The influence of matrix concentration and solvent composition on the results of MALDI MSI, with the aid of wetā€interface matrix deposition

Journal of Mass Spectrometry

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The influence of matrix concentration and solvent composition on the results of MALDI MSI, with the aid of wetā€interface matrix deposition

Abstract

Imaging mass spectrometry is a powerful technique for the molecular analysis of tissue sections. As in many analytical methods, sample preparation is one of the main and most important steps to obtain results of good quality. Usually, the matrix concentration and solvent composition in different studies are taken for granted without any further consideration. In our studies, we aimed to find how matrix concentration and a type of solvent influence the signal. Moreover, we also aimed to find the relationship between these parameters, how they influence the spectra, and how they influence obtained ion maps. In our experiments, we used SunCollectĀ®, which is a commercially available wet-interface system for matrix deposition. We decided to choose two matrix concentrations (2,5-dihydroxybenzoic acid [DHB]: 15 and 25ā€‰mg/mL; 9-aminoacridine [9AA]: 7 and 5Ā mg/mL) and two different water solutions of solvents in two different percentages for the matrices (DHB: 50% and 70% of methanol [MeOH] and acetonitrile [ACN]; 9AA 70% and 50% of ethanol [EtOH] and MeOH). In the end, the influence of these parameters on obtained spectra and ion maps was assessed.

Przemyslaw Mielczarek,
Piotr Suder,
Igor Kotsan,
Anna Bodzonā€Kulakowska
March 27, 2023
https://onlinelibrary.wiley.com/doi/10.1002/jms.4916?af=R

Quantitative proteomics I.: Concept, design, and planning of quantitative proteomics experiments

Journal of Mass Spectrometry

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Quantitative proteomics I.: Concept, design, and planning of quantitative proteomics experiments

Journal of Mass Spectrometry, Volume 58, Issue 4, April 2023.

Simon SugƔr,
Laszlo Drahos,
Karoly Vekey
March 27, 2023
https://onlinelibrary.wiley.com/doi/10.1002/jms.4907?af=R

Impact of wavelength and spot size on laser depth of focus: Considerations for mass spectrometry imaging of nonā€flat samples

Journal of Mass Spectrometry

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Impact of wavelength and spot size on laser depth of focus: Considerations for mass spectrometry imaging of nonā€flat samples

Abstract

Biospecimens with nearly flat surfaces on a flat stage are typically required for laser-based mass spectrometry imaging (MSI) techniques. However, sampling stages are rarely perfectly level, and accounting for this and the need to accommodate non-flat samples requires a deeper understanding of the laser beam depth of focus. In ablation-based MSI methods, a laser is focused on top of the sample surface, ensuring that the sample is at the focal point or remains within depth of focus. In general, the depth of focus of a given laser is related to the beam quality (M
2) and the wavelength (Ī»). However, because laser is applied on a biological sample, other variables can also impact the depth of focus, which could affect the robustness of the MSI techniques for diverse sample types. When the height of a sample ranges outside of the depth of focus, ablated area and the corresponding ion abundances may vary as well, increasing the variability of results. In this tutorial, we examine the parameters and equations that describe the depth of focus of a Gaussian laser beam. Additionally, we describe several approaches that account for surface roughness exceeding the depth of focus of the laser.

Alena N. Joignant,
Ying Xi,
David C. Muddiman
March 27, 2023
https://onlinelibrary.wiley.com/doi/10.1002/jms.4914?af=R

Localization of cyclopropyl groups and alkenes within glycerophospholipids using gasā€phase ion/ion chemistry

Journal of Mass Spectrometry

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Localization of cyclopropyl groups and alkenes within glycerophospholipids using gasā€phase ion/ion chemistry

Abstract

Shotgun lipid analysis using electrospray ionization tandem mass spectrometry (ESI-MS/MS) is a common approach for the identification and characterization of glycerophohspholipids GPs. ESI-MS/MS, with the aid of collision-induced dissociation (CID), enables the characterization of GP species at the headgroup and fatty acyl sum compositional levels. However, important structural features that are often present, such as carbonā€“carbon double bond(s) and cyclopropane ring(s), can be difficult to determine. Here, we report the use of gas-phase charge inversion reactions that, in combination with CID, allow for more detailed structural elucidation of GPs. CID of a singly deprotonated GP, [GPā€‰āˆ’ā€‰H]āˆ’, generates FA anions, [FAā€‰āˆ’ā€‰H]āˆ’. The fatty acid anions can then react with doubly charged cationic magnesium tris-phenanthroline complex, [Mg(Phen)3]2+, to form charge inverted complex cations of the form [FAā€‰āˆ’ā€‰Hā€‰+ā€‰MgPhen2]+. CID of the complex generates product ion spectral patterns that allow for the identification of carbonā€“carbon double bond position(s) as well as the sites of cyclopropyl position(s) in unsaturated lipids. This approach to determining both double bond and cyclopropane positions is demonstrated with GPs for the first time using standards and is applied to lipids extracted from Escherichia coli.

