Article
Clinical Neurology
Irep Uras, Merve Karayel-Basar, Betul Sahin, Ahmet Tarik Baykal
Summary: Alzheimer's disease (AD) is a debilitating neurodegenerative disorder characterized by memory deficit and dementia. In this study, the spatial proteomic differences in the neonatal 5xFAD brain tissue were investigated using MALDI-MSI coupled to LC-MS/MS, and the differentially expressed proteins (DEPs) associated with AD were identified. The results showed a remarkable resemblance in the protein expression profiles of neonatal 5xFAD brain compared to AD patient specimens or AD mouse models, suggesting that molecular alterations in the AD brain existed even at birth and certain proteins may serve as neurodegenerative presages in neonatal AD brain.
ALZHEIMERS & DEMENTIA
(2023)
Article
Biochemical Research Methods
Peipei Zhu, Xiaofeng Wu, Ruo-Yu Zhang, Chuan-Chih Hsu, Zhong-Yin Zhang, W. Andy Tao
Summary: Protein phosphatases are important in cellular processes, but studying their substrates and mechanisms is challenging. This study introduces a novel strategy to identify substrates of SHP2 using quantitative proteomics methods, and discovers new substrates.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Agriculture, Dairy & Animal Science
Jiale Sui, Jing Xiao, Xinping Chang, Yisha Xu, Jinqiu Wang, Fang Geng
Summary: Chicken egg yolk granules (EYG) are rich in proteins, phospholipids, and minerals compared to egg yolk. Proteomic analysis of EYG revealed the identification of phosphorylation and N-glycosylation sites on various proteins, providing new insights into the structure and function of EYG. This study contributes to the development and utilization of EYG.
Article
Biochemistry & Molecular Biology
Chia-Ru Chung, Hsin-Yao Wang, Po-Han Chou, Li-Ching Wu, Jang-Jih Lu, Jorng-Tzong Horng, Tzong-Yi Lee
Summary: This study used an ensemble of multiple preprocessing methods to extract critical information from complicated mass spectrometry spectral data for identifying microorganisms and predicting antibiotic resistance. The ensemble method outperformed individual methods, achieving the highest accuracy on independent testing datasets. Important peaks related to antibiotic resistance could be detected, providing valuable information for further investigation of the resistance mechanism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Applied
Xue Yi Tan, Azizah Misran, Leona Daniela Jeffery Daim, Benjamin Yii Chung Lau
Summary: Four methods were evaluated to extract proteins from Musang King durian pulps, with acetone-phenol method producing the best results. Differential protein analyses revealed that 15 proteins were down-regulated and 3 proteins were up-regulated after a year of frozen storage. This study indicates that frozen storage affects protein expression in various functional aspects.
Article
Plant Sciences
Swetha Sudha Nagamalla, Malini Devi Alaparthi, Sunitha Mellacheruvu, Ravindar Gundeti, Jana Priya Sony Earrawandla, Someswar Rao Sagurthi
Summary: The study investigated the impact of drought stress on two cotton varieties, revealing that Bt cotton showed stronger drought tolerance compared to non-Bt cotton at the protein expression and physiological levels. This finding may aid in breeding new drought-tolerant and high-yielding cotton hybrid varieties.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
G. Guo, M. Papanicolaou, N. J. Demarais, Z. Wang, K. L. Schey, P. Timpson, T. R. Cox, A. C. Grey
Summary: Spatial proteomics using MALDI-MSI is a powerful tool for direct detection of protein distribution in tissues but faces challenges in peptide quantification and identification. The development of HIT-MAP provides an open-source bioinformatics workflow for accurate protein annotation and spatial mapping from MALDI-MSI data.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Dandan Jiang, Siqi Lv, Xue Han, Limei Duan, Jinghai Liu
Summary: Exfoliated magadiite nanosheets embedded with Fe3O4 were utilized to prepare Gd3+-immobilized magnetic magadiite nanosheets as an adsorbent for phosphopeptides enrichment. The 2D morphology of the adsorbent provided high surface area and abundant Gd3+ contents, leading to efficient phosphopeptides capture with low detection limit and stable enrichment performance. Further evaluation demonstrated the capability of the nanocomposite to enrich phosphopeptides from various biological samples.
