MS Experiments Research Articles

Sustainable valorisation of cigarette butts waste through pyrolysis: An insight into the pyrolytic products and subsequent aqueous heavy metals removal by pyrolytic char

In this study, cigarette butts (CB) waste was pyrolyzed over a wide temperature range (400–700 °C) using Pyro/GC–MS and slow pyrolysis experiments. The feedstock and char products were extensively investigated using TGA, elemental analysis, surface area and porosity analysis, SEM-EDS, XRD, and FT-IR, and subsequently tested for their ability to remove Ni (II) and Cu (II) from aqueous solutions. The Pyro/GC–MS analysis revealed the presence of several useful compounds including acids, esters and hydrocarbons. Char yields ranged from 26.6 to 20.1 wt%, and carbon contents varied from 65.3 to 60.8 wt%. The chars produced at medium temperatures (500-600 °C) were highly porous, with a specific surface area of 272.9–270.8 m2/g. The heavy metal adsorption studies revealed that CB 500 °C had the highest adsorption capacity of 13.8 mg/g with 53.4 % nickel removal, while CB 600 °C had the highest adsorption capacity of 23.4 mg/g with 94.7 % copper removal.

Enhanced Payload Localization in Antibody-Drug Conjugates Using a Middle-Down Mass Spectrometry Approach with Proton Transfer Charge Reduction.

Antibody-drug conjugates (ADCs) represent a novel class of immunoconjugates with growing therapeutic relevance, since they combine the efficacy of cytotoxic drugs with the specificity of antibodies. However, by design, ADCs introduce structural features into the monoclonal antibody scaffold that complicate their analysis. Payload attachment to cysteine or lysine residues can often result in product heterogeneity, regarding both the number of attached drug molecules and their conjugation site, necessitating the use of state-of-the-art MS instrumentation to elucidate their complexity. In middle-down mass spectrometry (MD MS), the gas-phase sequencing of ∼25 kDa ADC subunits with different ion activation techniques generally produces rich fragmentation mass spectra; however, spectral congestion can cause some fragment ions to go undetected, including those that can pinpoint the exact location of payload conjugation sites. Proton transfer charge reduction (PTCR) can substantially simplify fragment ion spectra, thereby unveiling the presence of product ions whose signals were previously suppressed. Herein, we present an MD MS strategy relying on the use of PTCR to investigate a cysteine-based ADC mimic with a variable drug-to-antibody ratio, targeting the unambiguous localization of payload conjugation sites. Unlike traditional tandem MS experiments (MS2), which could not provide a complete map of conjugation sites, a single PTCR-based experiment (MS3) proved to be sufficient to achieve this goal across all variably modified ADC subunits, including isomeric ones. Combining the results obtained from orthogonal ion activation techniques followed by PTCR further strengthened the confidence in the assignments.

The O-GlcNAc database: introducing new features and tools developed from community feedback.

O-GlcNAc is a reversible post-translational modification found on serine and threonine residues of nucleocytoplasmic proteins. Four years ago, we released the O-GlcNAc Database( oglcnac.mcw.edu ), a comprehensive catalog of O-GlcNAcylated proteins that has become one of the most cited resources in the field, with hundreds of unique users per month. We are now presenting an updated O-GlcNAc Database, which includes nearly 20,000 O-GlcNAcylated proteins and 48 species, marking substantial growth in data volume and scope. This paper presents the most noteworthy features implemented over the last year, often originating from feedback from the O-GlcNAc community. Among these features, we provide a brief overview of the database content, introduce our new protein viewer mode, and discuss the implementation of subcellular localization information and its applications in the O-GlcNAc score. We also provide an interface to use CytOVS, a tool designed to evaluate and sort O-GlcNAcome datasets derived from MS experiments. In conclusion, this new and improved O-GlcNAc Database represents a significant advancement in providing a comprehensive and expanded resource for researchers in the field of O-GlcNAc biology.

