrophage, mice, and lung within the full text were assessed. While some of these studies highlight the presence of disease-relevant pathogenic macrophages in the airspaces, others emphasize a protective role for macrophages in O₃-induced lung diseases. Moreover, a comprehensive list of currently known macrophage-specific roles in O₃-induced lung diseases is included in this review and the significant knowledge gaps that still exist in the field are outlined. In conclusion, there is a vital need in this field for additional policy-relevant scientific information, including mechanistic studies to further define the role of macrophages in response to O₃.

Simultaneous Enhancement of Near-Infrared Emission and Dye Photodegradation in a Racemic Aspartic Acid Compound via Metal-Ion Modification

Changing functionalities of materials using simple methods is an active area of research, as it is "green" and lowers the developing cost of new products for the enterprises. A new small molecule racemic N,N-dimethyl aspartic acid has been prepared. Its structure is determined by single-crystal X-ray diffraction. It is characterized by FTIR, XPS, ¹H NMR, and mass spectroscopy. Its near-infrared luminescence can be enhanced by the combination of metal ions, including Dy³⁺, Gd³⁺, Nd³⁺, Er³⁺, Sr³⁺, Y³⁺, Zn²⁺, Zr⁴⁺, Ho³⁺, Yb³⁺, La³⁺, Pr⁶⁺/Pr³⁺, and Sm³⁺ ions. An optical chemistry mechanism upon interaction between the sensitizer and activator is proposed. Furthermore, the association of Ca²⁺, Sr²⁺, or Zr⁴⁺ ions to the molecule enhanced its photodegradation for dyes under white-light irradiation. Specifically, rhodamine 6G can be degraded by the Ca²⁺-modified molecule; rhodamine B, rhodamine 6G, and fluorescein sodium salt can be degraded by the Sr²⁺- or Zr⁴⁺-modified molecule. This surprising development opens a way in simultaneously increasing NIR luminescence and the ability of dye photodegradation for the investigated molecule.

Peroxymonosulfate Oxidizes Amino Acids in Water without Activation

A variety of peptidic and proteinaceous contaminants (e.g., proteins, toxins, pathogens) present in the environment may pose risk to human health and wildlife. Peroxymonosulfate is a strong oxidant (E_H⁰ = 1.82 V for HSO₅^-, the predominant species at environmental pH values) that may hold promise for the deactivation of proteinaceous contaminants. Relatively little quantitative information exists on the rates of peroxymonosulfate reactions with free amino acids. Here, we studied the oxidation of 19 of the 20 standard proteinogenic amino acids (all except cysteine) by peroxymonosulfate without explicit activation. Reaction half-lives at pH 7 ranged from milliseconds to hours. Amino acids possessing sulfur-containing, heteroaromatic, or substituted aromatic side chains were the most susceptible to oxidation by peroxymonosulfate, with rates of transformation decreasing in the order methionine > tryptophan > tyrosine > histidine. The rate of tryptophan oxidation did not decrease in the presence of an aquatic natural organic matter. Singlet oxygen resulting from peroxymonosulfate self-decomposition, while detected by electron paramagnetic resonance spectroscopy, was unlikely to be the principal reactive species. Our results demonstrate that peroxymonosulfate is capable of oxidizing 19 amino acids without explicit activation and that solvent-exposed methionine and tryptophan residues are likely initial targets of oxidation in peptides and proteins.

Bridging the Knowledge Gap for the Impact of Non-Thermal Processing on Proteins and Amino Acids

Proteins represent one of the major food components that contribute to a wide range of biophysical functions and dictate the nutritional, sensorial, and shelf-life of food products. Different non-thermal processing technologies (e.g., irradiation, ultrasound, cold plasma, pulsed electric field, and high-pressure treatments) can affect the structure of proteins, and thus their solubility as well as their functional properties. The exposure of hydrophobic groups, unfolding followed by aggregation at high non-thermal treatment intensities, and the formation of new bonds have been reported to promote the modification of structural and functional properties of proteins. Several studies reported the reduction of allergenicity of some proteins after the application of non-thermal treatments. The composition and concentration of free amino acids could be changed after non-thermal processing, depending on the processing time and intensity. The present review discusses the effects of different non-thermal treatments on protein properties in detail, and highlights the opportunities and disadvantages of these technologies in relation to protein functionality.

