Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics

David J. Clark, Yingwei Hu, William Bocik, Lijun Chen, Michael Schnaubelt, Rhonda Roberts, Punit Shah, Gordon Whiteley, Hui Zhang

Research output: Contribution to journalArticlepeer-review


Reference 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.

Original languageEnglish (US)
Pages (from-to)2205-2215
Number of pages11
JournalJournal of proteome research
Issue number6
StatePublished - Jun 1 2018


  • clinical proteomics
  • mass spectrometry
  • proteomics reference material

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)


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