Analytical Window Research Articles

Data-Independent Acquisition Shortens the Analytical Window of Single-Cell Proteomics to Fifteen Minutes in Capillary Electrophoresis Mass Spectrometry.

Separation in single-cell mass spectrometry (MS) improves molecular coverage and quantification; however, it also elongates measurements, thus limiting analytical throughput to study large populations of cells. Here, we advance the speed of bottom-up proteomics by capillary electrophoresis (CE) high-resolution mass spectrometry (MS) for single-cell proteomics. We adjust the applied electrophoresis potential to readily control the duration of electrophoresis. On the HeLa proteome standard, shorter separation times curbed proteome detection using data-dependent acquisition (DDA) but not data-independent acquisition (DIA) on an Orbitrap analyzer. This DIA method identified 1161 proteins vs 401 proteins by the reference DDA within a 15 min effective separation from single HeLa-cell-equivalent (∼200 pg) proteome digests. Label-free quantification found these exclusively DIA-identified proteins in the lower domain of the concentration range, revealing sensitivity improvement. The approach also significantly advanced the reproducibility of quantification, where ∼76% of the DIA-quantified proteins had <20% coefficient of variation vs ∼43% by DDA. As a proof of principle, the method allowed us to quantify 1242 proteins in subcellular niches in a single, neural-tissue fated cell in the live Xenopus laevis (frog) embryo, including many canonical components of organelles. DIA integration enhanced throughput by ∼2-4 fold and sensitivity by a factor of ∼3 in single-cell (subcellular) CE-MS proteomics.

Quantification of 68 elements in river water monitoring samples in single-run measurements

Triple-quadrupole inductively coupled plasma mass spectrometry (ICP-QQQ-MS) is a unique analytical technique which is, next to speciation analyses, applied for the determination of total element concentrations in several matrices. Due to its wide linear range, short analysis times, and the collision-reaction gas technology, it is capable of addressing a high number of analytes in a single run with sufficient low limits of quantification for river water monitoring. Over the last decades, the focus of the environmental monitoring changed from “traditional” and regulated analytes to elements of possibly rising concern from new applications such as the so-called technology-critical elements (TCE). By widening the analytical window of this method for applications in networks of future river water monitoring, a better understanding of natural transport processes and global biogeochemical element cycles will be established and the total number of methods can be reduced. During method development and validation, certified reference materials, calibration check solutions, and spiked river water samples from 12 major German rivers covering different catchment areas were measured and evaluated with the three cell gases He, H2 and O2. The method delivers a best as possible undisturbed simultaneous determination for 68 out of 71 target analytes with recoveries in an accepted range of 80–120% for river water samples (dissolved fraction; <0.45 μm). After comprehensive evaluation, we offer a novel best-practice multi-element method for river water monitoring with the goal of fostering the exchange and discussion between practitioners in long-term river monitoring. It enables the readers to create their own methods based on the scientific needs to monitor elemental “fingerprints” of rivers and their catchments.

Scales of disaster: Intimate social contracts on the margins of the postcolonial state

Geographical scholarship highlights social contracts as a valuable lens on the dynamic and contested balance of rights and responsibilities between risk governance players. We apply this lens to post-disaster response and reconstruction, which provides an ‘analytical window’ to better understand the types of relationship frameworks between the state and its citizens in postcolonial contexts. Using two post-disaster contexts, Mindanao in southern Philippines and the Andaman Islands in southern India, we uncover intimate social contracts on the margins of the postcolonial state. The article complicates structural scalar analysis of state–citizen relations, arguing that respondents in our field sites do not engage at a ‘local’ level with a sub-national social contract or at a ‘national’ level with a central social contract. Rather our empirical work demonstrates that intimate social contracts are found in the intertwining of central government policy, personal relationships and organisational abilities of local community leaders.

