pr8b00165_si_002.xlsx (40.82 MB)
Evaluation of NCI‑7 Cell Line Panel as a Reference Material for Clinical Proteomics
dataset
posted on 2018-05-02, 00:00 authored by David J. Clark, Yingwei Hu, William Bocik, Lijun Chen, Michael Schnaubelt, Rhonda Roberts, Punit Shah, Gordon Whiteley, Hui ZhangReference materials are vital to
benchmarking the reproducibility
of clinical tests and essential for monitoring laboratory performance
for clinical proteomics. The reference material utilized for mass
spectrometric analysis of the human proteome would ideally contain
enough proteins to be suitably representative of the human proteome,
as well as exhibit a stable protein composition in different batches
of sample regeneration. Previously, The Clinical Proteomic Tumor Analysis
Consortium (CPTAC) utilized a PDX-derived comparative reference (CompRef)
materials for the longitudinal assessment of proteomic performance;
however, inherent drawbacks of PDX-derived material, including extended
time needed to grow tumors and high level of expertise needed, have
resulted in efforts to identify a new source of CompRef material.
In this study, we examined the utility of using a panel of seven cancer
cell lines, NCI-7 Cell Line Panel, as a reference material for mass
spectrometric analysis of human proteome. Our results showed that
not only is the NCI-7 material suitable for benchmarking laboratory
sample preparation methods, but also NCI-7 sample generation is highly
reproducible at both the global and phosphoprotein levels. In addition,
the predicted genomic and experimental coverage of the NCI-7 proteome
suggests the NCI-7 material may also have applications as a universal
standard proteomic reference.