Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes

Stefani N Thomas, Betty Friedrich, Michael Schnaubelt, Daniel W. Chan, Hui Zhang, Ruedi Aebersold

Research output: Contribution to journalArticlepeer-review

7 Scopus citations

Abstract

The National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium (CPTAC) established a harmonized method for large-scale clinical proteomic studies. SWATH-MS, an instance of data-independent acquisition (DIA) proteomic methods, is an alternate proteomic approach. In this study, we used SWATH-MS to analyze remnant peptides from the original retrospective TCGA samples generated for the CPTAC ovarian cancer proteogenomic study. The SWATH-MS results recapitulated the confident identification of differentially expressed proteins in enriched pathways associated with the robust Mesenchymal high-grade serous ovarian cancer subtype and the homologous recombination deficient tumors. Hence, SWATH/DIA-MS presents a promising complementary or orthogonal alternative to the CPTAC proteomic workflow, with the advantages of simpler and faster workflows and lower sample consumption, albeit with shallower proteome coverage. In summary, both analytical methods are suitable to characterize clinical samples, providing proteomic workflow alternatives for cancer researchers depending on the context-specific goals of the studies.

Original languageEnglish (US)
Article number101079
JournaliScience
Volume23
Issue number6
DOIs
StatePublished - Jun 26 2020

Keywords

  • Biological Sciences
  • Cancer Systems Biology
  • Proteomics

ASJC Scopus subject areas

  • General

Fingerprint

Dive into the research topics of 'Orthogonal Proteomic Platforms and Their Implications for the Stable Classification of High-Grade Serous Ovarian Cancer Subtypes'. Together they form a unique fingerprint.

Cite this