21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: A National Resource for Ultrahigh Resolution Mass Analysis

Deciphering linkages between DON and the microbial community for nitrogen removal using two green sorption media in a surface water filtration system

The presence of dissolved organic nitrogen (DON) in stormwater treatment processes is a continuous challenge because of the intertwined nature of its decomposition, bioavailability, and biodegradability and its unclear molecular characteristics. In this paper, 21 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in combination with quantitative polymerase chain reaction was applied to elucidate the molecular change of DON and microbial population dynamics in a field-scale water filtration system filled with two specialty adsorbents for comparison in South Florida where the dry and wet seasons are distinctive annually. The adsorbents included CPS (clay-perlite and sand sorption media) and ZIPGEM (zero-valent iron and perlite-based green environmental media). Our study revealed that seasonal effects can significantly influence the dynamic characteristics and biodegradability of DON. The microbial population density in the filter beds indicated that three microbial species in the nitrogen cycle were particularly thrived for denitrification, dissimilatory nitrate reduction to ammonium, and anaerobic ammonium oxidation via competition and commensalism relationships during the wet season. Also, there was a decrease in the compositional complexity and molecular weight of the DON groups (CnHmOpN1, CnHmOpN2, CnHmOpN3, and CnHmOpN4), revealed by the 21 T FT-ICR MS bioassay, driven by a microbial population quantified by polymerase chain reaction from the dry to the wet season. These findings indirectly corroborate the assumption that the metabolism of microorganisms is much more vigorous in the wet season. The results affirm that the sustainable materials (CPS and ZIPGEM) can sustain nitrogen removal intermittently by providing a suitable living environment in which the metabolism of microbial species can be cultivated and enhanced to facilitate physico-chemical nitrogen removal across the two types of green sorption media.

Experimental Validation of Comprehensive Calculation for High-Resolution Linear MALDI-TOF Mass Spectrometry

This work discusses the effectiveness of the previously developed comprehensive calculation model to optimize linear MALDI-TOF mass spectrometers. The model couples space- and velocity-focusing to precisely analyze the flight-time distribution of ions and predict optimal experimental parameters for the highest mass resolving power. Experimental validation was conducted using a laboratory-made instrument to analyze CsI3 and angiotensin I ions in low to medium m/z range. The results indicate that the predicted optimal extraction voltage and delay were reasonably accurate and effective. In the low m/z range, the peak width obtained using optimal parameters reached the sub nanosecond range, corresponding to a mass resolving power of 10 000-17 000, or 20 000-34 000 if shot-to-shot random fluctuations were minimized by the dynamic data correction method. The observed optimal mass resolving power in the current experiment is 4.8-7.8 times that of commercial instruments. Practical limitations resulting in the gap between the observed and theoretical ultimate mass resolving power are discussed.

Fire Impacts on the Soil Metabolome and Organic Matter Biodegradability

Global wildfire activity has increased since the 1970s and is projected to intensify throughout the 21st century. Wildfires change the composition and biodegradability of soil organic matter (SOM) which contains nutrients that fuel microbial metabolism. Though persistent forms of SOM often increase postfire, the response of more biodegradable SOM remains unclear. Here we simulated severe wildfires through a controlled "pyrocosm" approach to identify biodegradable sources of SOM and characterize the soil metabolome immediately postfire. Using microbial amplicon (16S/ITS) sequencing and gas chromatography-mass spectrometry, heterotrophic microbes (Actinobacteria, Firmicutes, and Protobacteria) and specific metabolites (glycine, protocatechuate, citric cycle intermediates) were enriched in burned soils, indicating that burned soils contain a variety of substrates that support microbial metabolism. Molecular formulas assigned by 21 T Fourier transform ion cyclotron resonance mass spectrometry showed that SOM in burned soil was lower in molecular weight and featured 20 to 43% more nitrogen-containing molecular formulas than unburned soil. We also measured higher water extractable organic carbon concentrations and higher CO2 efflux in burned soils. The observed enrichment of biodegradable SOM and microbial heterotrophs demonstrates the resilience of these soils to severe burning, providing important implications for postfire soil microbial and plant recolonization and ecosystem recovery.

Special Issue with Research Topics on "Recent Analysis and Applications of Mass Spectra on Biochemistry"

Analytical mass spectrometry applies irreplaceable mass spectrometric (MS) methods to analytical chemistry and chemical analysis, among other areas of analytical science [...].

Controls of Mineral Solubility on Adsorption-Induced Molecular Fractionation of Dissolved Organic Matter Revealed by 21 T FT-ICR MS

Mineral adsorption-induced molecular fractionation of dissolved organic matter (DOM) affects the composition of both DOM and OM adsorbed and thus stabilized by minerals. However, it remains unclear what mineral properties control the magnitude of DOM fractionation. Using a combined technique approach that leverages the molecular composition identified by ultrahigh resolution 21 T Fourier transform ion cyclotron resonance mass spectrometry and adsorption isotherms, we catalogue the compositional differences that occur at the molecular level that results in fractionation due to adsorption of Suwannee River fulvic acid on aluminum (Al) and iron (Fe) oxides and a phyllosilicate (allophane) species of contrasting properties. The minerals of high solubility (i.e., amorphous Al oxide, boehmite, and allophane) exhibited much stronger DOM fractionation capabilities than the minerals of low solubility (i.e., gibbsite and Fe oxides). Specifically, the former released Al3+ to solution (0.05-0.35 mM) that formed complexes with OM and likely reduced the surface hydrophobicity of the mineral-OM assemblage, thus increasing the preference for adsorbing polar DOM molecules. The impacts of mineral solubility are exacerbated by the fact that interactions with DOM also enhance metal release from minerals. For sparsely soluble minerals, the mineral surface hydrophobicity, instead of solubility, appeared to be the primary control of their DOM fractionation power. Other chemical properties seemed less directly relevant than surface hydrophobicity and solubility in fractionating DOM.

Using landfill leachate to indicate the chemical and biochemical activities in elevated temperature landfills

Landfill leachate properties contain important information and can be a unique indicator for the chemical and biochemical activities in landfills. In the recent decade, more landfills are experiencing elevated temperature, causing an imbalance in the decomposition of solid waste and affecting the properties of the landfill leachate. This study analyzes the properties of leachate from two landfills that were experiencing elevated temperature (ETLFs), samples were collected from both elevated temperature impacted and non-impacted areas in each landfill. The accumulation of volatile fatty acids (VFA) in leachates from elevated temperature impacted areas of both landfill sites revealed that methanogenesis was inhibited by the elevated temperature, which was further confirmed by the more acidic pH, higher H/C elemental ratio, and lower degree of aromaticity of the elevated temperature impacted leachates. Also, carbohydrates depletion indicated possible enhancement of hydrolysis and acidogenesis by elevated temperature, which was supported by compositional comparison of isolated acidic species by negative-ion electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICRMS) at 21 T derived from both elevated temperature impacted and non-impacted areas in the same landfill site. Furthermore, leachate organics fractionation showed that leachates not impacted by elevated temperature contain less hydrophilic fraction and more humic fraction than elevated temperature-impacted leachates for both ETLFs.