ZIFs@MIL-101/urea-derived magnetic FeCo nitrogen-rich carbon as an effective and stable catalyst for peroxymonosulfate activation

High efficiency and stability are key issues in heterogeneous metal catalytic materials/peroxymonosulfate (PMS) systems during wastewater degradation. However, catalytic materials that are difficult to recover and metal leaching can cause secondary contamination of water bodies. Herein, we designed the magnetic FeCo nitrogen-rich carbon (FeCo-NC) obtained by layer-by-layer encapsulation, followed by urea encapsulation of in situ grown MOF-in-MOF and carbonization. The CoFe2O4 crystalline nature of FeCo-NC was confirmed by X-ray diffraction (XRD), high-resolution transmission electron microscopy (HRTEM), and selected angle electron diffraction (SAED) results, which is responsible for the magnetic properties of FeCo-NC. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) present that the material's morphology transforms from dodecahedral ZIF-67 to spindle-shaped ZIF-67@MIL-101 and then to octahedral FeCo-NC. Compared with FeCo-C and ZIF-67@MIL-101, the removal efficiency of FeCo-NC was maintained at 78.6 % after 10 consecutive cycles, with only a 17 % loss of raw material. The Fe and Co leaching amounts in the FeCo-NC/PMS system were approximately 0.6 and 0.1 mg/L, respectively, much lower than China's Fe and Co emission standards. FeCo-NC characterization and TC degradation results demonstrated that magnetic CoFe2O4 nanoparticles formed on the surface or inside the FeCo-NC could effectively inhibit metal (Fe and Co) loss and be easily regenerated in multiple degradation cycles. The mechanism and degradation routes in the FeCo-NC/PMS/ TC system, including the radical/nonradical pathways, Fe/Co valence change, and electron transfer, were further investigated by electron paramagnetic resonance experiments, electrochemical analyses, in situ Raman spectroscopy, and HPLC–MS experiments.

B-166 Differentiation of Aziridine Functionality from Related Functional Groups in Protonated Analytes by Using Selective Ion-Molecule Reactions

Abstract Background The development of better methods for the rapid and reliable identification of unknown compounds in mixtures is urgently needed in drug development. Aziridines, in particular, are used for drug synthesis but are potentially mutagenic and carcinogenic compounds. However, the detection and identification of these compounds pose challenges for many analytical methods, such as Nuclear Magnetic Resonance (NMR) spectroscopy, Fourier-transform infrared spectroscopy (FT-IR), and X-ray crystallography. These techniques are time-consuming and often require large quantities of highly pure compounds. Methods Therefore, this study demonstrates that selective gas-phase ion-molecule reactions of protonated analytes with neutral tris(dimethylamino)borane (TDMAB), followed by diagnostic collision-activated dissociation (CAD), can be used to differentiate aziridines from structurally related compounds in a modified linear quadrupole ion trap (LQIT) mass spectrometer. The experiments were performed using an atmospheric pressure chemical ionization (APCI) source in positive ion detection mode. TDMAB was purchased from Sigma-Aldrich and used without purification. It was introduced into the ion trap (2 mtorr of helium buffer gas) via an external reagent mixing manifold through a syringe pump at a flow rate of 10 μL h-1 and diluted with helium before entering the ion trap through a variable leak valve. All analytes were prepared at a concentration of 1 mM in methanol. The protonated analytes were transferred into the ion trap, isolated, and allowed to react with TDMAB (MS2 experiments). Results Product ions formed upon reactions of the analyte ions with TDMAB were subjected to a collision-activated dissociation (CAD) experiment (MS3 experiments). CAD on product ions produced diagnostic fragment ions with 25- and 43 m/z-units lower m/z values than the adduct - DMA product ions. Quantum chemical calculations were employed using the Gaussian 16 program calculated at the M06-2X/6-311++G(d,p) level of theory to provide theoretical foundation and to explore the underlying mechanisms of the observed gas-phase reactions. None of the tested structurally related analytes produced a similar fragmentation pattern Conclusions The innovative approach presented in this study offers a promising avenue for enhancing efficiency and accuracy in drug development. The successful differentiation of aziridine is an alternative method in overcoming the limitation of traditional techniques. The findings from the research contributes to the advancement of analytical techniques, addressing critical issues in identifying impurities in drug products. The versatility of the methods extends beyond drug developments, making it applicable in various other fields such as in molecular diagnostics, metabolism and laboratory medicines.

