ArticleAnalytical chemistry2020
Development and Comparative Evaluation of Endolysosomal Proximity Labeling-Based Proteomic Methods in Human iPSC-Derived Neurons.
Article in Analytical chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 36 citations in OpenAlex.
- The Kaposi's sarcoma-associated herpesvirus viral genome packaging accessory factor ORF68 forms cytoplasmic puncta dependent on the viral tyrosine kinase.bioRxiv : the preprint server for biology · 2026Article
- Cell type-resolved proteomics reveals intra- and intercellular signaling in Alzheimer's disease.bioRxiv : the preprint server for biology · 2026Article
- Proximity labeling in neuroscience: decoding molecular landscapes for precision neurology.Translational neurodegeneration · 2026Review
- The Glycosaminoglycan-Dependent Interactome of Neurexin-1 in Human Fetal Glial Cells.Proteoglycan research · 2025Article
- Overcoming Analytical Challenges in Proximity Labeling Proteomics.Journal of mass spectrometry : JMS · 2025Review
- Spatiotemporal proteomics reveals the biosynthetic lysosomal membrane protein interactome in neurons.Nature communications · 2024Article
- KIF1C facilitates retrograde transport of lysosomes through Hook3 and dynein.Communications biology · 2024Article
- Multiomics Evaluation of Human iPSCs and iPSC-Derived Neurons.Journal of proteome research · 2024Article
- Benchmarking and Automating the Biotinylation Proteomics Workflow.Research square · 2024Article
- Immunoproximity biotinylation reveals the axon initial segment proteome.Nature communications · 2023Article
- Axonal transport of autophagosomes is regulated by dynein activators JIP3/JIP4 and ARF/RAB GTPases.The Journal of cell biology · 2023Article
- Multi-modal proteomic characterization of lysosomal function and proteostasis in progranulin-deficient neurons.Molecular neurodegeneration · 2023Article
- Chemical and Biological Strategies for Profiling Protein-Protein Interactions in Living Cells.Chemistry, an Asian journal · 2023Review
- Quantitative Measurement of Transthyretin Mistargeting by Proximity Labeling and Parallel Reaction Monitoring.Frontiers in chemical biology · 2023Article
- Deciphering Spatial Protein-Protein Interactions in Brain Using Proximity Labeling.Molecular & cellular proteomics : MCP · 2022Review
- Protein Contaminants Matter: Building Universal Protein Contaminant Libraries for DDA and DIA Proteomics.Journal of proteome research · 2022Article
- Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling.Nature communications · 2022Article
- Characterization of Neuronal Lysosome Interactome with Proximity Labeling Proteomics.Journal of visualized experiments : JoVE · 2022Article
- Thiol-Cleavable Biotin for Chemical and Enzymatic Biotinylation and Its Application to Mitochondrial TurboID Proteomics.Journal of the American Society for Mass Spectrometry · 2021Article
- Clinical Insights into Mitochondrial Neurodevelopmental and Neurodegenerative Disorders: Their Biosignatures from Mass Spectrometry-Based Metabolomics.Metabolites · 2021Review
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Proximity-based in situ labeling techniques offer a unique way to capture both stable and transient protein-protein and protein-organelle interactions. Combining this technology with mass spectrometry (MS)-based proteomics allows us to obtain snapshots of molecular microenvironments with nanometer resolution, facilitating the discovery of complex and dynamic protein networks. However, a number of technical challenges still exist, such as interferences from endogenously biotinylated proteins and other highly abundant bystanders, how to select the proper controls to minimize false discoveries, and experimental variations among biological/technical replicates. Here, we developed a new method to capture the proteomic microenvironment of the neuronal endolysosomal network by knocking in (KI) an engineered ascorbate peroxidase (APEX) gene to the endogenous locus of lysosome-associated membrane protein 1 (LAMP1). We found that normalizing proximity labeling proteomics data to the endogenously biotinylated protein (PCCA) can greatly reduce variations and enable fair comparisons among different batches of APEX labeling and different APEX probes. We conducted a comparative evaluation between this KI-LAMP1-APEX method and our two overexpression LAMP1-APEX probes, achieving complementary coverage of both known and new lysosomal membrane and lysosomal-interacting proteins in human iPSC-derived neurons. To summarize, this study demonstrated new analytical tools to characterize lysosomal functions and microenvironment in human neurons and filled critical gaps in the field for designing and optimizing proximity labeling proteomic experiments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.