Ultrahigh-Mass Resolution Mass Spectrometry Imaging with an Orbitrap Externally Coupled to a High-Performance Data Acquisition System

Matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI) is a powerful analytical tool that enables molecular sample analysis while simultaneously providing the spatial context of hundreds or even thousands of analytes. However, because of the lack of a separation step prior to ionization and the immense diversity of biomolecules, such as lipids, including numerous isobaric species, the coupling of ultrahigh mass resolution (UHR) with MSI presents one way in which this complexity can be resolved at the spectrum level. Until now, UHR MSI platforms have been restricted to Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers. Here, we demonstrate the capabilities of an Orbitrap-based UHR MSI platform to reach over 1,000,000 mass resolution in a lipid mass range (600-950 Da). Externally coupling the Orbitrap Q Exactive HF with the high-performance data acquisition system FTMS Booster X2 provided access to the unreduced data in the form of full-profile absorption-mode FT mass spectra. In addition, it allowed us to increase the time-domain transient length from 0.5 to 10 s, providing improvement in the mass resolution, signal-to-noise ratio, and mass accuracy. The resulting UHR performance generates high-quality MALDI MSI images and simplifies the identification of lipids. Collectively, these improvements resulted in a 1.5-fold increase in annotations, demonstrating the advantages of this UHR imaging platform for spatial lipidomics using MALDI-MSI.

Unraveling the persistence of deep podzolized carbon: Insights from organic matter characterization

Over a billion tons of terrestrial carbon (C) is stored in deep soils from the Southeastern Coastal Plain of the United States. While the size and extent of this pool, known as deep podzolized carbon (DPC), have been reported in recent studies, the stabilization mechanisms responsible for its persistence are unclear. The main hypothesis of DPC stabilization is that hydrology, specifically water table fluctuations in the phreatic zone, slow microbial degradation and promote C accumulation. This accounts for the characteristic properties and distribution of DPC and provides a mechanistic distinction between DPC and shallow podzolized C in the region's soils, however it has yet to be tested. We characterized the organic matter composition of the bulk and dissolved fractions of DPC using elemental analysis, solvent extraction, infrared spectroscopy, and high-resolution mass spectrometry. Consistent with past work, the majority of DPC organic matter was extractable by sodium pyrophosphate solution; the influence of metal association was also observable in the water extractable fraction of DPC with large species being preferentially removed and a low compound diversity compared to those from other horizons overlying DPC. Only water extractable species with low molecular mass (m/z < 375 Da) showed significant change in average nominal oxidation state of carbon (NOSC) values, indicative of oxygen-limitation influence on the processing of these species. Infrared spectroscopy revealed an increase in abundance of aliphatic (C-H:C-O) bonds relative to polysaccharide bonds with depth whereas aromatic (C=C:C-O) bonds decreased with depth in DPC relative to other subsurface horizons. Our work shows that DPC is significantly more refractory than overlying surface soil C, and yet slightly more labile than the subsoils above DPC. Together our results suggest that the maintenance of low redox conditions via persistent water saturation contributes to the stabilization and persistence of DPC.

N-containing dissolved organic matter promotes dissolved inorganic carbon supersaturation in the Yangtze River, China

Dissolved inorganic carbon (DIC) represents a major global carbon pool and the flux from rivers to oceans has been observed to be increasing. The effect of weathering with respect to increasing DIC has been widely studied in recent decades; however, the influence of dissolved organic matter (DOM) on increasing DIC in large rivers remains unclear. This study employed stable carbon isotopes and Fourier transform ion cyclotron mass spectrometry (FT-ICR MS) to investigate the effect of the molecular composition of DOM on the DIC in the Yangtze River. The results showed that organic matter is an important source of DIC in the Yangtze River, accounting for 40.0 ± 12.1 % and 32.0 ± 7.2 % of DIC in wet and dry seasons, respectively, and increased along the river by approximately three times. Nitrogen (N)-containing DOM, an important composition in DOM with a percentage of ∼40 %, showed superior oxidation state than non N-containing DOM, suggesting that the presence of N could improve the degradable potential of DOM. Positive relationship between organic sourced DIC (DICOC) and N-containing DOM formulae indicated that N-containing DOM is crucial to facilitate the mineralization of DOM to DICOC. N-containg molecular formular with low H/C and O/C ratio were positively correlated with DICOC further verified these energy-rich and biolabile compounds are preferentially decomposed by bacteria to produce DIC. N-containing components significantly accelerated the degradation of DOM to DICOC, which is important for understanding the CO2 emission and carbon cycling in large rivers.

Photo-Enhanced Oil Toxicity to Alcid Immune Function

Oil spills are devastating to seabirds, causing high levels of mortality and toxic physiological effects, especially to immune function. Sunlight exposure can further enhance the toxicity of oil to marine species by generating photodegradation products. Photo-enhanced oil toxicity to marine birds has not been studied. Therefore, the goal of the present study was to investigate the toxicity and photo-enhanced toxicity of oil to lymphocyte proliferation, macrophage phagocytosis, and reactive oxygen species production in three alcid species, common murres (Uria aalge), tufted puffins (Fratercula cirrhata), and horned puffins (Fratercula corniculata). Intrinsic factors (species, age, and sex) had a more significant effect on lymphocyte proliferation than exposure to oil or photoactivated oil. Macrophage phagocytosis was significantly reduced in oil and photoactivated oil treatments, whereas hydrogen peroxide production was significantly increased. Interestingly, nonphotoactivated oil stimulated significantly more hydrogen peroxide than photoactivated oil. The results suggest that alcid immune function could be variably influenced during an oil spill depending on the species, sex, and age of the bird as well as the season and level of sunlight exposure. Environ Toxicol Chem 2023;42:2701-2711. © 2023 SETAC.

