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At least 145 records · Page 8

Rapid Targeted Quantitation of Protein Overexpression with Direct Infusion Shotgun Proteome Analysis (DISPA-PRM)

While much effort has been placed on comprehensive quantitative proteome analysis, certain applications demand measurement of only a few target proteins from complex systems. Traditional approaches to targeted proteomics rely on nano-liquid chromatography (nLC) and targeted mass spectrometry (MS) methods, e.g., parallel reaction monitoring (PRM). However, the time requirement for nLC can limit throughput of targeted proteomics. To achieve rapid and high-throughput targeted methods, here we show that nLC separations can be eliminated and replaced with direct infusion shotgun proteome analysis (DISPA) using high-field asymmetric waveform ion mobility spectrometry (FAIMS) with PRM. We demonstrate application of DISPA-PRM for rapid targeted quantification of bacterial enzymes utilized in the production of biofuels by monitoring temporal expression in 72 metabolically engineered bacterial cultures in under 2.5 hours, with a measured dynamic range >1200-fold. Here, we conclude that DISPA-PRM presents a valuable innovative tool with results comparable to nLC-MS/MS, enabling fast and rapid detection of targeted proteins in complex mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

malbacR: A Package for Standardized Implementation of Batch Correction Methods for Omics Data

Mass spectrometry is a powerful tool for identifying and analyzing small molecules, such as metabolites and lipids, in com-plex biological samples. Liquid chromatography and gas chromatography mass spectrometry studies quite commonly in-volve large numbers of samples, which can require significant time for sample preparation and analyses. To accommodate such studies, the samples are commonly split into batches. Inevitably, variations in sample handling, temperature fluctua-tion, imprecise timing, column degradation and other factors result in systematic errors or biases of the measured abundances between the batches. Numerous methods are available via R packages to assist with batch correction for small molecule om-ics data; however, since these methods were developed by different research teams, the algorithms are available in separate R packages, each with different data input and output formats. We introduce the malbacR package which consolidates eleven common batch effect correction methods for small molecule omics data into one place so users can easily implement and compare: pareto scaling, power scaling, range scaling, ComBat, EigenMS, NOMIS, RUV-random, QC-RLSC, WaveI-CA2.0, TIGER, and SERRF. The malbacR package standardizes data input and output formats across these batch correction methods. The package works in conjunction with the pmartR package, allowing users to seamlessly include batch effect cor-rection in a pmartR workflow without needing any additional data manipulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Natural Abundance Isotope Ratio Measurements of Organic Molecules Using 21 T FTICR MS

Subtle variations in stable isotope ratios at natural abundance are challenging to measure but can yield critical insights into biological, physical, and geochemical processes. Well established methods, particularly multi-collector, gas-source or plasma isotope ratio mass spectrometry (IRMS) are the gold standard for stable isotope measurement but inherent limitations in these approaches make them ill-suited to determining site-specific and multiply substituted isotopic abundances of all but a few compounds, or to characterizing mixtures or larger intact molecules. Additionally, Fourier transform mass spectrometry (FTMS), namely Orbitrap mass spectrometry, has recently demonstrated the ability to measure natural abundance isotope ratios with chemically informative accuracy and precision. Here, we report the first use of Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) for the accurate (<1‰) and precise (<1‰ standard error) simultaneous determination of $δ$ 13 C and $δ$ 15 N in caffeine isotopologues and provide a discussion of the critical instrumental parameters necessary to make such measurements. Finally, we report the ability to make these measurements with online liquid chromatography, expanding the ability of this technique to explore mixtures in the future.

