Biogeochemical cycling of sulfur and iron constrains arsenic enrichment in groundwater: Microbial functionality and organic matter composition.

Novel molecular-level evidence of iodine binding to natural organic matter from Fourier transform ion cyclotron resonance mass spectrometry

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules. Graphical Abstract ᅟ.

Marine dissolved organic matter (DOM) represents a primary reservoir in the biogeochemical cycle, and marine microorganisms are essential to the transformation and long‐term sequestration of DOM as recalcitrant dissolved organic matter (RDOM). In China's marginal seas, DOM levels are affected by coastal productivity and terrestrial inputs, yet the molecular mechanisms driving the DOM to RDOM transformation remain insufficiently characterized. This study aimed to elucidate the mechanisms behind the DOM transformation mediated by marine microorganisms in the Bohai and Yellow Seas, particularly focusing on molecular‐level characterizations of microbial carbon cycling processes. Here, using 16S rDNA amplicon sequencing, we analyzed the bacterial communities across the surface and deep layers. Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS) was used to molecularly characterize the DOM. Our findings revealed distinct bacterial diversity and functional profiles between the surface and deep layers, with deep layers exhibiting higher microbial diversity. Furthermore, the deep layers were characterized by higher proportions of RDOM, with molecular indicators such as carboxyl‐rich alicyclic molecules (CRAM) suggesting enhanced carbon stability. This study highlights the role of microbial processes in shaping the molecular characteristics of DOM across depths, supporting the microbial carbon pump (MCP) framework and characterizing the Bohai and Yellow Seas as significant carbon sinks in the coastal region. These findings advance our mechanistic understanding of oceanic carbon sequestration, particularly in coastal marginal seas.

We examine suspected molecular transformations of thermally treated Athabasca bitumen heavy vacuum gas oil (HVGO) by ultrahigh-resolution negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Liquid products from HVGOs treated under an inert N2 atmosphere at temperatures of 300, 325, 350, and 400 °C were each characterized by class (heteroatom content), type (double-bond equivalents = number of rings plus double bonds to carbon), and carbon number distribution. In addition, the inert N2 sweep gas of the autoclave was collected, condensed, and analyzed. The total acid number (TAN) of the HVGO liquid products decreases with an increasing treatment temperature (from 4.13 at 300 °C to 1.46 at 400 °C), indicative of potential carboxylic acid decomposition. The highly abundant O2 class contains species with DBE = 3; however, no compositional changes occur with increased treatment temperature. A bimodal DBE distribution is observed for the S1O2 class, suggesting two possible stable core structures. Only low relative abundance classes show slight changes with thermal treatment. Condensed nitrogen sweep gas obtained at 350 and 400 °C contains highly abundant O2 species with DBE of 3 and but at lower carbon number. Similarly, the condenser product S1O2 classes display the same bimodal DBE distributions as the HVGO liquid products but with lower carbon number (∼18−27 for condenser versus ∼25−35 for the liquid products). The similarity of the O2 speciation in the HVGO liquid products after thermal treatment combined with the detailed analysis of the condenser products suggests that the gross decrease in total acid number (TAN) at higher temperature is due to global (class, DBE, and carbon number indiscriminant) decomposition of the naphthenic acids as well as a small contribution from the loss of the lower boiling, lower carbon number acids by simple distillation.

Organic solid deposition control (OSDC) is a live oil test capable of simulating the production conditions of oil streams and can generate asphaltene deposits under production system conditions. OSDC can also simulate gas lift conditions because the producers are looking for artificial lift methods to produce oil from low-energy reservoirs. In this paper, we present the first compositional study on the OSDC deposits under gas lift conditions and compare it to C7 asphaltenes from the same crude oil precipitated in the laboratory, by use of ultra-high-resolution Fourier transform ion cyclotron resonance mass spectrometry. Furthermore, deposits collected from chemically treated fluids were also studied. The negative-ion mass spectra of OSDC deposits from untreated crude oil and asphaltene inhibitor (AI)-treated crude oil are richer in acidic species, such as the Ox and SxOy polar classes, relative to the parent crude oil. The molecular-weight differences for treated deposits relative to the untreated sample ...

