Article
Biochemical Research Methods
Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev, Jason Derks, Edward Emmott, Alexander M. Franks, Alexander R. Ivanov, Ryan T. Kelly, Luke Khoury, Andrew Leduc, Michael J. MacCoss, Peter Nemes, David H. Perlman, Aleksandra A. Petelski, Christopher M. Rose, Erwin M. Schoof, Jennifer Van Eyk, Christophe Vanderaa, John R. R. Yates III, Nikolai Slavov
Summary: Analyzing proteins from single cells by tandem mass spectrometry (MS) has the potential to accurately quantify thousands of proteins across thousands of single cells. However, various factors affecting experimental design, sample preparation, data acquisition and analysis may undermine the accuracy and reproducibility of the results. Best practices, quality controls, and data-reporting recommendations are proposed to enhance the reliability of quantitative workflows for single-cell proteomics.
Article
Multidisciplinary Sciences
Yuliya Korolkova, Alexander Mikov, Anna Lobas, Elizaveta Solovyeva, Alexey Surin, Yaroslav Andreev, Mikhail Gorshkov, Sergey Kozlov
Summary: This study conducted transcriptome and proteome analysis on the venom of Tibellus oblongus spider, revealing the presence of several new toxins.
Review
Nutrition & Dietetics
Ana G. Abril, Manuel Pazos, Tomas G. Villa, Pilar Calo-Mata, Jorge Barros-Velazquez, Monica Carrera
Summary: Bioactive peptides have various health benefits and can be identified and quantified through proteomics. They have the potential to be a source of novel drugs and ingredients in food and pharmaceuticals.
Article
Chemistry, Applied
Tessa B. Moyer, Wyatt J. Schug, Leslie M. Hicks
Summary: This study utilizes in silico predictions, proteomics, and simulated gastrointestinal digestions to identify digestion resistant cysteine-rich peptides (CRPs) within Amaranthus hypochondriacus seeds. Thirteen in silico predicted CRPs were detected in a seed extract, providing evidence for the translation of five CRP families. Mature forms of six CRPs were characterized via top-down proteomics, revealing multiple post translational modifications. All six peptides demonstrated resistance to simulated gastrointestinal digestion, suggesting that A. hypochondriacus CRPs may exhibit bioactivity after consumption and should be prioritized for further characterization.
Article
Food Science & Technology
Giovanna Lippe, Barbara Prandi, Tiziana Bongiorno, Francesca Mancuso, Emilio Tibaldi, Andrea Faccini, Stefano Sforza, Mara Lucia Stecchini
Summary: The study found that a starvation period before slaughtering in farmed sea bream affects quality attributes, with starved fish fillets showing higher susceptibility to protein degradation at slaughter, leading to increased in vitro gastric digestibility at 4 degrees Celsius storage. Additionally, using UHPLC-MS/MS, it was discovered that starvation may increase the levels of ACE-inhibitor gastric-resistant bioactive peptides in sea bream fillets.
EUROPEAN FOOD RESEARCH AND TECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Emmanouil Mavrogeorgis, Harald Mischak, Agnieszka Latosinska, Justyna Siwy, Vera Jankowski, Joachim Jankowski
Summary: In recent years, CE-MS has been increasingly used in clinical research for chronic and age-associated diseases, allowing for comprehensive assessment of small molecular weight proteins and peptides. The study evaluated the analytical performance of CE-MS in terms of reproducibility, variability, and efficiency in peptide detection, showing high correlation among different runs and low variation in signal intensity. These findings support the value of CE-MS for clinical application.
