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

IScience
Stefani N ThomasRuedi Aebersold

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.

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Citations

Mar 7, 2021·Journal of Personalized Medicine·Christen A KhellaMichael L Gatza
May 11, 2021·Frontiers in Cell and Developmental Biology·Martin Roszkowski, Isabelle M Mansuy
Jun 8, 2021·Molecular Therapy Oncolytics·Xiao-Li YangDa Fu

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Methods Mentioned

BETA
histone acetylation
two-hybrid
affinity
co-immunoprecipitation
biopsies

Software Mentioned

Perseus
MS
mclust )
CPTAC
STRING
WGCNA
DIA
mclust
SWATH
Umpire

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