De’Shovon M. Shenault,
Scott A. McLuckey,
Elissia T. Franklin
March 27, 2023
https://onlinelibrary.wiley.com/doi/10.1002/jms.4913?af=R

Improved whole rock low detection limit gold analysis by LA-ICP-MS utilizing pressed-powder-pellets

International Journal of Mass Spectrometry

ScienceDirect Publication: International Journal of Mass Spectrometry

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Improved whole rock low detection limit gold analysis by LA-ICP-MS utilizing pressed-powder-pellets

Publication date: June 2023

Source: International Journal of Mass Spectrometry, Volume 488

Author(s): C.G.C. Patten, A. Beranoaguirre, S. Hector, D. Gudelius, J. Kolb, E. Eiche

March 26, 2023
https://www.sciencedirect.com/science/article/pii/S1387380623000301?dgcid=rss_sd_all

Ultraā€low current electrospray ionization of chloroform solution for the analysis of perfluorinated sulfonic acids

Rapid Communications in Mass Spectrometry

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Ultraā€low current electrospray ionization of chloroform solution for the analysis of perfluorinated sulfonic acids

Rationale

Femtoamp and picoamp electrospray ionization (ESI) characteristics of a nonpolar solvent were explored. The direct ESI mass spectrometry analysis of chloroform extract solution enabled rapid analysis of perfluorinated sulfonic acid analytes in drinking water.

Methods

Neat chloroform solvent and extracts were directly used in a typical wire-in ESI setup using micrometer emitter tips. Ionization currents were measured with femtoamp sensitivity while ramping the spray voltage from 0 to āˆ’5000ā€‰V. Methanol was used as a comparison to illustrate theĀ characteristics of electrospraying chloroform. The effects of spray voltage and inlet temperature were studied. A liquidā€“liquid extraction workflow was developed to analyze perfluorooctanoate sulfonate (PFOS) in drinking water using an ion-trap mass spectrometer.

Results

The ionization onset of chloroform solution was 41ā€‰Ā±ā€‰17ā€‰fA at 300ā€‰V. The ionization current gradually increased with voltage while remaining below 100ā€‰pA when using voltages up to āˆ’5000ā€‰V. The ion signal of PFOS was significantly enhanced to improve the limit of detection (LoD) to 25ā€‰ppt in chloroform. Coupled with a liquidā€“liquid extraction workflow, LoD of 0.38ā€“5.1Ā ppt and a quantitation range of 5ā€“400ā€‰ppt were achieved for perfluorinated sulfonic compounds in 1-ml water samples.

Conclusions

Femtoamp and picoamp modes expand the solvent compatibility range of ESI and can enable quantitative analysis in parts per trillion (ppt) concentrations.

Taoqing Wang,
Huishan Li,
Nicholas Allen,
Ian Ferraro,
Anyin Li
March 26, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9501?af=R

Equilibrium isotope fractionation factors of H exchange between steam and soil clay fractions

Rapid Communications in Mass Spectrometry

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Equilibrium isotope fractionation factors of H exchange between steam and soil clay fractions

Rationale

Steam equilibration overcomes the problem of the traditional measurements of H isotope compositions, which leave an arbitrary amount of adsorbed water in the sample, by controlling for the entire exchangeable H pool, including adsorbed water and hydroxyl-H. However, the use of steam equilibration to determine nonexchangeable stable H isotope compositions in environmental media (expressed as Ī“
2Hn values) by mathematically eliminating the influence of exchangeable H after sample equilibration with waters of known H-isotopic composition requires the knowledge of the equilibrium isotope fractionation factor between steam-H and exchangeable H of the sample (Ī±ex-w), which is frequently unknown.

