Article
Immunology
Lenka Pacakova, Karel Harant, Petr Volf, Tereza Lestinova
Summary: This study compared the proteome of Leishmania mexicana amastigotes from lesion of infected BALB/c mice with alternately cultivated amastigotes. Significant differences in the abundance of metabolic enzymes, virulence factors and proteins involved in translation and condensation of DNA were observed, with axenic amastigotes showing the most pronounced differences compared to lesion-derived amastigotes, and macrophage-derived amastigotes mostly intermediate between the two.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Marine & Freshwater Biology
Eric Bollinger, Jochen P. Zubrod, Marco Konschak, Ralf Schulz, Mirco Bundschuh
Summary: Stable isotope analysis is an important technique in food web ecology, but its effectiveness can be unclear in complex systems. The use of heavy isotope tracers has been suggested as a way to enhance the utility of stable isotope analysis, but this study found that labeling could potentially affect isotopic fractionation and bias conclusions. While the physiological and activity levels of organisms in autotrophy-based and detritus-based aquatic food webs were not significantly affected by labeling, the study supported the isotopic redundancy hypothesis, which suggests that metabolic processes can be altered by discrete quantum mechanical states.
AQUATIC TOXICOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Xiao-Yu Wang, Chun-Jing Chen, Yao-Hui He, Lian-Shuai Ding, Yi-Fan Wu, Cheng-Ting Huang, Jun Wu, Rong Ding, Yu-Hua Xue, Zhi-Wei Lin, Peng-Xiang Xu, Yi-Le Wu, Wen Liu, Ji-Jun Li, Si-Ming Chen, Yu-Fen Zhao, Ji-Yang Dong, Qiang Zhou, Xiang Gao
Summary: Stable isotope chemical labeling methods have limitations in high sensitivity detection for quantitative proteomics. A novel isobaric stable isotope N-phosphorylation labeling strategy (iSIPL) was developed for precise quantitative proteome analysis with high sensitivity and accuracy. iSIPL strategy was successfully applied to analyze the dynamics of protein-protein interactions in the transactivation of HIV-1 provirus.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Biochemistry & Molecular Biology
Pan Fang, Yanlong Ji, Thomas Oellerich, Henning Urlaub, Kuan-Ting Pan
Summary: Protein glycosylation plays a key role in physiological and pathological processes. Mass spectrometry-based glycoproteomics has become an essential tool for studying glycosylation changes. This article summarizes recent advancements in quantification strategies and proposes a strategy for multilayered glycopeptide quantification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Jonathan B. Thacker, Chenchen He, Subramaniam Pennathur
Summary: A novel quantitative analytical strategy was developed and validated for measuring potential biomarkers in cells. The study successfully determined the concentrations of the biomarkers and validated the method for accuracy and stability. Additionally, the use of benzoyl chloride for chemical isotope labeling in cells was reported for the first time.
JOURNAL OF SEPARATION SCIENCE
(2021)
Article
Chemistry, Multidisciplinary
Jiangming Huang, Biyun Jiang, Mingqi Liu, Pengyuan Yang, Weiqian Cao
Summary: gQuant is an automated tool for processing MALDI-MS-based glycan isotope labeling data, designed with dedicated algorithms to improve efficiency, accuracy, and convenience. It showed the ability to process data quickly and accurately in testing, providing a user-friendly interface.
FRONTIERS IN CHEMISTRY
(2021)
Review
Spectroscopy
Xiaobo Tian, Hjalmar P. Permentier, Rainer Bischoff
Summary: This article summarizes the advances in liquid chromatography and mass spectrometry in proteome quantification approaches, focusing on the principles, benefits, and limitations of chemical isotope labeling-based methods. It also discusses the potential and limitations of multiplex isotope labeling approaches for data-independent acquisition mode.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Chemistry, Analytical
Kodai Beppu, Daichi Saito, Yoshio Muguruma, Miki Takahashi, Shuichi Harada, Koichi Inoue
Summary: This study developed a new stable isotope labeling method for analyzing residual antibiotics in bacteria culture, achieving acceptable recovery rates and representing a significant improvement over previous methods.
ANALYTICAL SCIENCES
(2021)
Article
Microbiology
Dariia Vyshenska, Pranav Sampara, Kanwar Singh, Andy Tomatsu, W. Berkeley Kauffman, Erin E. Nuccio, Steven J. Blazewicz, Jennifer Pett-Ridge, Katherine B. Louie, Neha Varghese, Matthew Kellom, Alicia Clum, Robert Riley, Simon Roux, Emiley A. Eloe-Fadrosh, Ryan M. Ziels, Rex R. Malmstrom
Summary: Answering the questions, who is eating what? and who is active? within complex microbial communities is essential for modeling, predicting, and modifying microbiomes for improved human and planetary health. Stable isotope probing can be used to track the incorporation of labeled compounds into cellular DNA during microbial growth to address these questions. However, traditional stable isotope methods face challenges in establishing links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. This study presents an experimental and analytical workflow that improves the detection of metabolically active microorganisms and provides better quantitative estimates of genome-resolved isotope incorporation, thus refining ecosystem-scale models for carbon and nutrient fluxes within microbiomes.
