Deciphering Host-Parasite Interplay in Leishmania Infection through a One Health View of Proteomics Studies on Drug Resistance.

Recent efforts in the study of vector-borne parasitic diseases (VBPDs) have emphasized an increased consideration for preventing drug resistance and promoting the environmental safety of drugs, from the beginning of the drug discovery pipeline. The intensive use of the few available antileishmanial drugs has led to the spreading of hyper-resistant Leishmania infantum strains, resulting in a chronic burden of the disease. In the present work, we have investigated the biochemical mechanisms of resistance to antimonials, paromomycin, and miltefosine in three drug-resistant parasitic strains from human clinical isolates, using a whole-cell mass spectrometry proteomics approach. We identified 14 differentially expressed proteins that were validated with their transcripts. Next, we employed functional association networks to identify parasite-specific proteins as potential targets for novel drug discovery studies. We used SeqAPASS analysis to predict susceptibility based on the evolutionary conservation of protein drug targets across species. MATH-domain-containing protein, adenosine triphosphate (ATP)-binding cassette B2, histone H4, calpain-like cysteine peptidase, and trypanothione reductase emerged as top candidates. Overall, this work identifies new biological targets for designing drugs to prevent the development of Leishmania drug resistance, while aligning with One Health principles that emphasize the interconnected health of people, animals, and ecosystems.

Data acquisition approaches for single cell proteomics.

Single-cell proteomics (SCP) aims to characterize the proteome of individual cells, providing insights into complex biological systems. It reveals subtle differences in distinct cellular populations that bulk proteome analysis may overlook, which is essential for understanding disease mechanisms and developing targeted therapies. Mass spectrometry (MS) methods in SCP allow the identification and quantification of thousands of proteins from individual cells. Two major challenges in SCP are the limited material in single-cell samples necessitating highly sensitive analytical techniques and the efficient processing of samples, as each biological sample requires thousands of single cell measurements. This review discusses MS advancements to mitigate these challenges using data-dependent acquisition (DDA) and data-independent acquisition (DIA). Additionally, we examine the use of short liquid chromatography gradients and sample multiplexing methods that increase the sample throughput and scalability of SCP experiments. We believe these methods will pave the way for improving our understanding of cellular heterogeneity and its implications for systems biology.

Development of a sensitive LC-MS/MS assay to support human microdose study for an oral agonist of the GLP-1 receptor.

Aim: The purpose of this work was to determine the feasibility of supporting a clinical microdose study for PF-06882961 (danuglipron), an oral small molecule agonist of the GLP-1 receptor, by LC-MS/MS. Methodology: Statistical instrument parameter optimization using response surface methodology was employed to develop a LC-MS/MS method for the analyte, PF-06882961. Results: An LC-MS/MS method was developed and validated to support a proof of concept microdose pharmacokinetics preclinical study in monkeys, administered PF-06882961 (0.005 mg total, average dose = 0.0007 mg/kg) via intravenous bolus injection. Conclusion: The present study demonstrated the feasibility of analyzing human microdose plasma samples for PF-06882961 by LC-MS/MS, instead of accelerator mass spectrometry, thereby reducing cost and eliminating synthesis and exposure to 14C labeled material.

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Sputum proteomics in lung disorders.

Lung diseases affect pulmonary and respiratory function and are caused by bacterial viral and fungal infection as well as environmental factors. Unfortunately, symptom overlap between various pulmonary diseases often prevents clear differentiation and uncertain diagnosis. Accordingly, identification of specific markers of inflammatory activity in early disease stage could potential unveil the intrinsic molecular mechanisms of the underlying pathology. Proteomic studies aimed at understanding the genetic/environmental contributions to the development and progression of lung diseases represent a promising approach for diagnosis and treatment. The fluid phase of sputum represents a rich protein source and is frequently used in these studies. This chapter addresses causes of lung disorders, sputum composition, collection and processing as well as the clinical significance and challenges associated with the presence of interfering factors. Basics of proteomics and mass spectrometry are also described, together with the analytical approaches to investigate the sputum proteome. Finally, we explore the application of sputum proteomics in severe lung disorders including COVID-19 infection, chronic obstructive pulmonary disease, asthma, cystic fibrosis, lung cancer and tuberculosis.

Full-Dimensional Analysis of Gaseous Products to Unlocking In Depth Thermal Runaway Mechanism of Li-Ion Batteries.