Methods

We developed a new method to determine the Ī±ex-w values for clay minerals, topsoil clay fractions, and mica by manipulating the contributions of exchangeable H to the total H pool via different degrees of post-equilibration sample drying. We measured the Ī“
2H values of steam-equilibrated mineral and soil samples using elemental analyzer-pyrolysis-isotope ratio mass spectrometry.

Results

The Ī±ex-w values of seven clay minerals ranged from 1.071 to 1.140, and those of 19 topsoil clay fractions ranged from 0.885 to 1.216. The Ī±ex-w value of USGS57 biotite, USGS58 muscovite, and of cellulose was 0.965, 0.871, and 1.175, respectively. The method did not work for kaolinite, because its small exchangeable H pool did not respond to the selected drying conditions. Structurally different mineral groups such as two- and three-layer clay minerals or mica showed systematically different Ī±ex-w values. The Ī±ex-w value of the topsoil clay fractions correlated with the soil clay content (rĀ =Ā 0.63, PĀ =ā€‰0.004), the local mean annual temperature (rā€‰=ā€‰0.68, PĀ =ā€‰0.001), and the Ī“
2H values of local precipitation (rā€‰=ā€‰0.72, PĀ <ā€‰0.001), likely to reflect the different clay mineralogy under different weathering regimes.

Conclusions

Our new Ī±ex-w determination method yielded realistic results in line with the few previously published values for cellulose. The determined Ī±ex-w values were similar to the widely assumed values of 1.00ā€“1.08 in the literature, suggesting that the adoption of one of these values in steam equilibration approaches is appropriate.

Stefan Merseburger,
Arnim Kessler,
Yvonne Oelmann,
Wolfgang Wilcke
March 26, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9499?af=R

Inadequate Definition of the Limit of Quantification Applied for the Quantification of Perfluoroalkyl Substances in Food by LCā€MS/MS May Compromise the Reliability of the Data Requested by the European Regulation

Rapid Communications in Mass Spectrometry

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Inadequate Definition of the Limit of Quantification Applied for the Quantification of Perfluoroalkyl Substances in Food by LCā€MS/MS May Compromise the Reliability of the Data Requested by the European Regulation

Liquid chromatography tandem mass spectrometry (LC-MS/MS) is a widespread technology used for the quantitative determination of per- and polyfluoroalkyl substances (PFAS) in foodstuffs. Specifically, LC-MS/MS offers attractive performance combining the sensitivity and selectivity required by the European Union for testing perfluorooctane sulfonic acid (PFOS), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA) and perfluorohexane sulfonic acid (PFHxS) with maximum limits of quantification (LOQs) in the sub part-per-billion (Ī¼g/kg) or the part-per-trillion (ng/kg) domains. In this article we highlight the important diversity in LOQ definitions applied in LC-MS/MS methods described in the literature that raise concerns about the capability of some of those to generate reliable data requested by the European regulation. Here, we point the risk of false response or misquantification if criteria for assessing LOQ suffer from a lack of rigor. We emphasize the need to use PFAS-free samples spiked with the analyte(s) of interest and the application of identification criteria according to official documents for a sound measurement of the LOQ.

Thierry Delatour,
Xanthippe Theurillat,
BjĆørn Eriksen,
Claudia Mujahid,
Pascal Mottier
March 26, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9507?af=R

Rapid onā€site detection of persistent organic pollutants using multiā€walled carbon nanotubeā€modified paper spray ionization and a miniature mass spectrometer

Rapid Communications in Mass Spectrometry

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Rapid onā€site detection of persistent organic pollutants using multiā€walled carbon nanotubeā€modified paper spray ionization and a miniature mass spectrometer

RATIONALE

Rapid on-site detection of persistent organic pollutants (POPs) is highly desirable for environmental protection.

METHODS

Herein, a rapid on-site analytical workflow was developed for the investigation of polycyclic aromatic hydrocarbons (PAHs) and perfluorinated compounds (PFCs) using multi-walled carbon nanotube (MWCNT)-modified paper spray ionization (PSI) coupled with a miniature ion trap mass spectrometer. Critical parameters regarding PSI and miniature mass spectrometry analysis were optimized.

RESULTS

The analytical performance of the developed method was evaluated under optimized conditions, obtaining a short analysis duration of less than 1 min, sufficient linearity with correlation coefficients greater than 0.99, acceptable recovery rates of 93.1ā€“105.8% with relative standard deviations of between 3.5ā€“10.3%, and reasonable sensitivity with limits of detection and quantitation of 2ā€“200 Ī¼g/L and 5ā€“500 Ī¼g/L, respectively.