Intramolecular hydrogen bonds between a phosphate group and charged residues play a crucial role in the chemistry of phosphorylated peptides, driving the species to specific conformations and affecting the exposure of the phosphate moiety. The nature and extent of these interactions can be investigated by measuring the reactivity of phosphate groups toward selected substrates in the gas phase. We used Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass spectrometry (MS) to perform a systematic study on the gas-phase ionic reactivity of phosphorylated amino acids and peptides with triethoxyborane (TEB). Ions of interest were generated by electrospray ionization (ESI), isolated in the cell of the FT-ICR mass spectrometer, and allowed to react with a stationary pressure of TEB. The temporal evolution of the reaction was monitored and thermal rate constants were derived. The structure of the ionic products was confirmed by Collision-Induced Dissociation (CID) tandem mass spectrometry (MS/MS). TEB was found to react with the phosphate of protonated phosphorylated amino acids and peptides by an addition-elimination pathway. The kinetic efficiency of the reaction showed a positive correlation with the charge state of the reagent ion, suggesting the existence of charge-state-dependent exposure of the phosphate groups towards the incoming neutral during the reaction. Isomeric phosphorylated peptides, only differing for the position of the modified serine residue, showed markedly different kinetic efficiencies. The ability of a phosphorylated species to react with TEB depends on the ease of access to the phosphate moiety in the corresponding gaseous ion. Measuring the kinetic efficiency of such reactions can represent a valuable tool to explore the accessibility of phosphate groups in biomolecules.

Vanadyl porphyrins are detected and characterized by their double-bond equivalents (DBE = number of rings plus double bonds) and carbon number in an unfractionated (raw) asphaltene and unaltered South American crude oil. Atmospheric pressure photoionization (APPI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) provides the high mass-resolving power (450 000−650 000 at m/z 500) and accurate mass (<300 ppb) to unambiguously assign elemental compositions to each of more than 10 000 peaks in each mass spectrum. Kendrick mass sorting revealed unusually high mass errors for peaks assigned to high DBE O2 species as well as a suspicious bimodal distribution in plots of DBE versus carbon number for all O2 species. Inclusion of vanadium in the chemical formula assignment resolved the bimodal distribution into lower DBE O2 species and vanadyl porphyrins, with a subsequent decrease in mass assignment errors to the same level as those for the thousands of other identified species. Vanadyl porp...

Integrated evaluation of the reactive oxygen species (ROS) production characteristics in one large lake under alternating flood and drought conditions

The archaeal minichromosomal maintenance (MCM) helicase from Sulfolobus solfataricus (SsoMCM) is a model for understanding structural and mechanistic aspects of DNA unwinding. Although interactions of the encircled DNA strand within the central channel provide an accepted mode for translocation, interactions with the excluded strand on the exterior surface have mostly been ignored with regard to DNA unwinding. We have previously proposed an extension of the traditional steric exclusion model of unwinding to also include significant contributions with the excluded strand during unwinding, termed steric exclusion and wrapping (SEW). The SEW model hypothesizes that the displaced single strand tracks along paths on the exterior surface of hexameric helicases to protect single-stranded DNA (ssDNA) and stabilize the complex in a forward unwinding mode. Using hydrogen/deuterium exchange monitored by Fourier transform ion cyclotron resonance MS, we have probed the binding sites for ssDNA, using multiple substrates targeting both the encircled and excluded strand interactions. In each experiment, we have obtained >98.7% sequence coverage of SsoMCM from >650 peptides (5-30 residues in length) and are able to identify interacting residues on both the interior and exterior of SsoMCM. Based on identified contacts, positively charged residues within the external waist region were mutated and shown to generally lower DNA unwinding without negatively affecting the ATP hydrolysis. The combined data globally identify binding sites for ssDNA during SsoMCM unwinding as well as validating the importance of the SEW model for hexameric helicase unwinding.

Cryoconite in mountain glaciers plays important roles in glacial ablation and biogeochemical cycles. In this study, the composition and sources of dissolved organic matter (DOM) in cryoconite from the ablation regions of two Tibetan Plateau glaciers were determined using electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and fluorescence spectrometry. A marked absorbance between 300 and 350 nm in the DOM absorption spectra was observed which was consistent with microbe-derived mycosporine-like amino acids. Fluorescence excitation-emission matrices showed that DOM had intense signals at protein-like substance peaks and weak signals at humic-like substance peaks. The high-resolution mass spectra of FT-ICR-MS showed cryoconite DOM from both glaciers contained diverse lignins, lipids, proteins, and unsaturated hydrocarbons. The lipids and proteins were consistent with material from microbial sources, and the lignins and unsaturated hydrocarbons were probably from vascular plant material supplied in atmospheric aerosols and debris from around the glaciers. Almost one-third of the identified DOM molecules had low C/N ratios (≤20), indicating their high bioavailability. Using a conservative cryoconite distribution on Chinese mountain glacier surfaces (6%) and an average debris mass per square meter of cryoconite (292 ± 196 g m-2), we found that the amount of DOC produced in cryoconite on Chinese glaciers as much as 0.23 ± 0.1 Gg per cryoconite formation process. This dissolved organic carbon may absorb solar radiation, accelerate glacial melting, and be an important source of bioavailable DOM to proglacial and downstream aquatic ecosystems.

