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.

Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer’s disease

“…For each batch, there were approximately 10,000 protein groups identified ( Fig. 1b), which was comparable to the depth achieved in the CPTAC protocol using different tissue sources 42,43 . The confidence of identification for peptide and protein is highly related with the number of PSMs and unique peptides.…”

Global quantitative analysis of the human brain proteome and phosphoproteome in Alzheimer’s disease

“…The total numbers of identified peptides, proteins and PSMs for all batches in the total proteome are listed in Table 1. For each batch, there were approximately 10,000 protein groups identified (Figure 1b), which was comparable to the depth achieved in the CPTAC protocol using different tissue sources 32,33 . The confidence of identification for peptide and protein is highly related with the number of PSMs and unique peptides.…”

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

“…A reference sample was created by pooling an aliquot from individual ccRCC tumors and NAT samples (90 tumors and 72 NATs, representing ~90% of the sample cohort), labeled with the TMT-131 reagent, and included in all TMT 10-plexes as a pooled reference channel. Two internal quality control (QC) samples, a single, independently-acquired chromophobe renal cell carcinoma (chRCC) tumor sample and an NCI-7 Cell Line Panel sample ( Clark et al, 2018 ), were prepared and interspersed among all TMT 10-plex sets. 110 ccRCC tumor and 84 NAT samples with eight chromophobe QC aliquots and five NCI-7 QC aliquots were co-randomized to 23 TMT 10-plex sets.…”