Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer
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Updated: Feb 26, 2026
Preparation of Mitochondria from Ovarian Cancer Tissues and Control Ovarian Tissues for Quantitative Proteomics Analysis
Published on: November 18, 2019
Ehwang Song1, Yuqian Gao1, Chaochao Wu1
1Biological Sciences Division, Richland, WA 99354, USA.
Abstract:
Mass spectrometry (MS) based targeted proteomic methods such as selected reaction monitoring (SRM) are emerging as a promising tool for verification of candidate proteins in biological and biomedical applications. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute has investigated the standardization and analytical validation of the SRM assays and demonstrated robust analytical performance on different instruments across different laboratories. An Assay Portal has also been established by CPTAC to provide the research community a resource consisting of large sets of targeted MS-based assays, and a depository to share assays publicly. Herein, we report the development of 98 SRM assays that have been thoroughly characterized according to the CPTAC Assay Characterization Guidance Document; 37 of these passed all five experimental tests. The assays cover 70 proteins previously identified at the protein level in ovarian tumors. The experiments, methods and results for characterizing these SRM assays for their MS response, repeatability, selectivity, stability, and endogenous detection are described in detail. Data are available via PeptideAtlas, Panorama and the CPTAC Assay Portal.
Insights
The Clinical Proteomic Tumor Analysis Consortium developed 98 targeted mass spectrometry (MS) assays for ovarian cancer proteins. Of these, 37 assays met rigorous performance standards, advancing proteomic analysis in biomedical research.
Area of Science:
- Biochemistry
- Proteomics
- Analytical Chemistry
Background:
- Targeted mass spectrometry (MS) methods, like selected reaction monitoring (SRM), are crucial for verifying candidate proteins in biomedical research.
- The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has focused on standardizing and validating SRM assays for robust performance across various instruments and labs.
- CPTAC established an Assay Portal to share targeted MS assays with the research community.
Purpose of the Study:
- To report the development and comprehensive characterization of 98 SRM assays for targeted proteomic analysis.
- To evaluate these assays against the CPTAC Assay Characterization Guidance Document, assessing MS response, repeatability, selectivity, stability, and endogenous detection.
- To provide a resource of validated assays for the verification of 70 proteins identified in ovarian tumors.
Main Methods:
- Development of 98 SRM assays targeting 70 proteins previously identified in ovarian tumors.
- Rigorous characterization of each assay according to CPTAC guidelines, including MS response, repeatability, selectivity, stability, and endogenous detection.
- Validation experiments conducted across different instruments and laboratories to ensure robust analytical performance.
Main Results:
- 98 SRM assays were developed and characterized.
- 37 out of 98 developed assays successfully passed all five experimental tests outlined in the CPTAC Assay Characterization Guidance Document.
- The assays cover 70 proteins relevant to ovarian tumor proteomic profiles.
Conclusions:
- The study successfully developed and characterized a set of targeted mass spectrometry assays for ovarian cancer research.
- A significant portion of the developed assays (37/98) demonstrated robust analytical performance, meeting stringent validation criteria.
- These validated assays, available through public repositories, will aid in the verification of candidate proteins and advance proteomic applications in biomedical research.
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