07 ISOTOPE AND RADIATION SOURCES↗

Improved Single-Cell Proteome Coverage Using Narrow-Bore Packed NanoLC Columns and Ultrasensitive Mass Spectrometry

Single-cell proteomics can provide unique insights into biological processes by resolving heterogeneity that is obscured by bulk measurements. Gains in the overall sensitivity and proteome coverage through improvements in sample processing and analysis increase the information content obtained from each cell, particularly for less abundant proteins. Here we report on improved single-cell proteome coverage through the combination of the previously developed Nanodroplet Processing in One Pot for Trace Samples (nanoPOTS) platform with further miniaturization of liquid chromatography (LC) separations and implementation of an ultrasensitive latest-generation mass spectrometry (MS) instrument. Following nanoPOTS sample preparation, protein digest from single cells were separated using a 20-µm-i.d. in-house-packed nanoLC column. Separated peptides were ionized using an etched fused silica emitter capable of stable ionization at the ~20 nL/min flow rate provided by the LC separation. Ultrasensitive LC-MS analysis was achieved using the Orbitrap Eclipse Tribrid mass spectrometer. An average of 362 protein groups were identified by MS/MS from single HeLa cells, and 874 protein groups were identified using the Match Between Runs (MBR) feature of MaxQuant. This represents a >70% increase in label-free proteome coverage for single cells relative to previous efforts using larger-bore (30-µm-i.d.) LC columns coupled to a previous-generation MS (Orbitrap Fusion Lumos).

Cong, Yongzheng↗

Metabolites of Tobacco- and E-Cigarette-Related Nitrosamines Can Drive Cu 2+ -Mediated DNA Oxidation

Nitrosamine metabolites resulting from cigarette smoking and E-cigarette (E-cig) vaping cause DNA damage that can lead to genotoxicity. While DNA adducts of metabolites of nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N-nitrosonornicotine (NNN) are well-known tobacco-related cancer biomarkers, only a few studies implicate NNN and NNK in DNA oxidation in humans. NNK and NNN were found in the urine of E-cigarette users who never smoked cigarettes. This paper proposes the first chemical pathways of DNA oxidation driven by NNK and NNN metabolites in redox reactions with Cu 2+ and NADPH leading to reactive oxygen species (ROS). A microfluidic array with thin films of DNA and metabolic enzymes that make metabolites of NNN and NNK in the presence of Cu 2+ and NADPH was used to estimate relative rates of DNA oxidation. Detection by electrochemiluminescence (ECL) employed a new ECL dye [Os(tpy-benz-COOH) 2 ] 2+ that is selective for and sensitive to the primary DNA oxidation product 8-oxo-7,8-dihydro-2-deoxyguanosine (8-oxodG) in DNA. Enzyme–DNA films on magnetic beads were used to produce nitrosamine metabolites that enter ROS-forming redox cycles with Cu 2+ and NADPH, and liquid chromatography–mass spectrometry (LC–MS) was used to quantify 8-oxodG and identify metabolites. ROS were detected by optical sensors. Metabolites of NNK and NNN + Cu 2+ + NADPH generated relatively high rates of DNA oxidation. Lung is the exposure route in smoking and vaping, human lung tissue contains Cu 2+ and NADPH, and lung microsomal enzymes gave the highest rates of DNA oxidation in this study. Furthermore, E-cigarette vapor contains 6-fold more copper than that in cigarette smoke, which could exacerbate DNA oxidation.

59 BASIC BIOLOGICAL SCIENCES↗

Identification of Novel Microcystins Using High-Resolution MS and MS n with Python Code

Cyanotoxins called microcystins (MCs) are highly toxic and can be present in drinking water sources. Determining the structure of MCs is paramount because of its effect on toxicity. Though over 300 MC congeners have been discovered, many remain unidentified. In this work, a method is described for the putative identification of MCs using liquid chromatography (LC) coupled with high-resolution (HR) Orbitrap mass spectrometry (MS) and a new bottom-up sequencing strategy. Maumee River water samples were collected during a harmful algal bloom and analyzed by LC–MS with simultaneous HRMS and MS/MS. Unidentified ions with characteristic MC fragments (135 and 213 m/z) were recognized as possible novel MC congeners. An innovative workflow was developed for the putative identification of these ions. Python code was written to generate the potential structures of unidentified MCs and to assign ions after the fragmentation for structural confirmation. The workflow enabled the putative identification of eight previously reported MCs for which standards are not available and two newly discovered congeners, MC-HarR and MC-E(OMe)R.

