Ultrahigh-resolution Mass Spectrometry Data Research Articles

Computational Assessment of the Three-Dimensional Configuration of Dissolved Organic Matter Chromophores and Influence on Absorption Spectra.

The three-dimensional configuration of dissolved organic matter (DOM) is an important factor in determining the role of DOM in natural and engineered systems, yet there is still considerable uncertainty regarding the formation and potential stability of molecular aggregates within DOM. In this paper, we describe a computational assessment of the three-dimensional configuration of DOM. Specifically, we were interested in evaluating the hypothesis that DOM forms thermodynamically stable molecular aggregates that as a result were potentially shielded from water solvent molecules. Molecular dynamics simulations of DOM model compounds carefully selected based on ultrahigh-resolution mass spectrometry data revealed that, while DOM does indeed form molecular aggregates, the large majority of molecules (especially, O-atom bearing molecules) are solvent accessible. Additionally, these computations revealed that molecular aggregates are weak and dissociate when placed in organic solvents (tetrahydrofuran, methyl tert-butyl ether). Time-dependent density functional theory calculations demonstrated long-wavelength absorbance for both model DOM chromophores and their molecular aggregates. This study has important implications for determining the origin of DOM optical properties and for enhancing our collective understanding of DOM three-dimensional structures.

Dissolved organic matter sources in glacierized watersheds delineated through compositional and carbon isotopic modeling

AbstractClimate change is decreasing watershed glacial coverage throughout Alaska, impacting the biogeochemistry of downstream ecosystems. We collected streamwater fortnightly over the glacial runoff period from three streams of varying watershed glacier coverage (0–49%) and a subglacial outflow to assess how glacier recession impacts the relative contributions of glacier and terrestrial plant derived dissolved organic matter (DOM) inputs to streams. We show an increase in the fraction of old dissolved organic carbon (up to ∼ 3200 yr old radiocarbon age) with increasing glacial meltwater contribution to streamflow. We use a dual isotopic mixing model (δ13C and Δ14C) to quantify the relative contribution of terrestrial and glacial sources to streamwater DOM. The endmember contributions were further compared to DOM molecular compositional data from Fourier‐transform ion cyclotron resonance mass spectrometry to assess whether DOM composition can be linked to streamwater DOM source in watersheds with varying contributions of glacial runoff. This approach revealed the glacial fraction was positively correlated with percent relative abundance of heteroatom‐containing DOM molecular formulae, aliphatics, and peptide‐like formulae, while the terrestrial fraction was positively correlated with condensed aromatics and polyphenolics. These results provide information about how the retreat of mountain glaciers will impact the composition and thus biogeochemical role of DOM delivered to downstream ecosystems. Our findings highlight that combining an isotopic mixing model and ultrahigh resolution mass spectrometry data can provide novel insights into how changes in watershed landcover impact the source and chemical properties of streamwater DOM.

ICBM-OCEAN: Processing Ultrahigh-Resolution Mass Spectrometry Data of Complex Molecular Mixtures.

Untargeted molecular analyses of complex mixtures are relevant for many fields of research, including geochemistry, pharmacology, and medicine. Ultrahigh-resolution mass spectrometry is one of the most powerful tools in this context. The availability of open scripts and online tools for specific data processing steps such as noise removal or molecular formula assignment is growing, but an integrative tool where all crucial steps are reproducibly evaluated and documented is lacking. We developed a novel, server-based tool (ICBM-OCEAN, Institute for Chemistry and Biology of the Marine Environment, Oldenburg-complex molecular mixtures, evaluation & analysis) that integrates published and novel approaches for standardized processing of ultrahigh-resolution mass spectrometry data of complex molecular mixtures. Different from published approaches, we offer diagnostic and validation tools for all relevant steps. Among other features, we included objective and reproducible reduction of noise and systematic errors, spectra recalibration and alignment, and identification of likeliest molecular formulas. With 15 chemical elements, the tool offers high flexibility in formula attribution. Alignment of mass spectra among different samples prior to molecular formula assignment improves mass error and facilitates molecular formula confirmation with the help of isotopologues. The online tool and the detailed instruction manual are freely accessible at www.icbm.de/icbm-ocean.

KairosMS: A New Solution for the Processing of Hyphenated Ultrahigh Resolution Mass Spectrometry Data.

The use of hyphenated Fourier transform mass spectrometry (FTMS) methods affords additional information about complex chemical mixtures. Coeluted components can be resolved thanks to the ultrahigh resolving power, which also allows extracted ion chromatograms (EICs) to be used for the observation of isomers. As such data sets can be large and data analyses laborious, improved tools are needed for data analyses and extraction of key information. The typical workflow for this type of data is based upon manually dividing the total ion chromatogram (TIC) into several windows of usually equal retention time, averaging the signal of each window to create a single mass spectrum, extracting a peak list, performing the compositional assignments, visualizing the results, and repeating the process for each window. Through removal of the need to manually divide a data set into many time windows and analyze each one, a time-consuming workflow has been significantly simplified. An environmental sample from the oil sands region of Alberta, Canada, and dissolved organic matter samples from the Suwannee River Fulvic Acid (SRFA) and marine waters (Marine DOM) were used as a test bed for the new method. A complete solution named KairosMS was developed in the R language utilizing the Tidyverse packages and Shiny for the user interface. KairosMS imports raw data from common file types, processes it, and exports a mass list for compositional assignments. KairosMS then incorporates those assignments for analysis and visualization. The present method increases the computational speed while reducing the manual work of the analysis when compared to other current methods. The algorithm subsequently incorporates the assignments into the processed data set, generating a series of interactive plots, EICs for individual components or entire compound classes, and can export raw data or graphics for off-line use. Using the example of petroleum related data, it is then visualized according to heteroatom class, carbon number, double bond equivalents, and retention time. The algorithm also gives the ability to screen for isomeric contributions and to follow homologous series or compound classes, instead of individual components, as a function of time.