CONCLUSIONS

Considering these aspects, the present approach demonstrated a promising solution for rapid on-site detection of emerging POPs.

Xiangyu Guo,
Junfang Li,
Hua Bai,
Qiang Ma
March 26, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9509?af=R

EIā€MS fragmentation routes of CWCā€related organoarsenic compounds: The electron ionization and DFT studies

Rapid Communications in Mass Spectrometry

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EIā€MS fragmentation routes of CWCā€related organoarsenic compounds: The electron ionization and DFT studies

RATIONALE

For unambiguous identification of Chemical Weapons Convention-related chemicals in environmental and biological samples, access to mass spectra and expertise in spectral interpretation is required. As of today, there is no mass spectrum available for dialkyl alkylarsonodithioites in the literature. Therefore, it is essential to obtain spectral information about these compounds.

METHODS

The CWC-related organoarsenic compounds were synthesized and analyzed by GC-MS, and their retention index (RI) was calculated by Van Den Dool’s method. The relationship between RI and DFT-calculated polarizability (āŗ) and molecular weight was also studied. Electron ionization (EI) mode was used to investigate the general fragmentation patterns of the synthesized compounds. A DFT analysis of some major fragment ions was performed in order to confirm the fragmentation pathways.

RESULTS

A linear relationship between RI and āŗ is observed. The mass spectra of compounds 5-7 are affected by alkyl groups on sulfur and arsenic atom. The molecular ion of compounds 5-7 can be observed in their EI-MS with relatively good abundance. EI-MS studies revealed some interesting fragmentation pathways, such as the formation of arsenic analogue of benzilic and tropylium in EI-MS of chemicals 6.

CONCLUSIONS

By analyzing the mass spectra and RI values, it is possible to detect CWC-related chemicals in aqueous, blood, and urine samples during an on-site or off-site inspection.

Masomeh Eskandari,
Sajjad Mousavi Faraz,
Seyed Esmaeil Hosseini,
Shahram Moradi,
Hamid Saeidian
March 26, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9511?af=R

Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Likelihood-ratio test statistic for the finite-sample case in nonlinear ordinary differential equation models

Likelihood ratios are frequently utilized as basis for statistical tests, for model selection criteria and for assessing parameter and prediction uncertainties, e.g. using the profile likelihood. However, translating these likelihood ratios into p-values or confidence intervals requires the exact form of the test statistic’s distribution. The lack of knowledge about this distribution for nonlinear ordinary differential equation (ODE) models requires an approximation which assumes the so-called asymptotic setting, i.e. a sufficiently large amount of data. Since the amount of data from quantitative molecular biology is typically limited in applications, this finite-sample case regularly occurs for mechanistic models of dynamical systems, e.g. biochemical reaction networks or infectious disease models. Thus, it is unclear whether the standard approach of using statistical thresholds derived for the asymptotic large-sample setting in realistic applications results in valid conclusions. In this study, empirical likelihood ratios for parameters from 19 published nonlinear ODE benchmark models are investigated using a resampling approach for the original data designs. Their distributions are compared to the asymptotic approximation and statistical thresholds are checked for conservativeness. It turns out, that corrections of the likelihood ratios in such finite-sample applications are required in order to avoid anti-conservative results.
ToĢˆnsing, C., Steiert, B., Timmer, J., Kreutz, C.
March 26, 2023
http://biorxiv.org/cgi/content/short/2023.03.25.534223v1?rss=1

Clonal differences underlie variable responses to sequential and prolonged treatment

BioRxiv

bioRxiv Subject Collection: Systems Biology
This feed contains articles for bioRxiv Subject Collection "Systems Biology"

Clonal differences underlie variable responses to sequential and prolonged treatment

Cancer cells exhibit dramatic differences in gene expression at the single-cell level which can predict whether they become resistant to treatment. Treatment perpetuates this heterogeneity, resulting in a diversity of cell states among resistant clones. However, it remains unclear whether these differences lead to distinct responses when another treatment is applied or the same treatment is continued. In this study, we combined single-cell RNA-sequencing with barcoding to track resistant clones through prolonged and sequential treatments. We found that cells within the same clone have similar gene expression states after multiple rounds of treatment. Moreover, we demonstrated that individual clones have distinct and differing fates, including growth, survival, or death, when subjected to a second treatment or when the first treatment is continued. By identifying gene expression states that predict clone survival, this work provides a foundation for selecting optimal therapies that target the most aggressive resistant clones within a tumor.
Schaff, D. L., Fasse, A. J., White, P. E., Vander Velde, R. J., Shaffer, S. M.
March 26, 2023
http://biorxiv.org/cgi/content/short/2023.03.24.534152v1?rss=1