Complex Mixture Analysis of Emerging Contaminants Generated from Coal Tar- and Petroleum-Derived Pavement Sealants: Molecular Compositions and Correlations with Toxicity Revealed by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry

Pavement sealants are of environmental concern because of their complex petroleum-based chemistry and potential toxicity. Specifically, coal tar-derived sealants contain high concentrations of toxic/carcinogenic polycyclic aromatic hydrocarbons (PAHs) that, when weathered, can be transferred into the surrounding environment. Previous studies have demonstrated the effects of coal tar sealants on PAH concentration in nearby waterways and their harmful effects in aquatic ecosystems. Here, we investigate and compare the molecular composition of two different pavement sealants, petroleum asphalt- and coal tar-derived, and their photoproducts, by positive-ion (+) atmospheric pressure photoionization (APPI) and negative-ion (-) electrospray ionization (ESI) coupled with ultrahigh-resolution Fourier transform ion cyclotron resonance mass spectrometry to address species (high-boiling and/or high oxygen content) that lie outside the analytical window of other techniques due to ultra-high molecular complexity. In addition, we evaluate the toxicity of the water-soluble photoproducts by use of Microtox bioassay. The results demonstrate that the coal tar sealant contains higher amounts of PAHs and produces abundant water-soluble compounds, relative to unweathered materials, with a high abundance of PAH-like molecules of high toxicity. By comparison, the asphalt sealant produces fewer toxic water-soluble species, with molecular compositions that are consistent with natural dissolved organic matter. These results capture the mass, chemical diversity, toxicity, and source/photoproduct relationship of these compositionally complex emerging contaminants from the built environment.

Anisotropy of geochemical distributions characterized by irregular window-based local singularity analysis

Supporting the discovery of new resources to maintain the continuous development of human society is a long-term goal in mineral exploration. Geochemical data as an important geo-information carrier played significant roles in geographical information system (GIS)-based mineral prospectivity. Among the various analytical methodologies, local singularity analysis has been broadly discussed due to its high efficiency in the characterization of non-linear mineralization. Focusing on this topic, the current study first reviews local singularity analysis from its original proposition to recent progresses. Meanwhile, limitations in square and rectangular window-based singularity index α estimation algorithms are discussed. Based on this, analytical window parameters in U -statistics and algorithms to quantify the power-law relationship between the physical quantity and the measuring scale in local singularity are integrated. At each scale, optical elliptical windows along all azimuth angles are determined and further merged, which defines an irregular analytical window. Irregular windows at all scales are further applied to local singularity analysis that can consequently propose an irregular window-based singularity algorithm. Practical application in the Duolong mineral district, northern Tibet, China demonstrates well the comparable efficiency of weak anomaly identification with that of the original algorithm. More importantly, multiscale irregular windows can supplement delicate patterns to characterize anisotropic natures associated with mineralization. Thematic collection: This article is part of the Applications of Innovations in Geochemical Data Analysis collection available at: https://www.lyellcollection.org/cc/applications-of-innovations-in-geochemical-data-analysis

Comparison of Sample Preparation Techniques for the (−)ESI-FT-ICR-MS Analysis of Humic and Fulvic Acids

Soil organic matter (SOM) plays a key role in the global carbon and nitrogen cycles. Soil biogeochemistry is regularly studied by extracting the base-soluble fractions of SOM: acid-insoluble humic acid (HA) and acid-soluble fulvic acid (FA). Electrospray ionization-Fourier transform-ion cyclotron resonance-mass spectrometry (ESI-FT-ICR-MS) is commonly utilized for molecularly characterizing these fractions. Different sample preparation techniques exist for the analysis of HA and FA though questions remain regarding data comparability following different preparations. Comparisons of different sample preparation techniques here revealed that the negative-mode ESI-FT-ICR-MS analytical window can be skewed to detect different groups of molecules, with primary differences in oxygenation, aromaticity, and molecular weight. It was also observed that HA and FA from soils versus an aquatic matrix behaved very differently. Thus, we conclude that sample preparation techniques determined to be "most optimal" in our study are in no way universal. We recommend that future studies of HA and FA involve similar comparative studies for determining the most suitable sample preparation technique for their particular type of HA or FA matrices. This will enhance data comparability among different studies and environmental systems and ultimately allow us to better understand the complex composition of environmental matrices.