Accumulation of Terrestrial Dissolved Organic Matter Potentially Enhances Dissolved Methane Levels in Eutrophic Lake Taihu, China.

Inland waters play an important role for the storage of chromophoric dissolved organic matter (CDOM) and outgassing of methane (CH4). However, to date, linkages between the optical dynamics of CDOM and dissolved CH4 levels remain largely unknown. We used multi-year (2012-2014) seasonal data series collected from Lake Taihu and 51 connecting channels to investigate how CDOM optical dynamics may impact dissolved CH4 levels in the lake. High dissolved CH4 in the northwestern inflowing river mouths coincided with high underwater UV-vis light availability, dissolved organic carbon (DOC), chemical oxygen demand (COD), DOM aromaticity, terrestrial humic-rich fluorescence, in situ measured terrestrial CDOM, depleted dissolved oxygen (DO), stable isotopic δ2H, and δ18O compared with other lake regions. Our results further revealed positive relationships between dissolved CH4 and CDOM absorption at 350 nm, i.e. a(350), COD, DOC, terrestrial humic-rich fluorophores, and DOM aromaticity, and negative relationships between dissolved CH4 and DO, δ2H, and δ18O. The central lake samples showed a major contribution of terrestrial-sourced molecular formulas to the ultrahigh resolution mass spectrometry data, suggesting the presence of allochthonous DOM sources even here. We conclude that an elevated terrestrial CDOM input likely enhances dissolved CH4 levels in Lake Taihu.

Emergence of the Reactivity Continuum of Organic Matter from Kinetics of a Multitude of Individual Molecular Constituents.

The reactivity continuum (RC) model is a powerful statistical approach for describing the apparent kinetics of bulk organic matter (OM) decomposition. Here, we used ultrahigh resolution mass spectrometry data to evaluate the main premise of the RC model, namely that there is a continuous spectrum of reactivity within bulk OM, where each individual reactive type undergoes exponential decay. We performed a 120 day OM decomposition experiment on lake water, with an untreated control and a treatment preexposed to UV light, and described the loss of bulk dissolved organic carbon with RC modeling. The behavior of individual molecular formulas was described by fitting the single exponential model to the change in peak intensities over time. The range of the empirically derived apparent exponential decay coefficients (kexp) was indeed continuous. The character of the corresponding distribution, however, differed from the conceptual expectations, due to the effects of intrinsic averaging, overlaps in formula-specific loss and formation rates, and the limitation of the RC model to include apparently accumulating compounds in the analysis. Despite these limitations, both the RC model-simulated and empirical (mass spectrometry-derived) distributions of kexp captured the effects of preexposure to UV light. Overall, we present experimental evidence that the reactivity continuum within bulk OM emerges from a range of reactivity of numerous individual components. This constitutes direct empirical support for the major assumption behind the RC model of the natural OM decomposition.

Export of terrigenous dissolved organic matter in a broad continental shelf

AbstractExport of terrigenous dissolved organic matter (DOM) from rivers to the ocean plays an important role in the carbon cycle. Observations from six research cruises in 2014 were used to characterize the seasonal evolution of terrigenous DOM in the shallow and broad South Atlantic Bight (SAB) shelf. While DOM with a strong terrigenous molecular, optical and isotopic signature was restricted to a coastal band early in the year, a plume with terrigenous DOM extended further to the shelf break in late spring. The offshore transport of this terrigenous DOM was consistent with wind‐driven advection in a surface Ekman layer. On time scales spanning about 1 month, the traceable riverine DOM compounds were mostly resistant to bio‐ and photo‐degradation, and the decrease in their relative abundance over the shelf following peak river discharge during spring was consistent with dilution of the river plume due to entrainment of oceanic water associated with wind‐driven mixing. Comparisons between optical absorbance measurements and ultrahigh resolution mass spectrometry data revealed that the fraction of the DOM pool with a riverine signature in the SAB can be estimated using the spectral slope coefficient of chromophoric DOM in the 275–295 nm range. This finding opens up the possibility of observing the distribution of riverine DOM on the SAB shelf in high spatial resolution and by using remote sensing methods, a crucial step for quantifying shelf‐slope exchange and the fate of terrigenous DOM in shelf seas.

Using network analysis to discern compositional patterns in ultrahigh-resolution mass spectrometry data of dissolved organic matter.

Marine dissolved organic matter (DOM) has long been recognized as a large and dynamic component of the global carbon cycle. Yet, DOM is chemically varied and complex and these attributes present challenges to researchers interested in addressing questions about the role of DOM in global biogeochemical cycles. Organic matter extracts from seawater were analyzed by direct infusion with electrospray ionization into a Fourier transform ion cyclotron resonance mass spectrometer. Network analysis was used to quantify the number of chemical transformations between mass-to-charge values in each sample. The network of chemical transformations was calculated using the MetaNetter plug-in within Cytoscape. The chemical transformations serve as markers for the shared structural characteristics of compounds within complex DOM. Network analysis revealed that transformations involving selected sulfur-containing moieties and isomers of amino acids were more prevalent in the deep sea than in the surface ocean. Common chemical transformations were not significantly different between the deep sea and surface ocean. Network analysis complements existing computational tools used to analyze ultrahigh-resolution mass spectrometry data. This combination of ultrahigh-resolution mass spectrometry with novel computational tools has identified new potential building blocks of organic compounds in the deep sea, including the unexpected importance of dissolved organic sulfur components. The method described here can be readily applied by researchers to analyze heterogeneous and complex DOM. Copyright © 2016 John Wiley & Sons, Ltd.