Unravelling High-Molecular-Weight DBP Toxicity Drivers in Chlorinated and Chloraminated Drinking Water: Effect-Directed Analysis of Molecular Weight Fractions

As disinfection byproducts (DBPs) are ubiquitous sources of chemical exposure in disinfected drinking water, identifying unknown DBPs, especially unknown drivers of toxicity, is one of the major challenges in the safe supply of drinking water. While >700 low-molecular-weight DBPs have been identified, the molecular composition of high-molecular-weight DBPs remains poorly understood. Moreover, due to the absence of chemical standards for most DBPs, it is difficult to assess toxicity contributions for new DBPs identified. Based on effect-directed analysis, this study combined predictive cytotoxicity and quantitative genotoxicity analyses and Fourier transform ion cyclotron resonance mass spectrometry (21 T FT-ICR-MS) identification to resolve molecular weight fractions that induce toxicity in chloraminated and chlorinated drinking waters, along with the molecular composition of these DBP drivers. Fractionation using ultrafiltration membranes allowed the investigation of <1 kD, 1-3 kD, 3-5 kD, and >5 kD molecular weight fractions. Thiol reactivity based predictive cytotoxicity and single-cell gel electrophoresis based genotoxicity assays revealed that the <1 kD fraction for both chloraminated and chlorinated waters exhibited the highest levels of predictive cytotoxicity and direct genotoxicity. The <1 kD target fraction was used for subsequent molecular composition identification. Ultrahigh-resolution MS identified singly charged species (as evidenced by the 1 Da spacing in 13C isotopologues), including 3599 chlorine-containing DBPs in the <1 kD fraction with the empirical formulas CHOCl, CHOCl2, and CHOCl3, with a relative abundance order of CHOCl > CHOCl2 ≫ CHOCl3. Interestingly, more high-molecular-weight CHOCl1-3 DBPs were identified in the chloraminated vs chlorinated waters. This may be due to slower reactions of NH2Cl. Most of the DBPs formed in chloraminated waters were composed of high-molecular-weight Cl-DBPs (up to 1 kD) rather than known low-molecular-weight DBPs. Moreover, with the increase of chlorine number in the high-molecular-weight DBPs detected, the O/C ratio exhibited an increasing trend, while the modified aromaticity index (AImod) showed an opposite trend. In drinking water treatment processes, the removal of natural organic matter fractions with high O/C ratio and high AImod value should be strengthened to minimize the formation of known and unknown DBPs.

Advances in high-resolution mass spectrometry techniques for analysis of high mass-to-charge ions

A major challenge in modern mass spectrometry (MS) is achieving high mass resolving power and accuracy for precision analyses in high mass-to-charge (m/z) regions. To advance the capability of MS for increasingly demanding applications, understanding limitations of state-of-the-art techniques and their status in applied sciences is essential. This review summarizes important instruments in high-resolution mass spectrometry (HRMS) and related advances to extend their working range to high m/z regions. It starts with an overview of HRMS techniques that provide adequate performance for macromolecular analysis, including Fourier-transform, time-of-flight (TOF), quadrupole-TOF, and related data-processing techniques. Methodologies and applications of HRMS for characterizing macromolecules in biochemistry and material sciences are summarized, such as top-down proteomics, native MS, drug discovery, structural virology, and polymer analyses.

Radiolytically reworked Archean organic matter in a habitable deep ancient high-temperature brine

Investigations of abiotic and biotic contributions to dissolved organic carbon (DOC) are required to constrain microbial habitability in continental subsurface fluids. Here we investigate a large (101-283 mg C/L) DOC pool in an ancient (>1Ga), high temperature (45-55 °C), low biomass (102-104 cells/mL), and deep (3.2 km) brine from an uranium-enriched South African gold mine. Excitation-emission matrices (EEMs), negative electrospray ionization (-ESI) 21 tesla Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), and amino acid analyses suggest the brine DOC is primarily radiolytically oxidized kerogen-rich shales or reefs, methane and ethane, with trace amounts of C3-C6 hydrocarbons and organic sulfides. δ2H and δ13C of C1-C3 hydrocarbons are consistent with abiotic origins. These findings suggest water-rock processes control redox and C cycling, helping support a meagre, slow biosphere over geologic time. A radiolytic-driven, habitable brine may signal similar settings are good targets in the search for life beyond Earth.

Mass spectrometry-based proteomics as an emerging tool in clinical laboratories

Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.

Humid Evolution of Haze in the Atmosphere of Super-Earths in the Habitable Zone

Abstract Photochemical hazes are expected to form and significantly contribute to the chemical and radiative balance of exoplanets with relatively moderate temperatures, possibly in the habitable zone of their host star. In the presence of humidity, haze particles might thus serve as cloud condensation nuclei and trigger the formation of water droplets. In the present work, we are interested in the chemical impact of such a close interaction between photochemical hazes and humidity on the organic content composing the hazes and on the capacity to generate organic molecules with high prebiotic potential. For this purpose, we explore experimentally the sweet spot by combining N-dominated super-Earth exoplanets in agreement with Titan's rich organic photochemistry and humid conditions expected for exoplanets in habitable zones. A logarithmic increase with time is observed for the relative abundance of oxygenated species, with O-containing molecules dominating after 1 month only. The rapidity of the process suggests that the humid evolution of N-rich organic haze provides an efficient source of molecules with high prebiotic potential.

Hyphenation of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with separation methods: The art of compromises and the possible - A review

This review provides an overview of the online hyphenation of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) with separation methods to date. The online coupling between separation techniques (gas and liquid chromatography, capillary electrophoresis) and FT-ICR MS essentially raises questions of compromise and is not look as straightforward as hyphenation with other analyzers (QTOF-MS for instance). FT-ICR MS requires time to reach its highest resolving power and accuracy in mass measurement capabilities whereas chromatographic and electrophoretic peaks are transient. In many applications, the strengths and the weaknesses of each technique are balanced by their hyphenation. Untargeted "Omics" (e.g. proteomics, metabolomics, petroleomics, …) is one of the main areas of application for FT-ICR MS hyphenated to online separation techniques because of the complexity of the sample. FT-ICR MS achieves the required high mass measurement accuracy to determine accurate molecular formulae and resolution for isobar distinction. Meanwhile separation techniques highlight isomers and reduce the ion suppression effects extending the dynamic range. Even if the implementation of FT-ICR MS hyphenated with online separation methods is a little trickier (the art of compromise), this review shows that it provides unparalleled results to the scientific community (the art of the possible), along with raising the issue of its future in the field with the relentless technological progress.

Single-Cell and Subcellular Analysis Using Ultrahigh Resolution 21 T MALDI FTICR Mass Spectrometry

The mammalian brain contains ∼20,000 distinct lipid species that contribute to its structural organization and function. The lipid profiles of cells change in response to a variety of cellular signals and environmental conditions that result in modulation of cell function through alteration of phenotype. The limited sample material combined with the vast chemical diversity of lipids makes comprehensive lipid profiling of individual cells challenging. Here, we leverage the resolving power of a 21 T Fourier-transform ion cyclotron resonance (FTICR) mass spectrometer for chemical characterization of individual hippocampal cells at ultrahigh mass resolution. The accuracy of the acquired data allowed differentiation of freshly isolated and cultured hippocampal cell populations, as well as finding differences in lipids between the soma and neuronal processes of the same cell. Differences in lipids include TG 42:2 observed solely in the cell bodies and SM 34:1;O2 found only in the cellular processes. The work represents the first mammalian single cells analyzed at ultrahigh resolution and is an advance in the performance of mass spectrometry (MS) for single-cell research.