Lipid Biogeochemistry and Modern Lipidomic Techniques.

Lipids are structurally diverse biomolecules that serve multiple roles in cells. As such, they are used as biomarkers in the modern ocean and as paleoproxies to explore the geological past. Here, I review lipid geochemistry, biosynthesis, and compartmentalization; the varied uses of lipids as biomarkers; and the evolution of analytical techniques used to measure and characterize lipids. Advancements in high-resolution accurate-mass mass spectrometry have revolutionized the lipidomic and metabolomic fields, both of which are quickly being integrated into marine meta-omic studies. Lipidomics allows us to analyze tens of thousands of features, providing an open analytical window and the ability to quantify unknown compounds that can be structurally elucidated later. However, lipidome annotation is not a trivial matter and represents one of the biggest challenges for oceanographers, owing in part to the lack of marine lipids in current in silico databases and data repositories. A case study reveals the gaps in our knowledge and open opportunities to answer fundamental questions about molecular-level control of chemical reactions and global-scale patterns in the lipidscape.

Deciphering the Virus Signal Within the Marine Dissolved Organic Matter Pool.

Viruses are ubiquitously distributed in the marine environment, influencing microbial population dynamics and biogeochemical cycles on a large scale. Due to their small size, they fall into the oceanographic size-class definition of dissolved organic matter (DOM; <0.7 μm). The purpose of our study was to investigate if there is a detectable imprint of virus particles in natural DOM following standard sample preparation and molecular analysis routines using ultrahigh-resolution mass spectrometry (FT-ICR-MS). Therefore, we tested if a molecular signature deriving from virus particles can be detected in the DOM fingerprint of a bacterial culture upon prophage induction and of seawater containing the natural microbial community. Interestingly, the virus-mediated lysate of the infected bacterial culture differed from the cell material of a physically disrupted control culture in its molecular composition. Overall, a small subset of DOM compounds correlated significantly with virus abundances in the bacterial culture setup, accounting for <1% of the detected molecular formulae and <2% of the total signal intensity of the DOM dataset. These were phosphorus- and nitrogen-containing compounds and they were partially also detected in DOM samples from other studies that included high virus abundances. While some of these formulae matched with typical biomolecules that are constituents of viruses, others matched with bacterial cell wall components. Thus, the identified DOM molecular formulae were probably not solely derived from virus particles but were partially also derived from processes such as the virus-mediated bacterial cell lysis. Our results indicate that a virus-derived DOM signature is part of the natural DOM and barely detectable within the analytical window of ultrahigh-resolution mass spectrometry when a high natural background is present.

Characterisation of riverine dissolved organic matter using a complementary suite of chromatographic and mass spectrometric methods

Dissolved organic matter (DOM) plays a fundamental role in nutrient cycling dynamics in riverine systems. Recent research has confirmed that the concentration of riverine DOM is not the only factor regulating its functional significance; the need to define the chemical composition of DOM is a priority. Past studies of riverine DOM rested on bulk quantification, however technological advancements have meant there has been a shift towards analytical methods which allow the characterisation of DOM either at compound class or more recently molecular level. However, it is important to consider that all analytical methods only consider a defined analytical window. Thus, herein, we explore the use of a hierarchy of methods which can be used in combination for the investigation of a wide range of DOM chemistries. By using these methods to investigate the DOM composition of a range of streams draining catchments of contrasting environmental character, a wide range of compounds were identified across a range of polarities and molecular weight, thereby extending the analytical window. Through the elucidation of the DOM character in stream samples, information can be collected about likely the sources of DOM. The identification of individual key compounds within the DOM pool is a key step in the design of robust and informative bioassay experiments, used to understand in-stream ecosystem responses. This is critical if we are to assess the role of DOM as a bioavailable nutrient resource and/or ecotoxicological factor in freshwater.

Investigating the secondary care system burden of CRSwNP in sinus surgery patients with clinically relevant comorbidities using the HES database.

