Article
Biochemical Research Methods
Jinjun Gao, Yuan Liu, Fan Yang, Xuemin Chen, Benjamin F. Cravatt, Chu Wang
Summary: ABPP is a powerful chemical proteomic method for studying protein activity, modifications, and interactions, where accurate quantification is crucial. CIMAGE is a specialized quantification software for ABPP data analysis, providing efficient and accurate quantification with the ability to visualize results conveniently.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Paulina Grocholska, Marta Kowalska, Remigiusz Bachor
Summary: The analysis of saliva using metabolomics and proteomics is a valuable method for screening drugs, their metabolites, and biomarkers of diseases. Liquid chromatography coupled with mass spectrometry is the commonly used technique for saliva analysis. Challenges in identifying compounds by mass spectrometry and the need for isotopically labelled standards in quantitative analysis are discussed in this review. The advances and future prospects of mass spectrometry in salivary metabolomics and proteomics are presented, which can contribute to improved diagnostics and forensic investigations.
Article
Food Science & Technology
Jing Pu, Bingye Zhao, Xin Liu, Shugang Li, Beibei Wang, Di Wu, Jinqiu Wang, Fang Geng
Summary: This study comprehensively compared the protein profiles and properties of chicken egg white and its three components. The proteomes of thick and thin egg white are similar, but thick egg white has higher abundance of ovomucin subunits and lysozymes. The properties of thick and thin egg white are significantly different. Additionally, the chalaza component has higher abundance of insoluble proteins and lower abundance of soluble proteins, which explains its insolubility. These findings are important for further research and development of egg white, such as thinning of egg white, understanding changes in egg white properties, and differential application of thick and thin egg white.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Dianqin Xu, Xiaoyu Zhu, Ji Ren, Shan Huang, Ziwen Xiao, Hongmei Jiang, Yujie Tan
Summary: In this study, tandem mass tags-labeled quantitative proteomic technology and bioinformatics tools were used to analyze exfoliated cervical cells from normal and cervical cancer groups. A cancer-specific protein profile was established, leading to the identification of key proteins related to cervical cancer development. These differentially expressed proteins were found to be involved in various cellular processes and signaling pathways, laying the foundation for understanding the molecular mechanisms of cervical cancer.
JOURNAL OF PROTEOMICS
(2022)
Article
Biochemical Research Methods
Dmitry B. Eremin, Valery V. Fokin
Summary: Supercharging reagents can enhance protein ionization by increasing charge states and signal intensities, leading to improved sensitivity. This study presents a method of utilizing a dual-spray ionization source with DMSO as a supercharging reagent to expand in-source supercharging.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Applied
Sridevi Muralidharan, Yan Yee Poon, Graeme C. Wright, Paul A. Haynes, Nanju A. Lee
Summary: This study used mass spectrometry-based proteomic analysis on Australian peanut recombinant inbred lines and found significant protein expression differences between high and low polyphenol expressing RILs. Metabolic changes, including increased enzymatic breakdown of sugars and phenylalanine biosynthesis, were observed in polyphenol-rich RILs. The study also revealed overexpression of phenylpropanoid pathway and antioxidant enzymes, such as catalase, in the polyphenol-rich peanut phenotype.
Article
Cardiac & Cardiovascular Systems
Jingyuan Hou, Qiaoting Deng, Sudong Liu, Xiaohong Qiu, Xunwei Deng, Wei Zhong, Zhixiong Zhong
Summary: This study investigated the differences in plasma protein profiles between patients with in-stent restenosis (ISR), non-ISR patients, and healthy controls. The findings revealed several differentially abundant proteins that are involved in important biological processes and signaling pathways related to ISR. The identified proteins, including fetuin-B, apolipoprotein C-III (APOC3), and cholesteryl ester transfer protein (CETP), could potentially serve as early diagnostic biomarkers and therapeutic targets for ISR.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Biochemical Research Methods
Dongjin Qing, Yan Zhou, Yinghua Pan, Xinghai Yang, Jingcheng Li, Weiyong Zhou, Haifu Liang, Weiwei Chen, Lei Chen, Chunju Lu, Gaoxing Dai, Guofu Deng
Summary: This study identified several proteins regulated by grain length in indica rice using quantitative proteomics approach. The results revealed potential signaling pathways for grain size regulation and highlighted the inconsistency between transcription levels and protein content. These findings contribute to a better understanding of the mechanisms underlying grain length regulation in rice.
