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FFPE Proteomics

DESCRIPTION
SPECIFICATION
RESOURCES

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.

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

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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