Automated desorption electrospray ionization two-dimensional tandem mass spectrometry: Instrumentation and software for high throughput analysis

International Journal of Mass Spectrometry

ScienceDirect Publication: International Journal of Mass Spectrometry

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Automated desorption electrospray ionization two-dimensional tandem mass spectrometry: Instrumentation and software for high throughput analysis

Publication date: April 2023

Source: International Journal of Mass Spectrometry, Volume 486

Author(s): Eric T. Dziekonski, Thomas C. Sams, Lucas J. Szalwinski, L. Edwin Gonzalez, R. Graham Cooks

February 15, 2023
https://www.sciencedirect.com/science/article/pii/S1387380623000143?dgcid=rss_sd_all

Study of emerging chicken meat quality defects using OMICs: What do we know?

Journal of Proteomics

ScienceDirect Publication: Journal of Proteomics

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Study of emerging chicken meat quality defects using OMICs: What do we know?

Publication date: 30 March 2023

Source: Journal of Proteomics, Volume 276

Author(s): Xue Zhang, Sawyer Wyatt Smith, Lizzie R. Zaldivar, Dylan J. Lesak, M. Wes Schilling

February 15, 2023
https://www.sciencedirect.com/science/article/pii/S187439192300026X?dgcid=rss_sd_all

Identification of chemical constituents in pomegranate seeds based on ultra‐high‐performance supercritical fluid chromatography coupled with quadrupole time‐of‐flight mass spectrometry

Rapid Communications in Mass Spectrometry

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Identification of chemical constituents in pomegranate seeds based on ultra‐high‐performance supercritical fluid chromatography coupled with quadrupole time‐of‐flight mass spectrometry

Pomegranate seeds are a potential source of bioactive compounds. Nonetheless, most pomegranate seeds are discarded in the food processing industry, likely due to the lack of convincing data on their component analysis.

Methods

To reveal the main chemical constituents of pomegranate seeds, a reliable and sensitive method based on ultra-high-performance supercritical fluid chromatography coupled with electrospray ionization and quadrupole time-of-flight mass spectrometry (MS) was developed. A time-dependent MSE data acquisition mode was applied to acquire the mass spectrometric data. The chemical constituents were identified by an automatic retrieval of a traditional Chinese medicine library and relevant literature.

Results

A total number of 59 compounds, including fatty acids, sterols, vitamins, cerebrosides, phospholipids, flavonoids, phenylpropanoids, and others, were tentatively identified. Their possible fragmentation pathways and characteristic ions were proposed and elucidated.

Conclusions

The findings of this study, along with the developed methodology, could provide a reference for basic research on the pharmacodynamic substances of pomegranate seeds and shed light on their potential nutritional and therapeutic applications in the future.

Guoping Li,
Jing Chen,
Qing Yang,
Xuexin Yang,
Penglong Wang,
Haimin Lei,
Ma Mi,
Qiang Ma
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9482?af=R

Rapid Screening of High Priority N‐Nitrosamines in Pharmaceutical, Forensic, and Environmental Samples with PSI‐MS and FCSI‐MS

Rapid Communications in Mass Spectrometry

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Rapid Screening of High Priority N‐Nitrosamines in Pharmaceutical, Forensic, and Environmental Samples with PSI‐MS and FCSI‐MS

Rationale

The burgeoning concern of N-nitrosamine (NAM) contamination found in various pharmaceutical compositions has increased the demand for rapid and reliable screening methods to better assess the breadth of the problem. These carcinogenic compounds are also found in food, water, and soil, and they have been used in poison-related homicides.

Methods

A combination of complementary, ambient ionization methods, paper spray ionization (PSI) and filter cone spray ionization-mass spectrometry (FCSI-MS), was characterized towards trace-level residue screening of select NAMs (e.g., NDMA, NDEA, NDBA) directly from complex and problematic matrices of interest, including prescription and OTC tablets, drinking water, soil, and consumable goods. Spectral data for analyte confirmation and detection limit studies were collected on a Thermo LCQ Fleet ion trap mass spectrometer.

Results

PSI-MS and FCSI-MS readily produced mass spectral data marked by its simplicity (e.g., predominantly protonated molecular ions observed) and congruence with traditional ESI-MS spectra in under 2 minutes/sample. Both methods proved robust to the complex matrices tested, yielding ion signatures for target NAMs, as well as active pharmaceutical ingredients (APIs) for analyzed tablets, flavorants inherent to food products, etc. Low part-per-million (ppm) detection limits were observed but were shown dependent on sample composition.

