Formalin-Fixed Paraffin-Embedded (FFPE) tissue is one of the most common sample preservation formats in biomedical research and clinical pathology, widely used in tumor specimens, tissue microarrays, and retrospective cohort studies. However, due to protein denaturation, increased structural stability, and epitope masking caused by formaldehyde crosslinking, conventional protein extraction and digestion methods often fail to achieve effective lysis and efficient enzymatic digestion in FFPE samples, significantly compromising the sensitivity and reproducibility of downstream mass spectrometry analysis.
To improve the quality of proteomic data from FFPE samples, MtoZ Biolabs has developed a dedicated protein digestion kit designed for paraffin sections and curls and provided a one-stop solution covering deparaffinization, rehydration, lysis, crosslink reversal, and efficient digestion. The optimized buffer system and digestion strategy are fully compatible with NanoLC-MS/MS platforms, making it particularly suitable for low-input, high-throughput, and MS-grade proteomics applications.
Product Overview
The paraffin section/roll protein digestion kit is built upon an optimized lysis system and heat-induced crosslink reversal buffer, combined with MtoZ Biolabs' custom bead-assisted digestion strategy. This integrated approach enables efficient protein release and complete enzymatic digestion from FFPE tissue sections and curls. The specially designed deparaffinization/rehydration protocol and low-volume reaction system maximize protein preservation and are suitable for paraffin sections or tissue curls with a thickness of 10 μm.
Compared to traditional homemade protocols, the paraffin section/roll protein digestion kit significantly reduces hands-on time, improves inter-batch consistency, and minimizes human error. Its performance has been validated by mass spectrometry across various clinically sourced samples.
Product Details
|
Product Details |
Size |
Storage Conditions |
|
Dewaxing Solution |
30 mL×1 |
RT |
|
Absolute Ethanol |
30 mL×1 |
RT |
|
75% Ethanol |
30 mL×1 |
RT |
|
Lysis buffer |
10 mL×1 |
-20℃ |
|
Beads |
200 μL×1 |
4℃ |
Protocol
1. Dewaxing and Rehydration
Place the FFPE tissue section or curl into a 1.5 mL tube and add dewaxing solution until complete dewaxing is achieved. Then perform gradient ethanol washes until the sample reaches a pure water state.
2. Lysis and Crosslink Reversal
Add lysis buffer and heat at 95°C to reverse formaldehyde crosslinks and release proteins.
3. Alkylation
Add alkylation reagent to perform alkylation treatment.
4. Digestion Reaction
Subject the alkylated proteins to trypsin digestion following the bead-based digestion protocol at 37°C for 14-16 hours.
5. Digestion Termination and Sample Cleanup
Use a C18 tip or SPE column for desalting and purification to obtain MS-ready peptides.
Features and Benefits
1. Crosslink Reversal and Protein Release
Utilizes specialized lysis buffer and heat treatment to break formaldehyde-induced crosslinks and release proteins.
2. Unique Digestion System
Employs bead-based protein enrichment followed by trypsin digestion to enhance digestion efficiency and ensure thorough cleavage of low-abundance proteins.
3. High Throughput and Low Input Compatibility
Designed for trace FFPE sections or tissue curls, meeting the demands of high-throughput screening.
4. Compatibility with Mainstream Mass Spectrometry Platforms
Fully compatible with LC-MS/MS platforms such as Orbitrap and TripleTOF, ensuring high-quality data output.
Applications
- Proteomics analysis of FFPE tumor tissue samples
- Molecular biomarker research in clinical paraffin-embedded pathology sections
- Protein digestion preparation for microdissected tissue microarray samples
- Proteome preparation from low-input paraffin samples (e.g., fine-needle aspiration biopsies)
- Standardized proteomics pretreatment of retrospective cohort clinical samples
FAQs
Q1: Can the Kit Be Used on Stained Paraffin Sections?
A1: Yes, it can be used on H&E-stained samples; however, we recommend using unstained sections to avoid dye-related interference in MS signals. If stained samples are used, additional washing steps should be included to thoroughly remove residual dyes.
Q2: What Types of Tissue Samples Is The Kit Suitable for?
A2: The paraffin section/roll protein digestion kit is compatible with various paraffin sections and FFPE tissue samples, including but not limited to tumor tissues, normal tissues, and pathological tissues.
Q3: Can the Kit Process Scrolls of Multiple Tissue Sections?
A3: Yes, it supports processing up to ten 10-μm thick tissue scrolls. It is recommended to adjust the lysis buffer volume and enzyme amount based on the tissue density.