Mathematical models disentangle the role of IL-10 feedbacks in human monocytes upon proinflammatory activation

BioRxiv

bioRxiv Subject Collection: Systems Biology
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Mathematical models disentangle the role of IL-10 feedbacks in human monocytes upon proinflammatory activation

Inflammation is one of the vital mechanisms through which the immune system responds to harmful stimuli. During inflammation, pro and anti-inflammatory cytokines interplay to orchestrate fine-tuned, dynamic immune responses. The cytokine interplay governs switches in the inflammatory response and dictates the propagation of inflammation. Molecular pathways underlying the interplay are complex, and time-resolved monitoring of mediators and cytokines is necessary as a basis to study them in detail. Our understanding can be advanced by in silico models which enable to analyze the system of interactions and their dynamical interplay in detail. We, therefore, used a mathematical modeling approach to study the interplay between prominent pro and anti-inflammatory cytokines with a focus on Tumor Necrosis Factor (TNF) and Interleukin 10 (IL-10) in lipopolysaccharide (LPS)-primed primary human monocytes. Relevant time-resolved data were generated by experimentally adding or blocking IL-10 at different time points. The model was successfully trained and could predict independent validation data and was further used to perform in silico experiments to disentangle the role of IL-10 feedbacks in acute inflammation. We used the insight to obtain a reduced predictive model including only the necessary IL-10-mediated feedbacks. Finally, the validated reduced model was used to predict early IL-10 – TNF switches in the inflammatory response. Overall, we gained detailed insights into fine-tuning of inflammatory responses in human monocytes and present a model for further use in studying the complex and dynamic process of cytokine-regulated acute inflammation.
Nikaein, N., Tuerxun, K., Cedersund, G., Eklund, D., Kruse, R., Sarndahl, E., Nanberg, E., Thonig, A., Repsilber, D., Persson, A., Nyman, E., X-HiDE Consortium
March 26, 2023
http://biorxiv.org/cgi/content/short/2023.03.24.533939v1?rss=1

High versatility to meet conservation targets for biodiversity and hydrological services at the Riviera Maya, Quintana Roo, Mexico

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bioRxiv Subject Collection: Systems Biology
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High versatility to meet conservation targets for biodiversity and hydrological services at the Riviera Maya, Quintana Roo, Mexico

The ecosystem services (ES) framework has been proposed as an alternative to face the multiple challenges presented by biodiversity conservation, but the spatial conservation priorities of ES have been found to show low concordance levels with areas of high importance for biodiversity, which can lead to conflict during reserve design. To address this problem, the use of quantitative methods derived from systematic conservation planning has been proposed to identify spatial solutions that achieve the simultaneous representation of both elements in a spatially efficient manner. The aim of this study is to evaluate the differences between priority sites for biodiversity and hydrological ecosystem services (HES) using spatial prioritization models and to identify opportunities for co-benefits that allow an efficient conservation planning proposal, using as a case study the Riviera Maya, Mexico. The following hypothesis were tested by comparing models based on the prioritization algorithm Marxan: (1) Priority sites for biodiversity and HES are different, (2) HES priority sites adequately represent biodiversity conservation targets, and (3) integrating HES and biodiversity into one model is more efficient for representing conservation targets than combining the individual models for both elements. The results confirm: (1) Biodiversity and HES priority sites have different spatial patterns, sharing only 24% of priority sites, (2) HES priority sites achieve a high percentage (95%) of biodiversity conservation targets, showing that they can potentially be used for biodiversity representation, and (3) integrating HES and biodiversity into one model is more efficient to represent conservation targets than considering both elements individually (46% vs 66% of the study area). As there are no irreplaceable sites for biodiversity conservation, and less than 8% of the study area is covered by protected areas, there are clearly opportunities to align biodiversity and HES conservation actions at the Riviera Maya, Mexico. Despite the high context dependency of the spatial distribution of priority sites for biodiversity and HES, this study shows that the integration of conservation targets of both in the planning process can provide a solution to represent a high number of biodiversity and HES conservation targets.
Aguilar-Sanchez, J. A., Kolb, M.
March 26, 2023
http://biorxiv.org/cgi/content/short/2023.03.23.533929v1?rss=1