Conclusions

PSI-MS and FCSI-MS were successful in detecting trace-level NAMS in complex liquid- and solid-phase matrices with little to no prior preparation. This work suggests that these methodologies can provide a means for assessing problematic pharmaceutical adulterants/degradants for expedited quality control, as well as enhancing environmental stewardship efforts and forensic investigations.

Trevor J. McDaniel,
Jessica M. Holtz,
Ebenezer H. Bondzie,
Makoy Overfelt,
Patrick W. Fedick,
Christopher C. Mulligan
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9493?af=R

Geolocator tracking seabird migration and moult reveal large‐scale temperature‐driven isoscapes in the NE Atlantic

Rapid Communications in Mass Spectrometry

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Geolocator tracking seabird migration and moult reveal large‐scale temperature‐driven isoscapes in the NE Atlantic

RATIONALE

By combining precision satellite-tracking with blood sampling it has been possible to use seabirds to validate marine carbon and nitrogen isoscapes, but it is unclear whether a comparable approach using low precision light-level geolocators (GLS) and feather sampling can be similarly effective.

METHODS

Here we used GLS to identify wintering areas of northern gannets Morus bassanus and sampled winter grown feathers (confirmed from image analysis of non-breeding birds) to test for spatial gradients in Γ13C and Γ15N in the NE Atlantic.

RESULTS

By matching winter-grown feathers with non-breeding location of tracked birds we found latitudinal gradients in Γ13C and Γ15N in neritic waters. Moreover, isotopic patterns were best explained by sea surface temperature. Similar isotope gradients were found in fish muscle sampled at local ports.

CONCLUSIONS

Our study reveals the potential of using seabird GLS and feathers to reconstruct large scale isotopic patterns.

Kelly Atkins,
Stuart Bearhop,
Thomas W. Bodey,
W. James Grecian,
Keith Hamer,
Jorge M. Pereira,
Hannah Meinertzhagen,
Chris Mitchell,
Greg Morgan,
Lisa Morgan,
Jason Newton,
Richard B. Sherley,
Stephen C. Votier
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9489?af=R

The acquisition of thin sections of aƧaƭ (Euterpe oleracea Mart.) seed with elevated potassium content for molecular mapping by mass spectrometry imaging

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The acquisition of thin sections of aƧaƭ (Euterpe oleracea Mart.) seed with elevated potassium content for molecular mapping by mass spectrometry imaging

Rationale

Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) of tissues became popular in the last decade. Consequently, adapting sample preparation methods for different materials turned out to be a pivotal step for successful analysis due to the requirement of sample slices of 12–20 μm thickness. However, acquiring thin sections compatible with MALDI-IMS for unusual samples is challenging, as existing histological protocols may not be suitable, thus requiring new methods. AƧaĆ­ (Euterpe oleracea Mart.) seed is an example of a challenging material due to its toughness and resistance to crack, therefore our goal was to develop a methodology to obtain thin (12–20 μm) and entire sections of aƧaĆ­ seeds for MALDI-IMS analysis.

Methods

Different strategies were evaluated for obtaining thin sections of seeds, and the combination of the following steps was found to be the most suitable option: (i) softening of seeds by water immersion for 24 h; (ii) transversal cut of seeds to obtain half-seeds using a razor blade and a hammer; (iii) half-seeds imbibition in gelatin; (iv) samples sectioning using a cryostat at āˆ’20°C to obtain samples with 12–20 μm thickness; (v) collection of samples in an indium tin oxide-coated glass slide covered by double-sided copper tape to avoid sample wrapping and ensure adhesion after unfreezing; and (vi) storage of samples in a āˆ’80°C freezer, if necessary.

Results

This adapted sample preparation method enabled the analysis of aƧaƭ seeds by MALDI-IMS, providing spatial distribution of carbohydrates in the endosperm.

Conclusions

The adaptations developed for sample preparation will help investigate the metabolic and physiological properties of aƧaƭ seeds in future studies.