Mechanism insight into α-D-galactopyranose conversion to 5-hydroxymethyl furfural by combining Py-GC–MS experiments and theoretical calculations

Pyrolysis of biomass is a promising technique for producing various chemicals. During the fast pyrolysis of biomass, 5-hydroxymethyl furfural (5-HMF) is a significant product derived from holocellulose, which consists of cellulose and hemicellulose. In this study, the formation mechanism of 5-HMF was systematically revealed by combining fast pyrolysis experiments of 13C-labeled and unlabeled D-galactose and density functional theory calculations that α-D-galactopyranose was selected as the model compound for hemicellulose. Experimental results show the yield and concentration of 5-HMF gradually decrease as the temperature rises (≥400 °C). In addition, the origin of the C atoms in 5-HMF was determined. The aldehyde group and hydroxymethyl are primarily derived from C1 and C6 of D-galactose, respectively. Based on computational results, α-D-galactopyranose prefers to undergo a ring-opening reaction to form acyclic D-galactose with an energy barrier of 166.5 kJ/mol. (2R,3S,E)-2,3,5,6-tetrahydroxyhex-4-enal (C1-i2) and (2R,3S)-2,3,6-trihydroxy-5-oxohexanal (C1-i3) generated by D-galactose are important intermediates for 5-HMF formation. Because C1-i3 can readily form 5-HMF through successive dehydration at 3-OH+2-H site, cyclization, and dehydration at 5-OH+4-H site. In favorable paths, the aldehyde group of 5-HMF all comes from C1 of α-D-galactopyranose, which reasonably explains the experimental results. Overall, this study will be helpful to improve the formation mechanism of 5-HMF and to develop relevant pyrolysis techniques to prepare it.

UPLC-Q-TOF-MS/MS analysis of ophiobolins sesterterpenoids and bioactive analogs from Bipolaris eleusines

In order to elucidate the mass fragmentation patterns and unveil more undescribed ophiobolin analogs, the mass fragmentation patterns of ophiobolins were analyzed based on UPLC-Q-TOF-MS/MS experiments. Different kinds of rearrangements (including McLafferty rearrangement) were the main cleavage patterns. Twenty-six (9–31) analogs were then tentatively characterized based on their mass analysis, and three undescribed ophiobolins (6–8) and a known analogue (5) were isolated in target. Compound 5 possesses a rare polycyclic carbon skeleton only recently reported, and compound 6 contains an undescribed lactone ring system fused with A/B ring at C-3/C-21, whereas compounds 7 and 8 have a peroxyl group in the side chain, which is the first reported in all ophiobolins. Compounds 5 and 7 displayed significant cytotoxicity against MCF-7 cancer cells.

The temporal dynamics of familiar face recognition: Event-related brain potentials reveal the efficient activation of facial identity representations

While it is widely known that humans are typically highly accurate at recognizing familiar faces, it is less clear how efficiently recognition is achieved. In a series of three experiments, we used event-related brain potentials (ERP) in a repetition priming paradigm to examine the efficiency of familiar face recognition. Specifically, we varied the presentation time of the prime stimulus between 500 ms and 33 ms (Experiments 1 and 2), and additionally used backward masks (Experiment 3) to prevent the potential occurrence of visual aftereffects. Crucially, to test for the recognition of facial identity rather than a specific picture, we used different images of the same facial identities in repetition conditions. We observed clear ERP repetition priming effects between 300 and 500 ms after target onset at all prime durations, which suggests that the prime stimulus was sufficiently well processed to allow for facilitated recognition of the target in all conditions. This finding held true even in severely restricted viewing conditions including very brief prime durations and backward masks. We conclude that the facial recognition system is both highly effective and efficient, thus allowing for our impressive ability to recognise the faces that we know.