In this study, state-of-the-art on-line pyrolysis MS (OP-MS) equipped with temperature-controlled cold trap and on-line pyrolysis GC/MS (OP-GC/MS) injected through high-vacuum negative-pressure gas sampling (HVNPGS) programming are originally designed/constructed to identify/quantify the dynamic change of common permanent gases and micromolecule organics from the anode/cathode-electrolyte reactions during thermal runaway (TR) process, and corresponding TR mechanisms are further perfected/complemented. On LiCx anode side, solid electrolyte interphase (SEI) would undergo continuous decomposition and regeneration, and the R-H+ (e.g., HF, ROH, etc.) species derived from electrolyte decomposition would continue to react with Li/LiCx to generate H2. Up to above 200 °C, the O2 would release from the charged NCM cathode and organic radicals would be consumed/oxidized by evolved O2 to form COx, H2O, and more corrosive HF. On the contrary, charged LFP cathode does not present obvious O2 evolution during heating process and the unreacted flammable/toxic organic species would exit in the form of high temperature/high-pressure (HT/HP) vapors within batteries, indicating higher potential safety risks. Additionally, the in depth understanding of the TR mechanism outlined above provides a clear direction for the design/modification of thermostable electrodes and non-flammable electrolytes for safer batteries.

Determination of hATG8 Binding Selectivity of AIM (Autophagy-Interacting Motif) Peptides Using Native Electrospray Ionization Mass Spectrometry.

Establishing the hATG8 binding selectivity of AIM (autophagy-interacting motif) sequences found within autophagy system proteins provides insights into their biological roles, and in the case of disease-associated AIM mutations, potential pathophysiological mechanisms. Given the sometimes small differences in affinity for an individual AIM amongst the six hATG8 proteins, establishing AIM preferences can be experimentally challenging. We describe a native mass spectrometry method that is suitable for detecting such differences, using synthetic AIM peptides and recombinant hATG8 proteins, to probe hATG8-AIM interactions in the gas phase. Binding preferences of a single AIM peptide against multiple hATG8s, or two AIM peptides against a single hATG8 (e.g., wild-type versus mutant AIM), may be determined.

Extracellular Vesicle Isolation and Mass Spectrometry-Based Proteomic Analysis in Arabidopsis thaliana.

Extracellular vesicles (EVs) can transport various biological materials, including proteins, lipids, nucleic acids, and metabolites, through the unconventional protein secretion (UPS) pathway. Plant EVs can be classified into at least three major types: tetraspanin 8 (TET8)-positive EVs, penetration 1 (PEN1)-positive EVs, and exocyst-positive organelle (EXPO)-derived EVs. However, the research progress of plant EVs has been hindered due to the limitations inherent in EV isolation techniques. Moreover, since previous research on plant EVs has primarily focused on the interaction between plants and microbes, the biogenesis, transport, and secretion of plant EVs remain unexplored. Recent advances in centrifugation methods for extraction of apoplastic wash fluids, combined with mass spectrometry-based proteomic analysis, provide approaches to identify regulators and cargoes of plant EVs and thus serve as an important step for future studies on the biogenesis and function of plant EVs. Here, we illustrate detailed methods of EV isolation and mass spectrometry-based proteomic analysis in Arabidopsis.

Liquid chromatography-mass spectrometry quantification of phytochemicals in Withania somnifera using data-dependent acquisition, multiple-reaction-monitoring, and parallel-reaction-monitoring with an inclusion list.

Characterization of botanical extracts by mass spectrometry-based metabolomics analysis helps in determining the phytochemical composition that underlies their bioactivity and potential health benefits, while also supporting reproducibility of effects in clinical trials. The quantification of seven withanolides in Withania somnifera using three mass-spectrometry methods was evaluated using Deming regression. Two high-resolution time-of-flight mass spectrometry methods were used, one operating in data-dependent acquisition mode and the other in parallel-reaction-monitoring mode with an inclusion list. The two high-resolution time-of-flight mass spectrometry methods were compared to a multiple-reaction-monitoring method. We evaluated in-source fragmentation of steroidal glycosides and optimized the methods accordingly. A novel software approach to integrating parallel-reaction-monitoring data acquired with an inclusion list was developed. Combining and comparing quantitative results allowed for quantitative specificity, good precision, and adjustment of instrument source conditions for optimal quantification by multiple-reaction-monitoring mass spectrometry, an analytical method that is widely accessible in analytical and phytochemical laboratories.

