Project PXD003607

PRIDE Assigned Tags:
Biomedical Dataset



Ovarian Cancer Proteomics of FFPE Tissue


We have performed in-depth examination of single tissue sections from a collection of FFPE and Frozen treated tumors, as well as cell line material all originating from different subtypes of epithelial ovarian cancer (high-grade serous, clear cell, endometrioid). Data were prepared using a tandem mass tag 10plex protocol with MS3 analysis on an Orbitrap Fusion.

Sample Processing Protocol

Samples were prepared using a variation on the paramagnetic bead protocol, SP3, as described in the manuscript text. Samples were TMT labeled, fractionated with high-pH C18 RP chromatography, and the fractions analyzed using MS3 on an Orbitrap Fusion MS.

Data Processing Protocol

Data were initially processed using SEQUEST HT in the Proteome Discoverer software (v2.1). Results were processed further in the R programming language.


Christopher Hughes, BC Cancer Agency
Gregg Morin, Proteomics Head, British Columbia Cancer Research Centre ( lab head )

Submission Date


Publication Date



    Hughes CS, McConechy MK, Cochrane DR, Nazeran T, Karnezis AN, Huntsman DG, Morin GB. Quantitative Profiling of Single Formalin Fixed Tumour Sections: proteomics for translational research. Sci Rep. 2016 Oct 7;6:34949 PubMed: 27713570