Article
Chemistry, Medicinal
Md Abdus Shukur Imran, Monica Carrera, Sara Perez-Polo, Jaime Perez, Lorena Barros, Sonia Dios, Camino Gestal
Summary: The common octopus (Octopus vulgaris) is highly sought after for human consumption and has also been considered for aquaculture diversification. The octopus ink, a by-product in seafood processing, has been found to have antimicrobial and antioxidant properties. In this study, advanced proteomics techniques were used to create a reference dataset of peptides from octopus ink and investigate its bioactive potential. Various immune functioning proteins and bioactive peptides with potential health benefits, such as antimicrobial and antioxidant properties, were identified. These findings contribute to the development of pharmacological and functional food products.
Article
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana Belen Bravo, Maria del Pilar Chantada-Vazquez, Carmen Pena, Elio Diez-Feijoo, Pablo Hervella, Isabel Lema
Summary: This study utilized a qualitative approach to explore the tear proteome of patients with keratoconus (KC), finding that the expression of certain proteins in tears of KC patients differed from the control group. These differences were linked to processes such as cell death, oxidative damage, and inflammation.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Article
Biochemical Research Methods
Sergio Ciordia, Gloria Alvarez-Sola, Maria Rullan, Jesus M. Urman, Matias A. Avila, Fernando J. Corrales
Summary: The analysis of biological fluids for disease-related proteins is an important field of research. However, challenges exist, especially in complex matrices like bile. A new procedure described in this study significantly improves protein recovery from rat bile, providing valuable resources for further understanding disease molecular markers.
JOURNAL OF PROTEOMICS
(2021)
Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Article
Plant Sciences
Zdenek Perutka, Katerina Kaduchova, Ivo Chamrad, Jana Beinhauer, Rene Lenobel, Beata Petrovska, Veronique Bergougnoux, Jan Vrana, Ales Pecinka, Jaroslav Dolezel, Marek Sebela
Summary: Proteins play a crucial role in the structure and function of the nuclear genome, but our knowledge of their functions, especially in plant chromosomes, remains incomplete. A study using flow cytometry purified barley mitotic metaphase chromosomes and characterized their proteins, identifying various chromosomal proteins including histones and topoisomerase. This research enhances our understanding of plant chromosomal proteins and provides a basis for further functional characterization and comparative phylogenetic analyses.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Wen-Jen Lin, Pei-Chun Shen, Hsiu-Cheng Liu, Yi-Chun Cho, Min-Kung Hsu, I-Chen Lin, Fang-Hsin Chen, Juan-Cheng Yang, Wen-Lung Ma, Wei-Chung Cheng
Summary: LipidSig is a flexible and user-friendly web server designed to help users identify significant lipid-related features and advance the field of lipid biology through efficient data analysis and exploration of lipid characteristics.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Analytical
Carolina Rojas Ramirez, Jessica A. Espino, Lisa M. Jones, Daniel A. Polasky, Alexey I. Nesvizhskii
Summary: Monitoring protein structure before and after environmental alterations can provide insights into protein function. Fast photochemical oxidation of proteins (FPOP) coupled with mass spectrometry allows for monitoring of structural rearrangements by exposing proteins to radicals. However, the challenges of processing FPOP data have limited its proteome-scale uses. In this study, a computational workflow was developed to analyze FPOP data sets more efficiently, enabling the identification of modified peptide spectra at a faster rate than previous methods.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Joanna Perla-Kajan, Agata Malinowska, Jarosl Aw Zimny, Dominik Cysewski, Joanna Suszynska-Zajczyk, Hieronim Jakubowski
Summary: Protein N-homocysteinylation, a newly recognized post-translational modification, has been identified in both in vivo and in vitro settings in yeast. This modification, induced by elevated levels of Hcy-thiolactone, leads to significant changes in the yeast proteome and may contribute to cellular toxicity. The findings suggest that N-homocysteinylation and proteostasis dysregulation could play a role in Hcy-related pathophysiology in humans and animals.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Mehar Un Nissa, Nevil Pinto, Arijit Mukherjee, Panga Jaipal Reddy, Biplab Ghosh, Zhi Sun, Saicharan Ghantasala, Chetanya Chetanya, Sanjyot Vinayak Shenoy, Robert L. Moritz, Mukunda Goswami, Sanjeeva Srivastava
