Article
Oncology
Francesca Piaggio, Michela Croce, Francesco Reggiani, Paola Monti, Cinzia Bernardi, Marianna Ambrosio, Barbara Banelli, Mehmet Dogrusoez, Ralf Jockers, Domenico Bordo, Roberto Puzone, Silvia Viaggi, Domenico Coviello, Francesco B. Lanza, Martina Bartolucci, Andrea Petretto, Carlo Mosci, Rosaria Gangemi, Pieter A. van der Velden, Martine J. Jager, Ulrich Pfeffer, Adriana Amaro
Summary: This study investigated the impact of GNAQ and GNA11 gene mutations on the characteristics and prognosis of uveal melanoma. The results showed that GNA11 mutation was associated with worse prognosis and high-risk cytogenetic, mutational, and molecular tumor characteristics. Additionally, G-proteins encoded by GNAQ and GNA11 had different protein interaction partners, and differential DNA methylation might contribute to different progression risks.
EUROPEAN JOURNAL OF CANCER
(2022)
Article
Biochemical Research Methods
Isabelle Billault, Anouchka Gatin, Guillaume Van der Rest, Cecile Sicard-Roselli
Summary: In this study, four different di-tyrosine dimers were produced by radiolytical-induced oxidation. A new methodology combining UPLC-MS analysis, specific deuterium labelling and isotopic exchanges with the solvent was proposed to identify three different covalent cross-links and propose different new original di-tyrosine structures. Absorption and fluorescence characterizations consolidated the proposal.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Medicine, Legal
Can Hu, Hongcheng Mei, Hongling Guo, Ziyang Yu, Jun Zhu
Summary: The purification of ammonium nitrate (AN) samples through recrystallization has been shown to enhance stable isotope ratios and accurately distinguish AN samples from different cities and batches.
FORENSIC SCIENCE INTERNATIONAL
(2021)
Article
Biochemical Research Methods
Quynh-Trang Do, Ting-En Huang, Yi-Chen Liu, Jung-Hsiang Tai, Shu-Hui Chen
Summary: This study identified protein targets of CEs in estrogen-sensitive breast cancer cells using proteomics, revealing the mechanism of covalent adduct formation between CEs and proteins. The results suggest that CEs may downregulate proteins involved in metabolism or detoxification, indicating a negative correlation between CE-induced cellular damage and the expression of stress-alleviating proteins.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Freja Gronbaek-Thorsen, Camilla Jensen, Jesper Ostergaard, Laura Hyrup Moller, Bente Gammelgaard
Summary: A method for quantitation of OT and SeOT in human plasma using gradient elution LC-ICP-MS/MS was developed, with selenium-based analysis showing higher sensitivity and selectivity compared to sulfur-based analysis. Despite the relatively simpler setup of external calibration, IDA can compensate for instrument drift and changes in organic solvent concentration.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Alicia L. Richards, Manon Eckhardt, Nevan J. Krogan
Summary: Quantitative mass spectrometry (MS) techniques have enabled unbiased mapping of global changes in protein-protein interactions mediated by diseases, which can reveal disease mechanisms and identify new therapeutic targets.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemical Research Methods
Smarajit Mondal, Muthukumar Ramanathan, Weili Miao, Robin M. Meyers, Deepti Rao, Vanessa Lopez-Pajares, Zurab Siprashvili, David L. Reynolds, Douglas F. Porter, Ian Ferguson, Poornima Neela, Yang Zhao, Lindsey M. Meservey, Margaret Guo, Yen-Yu Yang, Lin Li, Yinsheng Wang, Paul A. Khavari
Summary: DNA-protein interactions play a crucial role in gene regulation and can be affected by DNA variants associated with polygenic diseases. A new method called PROBER has been developed to rapidly identify and quantify proteins associated with specific DNA sequences in living cells. PROBER utilizes high-copy episomes and proximity proteomics to accurately identify transcription factors and gene regulators associated with target DNA sequences and single-nucleotide variants. The method has been used to study the impact of cancer hotspot mutations on regulator associations.
Article
Oncology
Madison T. Wright, Lars Plate
Summary: The endoplasmic reticulum (ER) plays a crucial role in processing the human proteome, with mass spectrometry technology being key in understanding protein quality control mechanisms. There are still unexplored areas in ER proteostasis where mass spectrometry can be utilized to expand our understanding of protein quality control processes in diverse diseases.
EXPERIMENTAL CELL RESEARCH
(2021)
Article
Chemistry, Analytical
Goksu Ozcelikay, Ahmet Cetinkaya, Esen Bellur Atici, Sibel A. Ozkan
Summary: In this study, an electroanalytical quantification method for sugammadex was developed using molecular imprinting via the electropolymerization technique. The EP-MIP(SUG)/SPAuE sensor exhibited high sensitivity and specificity/selectivity, as demonstrated by its ability to detect sugammadex in biological fluids and differentiate it from similar molecules. The EP-MIP(SUG)/SPAuE sensor showed good analytical performance and validation parameters according to ICH guidelines, making it a promising tool for quantitative analysis of sugammadex in various samples.
ANALYTICAL METHODS
(2023)
Article
Chemistry, Analytical
Frederic Dewez, Edwin De Pauw, Ron M. A. Heeren, Benjamin Balluff
Summary: The multilabel approach in quantitative mass spectrometry imaging provides more accurate quantitation compared to a single-label approach, particularly when the target compound is unevenly distributed at a wide concentration range in the tissue.
