ArticleMolecular & cellular proteomics : MCP2020
Quantitative Profiling of the Human Substantia Nigra Proteome from Laser-capture Microdissected FFPE Tissue.
Article in Molecular & cellular proteomics : MCP, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 59 citations in OpenAlex.
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- Tau protein in Parkinson's disease: advances in phosphoproteomics and molecular dynamics simulations.Frontiers in aging neuroscience · 2026Review
- mGluR4-NPDC1 complex mediates α-synuclein fibril-induced neurodegeneration.Nature communications · 2025Article
- Spatial proteomics to discover aging-associated alterations in the renal tubulointerstitium.Clinical proteomics · 2025Article
- Spatial omics technology potentially promotes the progress of tumor immunotherapy.British journal of cancer · 2025Review
- Investigating proteogenomic divergence in patient-derived xenograft models of ovarian cancer.Scientific reports · 2025Article
- Advancements in single-cell RNA sequencing and spatial transcriptomics: transforming biomedical research.Acta biochimica Polonica · 2025Review
- Laser capture microdissection.Nature reviews. Methods primers · 2025Article
- Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker.Communications biology · 2024Article
- Tibial cortex transverse transport regulates Orai1/STIM1-mediated NO release and improve the migration and proliferation of vessels via increasing osteopontin expression.Journal of orthopaedic translation · 2024Article
- A mutation in the low-complexity domain of splicing factor hnRNPA1 linked to amyotrophic lateral sclerosis disrupts distinct neuronal RNA splicing networks.Genes & development · 2024Article
- Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine.Annual review of pharmacology and toxicology · 2024Review
- A Microdissection Protocol for Proteogenomic Analysis of Histological Sections to Advance Drug Development.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Deep topographic proteomics of a human brain tumour.Nature communications · 2023Article
- Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine-Exocrine Signaling Sphere of Influence.Molecular & cellular proteomics : MCP · 2023Article
- Microbial Pathogenesis in the Era of Spatial Omics.Infection and immunity · 2023Review
- Global Protein Profiling in Processed Immunohistochemistry Tissue Sections.International journal of molecular sciences · 2023Article
- Cell-Type-Specific Neuroproteomics of Synapses.Biomolecules · 2023Review
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. We first optimized the protocol for efficient LCM analysis of FFPE tissue specimens. The use of SDS containing extraction buffer in combination with the single-pot solid-phase-enhanced sample preparation (SP3) digest method gave the best results regarding protein yield and protein/peptide identifications. Microdissected FFPE human substantia nigra tissue samples (∼3,000 cells) were then analyzed, using tandem mass tag (TMT) labeling and LC-MS/MS, resulting in the quantification of >5,600 protein groups. Nigral proteins were classified and analyzed by abundance, showing an enrichment of extracellular exosome and neuron-specific gene ontology (GO) terms among the higher abundance proteins. Comparison of microdissected samples with intact tissue sections, using a label-free shotgun approach, revealed an enrichment of neuronal cell type markers, such as tyrosine hydroxylase and alpha-synuclein, as well as proteins annotated with neuron-specific GO terms. Overall, this study provides a detailed protocol for laser-capture proteomics using FFPE tissue and demonstrates the efficiency of LCM analysis of distinct cell subpopulations for proteomic analysis using low sample amounts.
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