The analytical solution for the optimum voltage on regularizing electrodes of the open dynamically harmonized cell

The Fourier transform ion cyclotron resonance method holds the lead in mass accuracy and resolving power among all other mass spectrometry methods. The dynamically harmonized cell is largely responsible for the supremacy. This cell has an ideal hyperbolic trapping potential after averaging over fast cyclotron motion. Recently we have introduced an open modification of the cell (especially useful with ultrahigh magnetic fields) and have found the analytical solution for the averaged potential inside it. The voltage on specific "regularizing" electrodes determines how close a potential is to the hyperbolic one. In this article, we find the optimal voltage on these "regularizing" electrodes analytically. This will assist with both further analysis and tuning of the trap after manufacturing.

The isotope distribution: A rose with thorns

The isotope distribution, which reflects the number and probabilities of occurrence of different isotopologues of a molecule, can be theoretically calculated. With the current generation of (ultra)-high-resolution mass spectrometers, the isotope distribution of molecules can be measured with high sensitivity, resolution, and mass accuracy. However, the observed isotope distribution can differ substantially from the expected isotope distribution. Although differences between the observed and expected isotope distribution can complicate the analysis and interpretation of mass spectral data, they can be helpful in a number of specific applications. These applications include, yet are not limited to, the identification of peptides in proteomics, elucidation of the elemental composition of small organic molecules and metabolites, as well as wading through peaks in mass spectra of complex bioorganic mixtures such as petroleum and humus. In this review, we give a nonexhaustive overview of factors that have an impact on the observed isotope distribution, such as elemental isotope deviations, ion sampling, ion interactions, electronic noise and dephasing, centroiding, and apodization. These factors occur at different stages of obtaining the isotope distribution: during the collection of the sample, during the ionization and intake of a molecule in a mass spectrometer, during the mass separation and detection of ionized molecules, and during signal processing.

Discovery of a biomarker for β-Thalassemia by HPLC-MS and improvement from Proton Transfer Reaction - Parallel Ion Parking

β-thalassemia is a quantitative hemoglobin (Hb) disorder resulting in reduced production of Hb A and increased levels of Hb A₂. Diagnosis of β-thalassemia can be problematic when combined with other structural Hb variants, so that the separation approaches in routine clinical centers are not sufficiently decisive to obtain accurate results. Here, we separate the intact Hb subunits by high-performance liquid chromatography, followed by top-down tandem mass spectrometry of intact subunits to distinguish Hb variants. Proton transfer reaction-parallel ion parking (PTR-PIP), in which a radical anion removes protons from multiply charged precursor ions and produces charge-reduced ions spanning a limited m/z range, was used to increase the signal-to-noise ratio of the subunits of interest. We demonstrate that the δ/β ratio can act as a biomarker to identify β-thalassemia in normal electrospray ionization MS1 and PTR-PIP MS1. The application of PTR-PIP significantly increases the sensitivity and specificity of the HPLC-MS method to identify δ/β ratio as a thalassemia biomarker.

Analysis of Isotopically Depleted Proteins Derived from Escherichia coli and Caenorhabditis elegans Cell Lines by Liquid Chromatography 21 T Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

Protein mass measurement by mass spectrometry is complicated by wide isotopic distributions that result from incorporation of heavy isotopes of C, H, N, O, and S, thereby limiting signal-to-noise ratio (SNR) and accurate intact mass determination, particularly for larger proteins [Fenselau et al. Anal. Chem. 1983, 55 (2), 353-356]. Observation of the monoisotopic mass-to-charge ratio (m/z) is the simplest and most accurate way to determine intact protein mass, but as mass increases, the relative abundance of the monoisotopic peak becomes so low that it is often undetectable. Here, we used an isotopically depleted growth medium to culture bacterial cells (Escherichia coli), resulting in isotopically depleted proteins. Isotopically depleted proteins show increased sequence coverage, mass measurement accuracy, and increased S/N of the monoisotopic peak by Fourier transform ion cyclotron resonance mass spectrometry analysis. We then grew Caenorhabditis elegans cells in a medium containing living isotopically depleted E. coli cells, thereby producing the first isotopically depleted eukaryotic proteins. This is the first time isotopic depletion has been implemented for four isotopes (¹H, ¹²C, ¹⁴N, and ¹⁶O), resulting in the highest degree of depletion ever used for protein analysis and further improving MS analysis.

Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling

The KRAS gene is one of the most frequently mutated oncogenes in human cancer and gives rise to two isoforms, KRAS4A and KRAS4B. KRAS post-translational modifications (PTMs) have the potential to influence downstream signaling. However, the relationship between KRAS PTMs and oncogenic mutations remains unclear, and the extent of isoform-specific modification is unknown. Here, we present the first top-down proteomics study evaluating both KRAS4A and KRAS4B, resulting in 39 completely characterized proteoforms across colorectal cancer cell lines and primary tumor samples. We determined which KRAS PTMs are present, along with their relative abundance, and that proteoforms of KRAS4A versus KRAS4B are differentially modified. Moreover, we identified a subset of KRAS4B proteoforms lacking the C185 residue and associated C-terminal PTMs. By confocal microscopy, we confirmed that this truncated GFP-KRAS4B^C185∗ proteoform is unable to associate with the plasma membrane, resulting in a decrease in mitogen-activated protein kinase signaling pathway activation. Collectively, our study provides a reference set of functionally distinct KRAS proteoforms and the colorectal cancer contexts in which they are present.

Food metabolomics: Latest hardware-developments for nontargeted food authenticity and food safety testing

The analytical requirements for food testing have increased significantly in recent years. On the one hand, because food fraud is becoming an ever-greater challenge worldwide, and on the other hand because food safety is often difficult to monitor due to the far-reaching trade chains. In addition, the expectations of consumers on the quality of food have increased, and they are demanding extensive information. Cutting-edge analytical methods are required to meet these demands. In this context, non-targeted metabolomics strategies using mass and nuclear magnetic resonance spectrometers (mass spectrometry [MS]) have proven to be very suitable. MS-based approaches are of particular importance as they provide a comparatively high analytical coverage of the metabolome. Accordingly, the efficiency to address even challenging issues is high. A variety of hardware developments, which are explained in this review, have contributed to these advances. In addition, the potential of future developments is highlighted, some of which are currently not yet commercially available or only used to a comparatively small extent but are expected to gain in importance in the coming years.

Generalization of an Open Dynamically Harmonized Cell for Ultrahigh FT ICR Resolution

FT ICR mass spectrometry is the leader in resolving power among all mass spectrometry methods. Introduction of the dynamically harmonized measuring cell─a closed-cylindrical cell with specifically shaped electrodes─helps to reach the resolving power of more than 10⁷ with a magnetic field of about 7 T. From the theory of FT ICR mass spectrometry it follows that the resolving power of this type of instrument depends linearly on the magnetic field under various conditions. However, the results obtained on this type of mass spectrometer with the maximum magnetic field achievable today did not show a proportional increase in resolving power. In one of our previous papers, we assumed that the reason for this was insufficient vacuum inside the cell, since vacuum quality should be at least proportional to the magnetic field, since the mean free run time decreases proportionally to the magnetic field growth. We have presented an open modification of the dynamically harmonized cell that can help improve the cell pumping conditions. However, the electric potential distribution inside this new cell is slightly different from the ideal (harmonic) one, obtained inside the closed version of the cell, and the resolving power may have been limited by this difference.