Felipe Lopes Brum,
Gabriel R. Martins,
Ronaldo Mohana‐Borges,
Ayla Sant’Ana da Silva
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9474?af=R

Metabolic study of selective androgen receptor modulator LY2452473 in thoroughbred horses for doping control

Rapid Communications in Mass Spectrometry

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Metabolic study of selective androgen receptor modulator LY2452473 in thoroughbred horses for doping control

RATIONALE

Since 2010, there has been an increasing number of adverse analytical findings related to selective androgen receptor modulators (SARMs) in competitive sports. It emphasizes the importance of comprehensive doping control analytical procedures that are capable of detecting SARM misuse.

METHODS

In this study, it is described how LY2452473, a selective androgen receptor modulator (SARM), was metabolized in thoroughbred horses after a single dose oral administration and in vitro with equine liver microsome preparations. An investigation of the metabolism of LY2452473 in horses’ urine, plasma, and hair matrices was carried out during the study. The plausible structures of the detected metabolites were postulated using high performance liquid chromatography-high resolution mass spectrometry.

RESULTS

Under the experimental conditions fifteen metabolites (twelve phase I, and three conjugates of phase I metabolites) were detected (M1–M15). The major phase I metabolites identified were formed by hydroxylation. Side chain dissociated and methylated metabolites were also detected. In phase II, the glucuronic acid and sulfonic acid conjugates of hydroxy LY2452473 were detected as the major metabolites. In vitro analysis has confirmed the presence of all metabolites found in vivo except for the methylated analogs M11 and M12. A peak concentration of LY2452473 (0.5 pg/mg) in proximal hair segments was achieved four weeks after administration, according to hair analysis.

CONCLUSIONS

Data obtained will aid in identifying LY2452473 and related substances faster, furthermore, the results will assist in checking for the illegal use of these substances in competitive sports.

Tajudheen K. Karatt,
M. Anwar Sathiq,
Saraswathy Laya,
Abdul Khader Karakka Kal,
Michael Benedict Subhahar,
Muhammed Ajeebsanu M.P,
Moses Philip,
Fatma Mohammed Graiban,
Marina Rodriguez Caveney
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/rcm.9491?af=R

Mass spectrometry analysis of phosphotyrosine‐containing proteins

Mass Spectrometry Reviews

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Mass spectrometry analysis of phosphotyrosine‐containing proteins

Abstract

Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.

Jiajia Li,
Xianquan Zhan
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21836?af=R

Recent developments and applications of selected ion flow tube mass spectrometryĀ (SIFT‐MS)

Mass Spectrometry Reviews

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Recent developments and applications of selected ion flow tube mass spectrometryĀ (SIFT‐MS)

Abstract

Selected ion flow tube mass spectrometryĀ (SIFT-MS) is now recognized as the most versatile analytical technique for the identification and quantification of trace gases down to the parts-per-trillion by volume, pptv, range. This statement is supported by the wide reach of its applications, from real-time analysis, obviating sample collection of very humid exhaled breath, to its adoption in industrial scenarios for air quality monitoring. This review touches on the recent extensions to the underpinning ion chemistry kinetics library and the alternative challenge of using nitrogen carrier gas instead of helium. The addition of reagent anions in the Voice200 series of SIFT-MS instruments has enhanced the analytical capability, thus allowing analyses of volatile trace compounds in humid air that cannot be analyzed using reagent cations alone, as clarified by outlining the anion chemistry involved. Case studies are reviewed of breath analysis and bacterial culture volatile organic compoundĀ (VOC), emissions, environmental applications such as air, water, and soil analysis, workplace safety such as transport container fumigants, airborne contamination in semiconductor fabrication, food flavor and spoilage, drugs contamination and VOC emissions from packaging to demonstrate the stated qualities and uniqueness of the new generation SIFT-MS instrumentation. Finally, some advancements that can be made to improve the analytical capability and reach of SIFT-MS are mentioned.

David Smith,
Patrik Španěl,
Nicholas Demarais,
Vaughan S. Langford,
Murray J. McEwan
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21835?af=R

The isotope distribution: A rose with thorns

Mass Spectrometry Reviews

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The isotope distribution: A rose with thorns

Abstract

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.

