Article
Agriculture, Multidisciplinary
Mahya Bahmani, Angela Juhasz, Utpal Bose, Mitchell G. Nye-Wood, Malcolm Blundell, Crispin A. Howitt, Michelle L. Colgrave
Summary: In this study, the proteome profile of barley grain and malt samples was investigated using SWATH-MS proteomics. The results showed that the C-hordein-reduced lines had a more significant impact on proteome level changes during malting. Upregulated proteins in C-hordein-reduced lines were mainly involved in the tricarboxylic acid cycle and fatty acid peroxidation processes. Proteomics approaches in hordein-reduced barley lines after malting also revealed additional changes in the proteome driven by the genetic background. These findings provide valuable insights for barley breeders and maltsters to optimize gluten-free grains in malt products.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemical Research Methods
Martina Milighetti, Lukas Krasny, Alex T. J. Lee, Gabriele Morani, Cornelia Szecsei, Yingtong Chen, Nafia Guljar, Frank McCarthy, Christopher P. Wilding, Amani Arthur, Cyril Fisher, Ian Judson, Khin Thway, Maggie C. U. Cheang, Robin L. Jones, Paul H. Huang
Summary: Proteomic profiling of STS patients across different histological subtypes using SWATH-MS revealed enrichment of specific gene sets in each subtype. A subgroup of STS cases with distinct protein expression profiles and poorer survival outcomes was identified. Comprehensive proteomic characterization may help identify histotype-specific profiles and new prognostic biomarkers in rare and challenging-to-treat diseases like STS.
JOURNAL OF PROTEOMICS
(2021)
Article
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana B. Bravo, Maria del Pilar Chantada-Vazquez, Ruben Varela-Fernandez, Paulo Avila-Gomez, Pablo Hervella, Isabel Lema
Summary: Utilizing SWATH-MS for tear protein quantification, dysregulated proteins involved in iron homeostasis, inflammatory-immune response, oxidative stress, and other biological processes were identified in patients with keratoconus. The study sheds light on the molecular mechanisms underlying the disease and highlights the potential therapeutic targets related to iron accumulation and tissue damage in keratoconus pathophysiology.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Biochemical Research Methods
Sarah K. Osama, Edward D. Kerr, Adel M. Yousif, Toan K. Phung, Alison M. Kelly, Glen P. Fox, Benjamin L. Schulz
Summary: Germination is a critical process for flowering plant reproduction and industrial malting, while seed dormancy can lead to inefficiencies in malt production. Proteomic analysis identified significant changes during germination, including a rapid decrease in proteins involved in desiccation tolerance and germination inhibition, as well as reductions in lipid, protein, and nutrient reservoir storage. These consistent changes between laboratory and industrial scales demonstrate the utility of laboratory-scale germination as a model system for industrial malt house processes.
JOURNAL OF PROTEOMICS
(2021)
Article
Agriculture, Multidisciplinary
Mahya Bahmani, Angela Juhasz, James Broadbent, Utpal Bose, Mitchell G. Nye-Wood, Ian B. Edwards, Michelle L. Colgrave
Summary: This study analyzed the proteome and malt characteristics of three barley lines grown in different locations in Western Australia using LC-MS. The results showed a correlation between genetics, growing locations, proteins, and traits such as malt yield.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Francesco Finamore, Antonella Cecchettini, Elisa Ceccherini, Giovanni Signore, Francesco Ferro, Silvia Rocchiccioli, Chiara Baldini
Summary: In this pilot study, SWATH-MS approach was used to monitor extracellular vesicles-enriched saliva sub-proteome in pSS patients, revealing 121 differentially expressed proteins with 82% upregulated and 18% downregulated in pSS samples, mainly related to immune-innate response. The results highlight the usefulness of EVs for discovering novel salivary-omic biomarkers and offer new perspectives for the identification of clinically relevant proteins in pSS.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Oncology
Jhajaira M. Araujo, Gabriel De la Cruz-Ku, Melanie Cornejo, Franco Doimi, Richard Dyer, Henry L. Gomez, Joseph A. Pinto
Summary: This study evaluated the prognostic capability of a 3-gene score in different subtypes of triple negative breast cancer (TNBC). The results showed that the score was able to predict the risk of distant recurrence in the immunomodulatory and mesenchymal stem-like subtypes. Additionally, a low score was associated with a high level of tumor-infiltrating lymphocytes.