Molecular Characterization of Organophosphorus Compounds in Wildfire Smoke Using 21-T Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

We present a detailed molecular characterization of organophosphorus compounds in ambient organic aerosol influenced by wildfire smoke. Biomass burning organic aerosol (BBOA) is an important source of phosphorus (P) to surface waters, where even a small imbalance in the P flux can lead to substantial effects on water quality, such as eutrophication, algal blooms, and oxygen depletion. We aimed to exploit the ultrahigh resolving power, mass accuracy, and sensitivity of Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) to explore the molecular composition of an ambient BBOA sample collected downwind of Pacific Northwest wildfires. The 21-T FT-ICR MS yielded 10 533 distinct formulae, which included molecular species comprising C, H, O, and P with or without N, i.e., organophosphorus compounds that have long been quantified in wildfire smoke but have not yet been characterized at the molecular level. The lack of detailed molecular characterization of organophosphorus compounds in BBOA is primarily due to their inherently low concentrations in aerosols and poor ionization efficiency in complex mixtures. We demonstrate that the exceptional sensitivity of the 21-T FT-ICR MS allows qualitative analysis of a previously uncharacterized fraction of BBOA without its selective concentration from the organic matrix, exemplifying the need for ultrahigh-resolution tools for a more detailed and accurate molecular depiction of such complex mixtures.

Impact of beaver ponds on biogeochemistry of organic carbon and nitrogen along a fire-impacted stream

Wildfires, which are increasing in frequency and severity in the western U.S., impact water quality through increases in erosion, and transport of nutrients and metals. Meanwhile, beaver populations have been increasing since the early 1900s, and the ponds they create slow or impound hydrologic and elemental fluxes, increase soil saturation, and have a high potential to transform redox active elements (e.g., oxygen, nitrogen, sulfur, and metals). However, it remains unknown how the presence of beaver ponds in burned watersheds may impact retention and transformation of chemical constituents originating in burned uplands (e.g., pyrogenic dissolved organic matter; pyDOM) and the consequences for downstream water quality. Here, we investigate the impact of beaver ponds on the chemical properties and molecular composition of dissolved forms of C and N, and the microbial functional potential encoded within these environments. The chemistry and microbiology of surface water and sediment changed along a stream sequence starting upstream of fire and flowing through multiple beaver ponds and interconnecting stream reaches within a burned high-elevation forest watershed. The relative abundance of N-containing compounds increased in surface water of the burned beaver ponds, which corresponded to lower C/N and O/C, and higher aromaticity as characterized by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The resident microbial communities lack the capacity to process such aromatic pyDOM, though genomic analyses demonstrate their potential to metabolize various compounds in the anaerobic sediments of the beaver ponds. Collectively, this work highlights the role of beaver ponds as biological "hotspots" with unique biogeochemistry in fire-impacted systems.

The Omnitrap Platform: A Versatile Segmented Linear Ion Trap for Multidimensional Multiple-Stage Tandem Mass Spectrometry

Multidimensional multiple-stage tandem processing of ions is demonstrated successfully in a novel segmented linear ion trap. The enhanced performance is enabled by incorporating the entire range of ion activation methods into a single platform in a highly dynamic fashion. The ion activation network comprises external injection of reagent ions, radical neutral species, photons, electrons, and collisions with neutrals. Axial segmentation of the two-dimensional trapping field provides access to a unique functionality landscape through a system of purpose-designed regions for processing ions with maximum flexibility. Design aspects of the segmented linear ion trap, termed the Omnitrap platform, are highlighted, and motion of ions trapped by rectangular waveforms is investigated experimentally by mapping the stability diagram, tracing secular frequencies, and exploring different isolation techniques. All fragmentation methods incorporated in the Omnitrap platform involving radical chemistry are shown to provide complete sequence coverage for partially unfolded ubiquitin. Three-stage (MS3) tandem mass spectrometry experiments combining collision-induced dissociation of radical ions produced by electron meta-ionization and further involving two intermediate steps of ion isolation and accumulation are performed with high efficiency, producing information rich spectra with signal-to-noise levels comparable to those obtained in a two-stage (MS2) experiment. The advanced capabilities of the Omnitrap platform to provide in-depth top-down MSn characterization of proteins are portrayed. Performance is further enhanced by connecting the Omnitrap platform to an Orbitrap mass analyzer, while successful integration with time-of-flight analyzers has already been demonstrated.

Improved Dynamic Range, Resolving Power, and Sensitivity Achievable with FT-ICR Mass Spectrometry at 21 T Reveals the Hidden Complexity of Natural Organic Matter

Fourier transform ion-cyclotron resonance mass spectrometry (FT-ICR MS) is the only mass analyzer that can resolve the molecular complexity of natural organic matter at the level of elemental composition assignment. Here, we leverage the high dynamic range, resolving power, resistance to peak coalescence, and maximum ion number and ion trapping duration in a custom built, 21 tesla hybrid linear ion trap /FT-ICR mass spectrometer for a dissolved organic matter standard (Suwanne River Fulvic Acid). We compare the effect of peak-picking threshold (3σ, 4σ, 5σ, and 6σ) on number of elemental composition assignments, mass measurement accuracy, and dynamic range for a 6.3 s transient across the mass range of m/z 200-1200 that comprises the highest achieved resolving power broadband FT-ICR mass spectrum collected to date. More than 36 000 species are assigned with signal magnitude greater than 3σ at root-mean-square mass error of 36 ppb, the most species identified reported to date for dissolved organic matter. We identify ¹⁸O and ¹⁷O isotopologues and resolve isobaric overlaps on the order of a few electrons across a wide mass range (up to m/z 1000) leveraging mass resolving powers (3 000 000 at m/z 200) only achievable by 21 T FT-ICR MS and increased by ∼30% through absorption mode data processing. Elemental compositions unique to the 3σ span a wide compositional range of aromaticity not detected at higher peak-picking thresholds. Furthermore, we leverage the high dynamic range at 21 T FT-ICR MS to provide a molecular catalogue of a widely utilized reference standard (SRFA) to the analytical community collected on the highest performing mass analyzer for complex mixture analysis to date. This instrument is available free of charge to scientists worldwide.

Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes

Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.

Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool

Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.