Decomposition and oxidation of methionine and tryptophan following irradiation with a nonequilibrium plasma jet and applications for killing cancer cells

We present evidence for the decomposition and oxidation of amino acids in aqueous solution following irradiation with a nonequilibrium plasma jet. Of 15 amino acids tested in cell culture medium, plasma irradiation induced a marked chemical change in methionine and tryptophan due to the effective production of reactive oxygen species by plasma-water interaction. We also report that plasma-treated methionine and tryptophan aqueous solutions can kill cancer cells, greatly decreasing the viability of human endometrial carcinoma (HEC-1) cancer cells due to the presence of decomposition or oxidation products generated from the amino acid. Plasma-treated methionine and tryptophan aqueous solutions also induced an anti-cancer effect on cancer-initiating cells.

Gas-Phase Fragmentation Reactions of Protonated Cystine using High-Resolution Tandem Mass Spectrometry

Cystine is an important biomolecule in living systems. Although collision-induced dissociation (CID)-based tandem mass spectrometry (MS/MS) is commonly applied for identification and quantification of cystine in both biomedical and nutritional studies, gas-phase fragmentation reactions of cystine in CID has remained unclear. This may lead to improper assay design, which may in turn result in inaccurate test results. In the present study, gas-phase fragmentation reactions of protonated cystine in CID were characterized using high-resolution MS/MS and pseudo MS³. Fragmentations started from cleavages of disulfide bond (S⁻S) and carbon⁻sulfur bond (C⁻S). When cleaving at the S⁻S, protonated cysteine was generated as one of the predominant fragmentation products. Minor fragmentations started from the loss of H₂O + CO and the loss of NH₃. Our results reveal that the m/z 74 fragment ion, which is commonly used as a product ion of the transition (precursor/product ion pair) in selected reaction monitoring (SRM) assay for quantifying cystine, comprises two isobaric fragments originating from different parts of cystine. This indicates the need for careful selection of a stable isotope-labeled cystine molecule as an internal standard for SRM assays. Here, we provide a clear picture of the fragmentation reactions of protonated cystine in CID. It can serve as a useful guidance for designing MS/MS-based assays for cystine testing.

Correlations between metabolism and structural elements of the alicyclic fentanyl analogs cyclopropyl fentanyl, cyclobutyl fentanyl, cyclopentyl fentanyl, cyclohexyl fentanyl and 2,2,3,3-tetramethylcyclopropyl fentanyl studied by human hepatocytes and LC-QTOF-MS

Recently, a number of fentanyl analogs have been implicated in overdose deaths in Europe and in the US. So far, little is known of the molecular behavior of the structurally related subgroup; the alicyclic fentanyls. In this study, reference standards of cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, and 2,2,3,3-tetramethylcyclopropyl fentanyl (TMCPF) at a final concentration of 5 µM were incubated with cryopreserved human hepatocytes (1 × 10⁶ cells/mL) for 0, 1, 3 and 5 h. The metabolites formed were identified by liquid chromatography-quadrupole time-of-flight mass spectrometry analysis. The most abundant biotransformation found was N-dealkylation (formation of normetabolites) and oxidation of the alicyclic rings. As ring size increased, the significance of N-dealkylation decreased in favor of alicyclic ring oxidation. An example of this was cyclopropyl fentanyl, with a three-carbon ring, whose normetabolite covered 82% of the total metabolic peak area and no oxidation of the alicyclic ring was observed. In contrast, TMCPF, with a seven-carbon ring structure, rendered as much as 85% of its metabolites oxidized on the alicyclic ring. Other biotransformations found included oxidation of the piperidine ethyl moiety and/or the phenethyl substructure, glucuronidation as well as amide hydrolysis to form metabolites identical to despropionyl fentanyl. Taken together, this study provides a base for understanding the metabolism of a number of structurally related fentanyl analogs formed upon intake.