Genetic and dietary modulators of the inflammatory response in the gastro-intestinal tract of the BXD mouse genetic reference population

BioRxiv

bioRxiv Subject Collection: Systems Biology
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Genetic and dietary modulators of the inflammatory response in the gastro-intestinal tract of the BXD mouse genetic reference population

Inflammatory gut disorders, including inflammatory bowel disease (IBD), can be impacted by dietary, environmental and genetic factors. While the incidence of IBD is increasing worldwide, we still lack a complete understanding of the gene-by-environment interactions underlying inflammation and IBD. Here, we profiled the colon transcriptome of 52 BXD mouse strains fed with a chow or high-fat diet (HFD) and identified a subset of BXD strains that exhibit an IBD-like transcriptome signature on HFD, indicating that an interplay of genetics and diet can significantly affect intestinal inflammation. Using gene co-expression analyses, we identified modules that are enriched for IBD-dysregulated genes and found that these IBD-related modules share cis-regulatory elements that are responsive to the STAT2, SMAD3, and REL transcription factors. We used module quantitative trait locus (ModQTL) analyses to identify genetic loci associated with the expression of these modules. Through a prioritization scheme involving systems genetics in the mouse and integration with external human datasets, we identified Muc4 and Epha6 as the top candidates mediating differences in HFD-driven intestinal inflammation. This work provides insights into the contribution of genetics and diet to IBD risk and identifies two candidate genes, MUC4 and EPHA6, that may mediate IBD susceptibility in humans.
Li, X., Morel, J.-D., Benegiamo, G., Poisson, J., Bachmann, A., Rapin, A., Williams, E. G., Perino, A., Schoonjans, K., Bou Sleiman, M. S., Auwerx, J.
March 26, 2023
http://biorxiv.org/cgi/content/short/2023.03.22.533818v1?rss=1

DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspaseā€9 inhibition in chondrogenic cells

Proteomics (Wiley)

Wiley: PROTEOMICS: Table of Contents

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DiaPASEF proteotype analysis indicates changes in cell growth and metabolic switch induced by caspaseā€9 inhibition in chondrogenic cells

Abstract

Caspase-9 is the major apical caspase responsible for triggering the intrinsic apoptotic pathway. Our previous study indicated that specific inhibition of caspase-9 caused microscopically evident alterations in appearance of the primary chondrogenic cultures which cannot be explained by decrease in apoptosis. To describe a complex molecular background of this effect, proteomics analysis of control and caspase-9 inhibitor-treated chondrogenic cultures was performed. Proteins were extracted, identified and quantified using LC-MS in both data dependent and data independent acquisition (DIA) mode. While directDIA analysis of diaPASEF data obtained using timsTOF Pro LC-MS system revealed 7849 protein groups (Qvalue<0.01), a parallel analysis of iTRAQ-2DLC-MS3 and conventional DIA-MS data identified only 5146 and 4098 protein groups, respectively, showing diaPASEF a superior method for the study. The detailed analysis of diaPASEF data disclosed 236/551 significantly down-/up- regulated protein groups after caspase-9 inhibition, respectively (|log2FC|>0.58, Qvalue<0.05). Classification of downregulated proteins revealed changes in extracellular matrix organization, collagen metabolism, and muscle system processes. Moreover, deregulations suggest a switch from glycolytic to lipid based metabolism in the inhibited cells. No essential changes were found in the proteins involved in apoptosis. The data indicate new non-apoptotic participation of caspases in chondrocyte homeostasis with potential applications in cartilage pathophysiology.

This article is protected by copyright. All rights reserved

Petr Lapcik,
Barbora Vesela,
David Potesil,
Katerina Dadakova,
Martina Zapletalova,
Petr Benes,
Pavel Bouchal,
Eva Matalova
March 25, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200408?af=R

Proteins and metabolites fingerprints of gestational diabetes mellitus forming proteinā€“metabolite interactomes are its potential biomarkers

Proteomics (Wiley)

Wiley: PROTEOMICS: Table of Contents

Table of Contents for PROTEOMICS. List of articles from both the latest and EarlyView issues.