Article
Biochemistry & Molecular Biology
Paulina Czaplewska, Aleksandra E. Bogucka, Natalia Musial, Dmitry Tretiakow, Andrzej Skorek, Dominik Stodulski
Summary: The study aimed to explore protein components of human submandibular gland sialoliths matrix. Qualitative analysis was carried out using FASP methodology. By analyzing fragmentation spectra and using PEAKS Studio program, 254 human proteins and 393 bacterial proteins were identified in the sialolith extracts. The SWATH methodology was successfully applied for relative quantitative analysis of human proteins in deposits, providing a basis for further research.
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
Oncology
Bethany Geary, Erin Peat, Sarah Dransfield, Natalie Cook, Fiona Thistlethwaite, Donna Graham, Louise Carter, Andrew Hughes, Matthew G. Krebs, Anthony D. Whetton
Summary: TARGET (tumour characterisation to guide experimental targeted therapy) aims to match cancer patients entering early phase clinical trials to the best treatment based on their genetics, reducing the need for recruiting more patients. The study developed a Wellness Score using blood samples to predict patient survival more accurately than traditional performance status measurements. This score showed promising results in predicting overall survival and warrants further evaluation in larger patient populations.
Article
Oncology
Ammara Muazzam, Davide Chiasserini, Janet Kelsall, Nophar Geifman, Anthony D. Whetton, Paul A. Townsend
Summary: Prostate cancer is the third most common cancer in men globally. The PSA is the main protein biomarker used for diagnosis, staging, and monitoring, but it can lead to inaccurate diagnosis and overtreatment. Therefore, identifying novel biomarkers for prostate cancer can help improve the understanding of diagnosis and risk assessment.
Article
Chemistry, Analytical
Premy Shanthamoorthy, Adamo Young, Hannes Rost
Summary: This study quantitatively investigated the conditions necessary for unique metabolite detection in complex backgrounds using three benchmarked mass spectrometry (MS) methods. The results showed that DIA outperformed MS1-only and MRM-based methods in terms of specificity. Additionally, collision energy was identified as an important factor influencing unambiguous compound detection.
ANALYTICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Laura Darie-Ion, Danielle Whitham, Madhuri Jayathirtha, Yashveen Rai, Anca-Narcisa Neagu, Costel C. Darie, Brindusa Alina Petre
Summary: Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is widely used in proteomics for the structural identification and characterization of proteins and peptides, including their modified forms. MALDI-MS and MALDI-MS/MS offer sensitive analysis of small and large molecules, enabling direct analysis of biological samples with minimal preparation. MALDI-MS/MS has greatly aided in understanding the molecular function and involvement in disease pathogenesis of peptides and proteins. This review highlights the applications of MALDI-MS and MALDI-MS/MS for analyzing biomedical relevant proteins and peptides, including the use of MALDI-MSI for spatial analysis of molecular weight proteins in tissues.
Review
Biochemistry & Molecular Biology
Ekaterina Mikhailovna Stakhneva, Evgeniia Vitalievna Striukova, Yulia Igorevna Ragino
Summary: Proteomic studies play a crucial role in investigating atherosclerotic cardiovascular diseases, identifying potential biomarkers, and offering novel diagnostic approaches.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Rocco J. Rotello, Timothy D. Veenstra
Summary: In the era of genomics research, mass spectrometry has become a vital tool for quantitatively comparing proteins within cells and organisms, despite the complexity of identifying quantitative changes in proteomes due to their dynamic nature and limitations in technology coverage. The combined development of sample preparation and MS methods has enabled the quantitation of thousands of proteins obtained from cells and organisms.