54 ENVIRONMENTAL SCIENCES↗

Desorption of Phosphate from Iron-Bearing Soil Minerals by a Plant Secondary Metabolite

In soils, phosphorus readily adsorbs to the surfaces of ubiquitous iron (oxyhydr)oxide minerals, rendering it less accessible to plants and microorganisms. Plants have a number of strategies to access iron, among them the secretion of redox-active metabolites from their roots. Although these strategies likely increase the bioavailability of surface-adsorbed phosphorus through reductive dissolution, their effect on phosphorus cycling has not yet been investigated. We tested the ability of fraxetin, a coumarin-type redox-active metabolite produced by the model plant Arabidopsis thaliana and other dicotyledon plant species, to reductively solubilize phosphate from the surface of ferrihydrite. Our findings show that, at low and neutral pH, fraxetin increased aqueous phosphate concentrations under both oxic and anoxic conditions; at high pH, it was only effective in anoxic experiments. Additionally, a combination of liquid chromatography–mass spectrometry and spectroscopic methods demonstrated substantial fraxetin adsorption to the mineral surface but showed that iron reduction did not alter the mineral structure or change the nature of the chemical environment of the phosphorus atom over short time scales. These results provide evidence that the secretion of redox-active metabolites from roots is likely to be an effective phosphorus acquisition tactic in iron-rich soils.

36 MATERIALS SCIENCE↗

Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi -Containing Consortium SDC-9

At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). In this work, metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with 13 C-/ 15 N-labeled peptides determined 1.8 × 10 3 TceA and 1.2 × 10 2 VcrA RDase molecules per Dhc cell. Ultimately, the MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and has potential utility in bioremediation monitoring regimes.

59 BASIC BIOLOGICAL SCIENCES↗

A Preprocessing Tool for Enhanced Ion Mobility–Mass Spectrometry-Based Omics Workflows

The ability to improve the data quality of ion mobility–mass spectrometry (IM-MS) measurements is of great importance for enabling modular and efficient computational workflows and gaining better qualitative and quantitative insights from complex biological and environmental samples. We developed the PNNL PreProcessor, a standalone and user-friendly software housing various algorithmic implementations to generate new MS-files with enhanced signal quality and in the same instrument format. Different experimental approaches are supported for IM-MS based on Drift-Tube (DT) and Structures for Lossless Ion Manipulations (SLIM), including liquid chromatography (LC) and infusion analyses. The algorithms extend the dynamic range of the detection system, while reducing file sizes for faster and memory-efficient downstream processing. Specifically, multidimensional smoothing improves peak shapes of poorly defined low-abundance signals, and saturation repair reconstructs the intensity profile of high-abundance peaks from various analyte types. Further, other functionalities are data compression and interpolation, IM demultiplexing, noise filtering by low intensity threshold and spike removal, and exporting of acquisition metadata. Several advantages of the tool are illustrated, including an increase of 19.4% in lipid annotations and a two-times faster processing of LC-DT IM-MS data-independent acquisition spectra from a complex lipid extract of a standard human plasma sample. The software is freely available at https://omics.pnl.gov/software/pnnl-preprocessor.