ANALYTICAL CHEMISTRY
(2021)
Article
Engineering, Environmental
Yufeng Gong, Diwen Yang, Holly Barrett, Jianxian Sun, Hui Peng
Summary: Advancements in nontargeted analysis have allowed for the detection of multiple chemical contaminants. However, environmental toxicology approaches are lacking, impeding the transition to health risk assessment. A protein-guided approach called APNA has been developed to screen bioactive chemical contaminants at the exposome-wide level. This approach utilizes a tagged functional protein to isolate and identify contaminants, leading to the discovery of new ligands and protein targets. A proposed framework, eCPIN, aims to establish a comprehensive map of interactions between chemical contaminants and human proteins to facilitate screening and identification at a proteome-wide level.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Biochemical Research Methods
Alexis Chang, Mario Leutert, Ricard A. Rodriguez-Mias, Judit Villen
Summary: Phosphotyrosine (pY) enrichment is critical for understanding cellular signaling through mass spectrometry-based proteomics. However, current methods are expensive and not highly reproducible. We present a new method called R2-pY that can handle multiple samples in parallel, has high reproducibility, and produces comprehensive proteomic and phosphoproteomic samples. R2-pY extends our previous proteomic sample preparation framework and allows for large-scale studies of pY signaling.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Cell Biology
Devanarayanan Siva Sankar, Joern Dengjel
Summary: Autophagy is a crucial cellular degradation process that helps in maintaining cellular homeostasis through the clearance of damaged organelles and harmful substances. Protein-protein interaction networks play a key role in regulating autophagy, contributing to the degradation process and maintaining cellular function.
Article
Chemistry, Analytical
Fenglong Jiao, Fangyuan Gao, Yuanyuan Liu, Zhiya Fan, Xiaochao Xiang, Chaoshuang Xia, Yayao Lv, Yuping Xie, Haihong Bai, Wanjun Zhang, Weijie Qin, Xiaohong Qian
Summary: Small extracellular vesicles (SEVs) are cell-derived nanometer-sized vesicles that play vital roles in diseases and biomarker research. Current techniques for SEVs isolation face challenges, but Ti4+-modified magnetic graphene-oxide composites may offer a new approach for phosphoproteome studies of SEVs.
Review
Biochemistry & Molecular Biology
Roberto Giambruno, Francesco Nicassio
Summary: Proximity ligation technologies are powerful tools for studying RNA-protein interactions in living cells. They use inducible enzymes to biotinylate molecules within a 20 nm range, allowing for easy purification and analysis. These methods have been widely used to map molecular interactions and can also be used to study post-transcriptional modifications.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemical Research Methods
Zikai Hao, Leyuan Li, Zhibin Ning, Xu Zhang, Janice Mayne, Kai Cheng, Krystal Walker, Hong Liu, Daniel Figeys
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2020)
Article
Biochemical Research Methods
Kai Cheng, Zhibin Ning, Xu Zhang, Leyuan Li, Bo Liao, Janice Mayne, Daniel Figeys
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2020)
Article
Microbiology
Leyuan Li, Zhibin Ning, Xu Zhang, Janice Mayne, Kai Cheng, Alain Stintzi, Daniel Figeys
Article
Cell Biology
Sabrina Robichaud, Garrett Fairman, Viyashini Vijithakumar, Esther Mak, David P. Cook, Alexander R. Pelletier, Sylvain Huard, Barbara C. Vanderhyden, Daniel Figeys, Mathieu Lavallee-Adam, Kristin Baetz, Mireille Ouimet
Summary: The study identified multiple lipid droplet-associated proteins involved in lipophagy in macrophages, highlighting their importance in the process. Targeting these proteins to enhance lipophagy for promoting cholesterol efflux in foam cells may represent a novel therapeutic strategy for atherosclerosis.
Article
Chemistry, Analytical
Xu Zhang, Kai Cheng, Zhibin Ning, Janice Mayne, Krystal Walker, Hao Chi, Charles L. Farnsworth, Kimberly Lee, Daniel Figeys
Summary: This study demonstrates that serial enrichment using motif antibodies can capture peptides containing lysine acetylation, propionylation, and succinylation from human gut microbiome samples, providing a new bioinformatic workflow for the study of lysine acylations in the microbiome. The characterization of modification-specific metaproteomes reveals differential distribution of lysine acylations in microbial species with different metabolic capabilities.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Amanda E. Starr, Shelley A. Deeke, Zhibin Ning, Joseph de Nanassy, Ruth Singleton, Eric Benchimol, David R. Mack, Alain Stintzi, Daniel Figeys
Summary: Proteomic and bioinformatic analyses were conducted on colon biopsies from treatment-naive pediatric patients with IBD to characterize disease pathogenesis, revealing distinct proteomic patterns in inflamed and noninflamed tissues. Comparing pre- and post-treatment proteomes from CD patients identified proteins associated with therapy response, such as creatine kinase B and basigin.
JOURNAL OF PROTEOME RESEARCH
(2021)
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
Biochemical Research Methods
Kai Cheng, Zhibin Ning, Leyuan Li, Xu Zhang, Joeselle M. Serrana, Janice Mayne, Daniel Figeys
Summary: The studies of microbial communities have become increasingly important in various fields, and metaproteomics is a powerful tool for interpreting the roles of community members. However, analyzing metaproteomic data sets at the genome resolution is still challenging. In this study, a specially designed tool called MetaLab-MAG was developed for characterizing microbiomes from metagenome-assembled genome databases.
JOURNAL OF PROTEOME RESEARCH
(2022)
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
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)