CURRENT PROTEIN & PEPTIDE SCIENCE
(2021)
Article
Dentistry, Oral Surgery & Medicine
Alejandro Lorenzo-Pouso, Susana B. Bravo, Javier Carballo, Maria del Pilar Chantada-Vazquez, Jose Bagan, Leticia Bagan, Cintia M. Chamorro-Petronacci, Mercedes Conde-Amboage, Rafael Lopez-Lopez, Abel Garcia-Garcia, Mario Perez-Sayans
Summary: This study investigated the salivary proteome in MRONJ patients and identified differentially expressed proteins. Three prioritized proteins were identified, which may serve as a potential biomarker panel for the prediction or diagnosis of MRONJ.
Article
Neurosciences
Fernando Laso-Garcia, Dolores Piniella, Frutos Mari Carmen Gomez-de, Laura Casado-Fernandez, Maria Perez-Mato, Elisa Alonso-Lopez, Laura Otero-Ortega, Susana Belen Bravo, Maria Del Pilar Chantada-Vazquez, Lucia Trilla-Fuertes, Juan angel Fresno-Vara, Blanca Fuentes, Exuperio Diez-Tejedor, Maria Gutierrez-Fernandez, Maria Alonso De Lecinana
Summary: Extracellular vesicles (EVs) play a role in intercellular communication and can serve as biomarkers for disease processes. In the context of intracerebral hemorrhage, studying the number and protein content of circulating EVs can provide insights into the underlying biological mechanisms of damage and repair, aiding in the identification of potential therapeutic targets.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2023)
Article
Dentistry, Oral Surgery & Medicine
Mario Perez-Sayans, Cintia M. Chamorro-Petronacci, Susana B. Bravo, Maria E. Padin-Iruegas, Esteban Guitian-Fernandez, Francisco Barros-Angueira, Rita Quintas-Rey, Abel Garcia-Garcia
Summary: This study describes the genetic variants associated with the development of head and neck cancer (HNC) and validates their molecular implications. A family of 3 generations, where 3 members had developed HNC, was observed. It was found that 6 out of 13 members carried the same mutation of CYP26B1, and lower levels of all-trans retinoic acid (atRA) were confirmed in their plasma.
Article
Astronomy & Astrophysics
A. Waza, J. Kjer, M. Peiteado, T. Jardiel, J. Iversen, K. Rasmussen, J. Merrison
Summary: In this laboratory investigation, the mobilization and suspension of Mars dust analogues under Martian conditions have been studied using laser based techniques. Direct mobilization of dust has been observed at low shear stress and high flux, while the dust resuspension fluxes are significantly lower. The study also observed the remobilization of deposited dust layers by saltating sand, which generated a large flux of dust through impact abrasion.
PLANETARY AND SPACE SCIENCE
(2023)
Article
Food Science & Technology
Manuela Alonso-Sampedro, Xesus Feas, Susana Belen Bravo, Maria Pilar Chantada-Vazquez, Carmen Vidal
Summary: Health risks caused by stings from the yellow-legged Asian hornet, Vespa velutina nigrithorax (VV), have raised concerns. However, little is known about the composition of its venom. This study analyzed the proteome profile of VV's venom sac and identified differential expression of proteins between future queens and workers.