59 BASIC BIOLOGICAL SCIENCES↗

Introducing Molecular Hypernetworks for Discovery in Multidimensional Metabolomics Data

Orthogonal separations of data from high-resolution mass spectrometry can provide insight into sample composition and address challenges of complete annotation of molecules in untargeted metabolomics. “Molecular networks” (MNs), as used in the Global Natural Products Social Molecular Networking platform, are a prominent strategy for exploring and visualizing molecular relationships and improving annotation. MNs are mathematical graphs showing the relationships between measured multidimensional data features. MNs also show promise for using network science algorithms to automatically identify targets for annotation candidates and to dereplicate features associated with a single molecular identity. Here, this paper introduces “molecular hypernetworks” (MHNs) as more complex MN models able to natively represent multiway relationships among observations. Compared to MNs, MHNs can more parsimoniously represent the inherent complexity present among groups of observations, initially supporting improved exploratory data analysis and visualization. MHNs also promise to increase confidence in annotation propagation, for both human and analytical processing. We first illustrate MHNs with simple examples, and build them from liquid chromatography- and ion mobility spectrometry-separated MS data. We then describe a method to construct MHNs directly from existing MNs as their “clique reconstructions”, demonstrating their utility by comparing examples of previously published graph-based MNs to their respective MHNs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Design and Preparation of Nematic Colloidal Particles

Colloidal systems are abundant in technology, in biomedical settings, and in our daily life. The so-called “colloidal atoms” paradigm exploits interparticle interactions to self-assemble colloidal analogs of atomic and molecular crystals, liquid crystal glasses, and other types of condensed matter from nanometer- or micrometer-sized colloidal building blocks. Nematic colloids, which comprise colloidal particles dispersed within an anisotropic nematic fluid host medium, provide a particularly rich variety of physical behaviors at the mesoscale, not only matching but even exceeding the diversity of structural and phase behavior in conventional atomic and molecular systems. This feature article, using primarily examples of works from our own group, highlights recent developments in the design, fabrication, and self-assembly of nematic colloidal particles, including the capabilities of preprogramming their behavior by controlling the particle’s surface boundary conditions for liquid crystal molecules at the colloidal surfaces as well as by defining the shape and topology of the colloidal particles. Here recent progress in defining particle-induced defects, elastic multipoles, self-assembly, and dynamics is discussed along with open issues and challenges within this research field.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantification of Metabolic Products from Microbial Hosts in Complex Media Using Optically Diffracting Hydrogels

In this work, we herein describe a highly versatile platform approach for the in situ and real-time screening of microbial biocatalysts for enhanced production of bioproducts using photonic crystal hydrogels. This approach was demonstrated by preparing optically diffracting films based on polymerized N-isopropylacrylamide that contracted in the presence of alcohols and organic acids. The hydrogel films were prepared in a microwell plate format, which allows for high-throughput screening, and characterized optically using a microwell plate reader. While demonstrating the ability to detect a broad range of relevant alcohols and organic acids, we showed that the response of the films correlated strongly with the octanol-water partition coefficient (log P) of the analyte. Differences in the secretion of ethanol and succinic acid from strains of Zymomonas mobilis and Actinobacillus succinogenes, respectively, were further detected via optical characterization of the films. These differences, which in some cases were as low as ~3 g/L, were confirmed by high-performance liquid chromatography, thereby demonstrating the sensitivity of this approach. Our findings highlight the potential utility of this multiplexed approach for the detection of small organic analytes in complex biological media, which overcomes a major challenge in conventional optical sensing methods.

09 BIOMASS FUELS↗

Exploring Fluoropyridine Electrolytes in Li–S Batteries: Balancing Performance and Stability across Temperatures

A novel high-donor 3-fluoropyridine (3FPy) electrolyte has been introduced for use in Li-S batteries, demonstrating an inhibition effect on the polysulfide shuttle, even without the addition of LiNO 3 . In this study, fluoropyridine electrolytes, including 2-fluoropyridine (2FPy) and 3FPy electrolytes, are studied using electrochemical analysis, mass spectrometry (MS), and high-performance liquid chromatography (HPLC) methods. Collision-induced dissociation spectra revealed that Li + preferentially solvates with different fluoropyridines, with 2FPy exhibiting a stronger interaction due to ortho-fluorine's influence, compared to 4FPy and 3FPy. However, MS and HPLC analyses showed that 2FPy is reactive with polysulfides, while 3FPy offers high solubility for polysulfides and sulfur without reacting with them at room temperature. Further, despite 3FPy performing well at room temperature, further electrochemistry studies at elevated (60 °C) and reduced (0 °C) temperatures reveal the challenges. At high temperatures, LiNO 3 is essential to suppress the polysulfide shuttle; and at low temperatures, the performance with the 3FPy electrolyte significantly lags behind that of the ether-based electrolyte.

