FFPE Proteomics
Project Workflow
FFPE sample analysis when there are suitable library construction samples:
- FFPE samples
- Dewaxing and rehydration
- Decrosslink
- Protein
- Enzymolysis
- LC-MS/MS DIA analysis
- Data analysis
FFPE sample analysis when there are no suitable library construction samples:
- FFPE samples
- Dewaxing and rehydration
- Decrosslink
- Protein
- Enzymolysis
- LC-MS/MS DDA analysis
- Data analysis
Mass Spectrometry Service Specification
FFPE Proteomics services are performed using nano-flow liquid chromatography and cutting-edge Q Exactive HF/HF-X mass spectrometer.
Sample Preparation and Services
The QC analysis of enzymatic hydrolysis is strictly controlled by LC-MS
DDA-Spectral Library generated using HPLC technology and sample fractionation
Quality Standard
Summary includes all methods and data analysis
Reports provided in Excel or PDF format, RAW files available upon request
Turn Around Time
Typical 5-6 weeks from sample QC acceptance to data report delivery
Sample Requirements
| SAMPLE TYPE | AMOUNT | NOTE | |
| Library construction samples | Fresh samples of relevent tissue | > 5 mg |
Results effect ranking: Fresh tissue > FFPE tissue block > FFPE slice |
| FFPE tissue block | > 1 mg | ||
| FFPE slice | Minimum: 150 mm2; 3 slices, thickness of 10 µm, >50 mm2 | ||
| Recommended: 500 mm2; 10 slices, thickness of 10 µm, >50 mm2 | |||
| DIA analysis samples | FFPE slice | ≥ 1 slice, thickness of 10 µm, > 50 mm2; non-staining or hematoxylin-eosin staining | FFPE samples transport at room temperature; Fresh tissue samples transport with dry ice |
| FFPE tissue block |
> 1 mg; non-staining |
||
|
LCM FFPE
(Laser capture microdissection)
|
cells > 5000; non-staining or hematoxylin-eosin staining | ||
* For samples which have been stored for more than one year, it is recommended that customers send 1-2 samples for pre-ex-periment to evaluate the samples.
DATA ANALYSIS
- Data analysis and validation performed with Mascot
- Protein identification and quantification list
- Differential proteins data statistics and volcano plot
- Principal component analysis (PCA) and cluster analysis
- Protein GO/COG/KOG/Pathway annotation
- GO/COG/KOG enrichment analysis of differential proteins
- Protein-protein interaction analysis
- Protein subcellular localization analysis
- Time series analysis
- Repeatability analysis