Article
Medicine, Research & Experimental
Fernando Laso-Garcia, Laura Casado-Fernandez, Dolores Piniella, Mari Carmen Gomez-de Frutos, Jone Karmele Arizaga-Echebarria, Maria Perez-Mato, Elisa Alonso-Lopez, Laura Otero-Ortega, Susana Belen Bravo, Maria del Pilar Chantada-Vazquez, Jose Avendano-Ortiz, Eduardo Lopez-Collazo, Maria Isabel Lumbreras-Herrera, Angelo Gamez-Pozo, Blanca Fuentes, Exuperio Diez-Tejedor, Maria Gutierrez-Fernandez, Maria Alonso de Lecinana
Summary: Treatment with EVs derived from blood can enhance recovery after intracerebral hemorrhage by downregulating immune system activation pathways and upregulating repair pathways, leading to better tissue preservation.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Astronomy & Astrophysics
Julia Martikainen, Olga Munoz, Teresa Jardiel, Juan Carlos Gomez Martin, Marco Peiteado, Yannick Willame, Antti Penttila, Karri Muinonen, Gerhard Wurm, Tim Becker
Summary: An advanced light-scattering model is presented to study the optical constants of Martian dust analogs. Laboratory measurements and simulations show that the shape of dust particles has a significant impact on the optical constants.
ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES
(2023)
Article
Immunology
Gabriel Torres Iglesias, Mireya Fernandez-Fournier, Lucia Botella, Dolores Piniella, Fernando Laso-Garcia, Mari Carmen Gomez-de Frutos, Beatriz Chamorro, Inmaculada Puertas, Antonio Tallon Barranco, Blanca Fuentes, Maria Alonso de Lecinana, Elisa Alonso-Lopez, Susana B. Bravo, Maria Eugenia Miranda-Carus, Ana Montero-Calle, Rodrigo Barderas, Exuperio Diez-Tejedor, Maria Gutierrez-Fernandez, Laura Otero-Ortega
Summary: Blood extracellular vesicles (EVs) derived from T cells and neurons have been identified as specific biomarkers in multiple sclerosis (MS). Proteomic analysis revealed MS-associated proteins in these EVs, which correlated with disease activity.
BRAIN BEHAVIOR AND IMMUNITY
(2023)
Article
Cell Biology
Maria J. Gonzalez-Rellan, Uxia Fernandez, Tamara Parracho, Eva Novoa, Marcos F. Fondevila, Natalia da Silva Lima, Lucia Ramos, Amaia Rodriguez, Marina Serrano-Macia, Gonzalo Perez-Mejias, Pilar Chantada-Vazquez, Cristina Riobello, Christelle Veyrat-Durebex, Sulay Tovar, Roberto Coppari, Ashwin Woodhoo, Markus Schwaninger, Vincent Prevot, Teresa C. Delgado, Miguel Lopez, Antonio Diaz-Quintana, Carlos Dieguez, Diana Guallar, Gema Fruhbeck, Irene Diaz-Moreno, Susana B. Bravo, Maria L. Martinez-Chantar, Ruben Nogueiras
Summary: Neddylation is a post-translational modification mechanism that regulates metabolism in the liver of mice and is associated with liver pathology in patients with type 2 diabetes. Fasting or calorie restriction leads to neddylation of phosphoenolpyruvate carboxykinase 1 (PCK1), affecting its metabolic activity.
Article
Endocrinology & Metabolism
Maria J. Gonzalez-Rellan, Tamara Parracho, Violeta Heras, Amaia Rodriguez, Marcos F. Fondevila, Eva Novoa, Natalia Lima, Marta Varela-Rey, Ana Senra, Maria D. P. Chantada-Vazquez, Cristina Ameneiro, Ganeko Bernardo, David Fernandez-Ramos, Fernando Lopitz-Otsoa, Jon Bilbao, Diana Guallar, Miguel Fidalgo, Susana Bravo, Carlos Dieguez, Maria L. Martinez-Chantar, Oscar Millet, Jose M. Mato, Markus Schwaninger, Vincent Prevot, Javier Crespo, Gema Fruhbeck, Paul Iruzubieta, Ruben Nogueiras
Summary: O-GlcNAcylation is a post-translational modification that affects protein function and localization, and its deregulation is associated with various human diseases. This study reveals the role of O-GlcNAcylation in the progression of NAFLD, providing new avenues for therapeutic intervention.