Jürgen Claesen,
Alan Rockwood,
Mikhail Gorshkov,
Dirk Valkenborg
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21820?af=R

Characterization of the degradation products of lignocellulosic biomass by using tandem mass spectrometry experiments, model compounds, and quantum chemical calculations

Mass Spectrometry Reviews

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Characterization of the degradation products of lignocellulosic biomass by using tandem mass spectrometry experiments, model compounds, and quantum chemical calculations

Abstract

Biomass-derived degraded lignin and cellulose serve as possible alternatives to fossil fuels for energy and chemical resources. Fast pyrolysis of lignocellulosic biomass generates bio-oil that needs further refinement. However, as pyrolysis causes massive degradation to lignin and cellulose, this process produces very complex mixtures. The same applies to degradation methods other than fast pyrolysis. The ability to identify the degradation products of lignocellulosic biomass is of great importance to be able to optimize methodologies for the conversion of these mixtures to transportation fuels and valuable chemicals. Studies utilizing tandem mass spectrometry have provided invaluable, molecular-level information regarding the identities of compounds in degraded biomass. This review focuses on the molecular-level characterization of fast pyrolysis and other degradation products of lignin and cellulose via tandem mass spectrometry based on collision-activated dissociation (CAD). Many studies discussed here used model compounds to better understand both the ionization chemistry of the degradation products of lignin and cellulose and their ions’ CAD reactions in mass spectrometers to develop methods for the structural characterization of the degradation products of lignocellulosic biomass. Further, model compound studies were also carried out to delineate the mechanisms of the fast pyrolysis reactions of lignocellulosic biomass. The above knowledge was used to assign likely structures to many degradation products of lignocellulosic biomass.

Jacob D. Guthrie,
Caroline E. R. Rowell,
Ruth O. Anyaeche,
Kawthar Z. Alzarieni,
Hilkka I. KenttƤmaa
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21832?af=R

Probing gas phase catalysis by atomic metal cations with flow tube mass spectrometry

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Probing gas phase catalysis by atomic metal cations with flow tube mass spectrometry

Abstract

The evolution and applications of flow tube mass spectrometry in the study of catalysis promoted by atomic metal ions are tracked from the pioneering days in Boulder, Colorado, to the construction and application of the ICP/SIFT/QqQ and ESI/qQ/SIFT/QqQ instruments at York University and the VISTA-SIFT instrument at the Air Force Research Laboratory. The physical separation of various sources of atomic metal ions from the flow tube in the latter instruments facilitates the spatial resolution of redox reactions and allows the separate measurement of the kinetics of both legs of a two-step catalytic cycle, while also allowing a view of the catalytic cycle in progress downstream in the reaction region of the flow tube. We focus on measurements on O-atom transfer and bond activation catalysis as first identified in Boulder and emphasize fundamental aspects such as the thermodynamic window of opportunity for catalysis, catalytic efficiency, and computed energy landscapes for atomic metal cation catalysis. Gas-phase applications include: the catalytic oxidation of CO to CO2, of H2 to H2O, and of C2H4 to CH3CHO all with N2O as the source of oxygen; the catalytic oxidation of CH4 to CH3OH with O3; the catalytic oxidation of C6H6 with O2. We also address the environmentally important catalytic reduction of NO2 and NO to N2 with CO and H2 by catalytic coupling of two-step catalytic cycles in a multistep cycle. Overall, the power of atomic metal cations in catalysis, and the use of flow tube mass spectrometry in revealing this power, is clearly demonstrated.

Voislav Blagojevic,
Gregory K. Koyanagi,
Diethard K. Bƶhme
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mas.21831?af=R

Multilevel Omics-Readouts of in vitro Perturbation Studies are Determined by Memory Effects from Subculture

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Multilevel Omics-Readouts of in vitro Perturbation Studies are Determined by Memory Effects from Subculture