Cold argon-oxygen plasma species oxidize and disintegrate capsid protein of feline calicivirus

Possible mechanisms that lead to inactivation of feline calicivirus (FCV) by cold atmospheric-pressure plasma (CAP) generated in 99% argon-1% O₂ admixture were studied. We evaluated the impact of CAP exposure on the FCV viral capsid protein and RNA employing several cultural, molecular, proteomic and morphologic characteristics techniques. In the case of long exposure (2 min) to CAP, the reactive species of CAP strongly oxidized the major domains of the viral capsid protein (VP1) leading to disintegration of a majority of viral capsids. In the case of short exposure (15 s), some of the virus particles retained their capsid structure undamaged but failed to infect the host cells in vitro. In the latter virus particles, CAP exposure led to the oxidation of specific amino acids located in functional peptide residues in the P2 subdomain of the protrusion (P) domain, the dimeric interface region of VP1 dimers, and the movable hinge region linking the S and P domains. These regions of the capsid are known to play an essential role in the attachment and entry of the virus to the host cell. These observations suggest that the oxidative effect of CAP species inactivates the virus by hindering virus attachment and entry into the host cell. Furthermore, we found that the oxidative impact of plasma species led to oxidation and damage of viral RNA once it becomes unpacked due to capsid destruction. The latter effect most likely plays a secondary role in virus inactivation since the intact FCV genome is infectious even after damage to the capsid.

Non-starch contents affect the susceptibility of banana starch and flour to ozonation

The properties of native flour and starch were compared and the changes in their properties were evaluated following ozonation at 100 and 200 ppm. X-ray diffraction analysis indicated that crystallinity index of both ozonated banana flour and starch decreased by 1.6%, B-type pattern of native banana flour and starch did not change following ozonation. The presence of higher amounts of non-starch components decreased the sensitivity of flour to the oxidation, as indicated by the lower carboxyl content compared to that of starch. The flour also required higher ozone concentration than starch to alter its properties, particularly pasting properties. Ozonation tended to increase peak, hold and final viscosity of both. A prominent change in the freeze thaw stability of both flour and starch following ozonation was the most encouraging result. Ozonation also improved the solubility of flour which was important to reduce cooking loss when applied in a range of food products. The solubility improvement in the flour might be linked to the formation of new binding following ozonation presumably involving protein present in the granule surface.

Discovery of 40 Classes of Per- and Polyfluoroalkyl Substances in Historical Aqueous Film-Forming Foams (AFFFs) and AFFF-Impacted Groundwater

Aqueous film-forming foams (AFFFs), containing per- and polyfluoroalkyl substances (PFASs), are released into the environment during response to fire-related emergencies. Repeated historical applications of AFFF at military sites were a result of fire-fighter training exercises and equipment testing. Recent data on AFFF-impacted groundwater indicates that ∼25% of the PFASs remain unidentified. In an attempt to close the mass balance, a systematic evaluation of 3M and fluorotelomer-based AFFFs, commercial products, and AFFF-impacted groundwaters from 15 U.S. military bases was conducted to identify the remaining PFASs. Liquid chromatography quadrupole time-of-flight mass spectrometry was used for compound discovery. Nontarget analysis utilized Kendrick mass defect plots and a "nontarget" R script. Suspect screening compared masses with those of previously reported PFASs. Forty classes of novel anionic, zwitterionic, and cationic PFASs were discovered, and an additional 17 previously reported classes were observed for the first time in AFFF and/or AFFF-impacted groundwater. All 57 classes received an acronym and IUPAC-like name derived from collective author knowledge. Thirty-four of the 40 newly identified PFAS classes derive from electrochemical fluorination (ECF) processes, most of which have the same base structure. Of the newly discovered PFASs found only in AFFF-impacted groundwater, 11 of the 13 classes are ECF-derived, and the remaining two classes are fluorotelomer-derived, which suggests that both ECF- and fluorotelomer-based PFASs are persistent in the environment.