Article
Food Science & Technology
Rui Chang, Chong Ma, Chao Yu, Qiang Zhang, Yanxin Li, Jinmao You, Shijuan Zhang
Summary: Estrogens in milk samples were extracted using a new IL-modified COF and analyzed by SIL method. The synthesized COF showed high adsorption capacity and effectively minimized matrix effect in the analysis of estrogens.
EUROPEAN FOOD RESEARCH AND TECHNOLOGY
(2021)
Article
Environmental Sciences
Yue Zhu, Wenmin Qiu, Yuhong Li, Jinjuan Tan, Xiaojiao Han, Longhua Wu, Yugen Jiang, Zhiping Deng, Chao Wu, Renying Zhuo
Summary: Sedum plumbizincicola is a herbaceous species capable of accumulating excessive cadmium, especially with up-regulation of transport proteins, in response to Cd exposure. The study identified and quantified Cd-responsive membrane proteins in root, stem, and leaf tissues, showing significant changes in transport proteins such as ABC transporters and aquaporins after Cd treatment. The results provide insights into the molecular mechanisms of Cd hyper-tolerance and hyper-accumulation in S. plumbizincicola for potential applications in genetic engineering for phytoremediation purposes.
Article
Chemistry, Applied
Rui Chang, Xueting Wang, Yanxin Li, Shijuan Zhang
Summary: Two pairs of stable isotope labeling (SIL) agents were synthesized and their mass spectrometry (MS) sensitivity enhancement effect was compared with a commercial reagent. CPTA with quaternary ammonium group exhibited higher MS sensitivity enhancement effect and was successfully used for SIL analysis of alkylamines in food and food packaging materials. The SIL strategy and the permanent charge of CPTA minimized the matrix effect, and the method showed good limits of detection, quantitation, recoveries, and low matrix effect.
Article
Chemistry, Analytical
Xiaoling Su, Deying Chen, Liang Li, Lanjuan Li
Summary: The study demonstrates that perfusion can significantly alter the liver metabolome, recommending the use of non-perfused liver for comprehensive liver metabolomics analysis for high coverage.
ANALYTICA CHIMICA ACTA
(2021)
Article
Pharmacology & Pharmacy
Sabrina Wohlfart, Michael Kilian, Philip Storck, Thomas Gutsmann, Klaus Brandenburg, Walter Mier
Summary: A novel method for precise quantification of Pep19-2.5 in biological samples has been developed in this study, which is crucial for the treatment of sepsis. The method utilizes mass spectrometry and labeled amino acid residues to reliably quantify the peptide content.
Review
Chemistry, Medicinal
Rheem A. Totah, Allan E. Rettie
Summary: Advancements in stable isotopes and mass spectrometry instrumentation over the past 50 years have had a significant impact on elucidating endogenous biochemical pathways and quantitative methodology in analytical chemistry. This manuscript focuses on the application of 2H, 13C, and 18O in understanding mechanisms of drug metabolism since the early 1980s, with examples from the work of Dr. Thomas Baillie. The latter part of the review also discusses the development of stable-label drugs that have recently been approved or are currently under development.
MEDICINAL CHEMISTRY RESEARCH
(2023)
Article
Chemistry, Analytical
Pan Luo, Zheyi Liu, Tingting Zhang, Xiaolei Wang, Jing Liu, Yiqiang Liu, Xiaohu Zhou, Yang Chen, Wenrui Dong, Chunlei Xiao, Yan Jin, Xueming Yang, Fangjun Wang
Summary: This study presents a novel method for peroxide-free photochemical oxidation of proteins (PPOP) mediated by chloride ions, which can sensitively monitor protein high-order structures and be applied to study protein-drug interfaces.
ANALYTICAL CHEMISTRY
(2022)
Article
Gastroenterology & Hepatology
Xu Zhang, Krystal Walker, Janice Mayne, Leyuan Li, Zhibin Ning, Alain Stintzi, Daniel Figeys
Summary: This study developed a rapid method for evaluating the viability of live microbiota in biobanks and found that long-term freezing in deoxygenated glycerol buffer has minimal detrimental effects on the cultivability of fecal microbiota.
