Article
Biochemical Research Methods
Andikan J. Nwosu, Santosh A. Misal, Thy Truong, Richard H. Carson, Kei G. Webber, Nathaniel B. Axtell, Yiran Liang, S. Madisyn Johnston, Kenneth L. Virgin, Ethan G. Smith, George Thomas, Terry Morgan, John C. Price, Ryan T. Kelly
Summary: This study modified a sample processing workflow to extract proteins from FFPE tissues and analyze protein expression. By optimizing the extraction conditions, a high-confidence proteome was obtained, and the protein coverage for FFPE tissues reached 88% compared to frozen tissues.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Yoonsung Joh, Kangbae Lee, Hyunwoo Kim, Heejin Park
Summary: A novel approach, called progressive search, efficiently obtains analysis results for updated databases in tandem mass spectrometry. Compared to performing a normal search from scratch, progressive search achieves the same results much faster.
BMC BIOINFORMATICS
(2023)
Article
Chemistry, Analytical
Daoyang Chen, Zhichang Yang, Xiaojing Shen, Liangliang Sun
Summary: Top-down proteomics (TDP) is an ideal approach for deciphering the histone code and requires new analytical tools with high-capacity separation and highly sensitive detection of proteoforms. In this study, capillary zone electrophoresis (CZE) -MS/MS was used to identify a large number of histone proteoforms with higher sensitivity compared to traditional methods.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Surendhar Reddy Chepyala, Xueyan Liu, Ka Yang, Zhiping Wu, Alex M. Breuer, Ji-Hoon Cho, Yuxin Li, Ariana Mancieri, Yun Jiao, Hui Zhang, Junmin Peng
Summary: JUMPt is a software package that uses an ODE-based mathematical model to determine reliable rates of protein degradation, taking into account amino acid recycling and fitting the kinetics of labeled amino acids and the whole proteome to derive individual protein half-lives. Multiple settings in the software allow for simple to comprehensive data inputs, enabling flexible analysis of half-lives.
ANALYTICAL CHEMISTRY
(2021)
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.
Article
Microbiology
Charlotte Mappa, Beatrice Alpha-Bazin, Olivier Pible, Jean Armengaud
Summary: Shotgun proteomics is a promising alternative technique for identifying pathogens and characterizing their antimicrobial resistance genes. Proteotyping microorganisms through tandem mass spectrometry is expected to be essential in modern healthcare, and it also plays a crucial role in developing new biotechnological applications through culturomics. Phylopeptidomics is a new strategy that improves the quantification of microbial contributions by estimating phylogenetic distances and calculating the ratio of shared peptides. The study established the limit of detection for tandem mass spectrometry proteotyping and demonstrated the independence of bacterial identification by phylopeptidomics from their growth stage and the robustness of the method in the presence of additional bacteria.
Article
Biochemistry & Molecular Biology
Zhuokun Du, Qianying Yang, Yuanyuan Liu, Sijie Chen, Hongxian Zhao, Haihong Bai, Wei Shao, Yangjun Zhang, Weijie Qin
Summary: N-glycosylation and phosphorylation are important posttranslational modifications in biological processes. Simultaneous characterization of these modifications is challenging, especially for tiny amount of samples obtained in tissue biopsy. This study introduces a new strategy for the efficient tandem enrichment of N-glycopeptides and phosphopeptides using HILIC and TiO2 microparticles.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Makoto Inoue, Hideaki Suzuki, Kohji Meno, Shan Liu, Tatsumi Korenaga, Kazuhiko Uchida
Summary: The study developed a blood test based on LC-MS/MS to detect plasma proteins that can be used to identify mild cognitive impairment and Alzheimer's disease. They identified eight plasma protein biomarkers that can differentiate between MCI and AD. The clinical potential of these biomarkers was evaluated using ROC analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Neurosciences
Changci Tong, Peifang Cong, Ying Liu, Xiuyun Shi, Lin Shi, Shun Mao, Yan Zhao, Mingxiao Hou, Yunen Liu
Summary: This study utilized TMT labeling combined with LC-MS/MS to identify differentially expressed proteins in rat brain tissues at various time points after chest blast exposure. A total of 6931 proteins were identified, with 255 showing differential expression. GO, KEGG, COG, and STRING analyses indicated that chest blast-induced brain damage involves multiple important biological processes and signaling pathways, such as inflammation, cell adhesion, phagocytosis, neuronal and synaptic damage, oxidative stress, and apoptosis.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2021)
Article
Microbiology
Clement Lozano, Melodie Kielbasa, Jean-Charles Gaillard, Guylaine Miotello, Olivier Pible, Jean Armengaud
Summary: The exploration of marine microorganisms and their functions is still in its infancy. The diversity they possess can provide a wealth of knowledge and resources, emphasizing the importance of developing efficient identification and characterization techniques. In this study, a cutting-edge proteotyping technique called phylopeptidomics was used to identify 26 microbial isolates from coastal water in the NW Mediterranean Sea. The study successfully classified all isolates at the species level and noted the presence of strains from the newly described Balneolaeota phylum.