The Zea mays PeptideAtlas: A New Maize Community Resource.

This study presents the Maize PeptideAtlas resource (www.peptideatlas.org/builds/maize) to help solve questions about the maize proteome. Publicly available raw tandem mass spectrometry (MS/MS) data for maize collected from ProteomeXchange were reanalyzed through a uniform processing and metadata annotation pipeline. These data are from a wide range of genetic backgrounds and many sample types and experimental conditions. The protein search space included different maize genome annotations for the B73 inbred line from MaizeGDB, UniProtKB, NCBI RefSeq, and for the W22 inbred line. 445 million MS/MS spectra were searched, of which 120 million were matched to 0.37 million distinct peptides. Peptides were matched to 66.2% of proteins in the most recent B73 nuclear genome annotation. Furthermore, most conserved plastid- and mitochondrial-encoded proteins (NCBI RefSeq annotations) were identified. Peptides and proteins identified in the other B73 genome annotations will improve maize genome annotation. We also illustrate the high-confidence detection of unique W22 proteins. N-terminal acetylation, phosphorylation, ubiquitination, and three lysine acylations (K-acetyl, K-malonyl, and K-hydroxyisobutyryl) were identified and can be inspected through a PTM viewer in PeptideAtlas. All matched MS/MS-derived peptide data are linked to spectral, technical, and biological metadata. This new PeptideAtlas is integrated in MaizeGDB with a peptide track in JBrowse.

Discrimination of Common E. coli Strains in Urine by Liquid Chromatography-Ion Mobility-Tandem Mass Spectrometry and Machine Learning.

Accurate identification of bacterial strains in clinical samples is essential to provide an appropriate antibiotherapy to the patient and reduce the prescription of broad-spectrum antimicrobials, leading to antibiotic resistance. In this study, we utilized the combination of a multidimensional analytical technique, liquid chromatography-ion mobility-tandem mass spectrometry (LC-IM-MS/MS), and machine learning to accurately identify and distinguish 11 Escherichia coli (E. coli) strains in artificially contaminated urine samples. Machine learning was utilized on the LC-IM-MS/MS data of the inoculated urine samples to reveal lipid, metabolite, and peptide isomeric biomarkers for the identification of the bacteria strains. Tandem MS and LC separation proved effective in discriminating diagnostic isomers in the negative ion mode, while IM separation was more effective in resolving conformational biomarkers in the positive ion mode. Using hierarchical clustering, the strains are clustered accurately according to their group highlighting the uniqueness of the discriminating biomarkers to the class of each E. coli strain. These results show the great potential of using LC-IM-MS/MS and machine learning for targeted omics applications to diagnose infectious diseases in various environmental and clinical samples accurately.

Evaluation of cerebrospinal fluid (CSF) and interstitial fluid (ISF) mouse proteomes for the validation and description of Alzheimer's disease biomarkers.

BACKGROUND: Mass spectrometry (MS)-based cerebrospinal fluid (CSF) proteomics is an important method for discovering biomarkers of neurodegenerative diseases. CSF serves as a reservoir for interstitial fluid (ISF), and extensive communication between the two fluid compartments helps to remove waste products from the brain. NEW METHOD: We performed proteomic analyses of both CSF and ISF fluid compartments using intracerebral microdialysis to validate and detect novel biomarkers of Alzheimer's disease (AD) in APPtg and C57Bl/6J control mice. RESULTS: We identified up to 625 proteins in ISF and 4,483 proteins in CSF samples. By comparing the biofluid profiles of APPtg and C57Bl/6J mice, we detected 37 and 108 significantly up- and downregulated candidates, respectively. In ISF, 7 highly regulated proteins, such as Gfap, Aldh1l1, Gstm1, and Txn, have already been implicated in AD progression, whereas in CSF, 9 out of 14 highly regulated proteins, such as Apba2, Syt12, Pgs1 and Vsnl1, have also been validated to be involved in AD pathogenesis. In addition, we also detected new interesting regulated proteins related to the control of synapses and neurotransmission (Kcna2, Cacng3, and Clcn6) whose roles as AD biomarkers should be further investigated. COMPARISON WITH EXISTING METHODS: This newly established combined protocol provides better insight into the mutual communication between ISF and CSF as an analysis of tissue or CSF compartments alone. CONCLUSIONS: The use of multiple fluid compartments, ISF and CSF, for the detection of their biological communication enables better detection of new promising AD biomarkers.