A new conceptual framework for the transformation of groundwater dissolved organic matter

Groundwater comprises 95% of the liquid fresh water on Earth and contains a diverse mix of dissolved organic matter (DOM) molecules which play a significant role in the global carbon cycle. Currently, the storage times and degradation pathways of groundwater DOM are unclear, preventing an accurate estimate of groundwater carbon sources and sinks for global carbon budgets. Here we reveal the transformations of DOM in aging groundwater using ultra-high resolution mass spectrometry combined with radiocarbon dating. Long-term anoxia and a lack of photodegradation leads to the removal of oxidised DOM and a build-up of both reduced photodegradable formulae and aerobically biolabile formulae with a strong microbial signal. This contrasts with the degradation pathway of DOM in oxic marine, river, and lake systems. Our findings suggest that processes such as groundwater extraction and subterranean groundwater discharge to oceans could result in up to 13 Tg of highly photolabile and aerobically biolabile groundwater dissolved organic carbon released to surface environments per year, where it can be rapidly degraded. These findings highlight the importance of considering groundwater DOM in global carbon budgets.

Characterization of large intact protein ions by mass spectrometry: What directions should we follow?

Theoretically, the gas-phase interrogation of whole proteoforms via mass spectrometry, known as top-down proteomics, bypasses the protein inference problem that afflicts peptide-centric proteomic approaches. Despite this obvious advantage, the application of top-down proteomics remains rare, mainly due to limited throughput and difficulty of analyzing proteins >30 kDa. Here we will discuss some of the problems encountered during the characterization of large proteoforms, and guided by a combination of theoretical background and experimental evidence we will describe some innovative data acquisition strategies and novel mass spectrometry technologies that can at least partially overcome such limitations.

Improving the Center Section Sequence Coverage of Large Proteins Using Stepped-Fragment Ion Protection Ultraviolet Photodissociation

Ultraviolet photodissociation (UVPD) mass spectrometry has gained attention in recent years for its ability to provide high sequence coverage of intact proteins. However, secondary dissociation of fragment ions, in which fragment ions subjected to multiple laser pulses decompose into small products, is a common phenomenon during UVPD that contributes to limited coverage in the midsection of protein sequences. To counter secondary dissociation, a method involving the application of notched waveforms to modulate the trajectories of fragment ions away from the laser beam, termed fragment ion protection (FIP), was previously developed to reduce the probability of secondary dissociation. This, in turn, increased the number of identified large fragment ions. In the present study, FIP was applied to UVPD of large proteins ranging in size from 29 to 55 kDa, enhancing the abundances of large fragment ions. A stepped-FIP strategy was implemented in which UVPD mass spectra were collected using multiple different amplitudes of the FIP waveforms and then the results from the mass spectra were combined. By using stepped-FIP, the number of fragment ions in the midsections of the sequences increased for all proteins. For example, whereas no fragment ions were identified in the middle section of the sequence for glutamate dehydrogenase (55 kDa, 55+ charge state), 10 sequence ions were identified by using UVPD-FIP.

Applications and advancements of FT-ICR-MS for interactome studies

The set of all intra- and intermolecular interactions, collectively known as the interactome, is currently an unmet challenge for any analytical method, but if measured, could provide unparalleled insight on molecular function in living systems. Developments and applications of chemical cross-linking and high-performance mass spectrometry technologies are beginning to reveal details on how proteins interact in cells and how protein conformations and interactions inside cells change with phenotype or during drug treatment or other perturbations. A major contributor to these advances is Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) technology and its implementation with accurate mass measurements on cross-linked peptide-pair precursor and fragment ions to enable improved identification methods. However, these applications place increased demands on mass spectrometer performance in terms of high-resolution spectral acquisition rates for on-line MSⁿ experiments. Moreover, FT-ICR-MS also offers unique opportunities to develop and implement parallel ICR cells for multiplexed signal acquisition and the potential to greatly advance accurate mass acquisition rates for interactome studies. This review highlights our efforts to exploit accurate mass FT-ICR-MS technologies with chemical cross-linking and developments being pursued to realize parallel MS array capabilities that will further advance visualization of the interactome.

Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms

Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with its ultrahigh mass-resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top-down, middle-down, and native MS-based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT-ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in-depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post-translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT-ICR MS and emerging applications, such as native top-down FT-ICR MS and high-throughput top-down FT-ICR MS-based proteomics at 21 T, are also covered. Historically, the information gleaned from FT-ICR MS analyses have helped provide biological insights. We predict FT-ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Fourier transform ion cyclotron resonance mass spectrometry at the true cyclotron frequency

Ion cyclotron resonance (ICR) cells provide stability and coherence of ion oscillations in crossed electric and magnetic fields over extended periods of time. Using the Fourier transform enables precise measurements of ion oscillation frequencies. These precisely measured frequencies are converted into highly accurate mass-to-charge ratios of the analyte ions by calibration procedures. In terms of resolution and mass accuracy, Fourier transform ICR mass spectrometry (FT-ICR MS) offers the highest performance of any MS technology. This is reflected in its wide range of applications. However, in the most challenging MS application, for example, imaging, enhancements in the mass accuracy of fluctuating ion fluxes are required to continue advancing the field. One approach is to shift the ion signal power into the peak corresponding to the true cyclotron frequency instead of the reduced cyclotron frequency peak. The benefits of measuring the true cyclotron frequency include increased tolerance to electric fields within the ICR cell, which enhances frequency measurement precision. As a result, many attempts to implement this mode of FT-ICR MS operation have occurred. Examples of true cyclotron frequency measurements include detection of magnetron inter-harmonics of the reduced cyclotron frequency (i.e., the sidebands), trapping field-free (i.e., screened) ICR cells, and hyperbolic ICR cells with quadrupolar ion detection. More recently, ICR cells with spatially distributed ion clouds have demonstrated attractive performance characteristics for true cyclotron frequency ion detection. Here, we review the corresponding developments in FT-ICR MS over the past 40 years.

PFAS Analysis with Ultrahigh Resolution 21T FT-ICR MS: Suspect and Nontargeted Screening with Unrivaled Mass Resolving Power and Accuracy

Per- and polyfluoroalkyl substances (PFASs) are a large family of thousands of chemicals, many of which have been identified using nontargeted time-of-flight and Orbitrap mass spectrometry methods. Comprehensive characterization of complex PFAS mixtures is critical to assess their environmental transport, transformation, exposure, and uptake. Because 21 tesla (T) Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers the highest available mass resolving power and sub-ppm mass errors across a wide molecular weight range, we developed a nontargeted 21 T FT-ICR MS method to screen for PFASs in an aqueous film-forming foam (AFFF) using suspect screening, a targeted formula database (C, H, Cl, F, N, O, P, S; ≤865 Da), isotopologues, and Kendrick-analogous mass difference networks (KAMDNs). False-positive PFAS identifications in a natural organic matter (NOM) sample, which served as the negative control, suggested that a minimum length of 3 should be imposed when annotating CF₂-homologous series with positive mass defects. We putatively identified 163 known PFASs during suspect screening, as well as 134 novel PFASs during nontargeted screening, including a suspected polyethoxylated perfluoroalkane sulfonamide series. This study shows that 21 T FT-ICR MS analysis can provide unique insights into complex PFAS composition and expand our understanding of PFAS chemistries in impacted matrices.

