FFPE Proteomics

Service Description

BGI has extensive experience in the field of FFPE proteomics of tumor heterogeneity research. We can process projects with low initial sample amount of only one slice of FFPE.

 

FFPE Proteomics

FFPE sample refers to the tissue sample treated with FFPE method, which can be stored steadily for decades at room temperature and is the gold standard for histopathological analysis1.

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

References

[1] Marchione D M, et al., HYPERsol: High-Quality Data from Archival FFPE Tissue for Clinical Proteomics. J Proteome Res, 2020 Feb 7; 19(2): 973–983.

How to order

Request a Quote

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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

    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

    Quality Standard

    • Summary includes all methods and data analysis
    • Reports provided in Excel or PDF format, RAW files available upon request
  • Turn Around Time

    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
relevant tissue

> 5 mg

Results effect ranking:
Fresh tissue > FFPE tissue block > FFPE slice

Library construction
samples-FFPE tissue block

> 1 mg

Results effect ranking:
Fresh tissue > FFPE tissue block > FFPE slice

Library construction
samples-FFPE slice

Minimum:150 mm2;
3 slices, thickness of 10 μm,
> 50 mm2
Recommend: 500 mm2;
10 slices, thickness of 10 μm,
> 50 mm2

Results effect ranking:
Fresh tissue > FFPE tissue block > FFPE slice

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

DIA analysis
samples-FFPE tissue block

> 1 mg; non-staining

FFPE samples transport at room temperature;
Fresh tissue samples transport with dry ice

DIA analysis
samples-LCM FFPE
(Laser capture microdissection)

Cells > 5000; non-staining or hematoxylin-eosin staining

FFPE samples transport at room temperature;
Fresh tissue samples transport with dry ice

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

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