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Last Updated: 06/04/15

Credentialing Plasma and Serum Biospecimen Banks for Proteomics Analysis

Subcontractor: University of California — San Francisco (UCSF)
Principal Investigator: Katherine Williams, Ph.D.
Co-Principal Investigator: Susan Fisher, Ph.D.

Dr. Williams and her group at UCSF investigated the effects of intrinsic protease and peptidase activities and their contribution to sample integrity, variability, and the ability to produce reproducible data in proteomics. The experimental approach was aimed at evaluating the impact of preanalytical variables on the proteolysis-driven changes in plasma proteins. The investigators hypothesized that the time-course changes in the composition and relative abundance of low molecular weight (LMW) components, i.e. peptides, provide an indication of the continuing proteolytic processes and may be used to measure and define sample integrity. The PI’s also developed a quality assurance program consisting of several parts: (i) generation and use of standard operating procedures (SOPs) for all protocols used for the project, (ii) detailed procedures for data acquisition, (iii) assay acceptance criteria (i.e., a set of descriptors and numerical quality metrics related to the technical performance of the assay that need to be met to include the data into the database), (iv) data analysis, and (v) record keeping.

Dr. Williams and her team introduced a panel of proteins that could be used as quality assessment measures for predicting and verifying protein integrity in repository samples. Specifically, their team emphasized the usefulness of their study to medical research and biomarker communities to assess the integrity of plasma and serum samples to be used for proteomics experiments. They compiled a set of proteins for quantitative assessment of the integrity of plasma and serum biospecimens for proteomics research. The data provided information on the utility of banked biospecimens for proteomics research and established a set of preanalytical processing conditions that contributed to best practices protocols for prospective serum and plasma collection, processing, and storage.

Hassis et al., Evaluating the effects of preanalytical variables on the stability of the human plasma proteome, Anal. Biochem., 478(1), June 2015; 14-22