Study 7 Downloads

Executed by the CPTAC Experimental Design and Statistics: Verification Studies Working Group, was a multi-laboratory study designed to assess performance metrics of multiplexed, protein-based Multiple Reaction Monitoring (MRM) assays, including recovery, precision, and limits of detection and quantitation. Although individual laboratories have demonstrated that MRM coupled with stable-isotope dilution mass spectrometry has suitable assay performance for quantitative measurements of candidate protein biomarkers in plasma, reproducibility and transferability of these assays across multiple laboratories has yet to be demonstrated. CPTAC Study 7 was an advanced consortium-wide (8 laboratories participated) follow-up study to the initial “feasibility” Study 4. Study 7 encompassed a three-tiered experimental protocol that progressively introduced sample preparation variables likely to affect inter- and intra-laboratory reproducibility, transferability, and sensitivity. The experimental design varied from 1) spiking digested plasma with 10 signature peptides representing 7 target proteins (samples prepared centrally at NIST), 2) spiking digested plasma with the 7 digested target proteins (samples prepared centrally at NIST), and finally 3) spiking the 7 intact target proteins into un-digested, neat plasma followed by combined digestion (samples prepared at each participating site). In Study 7, using common materials and standardized protocols, it was demonstrated that MS-based assays of proteins in plasma can be sensitive and highly reproducible across laboratories and instrument platforms. Here we provide the Study 7 data files to be used as benchmarks against which individual laboratories can compare their performance and evaluate new technologies for biomarker verification in plasma. Study 7 has been submitted to Nature Biotechnology for publication (Terri Addona, et al. “Multi-site Assessment of Precision and Sources of Variability of Multiple Reaction Monitoring-based Measurements: Toward Quantitative Protein Biomarker Verification in Human Plasma”.)

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• Study 8: Discovery WG
  (Yeast, No SOP) 
• Study 7: Verification WG (published study)
  
• Study 6: Discovery WG
  (Yeast+Sigma UPS 1, SOP 2.2) 
• Study 5: Discovery WG
  (Yeast+BSA, SOP 2.1) 
• Study 4: Verification WG (feasibility study)
  
• Study 3: Discovery WG
  (Yeast, SOP 2.0) 
• Study 2: Discovery WG
  (NCI-20, SOP 1.0) 
• Study 1: Discovery WG
  (NCI-20, No SOP)