AIMC Topic: Proteome
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Enrichment of extracellular vesicles using Mag-Net for the analysis of the plasma proteome.
Nature communications
Jul 1, 2025
Extracellular vesicles (EVs) in plasma are composed of exosomes, microvesicles, and apoptotic bodies. We report a plasma EV enrichment strategy using magnetic beads called Mag-Net. Proteomic interrogation of this plasma EV fraction enables the detect...
Ultradeep N-glycoproteome atlas of mouse reveals spatiotemporal signatures of brain aging and neurodegenerative diseases.
Nature communications
Jul 1, 2025
The current depth of site-specific N-glycoproteomics is insufficient to fully characterize glycosylation events in biological samples. Herein, we achieve an ultradeep and precision analysis of the N-glycoproteome of mouse tissues by integrating multi...
A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy.
Nature communications
May 30, 2025
Quantifying protein turnover is fundamental to understanding cellular processes and advancing drug discovery. Multiplex-DIA mass spectrometry (MS), combined with dynamic SILAC labeling (pulse-SILAC, or pSILAC) reliably measures protein turnover and d...
Integrated plasma and vegetation proteomic characterization of infective endocarditis for early diagnosis and treatment.
Nature communications
May 30, 2025
Infective endocarditis, a life-threatening condition, poses challenges for early diagnosis and personalized treatment due to insufficient biomarkers and limited understanding of its pathophysiology. Here, we performed proteomic profiling of plasma an...
Radiomic and proteomic signatures of body mass index on brain ageing and Alzheimer's-like patterns of brain atrophy.
EBioMedicine
May 27, 2025
BACKGROUND: The impact of high body mass index (BMI) states and associated proteomic factors on brain ageing and Alzheimer's disease (AD) remains unclear.
GLIO-Select: Machine Learning-Based Feature Selection and Weighting of Tissue and Serum Proteomic and Metabolomic Data Uncovers Sex Differences in Glioblastoma.
International journal of molecular sciences
May 2, 2025
Glioblastoma (GBM) is a fatal brain cancer known for its rapid and aggressive growth, with some studies indicating that females may have better survival outcomes compared to males. While sex differences in GBM have been observed, the underlying biolo...
Deep Visual Proteomics maps proteotoxicity in a genetic liver disease.
Nature
Apr 16, 2025
Protein misfolding diseases, including α1-antitrypsin deficiency (AATD), pose substantial health challenges, with their cellular progression still poorly understood. We use spatial proteomics by mass spectrometry and machine learning to map AATD in h...
Deep learning tools predict variants in disordered regions with lower sensitivity.
BMC genomics
Apr 12, 2025
BACKGROUND: The recent AI breakthrough of AlphaFold2 has revolutionized 3D protein structural modeling, proving crucial for protein design and variant effects prediction. However, intrinsically disordered regions-known for their lack of well-defined ...
Deciphering the dark cancer phosphoproteome using machine-learned co-regulation of phosphosites.
Nature communications
Mar 20, 2025
Mass spectrometry-based phosphoproteomics offers a comprehensive view of protein phosphorylation, yet our limited knowledge about the regulation and function of most phosphosites hampers the extraction of meaningful biological insights. To address th...
Proteomics and Machine Learning-Based Approach to Decipher Subcellular Proteome of Mouse Heart.
Molecular & cellular proteomics : MCP
Mar 18, 2025
Protein compartmentalization to distinctive subcellular niches is critical for cardiac function and homeostasis. Here, we employed a rapid and robust workflow based on differential centrifugal-based fractionation with mass spectrometry-based proteomi...
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