A comprehensive gas chromatography electron ionization high resolution mass spectrometry study of a new steroidal selective androgen receptor modulator (SARM) compound S42.

The synthetic 20-keto-steroid S42 (1) demonstrated selective androgen receptor modulator (SARM) properties in preclinical studies and, consequently, received growing attention also in the context of sports drug testing programs. Fundamental understanding of the behavior of S42 (1) and of relevant derivatives in gas chromatography-electron ionization MS experiments at high resolution (GC-EI-HRMS) is indispensable to develop a reliable qualitative and quantitative doping control method for S42 (1) and its metabolites in body fluid matrices. We present important fundamental mechanistic data on the EI fragmentation behavior of S42 (1) and of silyl ether derivatives as well as of stable isotope-labelled reference material.

A novel AIE-based mitochondria-targeting fluorescent probe for monitoring of the fluctuation of endogenous hypochlorous acid in ferroptosis models.

Ferroptosis is a way of cell death mainly due to the imbalance between the production and degradation of lipid reactive oxygen species, which is closely associated with various diseases. Endogenous hypochlorous acid (HOCl) mainly produced in mitochondria is regarded as an important signal molecule of ferroptosis. Therefore, monitoring the fluctuation of endogenous HOCl is beneficial to better understand and treat ferroptosis-related diseases. Inspired by the promising aggregation-induced emission (AIE) properties of tetraphenylethene (TPE), herein, we rationally constructed a novel AIE-based fluorescent probe, namely QTrPEP, for HOCl with nice mitochondria-targeting ability and high sensitivity and selectivity. Probe QTrPEP consisted of phenylborate ester and the AIE fluorophore of quinoline-conjugated triphenylethylene (QTrPE). HOCl can brighten the strong fluorescence through a specific HOCl-triggered cleavage of the phenylborate ester bond and release ofQTrPE, which has been demonstrated by MS, HPLC, and DLS experiments. In addition, combining QTrPE-doped test strips with a smartphone-based measurement demonstrated the excellent performance of the probe to sense HOCl. The obtained favorable optical properties and negligible cytotoxicity allowed the use of this probe for tracking of HOCl in three different cells. In particular, this work represents the first AIE-based mitochondria-targeting fluorescent probe for monitoring the fluctuation of HOCl in ferroptosis.

NCPbook: A comprehensive database of noncanonical peptides.

Noncanonical peptides (NCPs) are a class of peptides generated from regions previously thought of as noncoding, such as introns, 5' UTRs, 3' UTRs, and intergenic regions. In recent years, the significance and diverse functions of NCPs have come to light, yet a systematic and comprehensive NCP database remains absent. Here, we developed NCPbook (https://ncp.wiki/ncpbook/), a database of evidence-supported NCPs, which aims to provide a resource for efficient exploration, analysis, and manipulation of NCPs. NCPbook incorporates data from diverse public databases and scientific literature. The current version of NCPbook includes 180,676 NCPs across 29 different species, evidenced by MS, ribosome profiling, or molecular experiments. These NCPs are distributed across kingdoms, comprising 123,408 from 14 plant species, 56,999 from 7 animal species, and 269 from 8 microbial species. Furthermore, NCPbook encompasses 9,166 functionally characterized NCPs playing important roles in immunity, stress resistance, growth, and development. Equipped with a user-friendly interface, NCPbook allows users to search, browse, visualize, and retrieve data, making it an indispensable platform for researching NCPs in various plant, animal, and microbial species.

Therapeutic effect of Periploca forrestii on collagen-induced arthritis in rats through JAK2/Nf-κB pathway.