Contribution to the characterization of Opuntia spp. juices by LC-DAD-ESI-MS/MS

Opuntia spp. fruits are considered as health promoting foods due to the diversity of bioactive molecules found in these fruits. The composition in organic acids, flavonols and betalains in the Opuntia ficus-indica juice from a region of Portugal was accomplished for the first time by liquid chromatography and tandem mass spectrometry using an electrospray ionization source operating in negative and positive mode. The methodology used allowed the detection of 44 compounds, from which 32 were identified. Isorhamnetin derivatives were the dominant flavonol glycosides. A total of 9 betalains including 6 betaxanthins and 3 betacyanin were also detected in the fruit juice samples and indicaxanthin, betanin and isobetanin were the major pigments. Phenolic acid and phenylpyruvic acid derivatives were also identified. To our knowledge, it is the first time derivative compounds from piscidic acid, phenolic compounds and betalains are characterized in cactus pear juice using a single LC-DAD-ESI-MS/MS method.

Protein Cross-Linking and Oligomerization through Dityrosine Formation upon Exposure to Ozone

Air pollution is a potential driver for the increasing prevalence of allergic disease, and post-translational modification by air pollutants can enhance the allergenic potential of proteins. Here, the kinetics and mechanism of protein oligomerization upon ozone (O3) exposure were studied in coated-wall flow tube experiments at environmentally relevant O3 concentrations, relative humidities and protein phase states (amorphous solid, semisolid, and liquid). We observed the formation of protein dimers, trimers, and higher oligomers, and attribute the cross-linking to the formation of covalent intermolecular dityrosine species. The oligomerization proceeds fast on the surface of protein films. In the bulk material, reaction rates are limited by diffusion depending on phase state and humidity. From the experimental data, we derive a chemical mechanism and rate equations for a kinetic multilayer model of surface and bulk reaction enabling the prediction of oligomer formation. Increasing levels of tropospheric O3 in the Anthropocene may promote the formation of protein oligomers with enhanced allergenicity and may thus contribute to the increasing prevalence of allergies.

Applying the tools of chemistry (mass spectrometry and covalent modification by small molecule reagents) to the detection of prions and the study of their structure

Prions are molecular pathogens, able to convert a normal cellular prion protein (PrP(C)) into a prion (PrP(Sc)). The information necessary for this conversion is contained in the conformation of PrP(Sc). Mass spectrometry (MS) and small-molecule covalent reactions have been used to study prions. Mass spectrometry has been used to detect and quantitate prions in the attomole range (10⁻¹⁸ mole). MS-based analysis showed that both possess identical amino acid sequences, one disulfide bond, a GPI anchor, asparagine-linked sugar antennae, and unoxidized methionines. Mass spectrometry has been used to define elements of the secondary and tertiary structure of wild-type PrP(Sc) and GPI-anchorless PrP(Sc). It has also been used to study the quaternary structure of the PrP(Sc) multimer. Small molecule reagents react differently with the same lysine in the PrP(C) conformation than in the PrP(Sc) conformation. Such differences can be detected by Western blot using mAbs with lysine-containing epitopes, such as 3F4 and 6D11. This permits the detection of PrP(Sc) without the need for proteinase K pretreatment and can be used to distinguish among prion strains. These results illustrate how two important chemical tools, mass spectrometry and covalent modification by small molecules, are being applied to the detection and structural study of prions. Furthermore these tools are or can be applied to the study of the other protein misfolding diseases such as Alzheimer Disease, Parkinson Disease, or ALS.

Effect of chemical oxidation on the sorption tendency of dissolved organic matter to a model hydrophobic surface