The morphology of the pygidial glands and the chemical composition of their secretions of four sphodrine ground beetle species (Carabidae: Platyninae).

Ground beetles possess a pair of pygidial glands that produce and release secretions that play an important role in defense against predators. The morphology of these glands and the chemical composition of their products were studied in four species of the tribe Sphodrini: Calathus (Calathus) fuscipes (Goeze, 1777), C. (Neocalathus) cinctus Motschulsky, 1850, C. (N.) melanocephalus (Linnaeus, 1758) and Laemostenus (Antisphodrus) elongatus (Dejean, 1828). The morphological analyzes of the glands of the four taxa mentioned were carried out for the first time using bright-field and nonlinear microscopy. All morphological structures were precisely measured and photographed. The pygidial gland secretions of C. (C.) fuscipes and L. (A.) elongatus were analyzed for the first time using gas chromatography-mass spectrometry. A total of 30 compounds were detected from the extracts of pygidial gland secretions of the four Sphodrini species studied. The simplest chemical mixture was found in L. (A.) elongatus, while the most complex secretion was that of C. (C.) fuscipes. 1-Undecanol, which we were able to detect in all taxa examined here, and dodecyl butyrate, which was detected in the three Calathus species, have never before been detected in the secretions of ground beetles.

Antioxidant-related enzymes and peptides as biomarkers of metallic nanoparticles (eco)toxicity in the aquatic environment.

Increased awareness of the impact of human activities on the environment has emerged in recent decades. One significant global environmental and human health issue is the development of materials that could potentially have negative effects. These materials can accumulate in the environment, infiltrate organisms, and move up the food chain, causing toxic effects at various levels. Therefore, it is crucial to assess materials comprising nano-scale particles due to the rapid expansion of nanotechnology. The aquatic environment, particularly vulnerable to waste pollution, demands attention. This review provides an overview of the behavior and fate of metallic nanoparticles (NPs) in the aquatic environment. It focuses on recent studies investigating the toxicity of different metallic NPs on aquatic organisms, with a specific emphasis on thiol-biomarkers of oxidative stress such as glutathione, thiol- and related-enzymes, and metallothionein. Additionally, the selection of suitable measurement methods for monitoring thiol-biomarkers in NPs' ecotoxicity assessments is discussed. The review also describes the analytical techniques employed for determining levels of oxidative stress biomarkers.

Enantiomeric Analysis of Chiral Drugs Using Mass Spectrometric Methods: A Comprehensive Review.

Chirality plays a crucial role in the drug development process, influencing fundamental chemical and biochemical processes and significantly affecting our daily lives. This review provides a comprehensive examination of mass spectrometric (MS) methods for the enantiomeric analysis of chiral drugs. It thoroughly investigates MS-hyphenated techniques, emphasizing their critical role in achieving enantioselective analysis. Furthermore, it delves into the intricate chiral recognition mechanisms inherent in MS, elucidating the fundamental principles that govern successful chiral separations. By critically assessing the obstacles and potential benefits associated with each MS-based method, this review offers valuable insights for researchers navigating the complexities of chiral analysis. Both qualitative and quantitative approaches are explored, presenting a comparative analysis of their strengths and limitations. This review is aimed at significantly enhancing the understanding of chiral MS methods, serving as a crucial resource for researchers and practitioners engaged in enantioselective studies.

Performance Validation of the NeoBase 2 Non-Derivatized MSMS Assay Kit and Cutoff Values Establishment of Term and Preterm Neonates.

OBJECTIVE: NeoBase 2 Non-derivatized MSMS assay kit (NeoBase 2 kit) was used for newborn screening, the performance of the NeoBase 2 kit should be validated before its implementation in clinical diagnostic laboratories. METHODS: Leftover dried blood spot samples, quality control materials in the NeoBase 2 kit, and proficiency testing materials received from the NSQAP were used. Precision, accuracy, LOD, LLOQ, recovery, and stability were carried out to verify the performance of the Waters ACQUITY TQD MS/MS system with the NeoBase 2 kit for newborn screening. Cutoffs were determined and analytes requiring different cutoffs in preterm neonates were investigated. RESULTS: Within-run and between-run precisions ranged from 3.95% to 14.41%. The accuracy and stability were within 15%. All analytes demonstrated acceptable LOD, LLOQ, and recoveries. Cutoffs for term and preterm neonates were established. CONCLUSIONS: The performance of the NeoBase 2 kit is acceptable and can be implemented in clinical diagnostic laboratories.