Terrestrial dissolved organic matter inputs affect the nitrous oxide emission revealed by FT-ICR MS

The basic principles and recent advances in electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry are reviewed. A brief history of electrospray ionization is provided, along with a complete technical description of the technique, electrospray ionization variations, and advantages. Next, the fundamental principles of Fourier transform ion cyclotron resonance mass spectrometry are covered, including ion cyclotron motion, ion cyclotron resonance excitation, and image current detection. Instrumentation and methods used to couple these techniques are then described. Topics include ion source configuration, ion transport through a strong magnetic field gradient, and ion trapping methods. The article concludes with selected applications that highlight the strengths of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.

Baidianling Capsule, which is made from 16 Chinese herbs, has been widely used for treating vitiligo clinically. In this study, the sensitive and rapid method has been developed for the analysis of chemical components in Baidianling Capsule by gas chromatography-mass spectrometry in combination with retention indices and high-performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry. Firstly, a total of 110 potential volatile compounds obtained from different extraction procedures including alkanes, alkenes, alkynes, ketones, ethers, aldehydes, alcohols, phenols, organic acids, esters, furans, pyrrole, acid amides, heterocycles, and oxides were detected from Baidianling Capsule by gas chromatography-mass spectrometry, of which 75 were identified by mass spectrometry in combination with the retention index. Then, a total of 124 components were tentatively identified by high-performance liquid chromatography combined with Fourier transform ion cyclotron resonance mass spectrometry. Fifteen constituents from Baidianling Capsule were accurately identified by comparing the retention times with those of reference compounds, others were identified by comparing the retention times and mass spectrometry data, as well as retrieving the reference literature. This study provides a practical strategy for rapidly screening and identifying the multiple constituents of a complex traditional Chinese medicine.

Molecular characterization of compounds present in highly complex mixtures such as petroleum is proving to be one of the main analytical challenges. Heavy fractions, such as asphaltenes, exhibit immense molecular and isomeric complexity. Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) with its unequalled resolving power, mass accuracy and dynamic range can address the isobaric complexity. Nevertheless, isomers remain largely inaccessible. Therefore, another dimension of separation is required. Recently, ion mobility mass spectrometry has revealed great potential for isomer description. In this study, the combination of trapped ion mobility and Fourier transform ion cyclotron resonance mass spectrometry (TIMS-FTICR) is used to obtain information on the structural features and isomeric diversity of vanadium petroporphyrins present in heavy petroleum fractions. The ion mobility spectra provided information on the isomeric diversity of the different classes of porphyrins. The determination of the collision cross section (CCS) from the peak apex allows us to hypothesize about the structural aspects of the petroleum molecules. In addition, the ion mobility signal full width at half maximum (FWHM) was used as a measure for isomeric diversity. Finally, theoretical CCS determinations were conducted first on core structures and then on alkylated petroporphyrins taking advantage of the linear correlation between the CCS and the alkylation level. This allowed the proposal of putative structures in agreement with the experimental results. The authors believe that the presented workflow will be useful for the structural prediction of real unknowns in highly complex mixtures.

Nine marine and two terrestrial oils from the Tarim Basin in Western China were analyzed by Fourier transform ion cyclotron resonance mass spectrometry. Sulfur compounds with 8–47 carbon atoms and double-bond equivalent (DBE) values of 0–21 are abundant in the crude oils. The most abundant sulfur species in Tazhong marine oils are S1 species (80.57–85.22%), followed by O1S1 (6.95–14.78%) and S2 (0.71–6.69%) species. The dominant species in Yingmaili terrestrial oils are S1 (51.41–52.76%), O1S1 (26.83–35.27%) and O2S1 (11.97–21.76%) species; no S2 species were detected. The results suggest that the sulfur compounds present in oil vary with the oil type. For the S1 and S2 species, as the thermal maturity increased, the degree of condensation increased, and the median and range of the number of carbon atoms decreased. Compounds with DBE values of 9, which are most likely dibenzothiophenes, became concentrated as the thermal maturity increased. Therefore, the unusually high abundance of dibenzothiophenes in the Lower Ordovician oils could be related to the thermal maturity. The TZ83 (O1) oil has an abnormal distribution of S1 species, and is characterized by sulfur species with relatively low DBE values (0–7). This abnormal distribution could be caused by thermochemical sulfate reduction, and a relatively high content of H2S in the associated gases and abundant sulfo-diamantane in the oil supported this theory. In conclusion, the thermal maturity, organic facies, paleoenvironment of the source rock, and possibly thermochemical sulfate reduction have a large impact on the sulfur compounds present in the oils. The O1S1/S1 and S2/S1 ratios could be used as indicators of the precursors/paleoenvironment, and C10–19/C20–50 DBE9 and DBE1,3,6 /DBE9 could be used as indicators of thermal maturity. Fourier transform ion cyclotron resonance mass spectrometry is very useful for detecting sulfur compounds, especially those with high molecular weights, in the crude oils. This technique has potential for determining the formation mechanisms of some unusual oils and the geochemical implications of the sulfur compounds they contain.