Chronic rhinosinusitis with nasal polyps (CRSwNP) is a chronic condition that can adversely affect quality of life for patients. There is no cure for CRSwNP, and patients may require intermittent systemic corticosteroids (SCS) and surgery in addition to intranasal treatment throughout their lifetime. This places a significant burden on the NHS which can be compounded by comorbid conditions such as asthma or NSAID-exacerbated respiratory disease (NERD). Patients with comorbidities are likely to experience higher rates of surgery and more secondary care visits. The aim of this study was to evaluate revision rates and the associated burden for patients with CRSwNP undergoing surgery and compare this to sub-cohorts of patients with comorbidities. This study has utilised the Hospital Episodes Statistics (HES) database across a ten-year time period (April 2010 to March 2020) to investigate the NHS resource use attributable to CRSwNP for all patients with the condition who have undergone sinus surgery, and to examine the burden of clinically relevant sub-groups. Our results showed that 101,054 patients underwent at least one sinus surgery in relation to their nasal polyps, with Kaplan Meier survival analysis estimating that the 10-year probability of revision is between 71-90% for comorbid patients, and 51% for non-comorbid patients. Patients with a relevant comorbid condition in addition to their CRSwNP were up to 4.7 times more likely to undergo at least one revision surgery during the ten-year analytical time window when compared to patients without a comorbidity. Further to this, comorbid patients had a higher tariff associated with their CRSwNP care across the analytical time window and were therefore likely to be more costly to the healthcare system. In conclusion, this study demonstrates that there is a high burden attached to CRSwNP-related sinus surgery and that comorbidities are a key driver of NHS resource use.

Stability of Wheat Floret Metabolites during Untargeted Metabolomics Studies.

A typical metabolomic analysis consists of a multi-step procedure. Variation can be introduced in any analysis segment if proper care in quality assurance is not taken, thus compromising the final results. Sample stability is one of those factors. Although sophisticated studies addressing sample decay over time have been performed in the medical field, they are emerging in plant metabolomics. Here, we focus on the stability of wheat floret extracts on queue inside an auto-injector held at 25 °C. The objective was to locate an analytical time window from extraction to injection with no significant difference occurring in the sample. Total ion current chromatograms, principal component analysis, and volcano plots were used to measure changes in the samples. Results indicate a maximum work window time of 7:45 h for Steele-ND wheat methanolic extractions in an auto-sampler at 25 °C. Comparisons showed a significant gradual increase in the number and intensity of compounds observed that may be caused by the degradation of other molecules in the sample extract. The approach can be applied as preliminary work in a metabolite profiling study, helping to set the appropriate workload to produce confident results.

A novel route for identifying starch diagenetic products in the archaeological record.

This work introduces a novel analytical chemistry method potentially applicable to the study of archaeological starch residues. The investigation involved the laboratory synthesis of model Maillard reaction mixtures and their analysis through Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS). Thus, starch from sixteen plant species were matured while reacting it with the amino acid glycine. The FTICR-MS analysis revealed > 5,300 molecular compounds, with numerous unique heteroatom rich compound classes, ranging from 20 (Zea mays) to 50 (Sorghum bicolor). These classes were investigated as repositories of chemical structure retaining source and process-specific character, linked back to botanical provenance. We discussed the Maillard reaction products thus generated, a possible pathway for the preservation of degraded starch, while also assessing diagenetic recalcitrance and adsorption potential to mineral surfaces. In some cases, hydrothermal experimentation on starches without glycine reveals that the chemical complexity of the starch itself is sufficient to produce some Maillard reaction products. The article concludes that FTICR-MS offers a new analytical window to characterize starchy residue and its diagenetic products, and is able to recognize taxonomic signals with the potential to persist in fossil contexts.

Expanding the Analytical Window for Biochar Speciation: Molecular Comparison of Solvent Extraction and Water-Soluble Fractions of Biochar by FT-ICR Mass Spectrometry.