The application of chemical oxidants may alter the sorption properties of dissolved organic matter (DOM), such as humic and fulvic acids, proteins, polysaccharides, and lipids, affecting their fate in water treatment processes, including attachment to other organic components, activated carbon, and membranes (e.g., organic fouling). Similar reactions with chlorine (HOCl) and bromine (HOBr) produced at inflammatory sites in vivo affect the fate of biomolecules (e.g., protein aggregation). In this study, quartz crystal microbalance with dissipation monitoring (QCM-D) was used to evaluate changes in the noncovalent interactions of proteins, polysaccharides, fatty acids, and humic and fulvic acids with a model hydrophobic surface as a function of increasing doses of HOCl, HOBr, and ozone (O3). All three oxidants enhanced the sorption tendency of proteins to the hydrophobic surface at low doses but reduced their sorption tendency at high doses. All three oxidants reduced the sorption tendency of polysaccharides and fatty acids to the hydrophobic surface. HOCl and HOBr increased the sorption tendency of humic and fulvic acids to the hydrophobic surface with maxima at moderate doses, while O3 decreased their sorption tendency. The behavior observed with two water samples was similar to that observed with humic and fulvic acids, pointing to the importance of these constituents. For chlorination, the highest sorption tendency to the hydrophobic surface was observed within the range of doses typically applied during water treatment. These results suggest that ozone pretreatment would minimize membrane fouling by DOM, while chlorine pretreatment would promote DOM removal by activated carbon.

Ionization characteristics of amino acids in direct analysis in real time mass spectrometry

Analytes used in DART mass spectrometry can be oxidized by hydrogen radicals HO˙ via oxygen attachment and hydrogen loss.

Identification of modified lysozyme peptides upon photo-oxidation by LC-TOF-MS

Protein oxidation can have major implications on the quality and safety of foods, but the majority of methods to evaluate oxidative damage lack specificity. Therefore, this study aimed to identify specific markers for protein oxidation. A well-characterized protein, lysozyme, was modified by photo-oxidation and subsequently hydrolyzed prior to peptide analysis by LC-TOF-MS. A semiquantitative analysis of the peptides indicated that from the seven peptides containing sensitive amino acids, two peptides (HGLDNYR and WWCNDGR) were highly affected upon photo-oxidation and have the potential to serve as markers for protein oxidation. Site-specific modifications enabled the description of the degradation pathway of several lysozyme peptides but also indicated that the surrounding amino acids and the 3D structure of the protein have an impact on the induced modifications. It is therefore advisable to evaluate protein oxidation on the intact protein.

Using isotopically-coded hydrogen peroxide as a surface modification reagent for the structural characterization of prion protein aggregates

The conversion of the cellular prion protein (PrP(C)) into aggregated ß-oligomeric (PrP(ß)) and fibril (PrP(Sc)) forms is the central element in the development of prion diseases. Here we report the first use of isotopically-coded hydrogen peroxide surface modification combined with mass spectrometry (MS) for the differential characterization of PrP(C) and PrP(β). (16)O and (18)O hydrogen peroxide were used to oxidize methionine and tryptophan residues in PrP(C) and PrP(β), allowing for the relative quantitation of the extent of modification of each form of the prion protein. After modification with either light or heavy forms of hydrogen peroxide (H2(16)O2 and H2(18)O2), the PrP(C) and PrP(β) forms of the protein were then combined, digested with trypsin, and analysed by LC-MS. The (18)O/(16)O signal intensity ratios were used to determine the relative levels of oxidation of specific amino acids in the PrP(C) and PrP(β) forms. Using this approach we have detected several residues that are differentially-oxidized between the native and β-oligomeric prion forms, allowing determination of the regions of PrP(C) involved in the formation of PrP(β) aggregates. Modification of these residues in the β-oligomeric form is compatible with a flip of the β1-H1-β2 loop away from amphipathic helices 2 and 3 during conversion.

BIOLOGICAL SIGNIFICANCE

Surface modification using isotopically-coded hydrogen peroxide has allowed quantitative comparison of the exposure of methionine and tryptophan residues in PrP(C) and PrP(ß) forms of prion protein. Detected changes in surface exposure of a number of residues have indicated portions of the PrP structure which undergo conformational transition upon conversion. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?