Article
Chemistry, Multidisciplinary
Pin-Lian Jiang, Cong Wang, Anne Diehl, Rosa Viner, Chris Etienne, Premchendar Nandhikonda, Leigh Foster, Ryan D. Bomgarden, Fan Liu
Summary: Cross-linking mass spectrometry (XL-MS) is a useful method for studying protein structures and interactions. However, its application in vivo is limited. To address this limitation, researchers have developed a new cross-linker called tBu-PhoX and established a tBu-PhoX-based XL-MS approach. This approach allows for the identification of a large number of cross-links in intact human cells with reduced analysis time.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Food Science & Technology
Yanchao Wang, Yaoguang Chang, Hu Hou, Jingfeng Wang, Changhu Xue
Summary: This review discusses the latest developments in proteomics technologies for solving problems in blue foods, such as traceability, quality, safety, and nutrition evaluation. It highlights the successful applications of proteomics strategies in addressing these critical issues and identifies the challenges and future development trends in the field.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Florian Leonardus Rudolfus Lucas, Kumar Sarthak, Erica Mariska Lenting, David Coltan, Nieck Jordy van der Heide, Roderick Corstiaan Abraham Versloot, Aleksei Aksimentiev, Giovanni Maglia
Summary: This study enhanced the capture frequency and discrimination of peptides by introducing aromatic amino acids into nanopores. Molecular dynamics simulations identified the sensing region and microscopic mechanisms of nanopores, as well as the effects of pore modification on peptide discrimination in FraC.
Article
Biochemical Research Methods
Sunkyu Choi, Atilio Reyes Romero, Fathima Mashood, Neha Goswami, Lotfi Chouchane, Frank Schmidt
Summary: Protein turnover, the balance between protein synthesis and degradation, is essential for cellular protein homeostasis. This study aimed to analyze protein turnover in adipocytes using time-dependent SILAC labeling. The results revealed associations between protein half-lives and various cellular processes, including energy metabolism, RNA splicing, and Golgi complex. These findings contribute to a better understanding of adipocyte proteome dynamics and protein homeostasis maintenance.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Food Science & Technology
Huiyan Zhang, Shizhe Qi, Wenhao Yu, Shan Zhao, Yan Jin, Qiancheng Zhao, Yanxia Qi
Summary: In this study, anchovy antimicrobial peptides (AAMPs) were prepared and optimised from anchovy extracts. Proteomics analysis identified 4 unique peptides with inhibitory activity against E. coli and S. aureus. This work established a useful workflow for discovering novel AMPs from fish proteins, which could contribute to the development of effective antibiotics.
INTERNATIONAL JOURNAL OF FOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sara Perez-Polo, Md Abdus Shukur Imran, Sonia Dios, Jaime Perez, Lorena Barros, Monica Carrera, Camino Gestal
Summary: This study conducted the first proteomic analysis of the common octopus skin mucus proteome, identifying proteins related to defense and discussing the potential application of bioactive peptides in biomedicine, pharmaceutical, and nutraceutical industry.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Diana Valeria Rossetti, Ilaria Inserra, Alessia Nestico, Federica Vincenzoni, Federica Iavarone, Irene Messana, Massimo Castagnola, Luca Massimi, Gianpiero Tamburrini, Massimo Caldarelli, Claudia Desiderio
Summary: The study aimed to explore the intact proteome of pediatric brain tumors of different WHO grades and localizations to understand the molecular mechanisms underlying the onset and progression of these pathologies. Proteomic analysis revealed statistically significant differences in protein/peptide levels between tumor histotypes, as well as the identification of naturally occurring fragments and post-translational modifications. This study contributes to elucidating the molecular profiles of the most common solid tumors affecting children.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Jens Fritsche, Daniel J. Kowalewski, Linus Backert, Frederik Gwinner, Sonja Dorner, Martin Priemer, Chih-Chiang Tsou, Franziska Hoffgaard, Michael Romer, Heiko Schuster, Oliver Schoor, Toni Weinschenk
Summary: Knowledge about the peptide repertoire presented by human leukocyte antigens (HLA) is crucial for unlocking target-specific cancer immunotherapies, but with increasing immunopeptidomics datasets, the risk of misidentification and false annotation of HLA ligands is rising. This study introduces computational and experimental methods to identify fake ligands and emphasizes the importance of system suitability and detection of source fragmentation events. By focusing on high-throughput sequence verification and quality control, the study aims to uncover limitations and pitfalls in existing datasets to identify true HLA ligands.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Review
Chemistry, Analytical
Rachel M. Miller, Lloyd M. Smith
Summary: Proteins are crucial actors in cells, and understanding the complexity of the proteome is important for scientific research and clinical applications. Mass spectrometry-based proteomics is a key method for protein analysis, but further advancements are needed for a more comprehensive view of the proteome.