25 ENERGY STORAGE↗

Chromatographic and Spectroscopic Study of the Interaction between Polysulfides and Copper Sulfides

To mitigate the “polysulfide shuttle” in lithium–sulfur batteries, different hosting materials that can interact with the polysulfide species physically or chemically have been widely investigated. Copper sulfides as one type of material are believed to have strong chemical interactions with the polysulfide species to consequently influence the performances of Li–S batteries. In this work, high-performance liquid chromatography (HPLC), electrospray ionization mass spectrometry (ESI/MS), scanning electron microscopy with energy-dispersive X-ray spectrometry (SEM-EDS), and inductively coupled plasma optical emission spectroscopy (ICP-OES) were used to systematically investigate the interactions between ether-based polysulfide solutions and copper sulfides (as well as silver sulfide). Furthermore, based on chromatographic and spectroscopic results, the interactions between polysulfides and Cu 2 S can be classified into two types of reactions: one is the redox reaction with the formation of CuS, while another is the complexation reaction with the formation of soluble LiCuS n (n ≥ 4). Contrarily, Ag 2 S (and CuS) shows no interactions with polysulfides. Accordingly, the cycling behaviors of Li–S batteries with copper sulfides as hosting materials or with copper as additives were explained reasonably.

25 ENERGY STORAGE↗

Nonthermal Plasma-Stimulated C–N Coupling from CH 4 and N 2 Depends on the Presence of Surface CH x and Plasma-Phase CN Species

Formation of C–N containing compounds from plasma-catalytic coupling of CH 4 and N 2 over various transition metals (Ni, Pd, Cu, Ag, and Au) is investigated using a multimodal spectroscopic approach, combining polarization-modulation infrared reflection–absorption spectroscopy (PM-IRAS) and optical emission spectroscopy (OES). Through sequential experiments utilizing CH 4 and N 2 nonthermal plasmas, we minimize plasma-phase reactions and identify key intermediates for C–N coupling on metal surfaces. Results show that simultaneous CH 4 and N 2 exposure with plasma stimulation produces surface C–N species. However, N 2 –CH 4 sequential exposure does not lead to C–N species formation, while CH 4 –N 2 sequential exposure reveals the presence of CH x surface species and CN radical species as key precursors to C–N species formation. From further analysis using X-ray photoelectron spectroscopy and liquid chromatography–mass spectrometry, the influence of exposure conditions on the degree of nitrogen incorporation and the nature of C–N species formed were revealed. The work highlights the importance of surface chemistry and exposure conditions in surface C–N coupling with plasma stimulation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Assessing Structural, Thermal, and Functional Characteristics of Marigold Flower Protein as a Sustainable Food Ingredient