Characterization of a Monoclonal Antibody by Native and Denaturing Top-Down Mass Spectrometry.

Established in recent years as an important approach to unraveling the heterogeneity of intact monoclonal antibodies, native mass spectrometry has been rarely utilized for sequencing these complex biomolecules via tandem mass spectrometry. Typically, top-down mass spectrometry has been performed starting from highly charged precursor ions obtained via electrospray ionization under denaturing conditions (i.e., in the presence of organic solvents and acidic pH). Here we systematically benchmark four distinct ion dissociation methods─namely, higher-energy collisional dissociation, electron transfer dissociation, electron transfer dissociation/higher-energy collisional dissociation, and 213 nm ultraviolet photodissociation─in their capability to characterize a therapeutic monoclonal antibody, trastuzumab, starting from denatured and native-like precursor ions. Interestingly, native top-down mass spectrometry results in higher sequence coverage than the experiments carried out under denaturing conditions, with the exception of ultraviolet photodissociation. Globally, electron transfer dissociation followed by collision-based activation of product ions generates the largest number of backbone cleavages in disulfide protected regions, including the complementarity determining regions, regardless of electrospray ionization conditions. Overall, these findings suggest that native mass spectrometry can certainly be used for the gas-phase sequencing of whole monoclonal antibodies, although the dissociation of denatured precursor ions still returns a few backbone cleavages not identified in native experiments. Finally, a comparison of the fragmentation maps obtained under denaturing and native conditions strongly points toward disulfide bonds as the primary reason behind the largely overlapping dissociation patterns.

Quantification of additives in beached plastic debris from Aotearoa New Zealand.

Plastics have become an essential part of modern society. Their properties can be easily manipulated by incorporating additives to impart desirable attributes, such as colour, flexibility, or stability. However, many additives are classified as hazardous substances. To better understand the risk of plastic pollution within marine ecosystems, the type and concentration of additives in plastic debris needs to be established. We report the quantification of thirty-one common plastic additives (including plasticisers, antioxidants, and UV stabilisers) in beached plastic debris collected across Aotearoa New Zealand. Additives were isolated from the plastic debris by solvent extraction and quantified using high-resolution liquid chromatography-mass spectrometry. Twenty-five of the target additives were detected across 200 items of debris, with plasticisers detected at the highest frequency (99 % detection frequency). Additives were detected in all samples, with a median of four additives per debris item. A significantly higher number of additives were detected per debris item for polyvinyl chloride (median = 7) than polyethylene or polypropylene (median = 4). The additives bis(2-ethylhexyl) phthalate, diisononyl phthalate, diisodecyl phthalate, and antioxidant 702 were detected at the highest concentrations (up to 196,930 µg/g). The sum concentration of additives per debris item (up to 320,325 µg/g) was significantly higher in polyvinyl chloride plastics (median 94,716 µg/g) compared to other plastic types, primarily due to the presence of phthalate plasticisers. Non-target analysis was consistent with the targeted analysis, indicating a higher number and concentration of additives in polyvinyl chloride debris items compared to all other polymer types. Feature identification indicated the presence of more additives than previously detected in the targeted analysis, including plasticisers (phthalate and non-phthalate), processing aids, and nucleating agents. This study highlights phthalates and polyvinyl chloride as key targets for consideration in ecotoxicology and risk assessments, and the development of policies to reduce the impacts of plastic pollution.

Genomic identification of expressed globulin storage proteins in oat.

Introduction: Oats, a highly nutritious cereal known for their health benefits, contain various macromolecules of significant biological value, including abundant and highly digestible proteins. Despite their importance, oat proteins have not been extensively studied. Here, we present a complete set of the expressed globulins genes, which code for the main storage protein in oats as well as their chromosomal positions. Methods: Published expressed sequence tags for globulins were used as queries in the Sang oat genome. In addition, globulin proteins were fractionated from oat flour by solvent extraction based on differential solubility with other classes of cereal proteins. The protein fractions were separated by gel electrophoresis and analyzed by tandem mass spectrometry to confirm their identity and expression in seed. Results and discussion: In total 32 globulin gene sequences were identified on the oat genome. Out of these, the expression on RNA level could be confirmed and 27 were also detected as expressed proteins by MS. Our results provide the most extensive set of salt-soluble oat globulin sequences to date, paving the way for further understanding their implications for human nutrition. In addition, a simple methodology to fractionate oat proteins is presented.