Enhanced Speciation of Pyrogenic Organic Matter from Wildfires Enabled by 21 T FT-ICR Mass Spectrometry

Wildfires affect soils through the formation of pyrogenic organic matter (pyOM) (e.g., char and soot). While many studies examine the connection between pyOM persistence and carbon (C) composition, nitrogen (N) transformation in wildfire-impacted systems remains poorly understood. Thermal reactions in wildfires transform biomass into a highly complex, polyfunctional, and polydisperse organic mixture that challenges most mass analyzers. High-field Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) is the only mass analyzer that achieves resolving powers sufficient to separate species that differ in mass by the mass of an electron across a wide molecular weight range (m/z 150-1500). We report enhanced speciation of organic N by positive-ion electrospray ionization (ESI) that leverages ultrahigh resolving power (m/Δm_50% = 1 800 000 at m/z 400) and mass accuracy (<10-100 ppb) achieved by FT-ICR MS at 21 T. Isobaric overlaps, roughly the mass of an electron (M_e^- = 548 μDa), are resolved across a wide molecular weight range and are more prevalent in positive ESI than negative ESI. The custom-built 21 T FT-ICR MS instrument identifies previously unresolved mass differences in C_cH_hN_nO_oS_s formulas and assigns more than 30 000 peaks in a pyOM sample. This is the first molecular catalogue of pyOM by positive-ion ESI 21 T FT-ICR MS and presents a method to provide new insight into terrestrial cycling of organic carbon and nitrogen in wildfire impacted ecosystems.

Constellation: An Open-Source Web Application for Unsupervised Systematic Trend Detection in High-Resolution Mass Spectrometry Data

The increasing popularity of high-resolution mass spectrometry has led to many custom software solutions to process, interpret, and reveal information from high-resolution mass spectra. Although there are numerous software packages for peak-picking, calibration, and formula-finding, there are additional layers of information available when it comes to detecting repeated motifs from polymers or molecules with repeating structures or products of chemical or biochemical transformations that exhibit systematic, serial chemical changes of mass. Constellation is an open-source, Python-based web application that allows the user first to expand their high-resolution mass data into the mass defect space, after which a trend finding algorithm is used for supervised or unsupervised detection of repeating motifs. Many adjustable parameters allow the user to tailor their trend-search to target particular chemical moieties or repeating units, or search for all potential motifs within certain limits. The algorithm has a built-in optimization routine to provide a good starting point for the main trend finding parameters before user customization. Visualization tools allow interrogation of the data and any trends/patterns to a highly specific degree and save publication-quality images directly from the interface. As Constellation is deployed as a web application, it is easily used by anyone with a web browser; no software download or high-powered computer is required, as computations are performed on a remote high-powered data server run by our group.

The Blood Proteoform Atlas: A reference map of proteoforms in human hematopoietic cells

Human biology is tightly linked to proteins, yet most measurements do not precisely determine alternatively spliced sequences or posttranslational modifications. Here, we present the primary structures of ~30,000 unique proteoforms, nearly 10 times more than in previous studies, expressed from 1690 human genes across 21 cell types and plasma from human blood and bone marrow. The results, compiled in the Blood Proteoform Atlas (BPA), indicate that proteoforms better describe protein-level biology and are more specific indicators of differentiation than their corresponding proteins, which are more broadly expressed across cell types. We demonstrate the potential for clinical application, by interrogating the BPA in the context of liver transplantation and identifying cell and proteoform signatures that distinguish normal graft function from acute rejection and other causes of graft dysfunction.

Characterization of Structural Hemoglobin Variants by Top-Down Mass Spectrometry and R Programming Tools for Rapid Identification

Hemoglobinopathies are one of the most prevalent genetic disorders, affecting millions throughout the world. These are caused by pathogenic variants in genes that control the production of hemoglobin (Hb) subunits. As the number of known Hb variants has increased, it has become more challenging to obtain unambiguous results from routine chromatographic assays employed in the clinical laboratory. Top-down proteomic analysis of Hb by mass spectrometry is a definitive method to directly characterize the sequences of intact subunits. Here, we apply "chimeric ion loading" to characterize Hb β subunit variants. In this technique, product ions derived from complementary dissociation techniques are accumulated in a multipole storage device before delivery to a 21 T Fourier-transform ion cyclotron resonance mass spectrometer for simultaneous detection. To further improve the efficiency of identification of Hb variants and localization of the mutation site(s), we developed an R programming script, "Variants Identifier", to search top-down data against a database containing accurate intact mass differences and diagnostic ions from investigated Hb variants. A second R script, "PredictDiag", was developed and employed to determine relevant diagnostic ions for additional Hb variants with known sequences. These two R scripts were successfully applied to the identification of a Hb δ-β fusion protein and other Hb variants. The combination of chimeric ion loading and the above R scripts enables rapid and reliable interpretation of top-down mass spectrometry data, regardless of activation type, for Hb variant identification.

Recent technological developments for native mass spectrometry

Native mass spectrometry (MS), the analysis of proteins and protein complexes from solutions that stabilize native solution structures, is a rapidly expanding area. There is strong evidence supporting the retention of proteins' native folds in the absence of solvent under the experimental timescales of MS experiments. Therefore, instrumentation has been developed to use gas-phase native-like protein ions to exploit the speed, sensitivity, and selectivity of mass spectrometry approaches to solve emerging problems in structural biology. This article reviews some of the recent advances and applications in gas-phase instrumentation for structural proteomics.

Towards Higher Sensitivity of Mass Spectrometry: A Perspective From the Mass Analyzers

Mass spectrometry (MS) is one of the most widely used analytical techniques in many fields. Recent developments in chemical and biological researches have drawn much attention to the measurement of substances with low abundances in samples. Continuous efforts have been made consequently to further improve the sensitivity of MS. Modifications on the mass analyzers of mass spectrometers offer a direct, universal and practical way to obtain higher sensitivity. This review provides a comprehensive overview of the latest developments in mass analyzers for the improvement of mass spectrometers' sensitivity, including quadrupole, ion trap, time-of-flight (TOF) and Fourier transform ion cyclotron (FT-ICR), as well as different combinations of these mass analyzers. The advantages and limitations of different mass analyzers and their combinations are compared and discussed. This review provides guidance to the selection of suitable mass spectrometers in chemical and biological analytical applications. It is also beneficial to the development of novel mass spectrometers.