Review
Biochemistry & Molecular Biology
Anca-Narcisa Neagu, Madhuri Jayathirtha, Emma Baxter, Mary Donnelly, Brindusa Alina Petre, Costel C. Darie
Summary: Mass spectrometry enables the analysis of proteins and peptides, including identification of mass, amino acid sequence, and post-translational modifications. In biomedical research, mass spectrometry can be used to identify relevant biomarkers for diagnostic and therapeutic purposes.
Article
Biochemical Research Methods
Dahang Yu, Zhe Wang, Kellye A. Cupp-Sutton, Yanting Guo, Qiang Kou, Kenneth Smith, Xiaowen Liu, Si Wu
Summary: A top-down TMT MS platform for confidently identifying and quantifying low molecular weight intact proteoforms in complex biological samples was developed by combining filter-SEC technique with high-performance size exclusion chromatography. This technique enables high-throughput analysis of intact proteoforms from Escherichia coli cell lysates, representing the first high-throughput TMT labeling-based, quantitative, top-down MS analysis suitable for complex biological samples.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Danting Liu, Shu Yang, Kanisha Kavdia, Jeffrey M. Sifford, Zhiping Wu, Boer Xie, Zhen Wang, Vishwajeeth R. Pagala, Hong Wang, Kaiwen Yu, Kaushik Kumar Dey, Anthony A. High, Geidy E. Serrano, Thomas G. Beach, Junmin Peng
Summary: A streamlined protocol has been developed to quantify over 9000 proteins with 0.5 μg of protein using 16-plex TMT coupled with LC/LC-MS/MS. Comparison with the standard protocol in 16 human brain tissue samples showed that the microgram-scale protocol had adequate sensitivity and reproducibility to detect differentially expressed proteins in disease-related pathways. This newly developed method holds promise for deep proteomic analysis at sub-microgram levels in biological and clinical samples.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Meletia Kallianta, Eftychia Pappa, Heleni Vastardis, Christos Rahiotis
Summary: Mass Spectrometry (MS) is a highly sensitive and universal analytical technique that has rapidly developed in recent decades. It has various applications in dentistry, including research on dental materials and agents, laboratory analysis of biospecimens, and real-time diagnostics in oral surgery and pathology. MS can provide valuable insights into the clinical behavior, toxicity, antimicrobial properties, and biomarkers of dental materials and agents. It is also effective in detecting biomarkers in saliva and providing a comprehensive understanding of cellular functions through metabolite analysis. Additionally, MS shows promising potential for surgical approaches to oral malignant disorders. Overall, MS has revolutionized dental research and has the potential to advance personalized dentistry.
Article
Biochemistry & Molecular Biology
Jacky M. K. Kwong, Joseph Caprioli, Joanne C. Y. Lee, Yifan Song, Feng-Juan Yu, Jingfang Bian, Ying-Hon Sze, King-Kit Li, Chi-Wai Do, Chi-Ho To, Thomas Chuen Lam
Summary: This study investigated the proteomic changes in the retina after optic nerve transection in rats. Using high-resolution mass spectrometry, they identified several differentially expressed proteins related to retinal ganglion cell damage, such as ALDH1A1 and SNCG.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)