Proteins and metabolites fingerprints of gestational diabetes mellitus forming proteinā€“metabolite interactomes are its potential biomarkers

Abstract

Gestational diabetes mellitus (GDM) is a consequence of glucose intolerance with an inadequate production of insulin that happens during pregnancy and leads to adverse health consequences for both mother and fetus. GDM patients are at higher risk for preeclampsia, and developing diabetes mellitus type 2 in later life, while the child born to GDM mothers are more prone to macrosomia, and hypoglycemia. The universally accepted diagnostic criteria for GDM are lacking, therefore there is a need for a diagnosis of GDM that can identify GDM at its early stage (first trimester). We have reviewed the literature on proteins and metabolites fingerprints of GDM. Further, we have performed proteinā€“protein, metaboliteā€“metabolite, and proteinā€“metabolite interaction network studies on GDM proteins and metabolites fingerprints. Notably, some proteins and metabolites fingerprints are forming strong interaction networks at high confidence scores. Therefore, we have suggested that those proteins and metabolites that are forming proteinā€“metabolite interactomes are the potential biomarkers of GDM. The proteinā€“metabolite biomarkers interactome may help in a deep understanding of the prognosis, pathogenesis of GDM, and also detection of GDM. The proteinā€“metabolites interactome may be further applied in planning future therapeutic strategies to promote long-term health benefits in GDM mothers and their children.

Bhaswati Chatterjee,
Suman S. Thakur
March 25, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200257?af=R

From the Laboratory to the Field: Chemical Analysis of Colored Smoke Pyrotechnic Formulations via Mass Spectrometry Techniques

Journal of Mass Spectrometry

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From the Laboratory to the Field: Chemical Analysis of Colored Smoke Pyrotechnic Formulations via Mass Spectrometry Techniques

Abstract

Smoke dyes are complex molecular systems that have the potential to form many molecular derivatives and fragments when deployed. The chemical analysis of smoke samples is challenging due to the adiabatic temperature of the pyrotechnic combustion and the molecular complexity of the physically dispersed reaction products. Presented here is the characterization of the reaction byproducts of a simulant Mk124 smoke signal on a multigram scale, which contain the dye disperse red 9 (1-(methylamino)anthraquinone), by ambient ionization mass spectrometry. Our previous work has examined the thermal decomposition of a simplified smoke system consisting of disperse red 9, potassium chlorate, and sucrose by anaerobic pyrolysis gas chromatography mass spectrometry performed at the laboratory milligram scale. The results from the lab scale test were compared to a fully functioned Mk124 in the field. To achieve this, Mk124 smokes were functioned in the presence of sampling swabs that collected byproduct residues from the smoke plume in the ambient environment. These swabs were then analyzed using ambient ionization mass spectrometry to identify the expended pyrotechnic residues, with particular interest in halogenated species. Previous work determined the toxicity of unforeseen byproducts identified on the laboratory scale, which were also detected in the field demonstrating the correlation of the laboratory testing to the fielded systems. By understanding the chemical composition of smokes and their reaction products, potential toxicity effects can be easily assessed, leading to safer formulations with improved performance. These results can help assess how smoke byproducts may impact Warfighter performance, personnel health, and the environment.

Patrick W. Fedick,
Kelly M. Thoreson,
Benjamin P. Wilkins,
Douglas M. Papenmeier,
Brian C. Bohrer,
Jonathan M. Dilger
March 25, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jms.4917?af=R

Editorial from Dominic M. Desiderio

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

Table of Contents for Mass Spectrometry Reviews. List of articles from both the latest and EarlyView issues.

Editorial from Dominic M. Desiderio

Mass Spectrometry Reviews, EarlyView.

Dom Desiderio
March 25, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21840?af=R

Innovations in Applications of Mass Spectrometry Impact Many Fields of Science.

Mass Spectrometry Reviews

Wiley: Mass Spectrometry Reviews: Table of Contents

Table of Contents for Mass Spectrometry Reviews. List of articles from both the latest and EarlyView issues.

Innovations in Applications of Mass Spectrometry Impact Many Fields of Science.

Abstract

I am pleased and honored that Dan Fabris has organized this special issue of reviews that reflect many of my research interests. I have been a member of the Editorial Advisory Board of Mass Spectrometry Reviews since 1994 and I regard reviews as an important component of the scientific method. Well done, they collect and integrate knowledge in a particular field and construct a factual foundation that directs and supports the next research frontier.

This article is protected by copyright. All rights reserved.

Catherine Fenselau Cotter
March 25, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21839?af=R