Kinetics and mechanism of oxidation of tryptophan by ferrate(VI)

Kinetics of the oxidation of tryptophan (Trp) and kynurenine (Kyn), precursors of nitrogenous disinfection byproducts (N-DBP), by ferrate(VI) (Fe(VI)O4(2-), Fe(VI)) were investigated over the acidic to basic pH range. The second-order rate constants decreased with increase in pH, which could be described by the speciation of Fe(VI) and Trp (or Kyn). The trend of pH dependence of rates for Trp (i.e., aromatic α-amino acid) differs from that for glycine (i.e., aliphatic α-amino acid). A nonlinear relationship between transformation of Trp and the added amount of Fe(VI) was found. This suggests that the formed intermediate oxidized products (OPs), identified by LC-PDA and LC-MS techniques, could possibly compete with Trp to react with Fe(VI). N-Formylkynurenine (NFK) at pH 7.0 and 4-hydroxyquinoline (4-OH Q) and kynurenic acid (Kyn-A) at pH 9.0 were the major OPs. Tryptophan radical formation during the reaction was confirmed by the rapid-freeze quench EPR experiments. The oxygen atom transfer from Fe(VI) to NFK was demonstrated by reacting Fe(18)O4(2-) ion with Trp. A proposed mechanism explains the identified OPs at both neutral and alkaline pH. Kinetics and OPs by Fe(VI) were compared with other oxidants (chlorine, ClO2(•), O3, and (•)OH).

Oxidation of methionine 216 in sheep and elk prion protein is highly dependent upon the amino acid at position 218 but is not important for prion propagation

We employed a sensitive mass spectrometry-based method to deconstruct, confirm, and quantitate the prions present in elk naturally infected with chronic wasting disease and sheep naturally infected with scrapie. We used this approach to study the oxidation of a methionine at position 216 (Met216), because this oxidation (MetSO216) has been implicated in prion formation. Three polymorphisms (Ile218, Val218, and Thr218) of sheep recombinant prion protein were prepared. Our analysis showed the novel result that the proportion of MetSO216 was highly dependent upon the amino acid residue at position 218 (I > V > T), indicating that Ile218 in sheep and elk prion protein (PrP) renders the Met216 intrinsically more susceptible to oxidation than the Val218 or Thr218 analogue. We were able to quantitate the prions in the attomole range. The presence of prions was verified by the detection of two confirmatory peptides: GENFTETDIK (sheep and elk) and ESQAYYQR (sheep) or ESEAYYQR (elk). This approach required much smaller amounts of tissue (600 μg) than traditional methods of detection (enzyme-linked immunosorbent assay, Western blot, and immunohistochemical analysis) (60 mg). In sheep and elk, a normal cellular prion protein containing MetSO216 is not actively recruited and converted to prions, although we observed that this Met216 is intrinsically more susceptible to oxidation.

Changes in fluorescence spectra of bioaerosols exposed to ozone in a laboratory reaction chamber to simulate atmospheric aging

A laboratory system for exposing aerosol particles to ozone and rapidly measuring the subsequent changes in their single-particle fluorescence is reported. The system consists of a rotating drum chamber and a single-particle fluorescence spectrometer (SPFS) utilizing excitation at 263 nm. Measurements made with this system show preliminary results on the ultra-violet laser-induced-fluorescence (UV-LIF) spectra of single aerosolized particles of Yersinia rohdei, and of MS2 (bacteriophage) exposed to ozone. When bioparticles are exposed in the chamber the fluorescence emission peak around 330 nm: i) decreases in intensity relative to that of the 400-550 nm band; and ii) shifts slightly toward shorter-wavelengths (consistent with further drying of the particles). In these experiments, changes were observed at exposures below the US Environmental Protection Agency (EPA) limits for ozone.

Combination of LC-MS- and GC-MS-based metabolomics to study the effect of ozonated autohemotherapy on human blood

Ozonated autohemotherapy (O3-AHT) is a medical approach during which blood obtained from the patient is ozonated and injected back into the body. Despite an increasing number of evidence that O3-AHT is safe, this type of therapy remains controversial. To extend knowledge about the changes in blood evoked by O3-AHT, LC-MS- and GC-MS-based metabolic fingerprinting was used to compare plasma samples obtained from blood before and after the treatment with potentially therapeutic concentrations of ozone. The procedure was performed in PVC bags utilized for blood storage to study also possible interactions between ozone and plastic. By use of GC-MS, an increase in lactic acid and pyruvic acid was observed, which indicated an increased rate of glycolysis. With LC-MS, changes in plasma antioxidants were observed. Moreover, concentrations of lipid oxidation products (LOP) and lysophospholipids were increased after ozone treatment. This is the first report of increased LOPs metabolites after ozonation of blood. Seven metabolites detected by LC-QTOF-MS only in ozonated samples could be considered as novel biomarkers of oxidative stress. Several plasticizers have been detected by both techniques in blood stored in PVC bags. PVC is known to be an ozone resistant material, but ozonation of blood in PVC bags stimulates leaching of plasticizers into the blood.

