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Updated: Aug 14, 2026
Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors
Published on: February 27, 2015
Identifying Abundant Immunotherapy and Other Targets in Solid Tumors: Integrating RNA-seq and Mass Spectrometry
Wei Zhao1, Matthew Fitzgibbon, Lindsay Bergan
1From the *Department of Systems Biology, MD Anderson Cancer Center, Houston, TX; and †Fred Hutchinson Cancer Research Center, Seattle, WA.
Abstract:
RNA-seq and mass-spectrometry proteomics combined with growing data repositories have greatly increased the capacity to identify candidate proteins or protein sequence variants that share properties of ideal therapy targets, which include being abundant in cancer cells, absent or rare in adult organs (especially vital organs), and shared by many patient tumors. RNA-seq and fixed content arrays can identify genes that are overexpressed or misexpressed in cancer. RNA-seq is uniquely suited to identifying cancer-specific sequence variants. We review factors relevant for determining whether products of genes that are abundant or differentially abundant in RNA-seq are concordant or discordant with proteins that are identified as abundant or differentially abundant in mass-spectrometry proteomics assays.
Insights
Identifying ideal cancer therapy targets requires matching abundant proteins in tumors with those absent in healthy organs. RNA-sequencing and mass spectrometry proteomics aid this discovery process.
Area of Science:
- Oncology
- Proteomics
- Genomics
Background:
- Growing data repositories enhance the identification of potential therapeutic targets.
- Ideal targets are abundant in cancer cells but rare in vital adult organs.
- Cancer-specific sequence variants and gene expression patterns are key.
Purpose of the Study:
- To review factors for determining concordance between RNA-sequencing and mass-spectrometry proteomics data for therapy target identification.
- To assess the suitability of RNA-sequencing for identifying cancer-specific protein variants.
- To evaluate gene products abundant in RNA-seq against proteins identified by proteomics.
Main Methods:
- Utilizing RNA-sequencing (RNA-seq) to identify gene expression and sequence variants.
- Employing mass-spectrometry proteomics to quantify protein abundance.
- Analyzing concordance between gene expression/variants and protein abundance data.
Main Results:
- RNA-seq and proteomics provide complementary data for therapy target discovery.
- RNA-seq excels at detecting cancer-specific sequence variants.
- Discordance between RNA-seq and proteomics data requires careful evaluation.
Conclusions:
- Integrating RNA-seq and proteomics is crucial for identifying robust cancer therapy targets.
- Careful analysis is needed to reconcile differences between transcriptomic and proteomic findings.
- This integrated approach advances the search for effective cancer treatments.