Article
Biochemistry & Molecular Biology
Yajun Hu, Jun Yao, Zening Wang, Hui Liang, Cunyu Li, Xinwen Zhou, Fengying Yang, Yang Zhang, Hong Jin
Summary: Trichosanthin (TCS), a Chinese herbal medicine, has been used in the treatment of gynecological diseases. In this study, the anticancer properties of TCS were tested using the human trophoblast cell line BeWo. MTT method was used for primary screening, and proteomics analysis was conducted to investigate the drug effect. The study identified several differentially expressed proteins and suggested potential pathways and signal transduction for disease treatment.
Article
Immunology
Laudine M. C. Petralia, Angela van Diepen, Dieu-Linh Nguyen, Lena A. Lokker, Erliyani Sartono, Sasisekhar Bennuru, Thomas B. Nutman, Kenneth Pfarr, Achim Hoerauf, Samuel Wanji, Jeremy M. Foster, Cornelis H. Hokke
Summary: Parasitic nematodes cause chronic disablement in humans worldwide. Current diagnostics for surveillance of filarial diseases have limitations, and improved assays are needed. We studied the glycan antigens of the parasite Brugia malayi and found that they triggered IgG responses. Our findings suggest potential for developing disease-specific diagnostics for filarial disease control.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Plant Sciences
Soumen Bhattacharjee, Ananya Chakrabarty, Durga Kora, Uthpal Krishna Roy
Summary: This study explored the impact of H2O2-induced redox manipulation on germinating rice seeds and found that the salt-resistant cultivar exhibited improved antioxidant-conjugated redox buffering and maintained redox homeostasis, while the salt-sensitive cultivar showed oxidative damage. The study also identified differentially expressed proteins that are involved in redox homeostasis, cell defense, photosynthesis, and energy metabolism. Overall, the study suggests the importance of H2O2 manipulation in regulating redox signaling and oxidative stress response during germination in rice seeds.
JOURNAL OF PLANT GROWTH REGULATION
(2023)
Article
Immunology
Xiaoyue He, Donghua Liu, Qicong Chen
Summary: The study identified the significant role of heat shock protein HSP90 in the melanin synthesis pathway of T.marneffei through proteomic analysis. The HSP90 inhibitor geldanamycin demonstrated effective inhibition of melanin production in T.marneffei yeast.
MICROBIAL PATHOGENESIS
(2021)
Review
Chemistry, Multidisciplinary
Chunxia Ma, Lei Xie, Xiao Wang, Kang Liang, Biao Kong
Summary: Functionalized mesoporous nanomaterials have diverse structural features and unique properties, making them widely applicable in MALDI-MS. Precisely controlling the factors in the assembly of mesoporous nanomaterials is crucial for achieving high-performance MALDI-MS. Significant progress has been made in the fabrication and properties of mesoporous nanomaterials in recent years.
Review
Chemistry, Analytical
M. Sejalon-Cipolla, P. Bruyat, S. Bregant, C. Malgorn, L. Devel, G. Subra, S. Cantel
Summary: MALDI-MS is crucial for detecting and identifying molecules involved in biological pathways, but many biomarkers remain undetectable due to various limitations. To overcome these challenges, labeling strategies and activity-based probes have been developed. Matrix-free derivatization techniques are currently gaining attention.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Microbiology
Eloise J. Busby, Ronan M. M. Doyle, Clara Leboreiro Babe, Kathryn A. A. Harris, Damien Mack, Gema Mendez-Cervantes, Denise M. M. O'Sullivan, Vicky Pang, Zahra Sadouki, Priya Solanki, Jim F. F. Huggett, Timothy D. D. McHugh, Emmanuel Q. Q. Wey
Summary: Managing the transmission of antimicrobial resistance requires reliable methods for tracking outbreaks. MALDI-TOF MS was compared with orthogonal approaches for strain typing, including WGS and FTIR, for Acinetobacter baumannii isolates associated with a healthcare-associated infection event. Reliable molecular typing methods can help to trace transmission routes and manage outbreaks.
