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Explore high-throughput methods to extract, quantify, and analyze proteins in formalin-fixed paraffin-embedded (FFPE) human tissue. Learn the techniques that are redefining research in pathology, oncology and neuroscience

🎓 What You'll Learn

Master advanced proteomic techniques using archived clinical tissue samples. Our educational platform breaks down complex laboratory processes into digestible, interactive lessons.

🔬 Key Topics Covered:

Protein extraction from FFPE tissue
Laser-based microdissection of histological regions
Tissue-based protein microarray fabrication
Mass spectrometry sample preparation
Bioinformatics integration with pathology data
Clinical and research applications

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📚 Featured Learning Modules


1. Intro to Tissue Proteomics
2. The FFPE Tissue Advantage
3. Laser Microdissection Techniques
4. Creating Protein Microarrays
5. Sample Prep for Mass Spectrometry
6. Data Integration & Analysis

Intro to Tissue Proteomics

Tissue proteomics is the study of proteins directly within biological tissues, offering insights into how proteins function and interact in their natural environment. Unlike genomics, which examines DNA, proteomics focuses on the active molecules that carry out cellular functions. Studying proteins in their native tissue environment especially using preserved clinical samples like FFPE reveals critical spatial and contextual information, helping researchers identify important protein markers and understand biological processes. This module introduces the basics of proteomics, its role in biological research, and why tissue-based analysis is vital for translating molecular data into meaningful understanding.

The FFPE Tissue Advantage

Formalin fixed paraffin-embedded (FFPE) tissue is the standard method for preserving tissue samples.
It maintains tissue structure and molecular content for decades.
Vast archives of FFPE samples are stored worldwide in laboratories.
These samples are linked to valuable metadata, enhancing research potential.
Historically, fixation made protein extraction difficult.
Modern techniques now enable efficient recovery of proteins from FFPE tissue.
This advancement allows retrospective studies and research on protein expression across diverse tissue types.
FFPE tissue supports wide-ranging biological and biomedical investigations.

Laser Microdissection Techniques

Laser microdissection is a highly precise method that allows researchers to isolate specific cell populations or regions from tissue sections under microscopic guidance. This technique is essential when working with complex tissues, where different cell types are intermixed. By targeting only the cells or regions of interest, scientists can obtain pure, uncontaminated samples for downstream proteomic analysis. Laser microdissection is fully compatible with FFPE tissue, preserving spatial resolution and enabling accurate molecular profiling from archival specimens.

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Creating Protein Microarrays

Protein microarrays created from tissue samples provide a powerful platform for high-throughput analysis of protein expression. In this approach, proteins extracted from well-defined regions of tissue often isolated by laser microdissection are printed onto glass slides in a highly organized array format. Each spot on the array represents a different tissue source, preserving specific cellular or tissue protein profiles. These arrays can then be probed with antibodies or other detection agents to study the presence, abundance, and modifications of target proteins. Tissue based protein microarrays enable comparative studies across hundreds of samples, offering scalable, quantitative insights into biological processes and biomarker discovery.

Sample Preparation for Mass Spectrometry

Preparing tissue samples for mass spectrometry is a critical step in obtaining accurate and reproducible proteomic data. Proteins must be efficiently extracted from the tissue, often after laser microdissection, and enzymatically digested typically using trypsin into peptides suitable for analysis. For FFPE samples, specialized protocols reverse crosslinking and recover proteins in a soluble form. The resulting peptide mixtures are cleaned and concentrated to remove interfering substances before injection into the mass spectrometer. Proper preparation ensures detection of low-abundance proteins with high sensitivity and specificity, enabling reliable identification and quantification across diverse tissue types.

Data Integration and Analysis

After proteins are identified and quantified, the next critical step is integrating proteomic data with sample metadata to extract meaningful biological insights. This involves mapping protein expression levels to information such as tissue type, developmental stage, or experimental conditions. Advanced bioinformatics tools visualize patterns, compare groups, and uncover biomarkers or functional pathways. By aligning molecular findings with annotated tissue images and metadata, researchers gain a better understanding of biological processes and molecular mechanisms. This module highlights the power of data integration in transforming raw proteomic data into actionable scientific knowledge.

Real-World Applications

Turn knowledge into action. Learn how tissue proteomics supports:

Biomarker discovery for various conditions
Profiling of neurological and cellular processes
Validation of targets for therapeutic development
Safety and toxicity assessment in research
Fundamental studies in biological systems

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Includes lab steps, microarray guides, and data analysis tools.

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