pFind Studio: a computational solution for mass spectrometry-based proteomics
2024
Scientific Data2024. de Oliveira Veloso Rezende, J{\'e}ssica et al.
Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Fiocruz Paran, Paran, Brazil
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Nature Communications2024. Chen, Ke et al.
Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai, 200032, China
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Structure2024. Ludzia, Patryk et al.
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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Nature Communications2024. Tang, Di et al.
Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
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Nature Communications2024. Le Bihan, Thierry et al.
Rapid Novor, Kitchener, ON, Canada
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Cell Discovery2024. Tan, Yangxia et al.
Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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Science Advances2024. Bayly-Jones, Charles et al.
Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
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Journal of Proteomics2024. Swati, Banerjee et al.
nstitute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nmst 542/2, 160 00 Praha, Czechia
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Nature Communications2024. Hayes, Brooke K et al.
Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, VIC, Australia
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Nature communications2024. Zhao, Lili et al.
CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, State Key Laboratory of Medical Proteomics, Dalian
ABSTRACT:Unlocking the intricacies of protein structures and interactions within the dynamic landscape of subcellular organelles presents a significant challenge. To address this, we introduce SPACX, a method for spatially resolved protein complex profiling via biocompatible chemical cross(x)-linking with subcellular isolation, designed to monitor protein conformation, interactions, and translocation in living cells. By rapidly capturing protein complexes in their native physiological state and efficiently enriching cross-linked peptides, SPACX allows comprehensive analysis of the protein interactome within living cells. Leveraging structure refinement with cross-linking restraints, we identify subcellular-specific conformation heterogeneity of PTEN, revealing dynamic differences in its dual specificity domains between the nucleus and cytoplasm. Furthermore, by discerning conformational disparities, we identify 83 cytoplasm-exclusive and 109 nucleus-exclusive PTEN-interacting proteins, each associated with distinct biological functions. Upon induction of ubiquitin-proteasome system stress, we observe dynamic alterations in PTEN assembly and its interacting partners during translocation. These changes, including the identification of components and interaction sites, are characterized using the SPACX approach. Notably, SPACX enables identification of unique interacting proteins specific to PTEN isoforms, including PTEN and PTEN-Long, through the determination of sequence-specific cross-linking interfaces. These findings underscore the potential of SPACX to elucidate the functional diversity of proteins within distinct subcellular sociology.
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