Data-Independent Acquisition Mass Spectrometry To Quantify Protein Levels in FFPE Tumor Biopsies for Molecular
Yeoun Jin Kim1, Steve M M Sweet1, Jarrett D Egertson2
1NantOmics , 9600 Medical Center Drive , Rockville , Maryland 20850 , United States.
Journal of Proteome Research
|November 28, 2018
Summary
Data-independent acquisition (DIA) mass spectrometry effectively profiles patient tumor proteomes from limited biopsies. This emerging proteomic assay quantifies biomarkers and aids therapeutic decision-making, outperforming traditional methods.
Area of Science:
- Proteomics and Mass Spectrometry
- Clinical Diagnostics and Biomarker Discovery
- Cancer Research
Background:
- Mass spectrometry (MS)-based protein quantitation is crucial for predicting therapy response using protein biomarkers in clinical settings.
- Selected reaction monitoring (SRM) is the established gold standard for targeted protein quantitation due to its high analytical performance.
- Data-independent acquisition (DIA) is an emerging MS technique offering proteome-wide profiling capabilities for clinical applications.
Purpose of the Study:
- To evaluate the utility of DIA for profiling patient-specific proteomes from limited formalin-fixed, paraffin-embedded (FFPE) tumor biopsies.
- To assess DIA's capability for targeted protein quantitation in clinical samples.
- To explore DIA's potential in informing therapeutic decisions and cancer subtyping.
Main Methods:
- Analysis of 12 FFPE tumor biopsies using DIA mass spectrometry.
- Global proteomic profiling to identify quantifiable proteins and biomarkers.
- Comparative analysis of DIA proteomic data with mRNA expression levels.
Main Results:
- DIA analysis successfully quantified 3713 proteins, including clinically actionable biomarkers.
- Global proteomic profiles enabled the differentiation of gastric from colorectal cancer specimens.
- DIA identified subtype-specific proteins with potential prognostic or diagnostic value and demonstrated accurate TUBB3 quantitation for therapeutic decision-making.
Conclusions:
- DIA mass spectrometry is a powerful tool for analyzing patient-specific proteomes from FFPE tumor biopsies, even with limited sample amounts.
- DIA offers a viable alternative to SRM for targeted quantitation and holds promise for clinical proteomic assays and biomarker discovery.
- The findings support the use of DIA for informing therapeutic strategies and understanding cancer heterogeneity.
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