Mass spectrometry-based omics technologies are of increasing relevance for drug discovery. The identification of significant molecular events is a prerequisite in order to map treatments effects to biological pathways for mode of action (MoA) deconvolution. The main contributors to statistical significance are the effect size and the variation of a given molecule. While the former is largely determined by the biological system and the drug treatment, the latter is controlled by the experimental workflow. The impact of sample preparation and instrumentation on variation are well described, but the impact of cell culture conditions on the variation of omics readouts is less explored. Here, we provide evidence that memory effects originating from subculture conditions during cell expansion before the perturbation influence the variation of multilevel omics readouts, including eicosadomics, proteomics and phosphoproteomics, as well as phenotypic parameters, e.g. cell growth and motility using a Cellwatcher system. The treatment was carried out in SW480 colon carcinoma cells with the clinically approved anticancer agent arsenic trioxide (ATO), which follows a multi-modal MoA. Experimental variation was assessed using two different subculture conditions. First, the cells were homogeneously expanded in the Log phase before the treatment. Second, the cells were heterogeneously expanded using cells in the Lag, Log and plateau phases of cell growth before the treatment. When comparing the homogeneous and heterogeneous subcultures, the coefficients of variation (CVs) of controls increased from 1% to 3% for eicosadomics, 11% to 23% for proteomics, 24% to 53% for phosphoproteomics, 5% to 13% for growth area occupied and 6% to 14% for cell motility. The ATO treatment did not considerably influence the number of identified molecules by mass spectrometry, nor the fold-change distributions after both subculture conditions. Therefore, the increased number of significant molecular events in drug treatments after homogeneous subculture seems to be mainly caused by the decrease in CVs. This in turn increased the information content in the obtained perturbation network, based on proteomics and phosphoproteomics data, from 58 to 321 causal conjectures after heterogeneous and homogeneous subcultures, respectively. Independently of the subculture conditions, the perturbation networks allowed for delineating the established MoA of ATO, including enhanced kinase signaling and reduced MYC-related gene expression, induction of heat shock proteins and cell cycle disruption. However, only the perturbation network after homogeneous subculture enabled the discovery of unprecedented drug effects, including down-regulation and quadruple dephosphorylation of the transcription factor RB1, among others. Also, the involvement of AP-1, which is central to the MoA of ATO was only detected after homogenous subculture. In summary, memory effects from subculture have broad relevance for MoA testing in drug discovery since they clearly manifest in molecular and phenotypic properties and their control enables a considerably enhanced MoA deconvolution, facilitating discovery efforts.
Bortel, P., Hagn, G., Skos, L., Bileck, A., Paulitschke, V., Paulitschke, P., Gleiter, L., Mohr, T., Gerner, C., Meier-Menches, S.
February 15, 2023
http://biorxiv.org/cgi/content/short/2023.02.13.528316v1?rss=1

Biphasic responses in cell signalling: A unified approach

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bioRxiv Subject Collection: Systems Biology
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Biphasic responses in cell signalling: A unified approach

Biphasic responses are encountered at all levels in biological systems. At the cellular level, biphasic dose-responses are widely encountered in cell signalling and post-translational modification systems and represent safeguards against over-activation or overexpression of species. In this paper we provide a unified theoretical synthesis of biphasic responses in cell signalling systems, by assessing signalling systems ranging from basic biochemical building blocks to canonical network structures to well-characterized exemplars on one hand, and examining different types of doses on the other. By using analytical and computational approaches applied to a range of systems across levels (described by broadly employed models) we reveal (i) design principles enabling the presence of biphasic responses, including in almost all instances, an explicit characterization of the parameter space (ii) structural factors which preclude the possibility of biphasic responses (iii) different combinations of the presence or absence of enzyme-biphasic and substrate-biphasic responses, representing safeguards against overactivation and overexpression respectively (iv) the possibility of broadly robust biphasic responses (v) the complete alteration of signalling behaviour in a network due to biphasic interactions between species (biphasic regulation) (vi) the propensity of different co-existing biphasic responses in the Erk signalling network. These results both individually and in totality have a number of important consequences for systems and synthetic biology.
Ramesh, V., Krishnan, J.
February 15, 2023
http://biorxiv.org/cgi/content/short/2023.02.13.528284v1?rss=1

Applying single‐cell highly multiplexed secretome proteomics to characterize immunotherapeutic products and predict clinical responses

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Applying single‐cell highly multiplexed secretome proteomics to characterize immunotherapeutic products and predict clinical responses

Abstract

Genetically and phenotypically identical immune cell populations can be highly heterogenous in terms of their immune functions and protein secretion profiles. The microfluidic chip-based single-cell highly multiplexed secretome proteomics enables characterization of cellular heterogeneity of immune responses at different cellular and molecular layers. Increasing evidence has demonstrated that polyfunctional T cells that simultaneously produce 2+ proteins per cell at the single-cell level are key effector cells that contribute to the development of potent and durable cellular immunity against pathogens and cancers. The functional proteomic technology offers a wide spectrum of cellular function assessment and can uniquely define highly polyfunctional cell subsets with cytokine signatures from live individual cells. This high-dimensional single-cell analysis provides deep dissection into functional heterogeneity and helps identify predictive biomarkers and potential correlates that are crucial for immunotherapeutic product design optimization and personalized immunotherapy development to achieve better clinical outcomes.