MOLECULAR METABOLISM
(2023)
Article
Astronomy & Astrophysics
T. Becker, J. Teiser, T. Jardiel, M. Peiteado, O. Munoz, J. Martikainen, J. C. Gomez Martin, J. Merrison, G. Wurm
Summary: This study examines the aerodynamic properties of particles generated from impacts on simulated Martian soil and finds that the settling velocity of these particles is slower than expected. Most of the particles are irregular aggregates, which explains the reduced settling velocity. These findings have important implications for understanding the dust in the Martian atmosphere and its effects.
PLANETARY SCIENCE JOURNAL
(2023)
Article
Biochemical Research Methods
Tanushree Halder, Elke Stroeher, Hui Liu, Yinglong Chen, Guijun Yan, Kadambot H. M. Siddique
Summary: Improving the root system of wheat is crucial for enhancing grain yield and climate resilience. This study identified proteins associated with root length and root mass in wheat using label-free quantitative proteomics. The findings revealed potential biomarkers that could be used for improving the root system of wheat.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Yinhua Pan, Quanqing Zou, Wu Yin, Zhen Huang, Yingzhu Zhao, Zongming Mo, Lihui Li, Jianrong Yang
Summary: A prognostic model of BC based on LNM-related genes was established in this study, providing guidance for prognosis evaluation and precise treatment of BC. The genes related to lymph node metastasis in BC are largely unknown and need further exploration. Searching for potential lymph node metastasis-related genes of BC will provide meaningful biomarkers for BC treatment. Our model, based on TCGA-BRCA data, effectively predicted patient outcomes and classified BC patients. The identified feature genes might have a predictive function in immunotherapy. The results of this study provide a new reference for the prognosis and treatment of BC patients with lymph node metastasis.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Qiushi Liang, Joon M. Pijnenburg, Erikjan Rijkers, Arnold G. Vulto, Ans T. van der Ploeg, Niek P. van Til, Eva C. Vlaar, Jeroen A. A. Demmers, W. W. M. Pim Pijnappel
Summary: Pompe disease is a lysosomal storage disorder characterized by glycogen accumulation in skeletal muscle, leading to profound pathology. This study showed that lentiviral gene therapy with LV-IGF2.GAAco can nearly completely correct disease-associated proteomic changes, supporting its future clinical development as a new treatment option for Pompe disease.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Chuang Liu, Wenjing Zhang, Qianli Dong, Haipeng Liu
Summary: This study fills the knowledge gap about the matrix proteins involved in the formation of mineralized exoskeletons in decapod crustaceans. By comparing with well-studied molluscan biomineralization proteins, it is proposed that decapod crustaceans evolved novel proteins while sharing some proteins with molluscs. This study provides insights into the evolution and adaptation of crustaceans and molluscs in forming their exoskeletons.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Rania D. Baka, Josipa Kules, Angelo Beletic, Vladimir Farkas, Dina Resetar Maslov, Blanka Beer Ljubic, Ivana Rubic, Vladimir Mrljak, Mark McLaughlin, David Eckersall, Zoe Polizopoulou
Summary: This study analyzed serum samples from dogs with epilepsy and identified potential markers of epilepsy, proteins involved in nerve tissue regeneration, and proteins altered by antiepileptic medication. The findings provide insight into the pathogenesis of epilepsy and the effects of medication on extracellular matrix proteins.
JOURNAL OF PROTEOMICS
(2024)
Article
Biochemical Research Methods
Viviane M. Codognoto, Fabiana F. de Souza, Thais R. Cataldi, Carlos A. Labate, Laiza S. de Camargo, Pedro H. Esteves Trindade, Roberto R. da Rosa Filho, Diego J. B. de Oliveira, Eunice Oba
Summary: This study aimed to compare urine proteomics from non- and pregnant buffaloes to identify potential biomarkers of early pregnancy. A total of 798 proteins were reported in the urine considering all groups, and the differential proteins play essential roles during pregnancy.
JOURNAL OF PROTEOMICS
(2024)