MICROBIOLOGY SPECTRUM
(2023)
Article
Oncology
Mitchell Acland, Noor A. Lokman, Clifford Young, Dovile Anderson, Mark Condina, Chris Desire, Tannith M. Noye, Wanqi Wang, Carmela Ricciardelli, Darren J. Creek, Martin K. Oehler, Peter Hoffmann, Manuela Klingler-Hoffmann
Summary: This study aimed to understand the molecular features of chemoresistance in ovarian cancer by comparing the proteome and metabolome of chemosensitive and chemoresistant cell lines. The analysis revealed perturbations in signalling and metabolic pathways in chemoresistant cells and identified a shared dysregulation in cytokine and type 1 interferon signalling. This research contributes to a deeper understanding of chemoresistance and could potentially help in developing better treatment strategies for ovarian cancer.
Article
Biochemical Research Methods
Yea-Rin Lee, Matthew T. Briggs, Clifford Young, Mark R. Condina, Julia S. Kuliwaba, Paul H. Anderson, Peter Hoffmann
Summary: This study utilized MALDI-MSI and LC-MS/MS to spatially map and identify specific degraded cartilage N-glycans in knee osteoarthritis patients for the first time. The identified N-glycans could potentially serve as diagnostic and prognostic biomarkers.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Quang Nghia Pham, Marnie Winter, Valentina Milanova, Clifford Young, Mark R. Condina, Peter Hoffmann, Nguyen T. H. Pham, Tran Thanh Tung, Dusan Losic, Benjamin Thierry
Summary: Here, we present an optimized protocol for immuno-magnetic enrichment of specific extracellular vesicle (EV) subtypes, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The results demonstrate efficient enrichment of target EVs with high protein recovery and low non-specific binding. This optimized method provides a low-cost, high-throughput approach for EV proteomic studies.
Article
Oncology
Georgia Arentz, Parul Mittal, Manuela Klingler-Hoffmann, Mark R. Condina, Carmela Ricciardelli, Noor A. Lokman, Gurjeet Kaur, Martin K. Oehler, Peter Hoffmann
Summary: Eighty percent of ovarian cancer patients respond to chemotherapy initially, but most experience relapse and die from acquired chemoresistance. In addition, 20% of patients are intrinsically resistant. A study found that the protein markers gelsolin (GSN), calmodulin (CALM1), and thioredoxin (TXN) were elevated in chemotherapy-responsive ovarian cancer tissues compared to non-responsive ones. The differential expression of these markers was confirmed in carboplatin-resistant cells, suggesting their potential as biomarkers for predicting chemotherapy response and understanding resistance mechanisms.
Article
Chemistry, Analytical
Yea-Rin Lee, Matthew T. T. Briggs, Julia S. S. Kuliwaba, Jakub Jagiello, Paul H. H. Anderson, Peter Hoffmann
Summary: This study aimed to investigate the N-glycan changes in subchondral trabecular bone of knee osteoarthritis (KOA) patients exposed to different joint loading forces using MALDI-MSI. The results demonstrated significant N-glycan alterations in the subchondral trabecular bone between the M-A and L-A regions. This is the first study to observe N-glycan changes under different joint loading forces in the KOA tibial plateau.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Santhni Subramaniam, Paul Joyce, Leigh Donnellan, Clifford Young, Anthony Wignall, Peter Hoffmann, Clive A. Prestidge
Summary: The inhalable administration of lipid nanoparticles is an effective strategy for localised delivery of therapeutics against various lung diseases. The influence of lipid nanoparticle composition and structure, as well as the presence of biologically relevant media, on their uptake in pulmonary cell lines is poorly understood. This study quantified the uptake of lamellar versus non-lamellar lipid nanoparticles in macrophages and lung epithelial cells and determined the influence of bronchoalveolar lavage fluid (BALF), containing native pulmonary protein and surfactant molecules. The findings provide insights into the role of biological fluid in regulating lipid nanoparticle uptake mechanisms, which can guide the development of optimal intracellular delivery systems for therapeutics via the pulmonary route.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Biochemical Research Methods
Yea-Rin Lee, Matthew T. Briggs, Julia S. Kuliwaba, Jakub Jagiello, Paul H. Anderson, Peter Hoffmann
Summary: Abnormal N-glycosylation plays an important role in multiple diseases, but its relationship with knee osteoarthritis (KOA) progression at the tissue level is poorly understood. This study quantified cartilage histomorphometric changes in FFPE tissue collected from KOA patients and analyzed N-glycans using MALDI-MSI. The results showed that complex-type N-glycans were associated with cartilage degeneration severity in KOA. These findings provide valuable insights into the cellular processes of KOA.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Sonia Sebastian, Manuela Klingler Hoffmann, Douglas Howard, Clifford Young, Jenni Washington, Harald Unterweger, Christoph Alexiou, Tyron Turnbull, Richard D'Andrea, Peter Hoffmann, Ivan Kempson
Summary: In this study, it was found that inert nanoparticles could antagonize the antioxidant mechanism of cancer cells. The impact on the glutathione-thioredoxin antioxidative pathway was observed, but it was temporary and cells quickly recovered after nanoparticle exposure ceased.