Rheumatoid arthritis (RA) is a chronic autoimmune disease that affects the body. Periploca forrestii was a miao ethnic drug in China that was used to treat arthritis for hundreds of years. But, the therapeutic mechanism is so far unknown. Therefore, the chemical component and effect of Periploca forrestii on arthritis in rats were studied using HPLC-QTOF MS, micro-CT, and other experiments in this paper. Male Sprague-Dawley rats were used to assess the in vivo activity. HPLC QTOF-MS was used to analyze the chemical profile of the P. forrestii (PF). Bovine type II collagen and Complete Freund's Adjuvant were used to stimulate and construct the collagen-induced arthritis (CIA) model. Three dosages of PF (100mg/kg, 200mg/kg, 400mg/kg) were used to evaluate in vivo activity. Methotrexate was used as the positive drug. H/E staining and micro-CT methods were used to monitor the pathological changes of CIA rats. ELISA method was used to assess the serum level of immune- and inflammation-related cytokines. Immunohistochemical experiments were used to test the gene expression in JAK and Nf-κB pathways. 42 compounds were identified from PF. PF administration lowered the increased spleen index compared with that of control and MTX groups, and partially restored body weight, reduced paw swelling, and arthritis score compared with the model group. Macroscopic assessment indicated inflamed paw with significant swelling in the model group, while the extent of inflammation and swelling was attenuated by both MTX and PF. H/E staining experiments demonstrated that pathological changes of synovial cells and infiltration of inflammatory cells were observed in the model group. In contrast, the MTX and PF treatment partially reversed these pathological changes. Micro-CT examination showed severe injuries and scars caused by inflammation for the model group, and in the high-dosage group (400mg/kg) the inflammation-caused injuries and scars were dramatically ameliorated. Mechanism study showed that PF restored Nf-κB phosphorylation and JAK2 expression compared with the model group. P. forrestii possesses a potent effect on CIA rats. Nf-κB and JAK2 pathways are involved in its protective effect on CIA.

Heterologous activation and metabolites identification of the pks7 gene cluster from Saccharopolyspora erythraea

The microbial genome remains a huge treasure trove for the discovery of diverse natural products. Saccharopolyspora erythraea NRRL23338, the industry producer of erythromycin, has a dozen of biosynthetic gene clusters whose encoding products are unidentified. Heterologous expression of one of the polyketide clusters pks7 in Streptomyces albus B4 chassis resulted in the characterization of its function responsible for synthesizing both 6-methylsalicyclic acid and 6-ethylsalicyclic acid. Meanwhile, two new 6-ethylsalicyclic acid ester derivatives were isolated as shunt metabolites. Their structures were identified by comprehensive analysis of MS and NMR experiments. Putative functions of genes within the pks7 BGC were also discussed.

DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes

Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP–MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP–MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP–MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex–complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.

Localizing Isomerized Residue Sites in Peptides with Tandem Mass Spectrometry.

Isomerized amino acid residues have been identified in many peptides extracted from tissues or excretions of humans and animals. These isomerized residues can play key roles by affecting biological activity or by exerting an influence on the process of aging. Isomerization occurs spontaneously and does not result in a mass shift. Thus, identifying and localizing isomerized residues in biological samples is challenging. Herein, we introduce a fast and efficient method using tandem mass spectrometry (MS) to locate isomerized residues in peptides. Although MS2 spectra are useful for identifying peptides that contain an isomerized residue, they cannot reliably localize isomerization sites. We show that this limitation can be overcome by utilizing MS3 experiments to further evaluate each fragment ion from the MS2 stage. Comparison at the MS3 level, utilizing statistical analyses, reveals which MS2 fragments differ between samples and, therefore, must contain the isomerized sites. The approach is similar to previous work relying on ion mobility to discriminate MS2 product ions by collision cross-section. The MS3 approach can be implemented using either ion-trap or beam-type collisional activation and is compatible with the quantification of isomer mixtures when coupled to a calibration curve. The method can also be implemented in combination with liquid chromatography in a targeted approach. Enabling the identification and localization of isomerized residues in peptides with an MS-only methodology will expand accessibility to this important information.