JOURNAL OF PROTEOMICS
(2023)
Article
Pharmacology & Pharmacy
Bridget L. Morse, John K. Fallon, Anil Kolur, Andrew T. Hogan, Philip C. Smith, Kathleen M. Hillgren
Summary: Hepatic clearance may be limited by organic anion transporting polypeptides (OATPs) and organic cation transporter 1 (OCT1), with little reported on OCT1 activity across species. Expression of transporters, including Oatps and Octs, varies between tissues in mice and rats, with higher Octs expression in the kidney compared to the liver. Liver partitioning of OCT1 substrates is lower in rodents compared to monkeys, reflecting species-dependent OCT1 activity.
Article
Chemistry, Analytical
Xuefei Zhong, Shruti Nayak, Lili Guo, Shivkumar Raidas, Yunlong Zhao, Rachel Weiss, Matthew Andisik, Chinnasamy Elango, Giane Sumner, Susan C. Irvin, Michael A. Partridge, Hong Yan, Sook E. Yen, Haibo Qiu, Yuan Mao, Albert Torri, Ning Li
Summary: REGEN-COV, a cocktail of two human monoclonal antibodies, has shown promising results in reducing SARS-CoV-2 viral load in COVID-19 patients. A liquid chromatography-mass spectrometry method was developed for the determination of REGEN-COV concentrations in serum samples from patients participating in clinical trials. The concentrations measured by this method were comparable to those measured by a validated immunoassay.
ANALYTICAL CHEMISTRY
(2021)
Article
Plant Sciences
Muhammad Afzal, Malte Sielaff, Valentina Curella, Manjusha Neerukonda, Khaoula El Hassouni, Detlef Schuppan, Stefan Tenzer, C. Friedrich H. Longin
Summary: The study analyzed the expression of 756 proteins across 150 wheat cultivars using proteomics and found that environmental conditions have a significant impact on protein expression. Wheat cultivars varied greatly in their protein profiles, with 114 proteins being crucial for bread quality and human health.
Article
Chemistry, Analytical
Casey J. Chen, Evan R. Williams
Summary: This study demonstrates the use of theta glass emitters to rapidly mix two solutions and measure the products using electrospray ionization mass spectrometry. The position of the emitter significantly affects the composition of the droplets and the reaction kinetics.
ANALYTICAL CHEMISTRY
(2023)
Article
Neurosciences
Sahil H. Shah, Lucio M. Schiapparelli, Satoshi Yokota, Yuanhui Ma, Xin Xia, Sahana Shankar, Sarah Saturday, Michael Nahmou, Catalina Sun, John Yates, Hollis T. Cline, Jeffrey L. Goldberg
Summary: In this study, a new in vivo quantitative measure of newly synthesized proteins was developed and applied to examine the changes in the retina after optic nerve injury. The results revealed a dynamic translational response within broader proteostasis regulation, enhancing our understanding of the cellular response to injury.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Juan J. Roman-Camacho, Juan C. Mauricio, Ines M. Santos-Duenas, Teresa Garcia-Martinez, Isidoro Garcia-Garcia
Summary: This study analyzed the protein profile of vinegar microbiota using liquid chromatography-tandem mass spectrometry, focusing on the Komagataeibacter species, particularly K. europaeus. The results showed that the majority of identified proteins involved in amino acid metabolism, protein biosynthesis, and energy production pathways increased their expression during the cycle loading phase and then decreased, with other proteins coming into play against acetic acid stress. These findings help predict the natural behavior of a microbial community in vinegar and contribute to obtaining a quality product.
Article
Biochemical Research Methods
Neil A. McCracken, Sarah A. Peck Justice, Aruna B. Wijeratne, Amber L. Mosley
Summary: The study introduces a user-friendly analysis of the melt shift calculation workflow and quantitatively assesses the impact of key steps in the analysis workflow on the final output list of stabilized and destabilized proteins. It also presents a more optimized analysis workflow, illustrating the importance of selected calculation steps on the final list of reported proteins of interest in a study. The development of the R based program Inflect offers a valuable resource for the research community to analyze data from TPP and CETSA experiments.
JOURNAL OF PROTEOME RESEARCH
(2021)