This article is protected by copyright. All rights reserved

Weiming Ni,
Edward X. Han,
Matthew Cyr,
Sean Mackay,
Jing Zhou
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200242?af=R

The mechanism of Pseudomonas aeruginosa outer membrane vesicle biogenesis determines their protein composition

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The mechanism of Pseudomonas aeruginosa outer membrane vesicle biogenesis determines their protein composition

Abstract

Gram-negative bacteria produce outer membrane vesicles (OMVs) and contain bacterial cargo including nucleic acids and proteins. The proteome of OMVs can be altered by various factors including bacterial growth stage, growth conditions, and environmental factors. However, it is currently unknown if the mechanism of OMV biogenesis can determine their proteome. In this study, we examined whether the mechanisms of OMV biogenesis influenced the production and protein composition of Pseudomonas aeruginosa OMVs. OMVs were isolated from three Pseudomonas aeruginosa strains that produced OMVs either by budding alone, by explosive cell lysis, or by both budding and explosive cell lysis. We identified that the mechanism of OMV biogenesis dictated OMV quantity. Furthermore, global proteomic analysis comparing the proteome of OMVs to their parent bacteria showed significant differences in the identification of proteins in bacteria and OMVs. Finally, we determined that the mechanism of OMV biogenesis influenced the protein composition of OMVs, as OMVs released by distinct mechanisms of biogenesis differed significantly to one another in their proteome and functional enrichment analysis. Overall, our findings reveal that the mechanism of OMV biogenesis is a main factor that determines the OMV proteome which may affect their subsequent biological functions.

This article is protected by copyright. All rights reserved

Lauren Zavan,
Haoyun Fang,
Ella L. Johnston,
Cynthia Whitchurch,
David Greening,
Andrew F. Hill,
Maria KaparakisLiaskos
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200464?af=R

Genetic and epigenetic control of the plant metabolome

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Genetic and epigenetic control of the plant metabolome

Abstract

Plant metabolites are mainly produced through chemical reactions catalysed by enzymes encoded in the genome. Mutations in enzyme-encoding or transcription factor-encoding genes can alter the metabolome by changing the enzyme’s catalytic activity or abundance, respectively. Insertion of transposable elements into non-coding regions has also been reported to affect transcription and ultimately metabolite content. In addition to genetic mutations, transgenerational epigenetic variations have also been found to affect metabolic content by controlling transcription of metabolism related genes. However, the majority of cases reported so far, in which epigenetic mechanisms are associated to metabolism, are non-transgenerational and are triggered by developmental signals or environmental stress. Although, accumulating research has provided evidence of strong genetic control of the metabolome, epigenetic control has been largely untouched. Here, we provide a review of the genetic and epigenetic control of metabolism with a focus on epigenetics. We discuss both transgenerational and non-transgenerational epigenetic marks regulating metabolism as well as prospects of the field of metabolic control where intricate interactions between genetics and epigenetics are involved.

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Koki Hayashi,
Saleh Alseekh,
Alisdair R. Fernie
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200104?af=R

Proteomic identification of intracellular vesicle trafficking and protein glycosylation requirements for lumen inflation in Ciona notochord

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Proteomic identification of intracellular vesicle trafficking and protein glycosylation requirements for lumen inflation in Ciona notochord

Abstract

Lumen formation and inflation are crucial steps for tubular organ morphogenesis, yet the underling mechanism remains largely unrevealed. Here, we applied 4D proteomics to screen the lumenogenesis-related proteins and revealed the biological pathways potentially that are involved in lumen inflation during notochord lumen formation in the ascidian Ciona savignyi. In total, 910 differentiated expressed proteins (DEPs) were identified before and after notochord lumen formation utilizing Mfuzz analysis. Those DEPs were grouped into four upregulated clusters based on their quantitative expression patterns; the functions of these proteins were enriched in protein metabolic and biosynthetic process, establishment of localization and vesicle-mediated transport. We analyzed the vesicle trafficking cluster and focused on the several vesicle transport hub proteins. In vivo function-deficient experiments showed that mutation of vesicle transport proteins resulted in an abnormal lumen in notochord development, demonstrating the crucial role of intracellular trafficking for lumen formation. Moreover, abundant extracellular matrix proteins were identified, the majority of which were predicted to be glycosylated proteins. Inhibition of glycosylation markedly reduced the lumen expansion rate in notochord cells, suggesting that protein glycosylation is essential for lumenogenesis. Overall, our study provides an invaluable resource and reveals the crucial mechanisms in lumen formation and expansion.