Cyclic interconversion of methionine containing peptide between oxidized and reduced phases monitored by reversed-phase HPLC and ESI-MS/MS

The cyclic oxidation and reduction of methionine (Met) containing peptides and proteins play important roles in biological system. This work was contributed to analysis the cyclic oxidation and reduction processes of a methionine containing peptide which is very likely to relate in the cell signal transduction pathways. To mimic the biological oxidation condition, hydrogen peroxide was used as the reactive oxygen species to oxidize the peptide. Reversed-phase high-performance liquid chromatography and mass spectrometry were employed to monitor the reactions and characterize the structural changes of the products. A rapid reduction procedure was developed by simply using KI as the reductant, which is green and highly efficient. By investigation of the cyclic oxidation and reduction process, our work provides a new perspective to study the function and mechanism of Met containing peptides and proteins during cell signaling processes as well as diseases.

Photocrosslinking between peptide-peptide or peptide-oligonucleotide by Ru(II)-TAP complexes

Ru(II)-TAP complexes have been shown to be very attractive compounds in the frame of developments of new anticancer drugs targeting the genetic material. This increasing interest originates from observations of covalent bond formations, triggered by photo-induced electron transfer (PET) between Ru(II)-TAP complexes and guanine bases of DNA. This photoreaction has recently been extended to the tryptophan (Trp) amino acid for future applications involving peptides. Thus, a double photo-addition of Trp residues of peptides on Ru(II) complexes is demonstrated by mass spectrometry with some structural issues. Such bi-adduct formations offer the possibility of photocrosslinking two Trp-containing biomolecules, which is investigated in this study. Thus, photocrosslinking between two complementary oligonucleotides (ODNs) derivatized by Trp-containing tripeptides is demonstrated by polyacrylamide gel electrophoresis (PAGE) in the presence of Ru(II)-TAP complexes. Both PAGE and MS indicate that such photocrosslinkings arise from two reaction pathways: either via the double addition of Trp residues on the Ru complex or from dimerization of Trp radicals. The competition between these two pathways depends on the experimental conditions. Heterobridgings between guanine bases and tryptophan residues mediated by Ru(II)-TAP complexes is also examined, opening the way to ODN-peptide photocrosslinkings.

Role of 2-oxo and 2-thioxo modifications on the proton affinity of histidine and fragmentation reactions of protonated histidine

A combination of electrospray ionisation (ESI), multistage and high-resolution mass spectrometry experiments was used to compare the gas-phase chemistry of the amino acids histidine (1), 2-oxo-histidine (2), and 2-thioxo-histidine (3). Collision-induced dissociation (CID) of all three different proton-bound heterodimers of these amino acids led to the relative gas-phase proton affinity order of: histidine >2-thioxo-histidine >2-oxo-histidine. Density functional theory (DFT) calculations confirm this order, with the lower proton affinities of the oxidised histidine derivatives arising from their ability to adopt the more stable keto/thioketo tautomeric forms. All protonated amino acids predominately fragment via the combined loss of H(2)O and CO to yield a(1) ions. Protonated 2 and 3 also undergo other small molecule losses including NH(3) and the imine HN=CHCO(2)H. The observed differences in the fragmentation pathways are rationalised through DFT calculations, which reveal that while modification of histidine via the introduction of the oxygen atom in 2 or the sulfur atom in 3 does not affect the barriers against the loss of H(2)O+CO, barriers against the losses of NH(3) and HN=CHCO(2)H are lowered relative to protonated histidine.