Article
Biochemistry & Molecular Biology
Annika Frauenstein, Stefan Ebner, Fynn M. Hansen, Ankit Sinha, Kshiti Phulphagar, Kirby Swatek, Daniel Hornburg, Matthias Mann, Felix Meissner
Summary: The study introduces a new experimental method (MIP-APMS) to explore the composition, interactions, and functional phenotypes of protein communities within cells. It identifies previously undescribed modifications and interactions in monocytes, revealing regulatory mechanisms of protein complexes in the immune system. Additionally, distinct mechanisms of action for small molecule inhibitors of p38 (MAPK14) are uncovered.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Lin Bai, Guojian Yang, Zhaoyu Qin, Jiacheng Lyu, Yunzhi Wang, Jinwen Feng, Mingwei Liu, Tongqing Gong, Xianju Li, Zhengyang Li, Jixi Li, Jun Qin, Wenjun Yang, Chen Ding
Summary: This study used a novel method to analyze the binding activity of transcription factors under DNA modifications and identified potential readers for 5fC-modified DNA. By quantifying the modified DNA-binding activity of 1039 TFs, it revealed the hierarchical networks between the transcriptional protein machinery and modified DNA.
Article
Multidisciplinary Sciences
John P. McGee, Pei Su, Kenneth R. Durbin, Michael A. R. Hollas, Nicholas W. Bateman, G. Larry Maxwell, Thomas P. Conrads, Ryan T. Fellers, Rafael D. Melani, Jeannie M. Camarillo, Jared O. Kafader, Neil L. Kelleher
Summary: This study introduces a semi-automated single-ion mass spectrometry workflow for top-down tandem mass spectrometry analysis directly from tissue microenvironments. The results demonstrate that this method can identify multiple proteoforms in tumor samples within a short period of time, and effectively identify proteoform signatures in tumor and stromal regions.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Jonathan G. Van Vranken, Jiaming Li, Dylan C. Mitchell, Jose Navarrete-Perea, Steven P. Gygi
Summary: Recent advances in mass spectrometry have enabled quantitative proteomics to become a powerful tool in drug discovery, with the development of solvent shift assays allowing for the establishment of target engagement and increased efficiency. Using this approach, specific targets of compounds with known mechanisms of action can be readily identified, and combining solvent proteome profiling with other methods can expand the screening capabilities for evidence of ligand binding in the proteome.
Article
Chemistry, Analytical
Giovanna Baron, Sofia Borella, Larissa Della Vedova, Serena Vittorio, Giulio Vistoli, Marina Carini, Giancarlo Aldini, Alessandra Altomare
Summary: This study aims to establish an analytical platform capable of extracting bioactive molecules from complex natural matrices, and successfully applies it to Scutellaria baicalensis extract. Through metabolomic and proteomic analysis, compounds adducted to the M-pro active site are identified, and molecular dynamics simulations provide insights into the binding mode of these compounds with M-pro.
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)
Review
Biochemical Research Methods
Zainab Noor, Seong Beom Ahn, Mark S. Baker, Shoba Ranganathan, Abidali Mohamedali
Summary: Accurate protein identification is crucial in proteomics, with mass spectrometry being the primary technique used. Understanding data generation and parameters used in computational tools is essential for proper protein identification. Bioinformatics and computational methodologies are also important for validating protein identification in proteomics.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Andrea Laguillo-Gomez, Enrique Calvo, Noa Martin-Cofreces, Marta Lozano-Prieto, Francisco Sanchez-Madrid, Jesus Vazquez
Summary: Open-search methods with prior knowledge improve identification performance of protein post-translational modifications by minimizing experimental errors and precursor mass assignation. The introduction of a novel approach enables the study of a wider variety of PTMs, including unknown or unexpected modifications.
JOURNAL OF PROTEOMICS
(2023)
Article
Biochemical Research Methods
Suresh Poudel, David Vanderwall, Zuo-Fei Yuan, Zhiping Wu, Junmin Peng, Yuxin Li
Summary: A computational pipeline JUMPptm was presented to extract PTMs from unenriched whole proteome. The deep brain proteome of Alzheimer's disease (AD) was analyzed using JUMPptm, revealing dysregulated PTM peptides during AD progression and establishing a valuable pan-PTM profile for AD research.
Article
Chemistry, Applied
Jana Unterhauser, Linda Ahammer, Tobias Rainer, Reiner Eidelpes, Sebastian Fuehrer, Bettina Nothegger, Claudia E. Covaciu, Valentina Cova, Anna S. Kamenik, Klaus R. Liedl, Thomas Mueller, Kathrin Breuker, Klaus Eisendle, Norbert Reider, Thomas Letschka, Martin Tollinger
Summary: Naturally occurring polyphenols can modify the molecular properties of food allergens. In the case of the major apple allergen Mal d 1, reactions with oxidized polyphenols result in the formation of a covalent adduct, leading to a loss of conformational IgE epitopes and reduced allergenicity. The modified allergen does not affect its three-dimensional fold or ligand binding, but partially covers an IgE epitope on its surface.
Article
Biochemistry & Molecular Biology
Jacky M. K. Kwong, Joseph Caprioli, Ying H. Sze, Feng J. Yu, King K. Li, Chi H. To, Thomas C. Lam
Summary: Retinal proteins associated with primary and secondary RGC degeneration were investigated using SWATH label-free and target-based mass spectrometry. Different proteomic profiles were found in response to localized optic nerve injury, indicating potential roles in RGC loss and cell death.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Christopher Burgoyne, Rob Smith
Summary: Glycans are important in biochemical processes, but the computational interpretation of glycans in mass spectrometry analysis can be challenging. The C++ implementation of the Sweet-SEQer algorithm, called C-SEQer, outperforms the original algorithm in terms of time and memory usage, making glycan analysis more efficient and effective. The implementation is freely available with an MIT license.
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
Biochemical Research Methods
Elke Debrie, Milan Malfait, Ralf Gabriels, Arthur Declerq, Adriaan Sticker, Lennart Martens, Lieven Clement
Summary: Reliable peptide identification is crucial in MS-based proteomics, and the TDA method is widely used for estimating the FDR. However, the assumptions of TDA are often not verified in practice, which can result in poor FDR control and negatively impact downstream data analysis. To address this issue, the TargetDecoy package is introduced, providing necessary functionality to assess the quality and assumptions of TDA for a given set of PSMs.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Issar Arab, William E. Fondrie, Kris Laukens, Wout Bittremieux
Summary: A key analysis task in mass spectrometry proteomics is matching tandem mass spectra to peptides using sequence database searching or spectral library searching. Machine learning is an increasingly popular postprocessing approach that improves identification of confident spectra. This study integrates semisupervised machine learning into the ANN-SoLo tool, an efficient spectral library search engine optimized for open modification searching. The machine learning approach boosts the identification of spectra in both standard and open searching, and provides insights into spectrum characteristics.
JOURNAL OF PROTEOME RESEARCH
(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)