Article
Microbiology
Caitlin M. A. Simopoulos, Zhibin Ning, Leyuan Li, Mona M. Khamis, Xu Zhang, Mathieu Lavallee-Adam, Daniel Figeys
Summary: Metaproteomics is a useful tool for studying microbial communities, but the data acquisition process can be time-consuming and resource-intensive. In this study, the researchers developed a computational framework called MetaProClust-MS1 to prioritize samples for follow-up analysis using tandem mass spectrometry (MS/MS). The framework successfully identified microbial responses and disease diagnostic features in gut microbiome data. The study also demonstrated the potential of MetaProClust-MS1 in clinical settings and large-scale metaproteomic screening.
Article
Microbiology
Zhongzhi Sun, Wenju Wang, Leyuan Li, Xu Zhang, Zhibin Ning, Janice Mayne, Krystal Walker, Alain Stintzi, Daniel Figeysa
Summary: The composition and function of the human gut microbiome are closely related to human health. Sugar substitute sweeteners, as commonly used food additives, have potential impacts on the functionality of the microbiome. This study systematically investigated the responses of the human gut microbiome to commonly used sugar substitute sweeteners and revealed the associations between sweetener properties and metaproteomic responses of individual microbiomes.
MICROBIOLOGY SPECTRUM
(2022)
Review
Nutrition & Dietetics
Kendra Hodgkinson, Faiha El Abbar, Peter Dobranowski, Juliana Manoogian, James Butcher, Daniel Figeys, David Mack, Alain Stintzi
Summary: Butyrate, produced by gut microbiota through fermentation of dietary fiber, serves as a key energy source for colonocytes. It has important roles in gastrointestinal health, impacting both host and microbial functions. Maintaining optimal butyrate levels improves gastrointestinal health by supporting colonocyte function, decreasing inflammation, maintaining the gut barrier, and promoting a healthy microbiome. However, increasing butyrate levels in humans and reversing negative outcomes have yielded mixed results, despite its protective actions in intestinal diseases.
CLINICAL NUTRITION
(2023)
Article
Chemistry, Analytical
Haonan Duan, Kai Cheng, Zhibin Ning, Leyuan Li, Janice Mayne, Zhongzhi Sun, Daniel Figeys
Summary: The human gut microbiome is a complex system consisting of hundreds of species, and metaproteomics is a useful tool for studying their expressed functions. However, many lower abundance species cannot be detected by current metaproteomic techniques, which is a challenge in metaproteomics. In this study, the researchers investigated the minimal abundance of a bacterium in a microbiome that can be detected by shotgun metaproteomics. They found that the number of identified peptides and peptide intensity from a 15N-labeled E. coli were linearly correlated with the spike-in levels, even at low abundances. They also discovered that the match-between-run strategy increased the number of quantified peptides, even for low-abundance species.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Lingqiang Zhou, Zheyi Liu, Yongjie Guo, Shiwen Liu, Heng Zhao, Shan Zhao, Chunlei Xiao, Shun Feng, Xueming Yang, Fangjun Wang
Summary: In this study, the effects of charge state and crown ether (CE) complexation on the gas-phase native-like protein structure were systematically investigated by integrating native mass spectrometry (nMS) with 193 nm ultraviolet photodissociation (UVPD). The results showed that CE complexation can greatly alleviate the structure disruption caused by the intramolecular solvation of charged side chains, resulting in a more stable and native-like protein structure in the gas phase.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Biochemical Research Methods
Binwen Sun, Zheyi Liu, Jin Liu, Shan Zhao, Liming Wang, Fangjun Wang
Summary: In this review, the authors provide an overview of common and emerging proteases used in proteomics analysis in the past 5 years. They focus on the unique cleavage features of these proteases and their specific applications in protein characterization, PTM discovery, and sequencing. Additionally, the authors summarize the use of proteases in structural proteomics and protein function analysis. They also discuss future directions for the development of new proteases and their applications in proteomics.
Article
Biochemical Research Methods
Marybeth Creskey, Leyuan Li, Zhibin Ning, Emily E. F. Fekete, Janice Mayne, Krystal Walker, Anna Ampaw, Robert Ben, Xu Zhang, Daniel Figeys
Summary: This study demonstrates that the TMT labeling procedures can be simplified by using pre-aliquoted dry TMT reagents, which achieve high labeling efficiency in both microbiome and mammalian cell line samples. The workflow was successfully applied to analyze 97 samples and consistently revealed microbiome responses. This study supports the use of pre-aliquoted, dried, and stored TMT reagents for robust quantitative proteomics and metaproteomics in high throughput applications.