The demand for sustainable and alternative protein sources has been on the rise, driving interest in the valorization of underutilized plants. This study evaluated Calendula officinalis (marigold), a common floral waste, as a sustainable alternative protein source for the food industry. The primary objective of this study was to investigate the physicochemical properties of protein fractions from Calendula officinalis flower to evaluate their potential as a novel protein ingredient. Extraction of the Calendula officinalis flower yielded 92.17% of the crude protein. A sequential extraction of albumin, globulin, glutelin, and prolamin from marigold flower revealed albumin as the dominant fraction (65.47%) and exhibited the highest protein functionality, including water-holding capacity (2.37 g/g), oil-holding capacity (2.49 g/g), and emulsifying capacity (65.22 mL/g). Compared with other protein fractions, glutelin showed a relatively high emulsifying and foaming capacity (EC: 59.13 mL/g; FC: 16.23%). Differential scanning calorimetry revealed high thermal stability for albumin (T p = 105.28 °C) and glutelin (T p = 97.6 °C). Sodium Dodecyl Sulfate–Polyacrylamide Gel Electrophoresis (SDS-PAGE) and Liquid Chromatography–Mass Spectrometry (LC-MS) confirmed the presence of abundant low-molecular-weight polypeptides (<37 kDa), which enhanced emulsification, while scanning electron microscopy revealed porous structures aligned with hydration properties. Antioxidant activity was higher in albumin and glutelin, linked to surface hydrophobicity. LC-MS/MS identified 33 short-chain proteins, including oxidoreductase proteins and lipid-transfer proteins. Findings highlight marigold flower proteins as a sustainable, functional ingredient for a diverse range of food applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring Approaches for Accelerated Mass Spectrometric Detection of Fluorochemicals from Aqueous Solutions Using Indirect, Adsorbent-Facilitated Desorption Ionization

There is a growing need for rapid, low-cost analytical tools to screen water supplies for persistent contaminants. Due to their ubiquitous presence in the environment and their detrimental effects on human health, there is a public interest in widespread testing for perfluoroalkyl substances (PFAS). However, the most common methods for PFAS analysis can be time-intensive, requiring a preconcentration step followed by liquid chromatography–mass spectrometry (LC–MS), and are cost-prohibitive for most members of the public. To address these challenges, this study explores a novel method for rapid analysis of aqueous analytes by concentrating analytes on solid adsorbents and detecting them using mass spectrometric analysis via desorption ionization directly from the adsorbent surface. We demonstrate this general approach of indirect solution analysis (ISA) with desorption electrospray ionization (ISA-DESI) and laser desorption ionization (ISA-LDI). Various adsorbent materials were screened, including commercial mesoporous carbons, alumina, and metal–organic frameworks (MOFs). Using ISA-DESI, we consistently detect concentrations as low as 5–100 parts per trillion (ppt) for perfluorooctanoic acid (PFOA) and 10–100 ppt for perfluoroundecanoic acid (PFUnDA). This approach enables rapid detection in under 5 min, making it suitable for applications requiring trace detection with fast response times. We further demonstrate the use of ISA-DESI on a range of environmentally relevant contaminants. Advantages of this indirect solution analysis approach include simplified sample preparation, accelerated analysis, and low cost with readily available materials, making it a promising tool to accelerate mass spectrometric PFAS detection for identifying contaminated sites, performing laboratory studies, and monitoring industrial waste streams.

Bays, Nathan Robert [Sandia National Laboratories ↗

Identification and Mitigation of Inhibitory Substances Contained in High-Salinity Crude Glycerol Generated from Biodiesel Production for Polyhydroxyalkanoate Synthesis by Haloferax mediterranei

High-salinity crude glycerol generated from biodiesel production poses significant challenges to microbial valorization due to inhibitory ingredients that severely limit microbial growth. This study identified and mitigated inhibitory substances contained in high-salinity glycerol sludge to enable its conversion to polyhydroxyalkanoates (PHAs) by the extreme halophilic archaeon Haloferax mediterranei. The long-chain fatty acids (LCFAs) were consistently identified as the primary inhibitors by liquid chromatography−mass spectrometry, Fourier transform infrared spectroscopy, and ultraviolet−visible spectroscopy. Acid precipitation at pH 2 efficiently removed these LCFAs, substantially reducing the required feedstock dilution from 23 to 3 times, improving PHA titer by 40%. Furthermore, this dilution reduction also increased the feedstock salinity utilization, achieving a 46% reduction in external salt supplementation for H. mediterranei growth. In contrast, overliming and arrested anaerobic digestion were confirmed to be ineffective in inhibitor removal. This study provides deep insights into inhibitor chemistry and presents acid precipitation as an effective pretreatment strategy for waste valorization of highsalinity crude glycerol.

LC-MS↗