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Zhuqing Wang,
Zicheng Tan,
Jianqing Bi,
Amei Liu,
An Jiang,
Bo Dong
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200460?af=R

Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

Proteomics (Wiley)

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Four‐dimensional proteomics analysis of human cerebrospinal fluid with trapped ion mobility spectrometry using PASEF

Abstract

A quadrupole time-of-flight mass spectrometer coupled with a trapped ion mobility spectrometry (timsTOF) operated in parallel accumulation-serial fragmentation (PASEF) mode has recently emerged as a platform capable of providing four dimensional (4D) features comprising of elution time, collision cross section (CCS), mass-to-charge ratio and intensity of peptides. The PASEF mode provides ∼100% ion sampling efficiency both in data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes without sacrificing sensitivity. In addition, targeted measurements using PASEF integrated parallel reaction monitoring (PRM) mode have also been described. However, only limited number of studies have used timsTOF for analysis of clinical samples. Although Orbitrap mass spectrometers have been used for biomarker discovery from cerebrospinal fluid (CSF) in a variety of neurological diseases, these Orbitrap-derived datasets cannot readily be applied for driving experiments on timsTOF mass spectrometers. We generated a catalog of peptides and proteins in human CSF in DDA mode on a timsTOF mass spectrometer and used these data to build a spectral library. This strategy allowed us to use elution times and ion mobility values from the spectral library to design PRM experiments for quantifying previously discovered biomarkers from CSF samples in Alzheimer’s disease. When the same samples were analyzed using a DIA approach combined with a spectral library search, a higher number of proteins were identified than in a library-free approach. Overall, we have established a spectral library of CSF as a resource and demonstrated its utility for PRM and DIA studies, which should facilitate studies of neurological disorders.

This article is protected by copyright. All rights reserved

Dong‐Gi Mun,
Rohit Budhraja,
Firdous A. Bhat,
Roman M. Zenka,
Kenneth L. Johnson,
Abhay Moghekar,
Akhilesh Pandey
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200507?af=R

Discriminating Alkylbenzene Isomers with Tandem Mass Spectrometry Using a Dielectric Barrier Discharge Ionization (DBDI) source

Journal of Mass Spectrometry

Wiley: Journal of Mass Spectrometry: Table of Contents

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

Discriminating Alkylbenzene Isomers with Tandem Mass Spectrometry Using a Dielectric Barrier Discharge Ionization (DBDI) source

Abstract

Soft ambient ionization sources generate reactive species that interact with analyte molecules to form intact molecular ions, which allows rapid, sensitive, and direct identification of the molecular mass. We used a dielectric barrier discharge ionization (DBDI) source with nitrogen at atmospheric pressure to detect alkylated aromatic hydrocarbon isomers (C8H10 or C9H12). Intact molecular ions [M]•+ were detected at 2.4 kVpp, but at increased voltage (3.4 kVpp) [M+N]+ ions were formed, which could be used to differentiate regioisomers by CID. At 2.4 kVpp, alkylbenzene isomers with different alkyl-substituents could be identified by additional product ions: ethylbenzene and -toluene formed [M-2H]+, isopropylbenzene formed abundant [M-H]+, and propylbenzene formed abundant C7H7+. At an operating voltage of 3.4 kVpp, ffragmentation of [M+N]+ by collision-induced dissociation (CID) led to neutral loss of HCN and CH3CN, which corresponded to steric hindrance for excited state N-atoms approaching the aromatic ring (C-H). The ratio of HCN to CH3N loss (interday RSD <20%) were distinct for ethylbenzene and ethyltoluene isomers. The greater the number of alkyl-substituents (C-CH3) and the more sterically hindered (meta>para>ortho) the aromatic core, the greater the loss of CH3CN relative to HCN was.

Begley Alina,
Zenobi,
Renato
February 15, 2023
https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/jms.4910?af=R