Article
Nanoscience & Nanotechnology
Jing Liu, Ji Lv, Zheyi Liu, Zheng Fang, Can Lai, Shan Zhao, Mingliang Ye, Fangjun Wang
Summary: In this study, it was discovered that interfacial hydrophobic hydration significantly enhances H-bond networks at the interface between a glycan-modified adsorbent and a methanol-water-acetonitrile ternary solution. This enhancement promotes the adsorbent-solution heterogeneous glycan-glycan recognition and interaction, leading to improved glycopeptide enrichment. Compared with the commonly used hydrophilic-interaction enrichment strategy, more intact N- and O-glycopeptides are identified and the enrichment recoveries are significantly increased. This study also provides in-depth profiling of N- and O-glycosylation on SARS-CoV-2 S1 and hACE2 proteins.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Multidisciplinary
Yu Bai, Zheyi Liu, Yuanqing Li, Heng Zhao, Can Lai, Shan Zhao, Kaixian Chen, Cheng Luo, Xueming Yang, Fangjun Wang
Summary: In this study, the dynamic molecular interactions and overall protein assembly of CDK12/CDK13-CycK complexes under the modulation of small molecule inhibitors were systematically investigated using the structural mass spectrometry (MS) methods of lysine reactivity profiling (LRP) and native MS (nMS). The complementary results of LRP and nMS provided essential structure insights, including inhibitor binding pocket, binding strength, interfacial molecular details, and dynamic conformation changes. The binding of the inhibitor SR-4835 destabilized the CDK12/CDK13-CycK interactions in an unusual allosteric activation way, offering a novel alternative for kinase activity inhibition. The study highlights the great potential of LRP combined with nMS for the evaluation and rational design of effective kinase inhibitors at the molecular level.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Biochemical Research Methods
Zheyi Liu, Shirui Yang, Lingqiang Zhou, Min He, Yu Bai, Shan Zhao, Fangjun Wang
Summary: Understanding the interplay between proteins and materials is crucial for a wide range of applications including safety evaluation of biomedical micro/nanomaterials, toxicity estimation, design of nano-drugs, and catalytic activity improvement of bio-inorganic functional hybrids. However, characterizing the molecular details of protein-micro/nanomaterial hybrids at the interface remains a significant challenge. This protocol presents a lysine reactivity profiling-mass spectrometry strategy to determine the interacting regions of a protein with micro/nanomaterials. Lysine residues, which are commonly found on hydrophilic protein surfaces, exhibit reactivity that depends on the accessibility of their amine groups. By analyzing the reactivity of lysine residues, useful information can be obtained about the protein localization orientation, interaction sequence regions, binding sites, and modulated protein structures in the protein-material hybrids. The protocol also includes optimized two-step isotope dimethyl labeling strategy, protein digestion, elution from materials, data processing, and interfacial structure analysis. The entire protocol takes approximately 3-5 days to complete, with the two-step isotope labeling steps requiring about 5 hours.
Article
Biochemical Research Methods
Kai Cheng, Zhibin Ning, Leyuan Li, Xu Zhang, Joeselle M. Serrana, Janice Mayne, Daniel Figeys
Summary: The research on microbial communities has gained attention in agriculture, environment, and human health. Metaproteomics has become a powerful tool to understand the roles of microbes through analyzing their expressed proteins. However, analyzing metaproteomic data at genome resolution is challenging due to the lack of efficient bioinformatics tools. Here, we introduce MetaLab-MAG, a specialized tool for microbiome characterization from metagenome-assembled genomes databases. MetaLab-MAG performs well compared to directly searching the gene catalog protein database, allowing quantification of genome-level microbiota compositions and supporting different quantification strategies. It overcomes the obstacles in metaproteomic data analysis and provides comprehensive information from microbiomes to researchers.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Zhongzhi Sun, Zhibin Ning, Kai Cheng, Haonan Duan, Qing Wu, Janice Mayne, Daniel Figeys
Summary: Metaproteomics studies functional changes in the human gut microbiome and peptide identification is a crucial step in this research. However, the large search space complicates peptide identification methods. This study constructed MetaPep, a core peptide database, and demonstrated its importance for human gut metaproteomics research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Xiong Chen, Shanping Ji, Zheyi Liu, Xiao Yuan, Congsheng Xu, Ruxi Qi, An He, Heng Zhao, Haiping Song, Chunlei Xiao, Weina Gao, Peng R. Chen, Ray Luo, Pengfei Li, Fangjun Wang, Xueming Yang, Ruijun Tian
Summary: Identification of the tyrosine phosphorylation (pY)-dependent interactome of immune co-receptors is crucial for understanding signal pathways involved in immunotherapy. In this study, a photoaffinity-based chemical proteomic approach was used to dissect the motif-specific cytoplasmic interactomes of CD28, a critical immune co-receptor. The study identified specific interactions of phospholipase PLCG1 with the Y191 motif and the kinase PKCq with the previously undefined pY218 motif. This synthetic CD28(cyto)-based photoaffinity proteomic approach can be applied to study other immune co-receptors with multiple pY sites.
CELL CHEMICAL BIOLOGY
(2022)