Biochar, a low-density yet carbon-rich material derived from different organic materials pyrolyzed under low or no oxygen conditions, has been widely studied as a soil amendment, for greenhouse gas mitigation and in remediation of trace element-contaminated soils. Molecular speciation of biochar compounds has been challenging due to low solubility, aggregation, and immense compositional polydispersity that challenges nearly all mass spectrometry methods routinely applied to carbon-based organic materials. Through a combined technique approach that applies advanced analytical strategies, we provide bulk and molecular characterization of Kentucky bluegrass biochar that can be applied to any biomass or biochar sample. First, we characterize Kentucky bluegrass biochar chemical functional groups by solid-state magic-angle spinning dynamic nuclear polarization NMR (MAS-DNP NMR) and resolve aromatic and aliphatic signals from the pyrogenic material and intact plant material. Next, we isolate water-soluble biochar species by solid-phase extraction followed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and identify highly polar, oxygen species across a wide carbon number range. Solvent fractionation of biochar further expands the compositional range and identifies condensed polycyclic aromatic species across nonpolar and polar classes detected by two ionization modes (-ESI and +APPI) by FT-ICR MS. Plotting biochar species with DBE versus carbon number highlights the pericondensed molecular structural motif that persists across numerous heteroatom classes and ionization modes. To the best of our knowledge, this is the first molecular level identification of nonfunctionalized PAHs in biochar extracts by APPI FT-ICR MS. Thus, we identify biochar species that span the same compositional space as coal, heavy oil asphaltenes, and coal tar and correspond to condensed ring PAHs.

Language Guerrillas: Signing Multilingualism into Action

This article opens an analytical window into the creation of multilingual guerrilla translations by participants in a preservice language teacher program at a public university in the United States. As an intervention responding to the prevalence of English monolingual signage on this highly diverse university campus, the college students invited a public audience into a joint critical interrogation of implicit institutional language policies, as their signage offered a necessarily incomplete and intentionally makeshift alternative to the official English displays. Inspired by the three-phase model of critical pedagogy, this grassroots endeavor embraced Freire’s notion of transformative praxis defined by the symbiotic relation of action and reflection. A closer examination of the scaffolding, which guided the planning and implementation, lends insight into activity design with the potential to nurture an activist aptitude among students. Comments from participants suggest that the conceptual stepping stones towards students’ collective critical engagement had a positive influence on their perception of language (teacher) advocacy and activism.

Application of adaptive parameterized S‐transform to delta sandstone reservoir identification

ABSTRACTTime–frequency analysis plays an important role in seismic interpretation and reservoir identification because it reveals the variation of seismic frequency contents over time. The S‐transform is recognized as an efficient method for seismic time–frequency analysis, but its frequency distribution biases the actual Fourier spectrum due to the linear frequency‐dependent term in the analytical window. In this paper, an improved S‐transform, named adaptive parameterized S‐transform, is proposed for identifying delta sandstone reservoirs. In the proposed method, three parameters are introduced into the S‐transform to better adjust the time–frequency resolution in different frequency bands. Then these parameters are selected adaptively by using the concentration measure to provide a highly energy‐concentrated time–frequency representation for seismic signals. Two synthetic examples validate the effectiveness of the proposed method. Analysis of field seismic data illustrates that it can provide a better reservoir interpretation with a high resolution. Comparisons between the wavelet transform, S‐transform, and modified S‐transform prove the superiority of the proposed method in describing reservoir distribution and decreasing the uncertainty of reservoir detection. This paper presents a complementary approach to current methods for reservoir detection and identification.

More than meets the eye: traditions, nucleus and peripheries of the biographical research field

The long and established roots of biographical research have been well documented, over the last decades, in a rich body of reflections about the main trends, traditions and contexts of production of the field within social sciences, including the identification of milestones and turns. Most of these notable analyses mapping the field’s key approaches and methods tend to be exclusively qualitatively driven, cross-disciplinary, and focused on particular research practices, national contexts. In this article, our aim is to make an innovative yet complementary contribution to the mapping of biographical research. Our contribution has a broader analytical window of observation by acknowledging not only the field’s main traditions and nucleus, but also its periphery and margins. We carried out a bibliometric analysis based on 1270 sociological publications written in English (journal articles, books and book chapters) and, through multivariate statistical analyses, identified three profiles. The Precursors, the founders of the field, define the key theoretical parameters of a sociological analysis of the relation between biography and society, while testing them empirically. The Engineers are the developers of the biographical method, by creating, producing and implementing methodological tools. The Explorers have a distinctive empirical focus, with publications illustrating the implementation of the bases developed by the Precursors and the Engineers in the collection of biographical data to study specific life contexts. All profiles have a singular contribution to the definition of the field’s structure, contents and dynamics in analytical, methodological and conceptual terms; thus, showing the many faces of biographical research.