Direct Infusion Metabolomics of the Photosystem and Chlorophyll Related Metabolites within a Drought Tolerant Plant Introduction of Glycine max

Drought is the most prolific form of abiotic stress that legumes and cereal plants alike can endure, and the planting of an improper cultivar at the beginning of a season can cause unexpected losses up to fifty percent under water deficient conditions. Herein, a plant introduction (PI) of an exotic cultivar of soybean (Glycine max), PI 567731, which demonstrates a slow wilting (SW) canopy phenotype in maturity group III, was profiled under drought conditions in field trials in Missouri against a drought susceptible check cultivar, Pana. Metabolomic profiling was carried out on samples of leaves from each of these cultivars at V5 and R2 growth stages both while irrigated and while under drought stress for three weeks. PI 567731 was observed to have differential phytochemical content, and enhanced levels of chlorophyll (Chl) a/b and pheophytin (Pheo) were profiled by direct infusion electrospray Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Indicating drought induced changes of the photosystem and photosynthetic capabilities alongside water preservation strategies are important within the SW phenotype drought response. Subsequent multivariate analysis was able to form predictive models, encompassing the variance of growth and drought stress of the cultivar. Moreover, the existence of unique Chl-related metabolites (CRM) (m/z > 900) were confirmed through tandem mass spectrometry. The resultant coordination of fatty acids to the core of the porphyrin ring was observed and played an unknown role in the proliferation of the photosynthesis. However, the relative ratio of the most abundant CRM is undisturbed by drought stress in PI 567731, in contrast to the drought susceptible cultivar. These results provide key insights into drought related metabolic mechanisms.

Clinical importance of high-mannose, fucosylated and complex N-glycans in breast cancermetastasis

BACKGROUND. Although aberrant glycosylation is recognized as a hallmark of cancer, glycosylation in clinical breast cancer (BC) metastasis has not yet been studied. While preclinical studies show that the glycocalyx coating of cancer cells is involved in adhesion, migration, and metastasis, glycosylation changes from primary tumor (PT) to various metastatic sites remain unknown in patients.

METHODS. We investigated N-glycosylation profiles in 17 metastatic BC patients from our rapid autopsy program. Primary breast tumor, lymph node metastases, multiple systemic metastases, and various normal tissue cores from each patient were arranged on unique single-patient tissue microarrays (TMAs). We performed mass spectrometry imaging (MSI) combined with extensive pathology annotation of these TMAs, and this process enabled spatially differentiated cell-based analysis of N-glycosylation patterns in metastatic BC.

RESULTS. N-glycan abundance increased during metastatic progression independently of BC subtype and treatment regimen, with high-mannose glycans most frequently elevated in BC metastases, followed by fucosylated and complex glycans. Bone metastasis, however, displayed increased core-fucosylation and decreased high-mannose glycans. Consistently, N-glycosylated proteins and N-glycan biosynthesis genes were differentially expressed during metastatic BC progression, with reduced expression of mannose-trimming enzymes and with elevated EpCAM, N-glycan branching, and sialyation enzymes in BC metastases versus PT.

CONCLUSION. We show in patients that N-glycosylation of breast cancer cells undergoing metastasis occurs in a metastatic site–specific manner, supporting the clinical importance of high-mannose, fucosylated, and complex N-glycans as future diagnostic markers and therapeutic targets in metastatic BC.

FUNDING. NIH grants R01CA213428, R01CA213492, R01CA264901, T32CA193145, Dutch Province Limburg “LINK”, European Union ERA-NET TRANSCAN2-643638.

A magnetic levitation based low-gravity simulator with an unprecedented large functional volume

Low-gravity environment can have a profound impact on the behaviors of biological systems, the dynamics of fluids, and the growth of materials. Systematic research on the effects of gravity is crucial for advancing our knowledge and for the success of space missions. Due to the high cost and the limitations in the payload size and mass in typical spaceflight missions, ground-based low-gravity simulators have become indispensable for preparing spaceflight experiments and for serving as stand-alone research platforms. Among various simulator systems, the magnetic levitation-based simulator (MLS) has received long-lasting interest due to its easily adjustable gravity and practically unlimited operation time. However, a recognized issue with MLSs is their highly non-uniform force field. For a solenoid MLS, the functional volume V_1%, where the net force results in an acceleration <1% of the Earth's gravity g, is typically a few microliters (μL) or less. In this work, we report an innovative MLS design that integrates a superconducting magnet with a gradient-field Maxwell coil. Through an optimization analysis, we show that an unprecedented V_1% of over 4000 μL can be achieved in a compact coil with a diameter of 8 cm. We also discuss how such an MLS can be made using existing high-T_c-superconducting materials. When the current in this MLS is reduced to emulate the gravity on Mars (g_M = 0.38g), a functional volume where the gravity varies within a few percent of g_M can exceed 20,000 μL. Our design may break new ground for future low-gravity research.

Online Coupling of Liquid Chromatography with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry at 21 T Provides Fast and Unique Insight into Crude Oil Composition

High magnetic field Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry provides the highest mass resolving power and mass measurement accuracy for detailed characterization of complex chemical mixtures. Here, we report the coupling of online liquid chromatography of complex mixtures with a 21 tesla FT-ICR mass spectrometer. The high magnetic field enables large ion populations to be analyzed for each spectrum for a high dynamic range, with 3.2 million mass resolving power at m/z 400 (6.2 s transient duration) or 1.6 million (3.1 s transient duration) while maintaining high mass accuracy for molecular formula assignment (root-mean-square assignment error < 0.150 ppm). Thousands of unique elemental compositions are assigned per mass spectrum, which can be grouped by the heteroatom class, double bond equivalents (the number of rings and double bonds to carbon), and carbon number. Figures of merit are discussed, as well as characterization of an Arabian heavy vacuum gas oil in terms of the ring number, compound class, double bond equivalents, and ion type. Consideration of elemental composition and retention order provides additional structural information.

Plastic Formulation is an Emerging Control of Its Photochemical Fate in the Ocean

Sunlight exposure is a control of long-term plastic fate in the environment that converts plastic into oxygenated products spanning the polymer, dissolved, and gas phases. However, our understanding of how plastic formulation influences the amount and composition of these photoproducts remains incomplete. Here, we characterized the initial formulations and resulting dissolved photoproducts of four single-use consumer polyethylene (PE) bags from major retailers and one pure PE film. Consumer PE bags contained 15-36% inorganic additives, primarily calcium carbonate (13-34%) and titanium dioxide (TiO₂; 1-2%). Sunlight exposure consistently increased production of dissolved organic carbon (DOC) relative to leaching in the dark (3- to 80-fold). All consumer PE bags produced more DOC during sunlight exposure than the pure PE (1.2- to 2.0-fold). The DOC leached after sunlight exposure increasingly reflected the ¹³C and ¹⁴C isotopic composition of the plastic. Ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry revealed that sunlight exposure substantially increased the number of DOC formulas detected (1.1- to 50-fold). TiO₂-containing bags photochemically degraded into the most compositionally similar DOC, with 68-94% of photoproduced formulas in common with at least one other TiO₂-containing bag. Conversely, only 28% of photoproduced formulas from the pure PE were detected in photoproduced DOC from the consumer PE. Overall, these findings suggest that plastic formulation, especially TiO₂, plays a determining role in the amount and composition of DOC generated by sunlight. Consequently, studies on pure, unweathered polymers may not accurately represent the fates and impacts of the plastics entering the ocean.