Article
Multidisciplinary Sciences
Qiaz Q. H. C. Hua, Clifford Young, Tara M. Pukala, Jasmin A. Martino, Peter Hoffmann, Bronwyn Gillanders, Zoe Doubleday
Summary: Proteomics is a powerful technique to study how organisms respond to biological perturbations, but its use in ecological studies has been limited due to inadequate protocols for sampling and preserving animal tissues from the field. We optimized a workflow and showed that sampling non-model organisms from remote field sites is achievable and can provide extensive proteomic coverage without compromising protein integrity.
Article
Biochemistry & Molecular Biology
Gaayathri Kumarasamy, Mohd Nazri Ismail, Sharifah Emilia Tuan Sharif, Christopher Desire, Parul Mittal, Peter Hoffmann, Gurjeet Kaur
Summary: Nearly 90% of cervical cancers are linked to HPV. Protein signatures were compared between normal cervix, HPV16/18-associated SIL, and SCC using LC-MS, identifying 3597 proteins. The transition from normal cervix to SIL showed downregulated differentially expressed proteins, while SIL to SCC showed upregulated proteins. PI3 kinase pathway, viral carcinogenesis, and necroptosis played important roles in cervical cancer development. Annexin A2 and cornulin were potential biomarkers, with cornulin exhibiting tumor suppressor characteristics.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Applied
Brooke A. Dilmetz, Christopher T. Desire, Jon Meneses, Manuela Klingler-Hoffmann, Clifford Young, Peter Hoffmann
Summary: This study found that bottle conditioning with yeast propagated until the post-diauxic shift (72 hours) resulted in improved longevity and foam stability of beer. The yeast propagated for 72 hours showed an upregulation of proteins involved in cellular respiration and stress pathways, indicating a response to cell stress.
Article
Chemistry, Applied
Wai C. D. Lau, Leigh Donnellan, Matthew Briggs, Thusitha Rupasinghe, John C. Harris, Julie E. Hayes, Peter Hoffmann
Summary: This study successfully applied MALDI mass spectrometry imaging (MALDI-MSI) technique combined with trapped ion mobility spectrometry (TIMS) to investigate the lipid composition and distribution in oats. The novel analytical technique overcomes challenges in sample preparation and lipid analysis, and has the potential to improve the discovery of biomarkers for grain quality.
Article
Biochemical Research Methods
Raman Kumar, Karthik S. Kamath, Luke Carroll, Peter Hoffmann, Jozef Gecz, Lachlan A. Jolly
Summary: The article describes an adaptable immunoprecipitation protocol for identifying protein-protein interactions, with a quantitative proteomics workflow for unbiased identification of co-immunoprecipitating proteins.
Article
Microbiology
Peter Cathro, Peter McCarthy, Peter Hoffmann, Stephen Kidd, Peter Zilm
Summary: Enterococcus faecalis cell membrane responds to extreme alkaline conditions by shifting carbohydrate metabolism and forming a protective capsule.
FEMS MICROBIOLOGY LETTERS
(2022)