Application of SO42–/Fe2O3-CuO solid superacid materials in cyclic compounds from wastewater: Performance and mechanism

In wastewater treatment, the degradation of refractory cyclic compounds by catalytic ozonation using sulfated solid superacid has not been thoroughly investigated. The doped S element alters the electronic activity and drives the ozone oxidation of recalcitrant organic pollutants, potentially leading to an increase in catalytic efficiency. This study aimed to develop a novel iron-copper sulfate (SO42–/Fe2O3-CuO) solid superacid composite to strengthen catalytic reactions. According to the characterization results, the embedding of SO42– enhanced the electron transfer inside the material, leading to more Lewis acid sites, which facilitated the catalytic decomposition of O3. The catalytic degradation and reaction kinetics experiments on quinoline verified the superior catalytic performance of the SO42–/Fe2O3-CuO system compared to other systems. Fluorescence, UV–Vis spectrophotometry, and EPR experiments demonstrated that the hydroxyl radicals (OH), superoxide radicals (O2−), and singlet oxygen (1O2) were generated in the SO42–/Fe2O3-CuO system, and their presence accelerated the redox cycling of Fe(III)/Fe(II) and Cu(II)/Cu(I). In addition, the possible degradation pathways of quinoline were verified by density functional theory (DFT) calculations, and the toxicity of intermediates was assessed by quantitative structure–activity relationship (QSAR) analysis. Finally, the applicability of the SO42–/Fe2O3-CuO catalytic system in bio-treated coking wastewater (BTCW) was validated. GC–MS experiments further confirmed that it was mainly the cyclic compounds that contributed to the removal rate during the catalytic process. In summary, this study demonstrated the significant potential of the SO42–/Fe2O3-CuO catalytic system in degrading refractory cyclic compounds, providing valuable technical support for the field of wastewater treatment.

Heteromeric Completive Self-Sorting in Coordination Cage Systems.

Heteroleptic coordination cages, nonstatistically assembled from a set of matching ligands, can be obtained by mixing individual components or via cage-to-cage transformations from homoleptic precursors. Based on the latter approach, we here describe a new level of self-sorting in coordination cage systems, namely, 'heteromeric completive self-sorting'. Here, two heteroleptic assemblies of type Pd2A2B2 and Pd2A2C2, sharing one common ligand component A but differing in the other, are shown to coexist in solution. This level of self-sorting can be reached either from a statistical mixture of assemblies based on some ligands B and C or, alternatively, following a first step of integrative self-sorting giving a distinct Pd2B2C2 intermediate. While subtle enthalpic factors dictate the outcome of the self-sorting, we found that it is controllable. From a unique set of three ligands, we demonstrate the transition from strict integrative self-sorting forming a Pd2AB2C cage to heteromeric completive self-sorting to give Pd2A2B2 and Pd2A2C2 by variation of the ligand ratio. Cage-to-cage transformations were followed by NMR and MS experiments. Single crystal X-ray structures for three new heteroleptic cages were obtained, impressively highlighting the versatility of ligand A to either form a π-stacked trans-figure-of-eight arrangement in Pd2A2B2 or occupy two cis-edges in Pd2A2C2 or only a single edge in Pd2AB2C. This study paves the way toward the control of heteroleptic cage populations in a systems chemistry context with emerging features such as chemical information processing, adaptive guest selectivity, or stimuli-responsive catalytic action.

Genome-guided purification of high amounts of the siderophore ornibactin and detection of potentially novel burkholdine derivatives produced by Burkholderia catarinensis 89T.

