Dataset Information

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

ABSTRACT: 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.

Dataset imported into MassIVE from https://cptac-data-portal.georgetown.edu/study-summary/S041 on 12/08/21

INSTRUMENT(S): Orbitrap Fusion Lumos, Q Exactive HF

ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090)

SUBMITTER: Hui Zhang

PROVIDER: MSV000088547 | MassIVE | Wed Dec 08 16:09:00 GMT 2021

REPOSITORIES: MassIVE

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

Clark David J DJ Hu Yingwei Y Bocik William W Chen Lijun L Schnaubelt Michael M Roberts Rhonda R Shah Punit P Whiteley Gordon G Zhang Hui H

Journal of proteome research 20180508 6

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) ...[more]

PMID: 29718670

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