What Is Refractory Organic Matter in the Ocean?

About 20% of the organic carbon produced in the sunlit surface ocean is transported into the ocean’s interior as dissolved, suspended and sinking particles to be mineralized and sequestered as dissolved inorganic carbon (DIC), sedimentary particulate organic carbon (POC) or “refractory” dissolved organic carbon (rDOC). Recently, the physical and biological mechanisms associated with the particle pumps have been revisited, suggesting that accepted fluxes might be severely underestimated (Boyd et al., 2019; Buesseler et al., 2020). Perhaps even more poorly understood are the mechanisms driving rDOC production and its potential accumulation in the ocean. On the basis of recent conflicting evidence about the relevance of DOC degradation in the deep ocean, we revisit the concept of rDOC in terms of its “refractory” nature in order to understand its role in the global carbon cycle. Here, we address the problem of various definitions and approaches used to characterize rDOC (such as turnover time in relation to the ocean transit time, molecule abundance, chemical composition and structure). We propose that rDOC should be operationally defined. However, we recognize there are multiple ways to operationally define rDOC; thus the main focus for unifying future studies should be to explicitly state how rDOC is being defined and the analytical window used for measuring rDOC, rather than adhering to a single operational definition. We also conclude, based on recent evidence, that the persistence of rDOC is fundamentally dependent on both intrinsic (chemical composition and structure, e.g., molecular properties), and extrinsic properties (amount or external factors, e.g., molecular concentrations, ecosystem properties). Finally, we suggest specific research questions aimed at stimulating research on the nature, dynamics, and role of rDOC in Carbon sequestration now and in future scenarios of climate change.

‘Putting heart’ into history and memory: Dialogues with Maya-Tseltal philosopher, Xuno López Intzin

In this article, the author shares her dialogues with the Maya-Tseltal scholar Xuno López Intzin, to open an analytical window to Non-Western conceptions of memory and time. It focuses on the cyclical conceptualization of time, and the embodied experience of history and memory of Maya peoples in the Chiapas Highlands. This Mayan perspective is explained by Xuno López Intzin, in an analytical dialogue with the author, who questions her own linear ethnohistorial perspectives. It aims to contribute to the decolonization of memory studies by giving an academic platform to this subaltern, nonlinear conception of time and history.

An Amplitude- and Frequency- Preserving S Transform

The time–frequency analysis is very useful for attenuation compensation, quality factor Q estimation, anomaly detection, and so on. Among plenty of time–frequency analysis methods, the S transform (ST) and its extensions are widely used because of their self-adjustable flexibility, compared with the short-time Fourier transform and Gabor transform. However, the traditional ST has a poor amplitude-preserving property near the boundary while being implemented in the time domain, because the partition of unity cannot be guaranteed. Besides, the frequency distribution biases the actual Fourier spectrum because of the linear-frequency-dependent term in the analytical window, which can decrease the accuracy of attenuation estimation. To preserve the amplitude and frequency, a new analytical window is designed, and the corresponding comprehensive window is derived in the time domain. The frequency-domain formulae are derived in detail for an efficient implementation, in which the time-domain convolution is achieved through multiplication. Numerical examples on the synthetic layered model and pseudorandom time series demonstrate the validity of the proposed method in amplitude- and frequency-preserving quantitatively. Examples at a well location of field data further demonstrate its frequency-preserving property qualitatively. Furthermore, the proposed method can have wide applications in exploration geophysics, seismology, or signal analysis fields, combining with the synchrosqueezing transform.

Introduction: Political Demography as an Analytical Window on our World

Introduction: Political Demography as an Analytical Window on our World