The increased availability of genome sequences has enabled the development of valuable tools for the prediction and identification of bacterial natural products. Burkholderia catarinensis 89T produces siderophores and an unknown potent antifungal metabolite. The aim of this work was to identify and purify natural products of B. catarinensis 89T through a genome-guided approach. The analysis of B. catarinensis 89T genome revealed 16 clusters putatively related to secondary metabolism and antibiotics production. Of particular note was the identification of a nonribosomal peptide synthetase (NRPS) cluster related to the production of the siderophore ornibactin, a hybrid NRPS-polyketide synthase Type 1 cluster for the production of the antifungal glycolipopeptide burkholdine, and a gene cluster encoding homoserine lactones (HSL), probably involved in the regulation of both metabolites. We were able to purify high amounts of the ornibactin derivatives D/C6 and F/C8, while also detecting the derivative B/C4 in mass spectrometry investigations. A group of metabolites with molecular masses ranging from 1188 to 1272Da could be detected in MS experiments, which we postulate to be new burkholdine analogs produced by B. catarinensis. The comparison of B. catarinensis BGCs with other Bcc members corroborates the hypothesis that this bacterium could produce new derivatives of these metabolites. Moreover, the quorum sensing metabolites C6-HSL, C8-HSL, and 3OH-C8-HSL were observed in LC-MS/MS analysis. The new species B. catarinensis is a potential source of new bioactive secondary metabolites. Our results highlight the importance of genome-guided purification and identification of metabolites of biotechnological importance.

Mercury binding to proteins disclosed by ESI MS experiments: The case of three organomercurials

Solution interactions of three organomercury compounds, i.e., methylmercury chloride, thimerosal and phenylmercury acetate, with a group of biochemically relevant proteins, namely cytochrome c (Cyt c), ribonuclease A (RNase A), carbonic anhydrase I (hCA I), superoxide dismutase (SOD), and serum albumin (HSA), were investigated using an established ESI MS approach. Temporal analysis of sample aliquots provided insight into the binding kinetics, while comparative analysis of the obtained mass spectra disclosed adduct formation of each mercurial with the tested proteins and the relative abundance of the species. The three organomercurials bind, exclusively and tightly, to free cysteine residues as no binding was observed in the case of proteins lacking such groups. hCA I, SOD and HSA formed distinct mercury adducts, preserving the Hg bound alkyl/aryl ligands; yet, the three organomercurials displayed significant differences in reactivity in relation to their chemical structure. The investigation was then extended to analyze the reactions with the C-terminal dodecapeptide of the enzyme human thioredoxin reductase, which contains a characteristic selenol-thiol moiety: tight Hg binding was observed. Notably, this peptide was able to remove effectively and completely the alkyl/aryl ligands of the three tested organomercurials; this behavior may be relevant to the detoxification mechanism of organomercurials in mammals. Finally, a competition experiment was carried out to establish whether protein bound mercury centers may be displaced by other competing metals. Interestingly, and quite unexpectedly, we observed that a protein bound mercury fragment may be partially displaced from its coordination site in hCA I by the medicinal gold compound auranofin.

Superoxide-responsive quinone methide precursors (QMP-SOs) to study superoxide biology by proximity labeling and chemoproteomics.

Superoxide is a reactive oxygen species (ROS) with complex roles in biological systems. It can contribute to the development of serious diseases, from aging to cancers and neurodegenerative disorders. However, it can also serve as a signaling molecule for important life processes. Monitoring superoxide levels and identifying proteins regulated by superoxide are crucial to enhancing our understanding of this growing field of redox biology and signaling. Given the high reactivity and very short lifetime of superoxide compared to other ROS in biological systems, proteins redox-modified by superoxide should be in close proximity to where superoxide is generated endogenously, i.e. superoxide hotspots. This inspires us to develop superoxide-specific quinone methide-based precursors, QMP-SOs, for proximity labeling of proteins within/near superoxide hotspots to image superoxide and profile proteins associated with superoxide biology by chemoproteomics. QMP-SOs specifically react with superoxide to generate an electrophilic quinone methide intermediate, which subsequently reacts with nucleophilic amino acids to induce a covalent tag on proteins, as revealed by liquid chromatography-mass spectrometry (LC-MS) and shotgun MS experiments. The alkyne handle on the covalent tag enables installation of fluorophores onto the tagged proteins for fluorescence imaging of superoxide in cells under oxidative stress. By establishing a chemoproteomics platform, QMP-SO-TMT, we identify DJ-1 and DLDH as proteins associated with superoxide biology in liver cancer cells treated with menadione. This work should provide insights into the crosstalk between essential cellular events and superoxide redox biology, as well as the design principles of quinone methide-based probes to study redox biology through proximity labeling and chemoproteomics.