Summary: Proteomic studies on Labeo rohita provided a comprehensive organ-based protein profiling, identifying a large number of proteins and global post-translational modifications. These findings offer important insights for basic and applied research in aquaculture field.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Analytical
Qianqian Wang, Xin Yan, Bin Fu, Ying Xu, Lingjun Li, Cheng Chang, Chenxi Jia
Summary: Characterization of protein arginine dimethylation is challenging due to its substoichiometric level. To address this, a targeted MS/MS workflow was established using the mNeuCode tag for proteome-wide discovery of dimethylation sites. By applying this approach, 176 arginine dimethylation sites on 70 proteins in HeLa cells were identified, including novel sites on the protein FAM98A. Deletion of FAM98A suppressed cell migration, and mutation of the dimethylation sites also showed this effect, suggesting the involvement of the PRMT1-FAM98A pathway. Our study highlights the potential of NeuCode-enabled techniques in targeted proteome analysis of substoichiometric biomolecules.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Tyler S. Larson, Thomas J. Diprospero, Gary L. Glish, Matthew R. Lockett
Summary: In this study, a novel method was used to investigate the lipid profile changes in oxaliplatin-sensitive and resistant cells, revealing significant increases in triglycerides and cholesterol esters caused by oxaliplatin, which were correlated with lipid droplet formation.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Ayako Takemori, Philipp T. Kaulich, Liam Cassidy, Nobuaki Takemori, Andreas Tholey
Summary: The combination of liquid chromatography (LC) and gas-phase separation by field-asymmetric ion mobility spectrometry (FAIMS) is a powerful proteoform separation system for top-down proteomics. In this study, an in-depth top-down proteomics workflow, GeLC-FAIMS-MS, was presented, which utilized a molecular-weight-based proteome fractionation approach using SDS-poly-acrylamide gel electrophoresis. The authors optimized the MS parameters for each gel band and compensating voltage (CV) to improve the identification of proteoforms. They also developed a simple and cost-effective method, combining the PEPPI protocol with an AnExSP method, for stain and SDS removal. Results showed that this method was better suited for low-molecular-weight proteoforms, while a methanol-chloroform-water (MCW)-based protocol showed advantages for higher-molecular-weight proteoforms.
ANALYTICAL CHEMISTRY
(2022)
Review
Immunology
Laura A. Solt
Summary: T cells transition from a quiescent state to active proliferation and effector function upon exposure to cognate antigen, a process tightly controlled by signal transduction pathways. Dysregulation of these events can mediate disease, and recent sequencing advances at the single-cell level have improved our understanding of T cell biology.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Agriculture, Multidisciplinary
Xianlin Han, Hongping Ye
Summary: Although triglycerides play important roles in cellular growth, metabolism, and function, accurately identifying their molecular species and quantities remains a challenge.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Dany Dominguez-Perez, Daniela Almeida, Josef Wissing, Andre M. Machado, Lothar Jansch, Agostinho Antunes, Luis Filipe Castro, Vitor Vasconcelos, Alexandre Campos, Isabel Cunha
Summary: This study focused on the adhesive system of the stalked goose barnacle L. anatifera, identifying a variety of proteins including cement specific adhesive proteins, proteases, protease inhibitors, and other structural proteins. Through shotgun proteomic analysis, the researchers identified and quantified peptide sequences in the adhesive gland and cement, providing insight into the composition of the adhesive proteins. The study also identified unannotated proteins with similar properties to known CPs and demonstrated the importance of Principal Components Analysis in identifying non-conserved adhesive proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)