Plasma is a rich source of protein biomarkers used to reveal disease biology. However, identifying and verifying biomarkers in plasma proteomics has challenges due to the wide range of protein concentrations. Thermo Fisher Scientific delivers a new set of performance standards for plasma proteomics-based verification, with deep proteome coverage, fast throughput, and accurate and precise quantitation. The combination of the Thermo Scientific Orbitrap Astral mass spectrometer performing discovery-based profiling while the Thermo Scientific Stellar mass spectrometer performs targeted quantitative analysis presents a new strategy to better evaluate putative biomarker candidates. Introduction of PRM Conductor tool in Skyline software further streamlines conversion of discovery to verification workflows between the two instruments for increased productivity.
The workflow is demonstrated using a newly developed extracellular vesicle enrichment protocol. Data-independent acquisition (DIA) enables new depths of plasma proteome profiling with more than 5,000 proteins in 60 minutes.
While mass spectrometry is often envisioned as an unbiased discovery platform for protein quantitation, many use the technology for directed quantitation of biologically relevant, predefined targets. Targeted methods based on parallel reaction monitoring (PRM) can be superior in terms of precision, accuracy, reproducibility, dynamic range, and specificity relative to DIA to increase confidence in determining the final set of putative biomarkers to transition to the validation stage of translational research.
This webcast will describe the development of PRM assays and demonstrate the ability to measure >700 proteins using >1,500 peptides in plasma on a novel hybrid nominal mass resolution tandem mass spectrometer, as well as demonstrate the statistical power in finding quantitative differences in a pilot Alzheimer’s disease cohort compared with DIA.
Learn:
- How to extend plasma proteome coverage using new enrichment strategies and new mass spectrometers for discovery
- How to efficiently and effectively transfer discovery-based plasma proteins for robust targeted quantitative analysis
- The analytical capabilities of a novel hybrid nominal mass resolution tandem mass spectrometer
About the presenter
Dr. Michael MacCoss, Professor of Genome Sciences, University of Washington
Dr. Michael MacCoss’s primary area of expertise is in protein biochemistry, nanoflow liquid chromatography, mass spectrometry instrumentation, and computational mass spectrometry data analysis. He has more than 30 years of mass spectrometry experience that bridges the fields of protein mass spectrometry, isotope ratio mass spectrometry, and quantitative mass spectrometry. The MacCoss laboratory actively applies these tools to essential areas of biology, including the basic biology of aging, neurodegenerative disease, protein-protein interactions, insulin signaling, measurement of protein half-life, transcriptional regulation, characterization of post-translational modifications, proteogenomics, and clinical diagnostics.