Global Proteome Analysis of the NCI-60 Cell Line Panel
Open accessAbstract
The NCI-60 cell line collection is a very widely used panel for the study of cellular mechanisms of cancer in general and in vitro drug action in particular. It is a model system for the tissue types and genetic diversity of human cancers and has been extensively molecularly characterized. Here, we present a quantitative proteome and kinome profile of the NCI-60 panel covering, in total, 10,350 proteins (including 375 protein kinases) and including a core cancer proteome of 5,578 proteins that were consistently quantified across all tissue types. Bioinformatic analysis revealed strong cell line clusters according to tissue type and disclosed hundreds of differentially regulated proteins representing potential biomarkers for numerous tumor properties. Integration with public transcriptome data showed considerable similarity between mRNA and protein expression. Modeling of proteome and drug-response profiles for 108 FDA-approved drugs identified known and potential protein markers for drug sensitivity and resistance. To enable community access to this unique resource, we incorporated it into a public database for comparative and integrative analysis (http://wzw.tum.de/proteomics/nci60).
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Data from several large-scale, high-resolution, FDR-controlled cellular proteome projects show coverage saturating at approximately 11,000.
“This analysis is supported by data from several large scale, high-resolution, FDR-controlled cellular proteome projects, where the coverage saturated at approximately 11,000 (refs. 15,18,45,46).”
From Cell type- and brain region-resolved mouse brain proteome (2015) · cites this paper as [45]
The NCI-60 proteome analysis (Figure 1, p. 2) identifies 10,350 distinct proteins, approximately 11,000, and Protein Identification and Quantification (p. 10) specifies a maximum 1% false discovery rate. The paper does not show that coverage saturated at that level; its total is a measured yield, not an established saturation point. It is one of several projects cited by the sentence, so it need not itself report results from several projects. (LLM, conf=0.84)
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References 86 · Cited by 302
- Authors
- Gholami, A. M., Hahne, H., Wu, Z., Auer, F. J., Meng, C., Wilhelm, M., & Kuster, B.
- Affiliations
- Technical University of Munich (DE)
- Corresponding author
- Gholami, Amin Moghaddas
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2013-08
- Volume
- 4
- Issue
- 3
- Pages
- 609-620
- ISSN
- 2211-1247 (ISSN-L)
- OpenAlex
- W1992014004
- Cited by
- 302
- References
- 86
- Citations by year
- 2026: 5 · 2025: 11 · 2024: 21 · 2023: 14 · 2022: 23 · 2021: 19 · 2020: 17 · 2019: 29 · 2018: 27 · 2017: 42 · 2016: 25 · 2015: 35 · 2014: 30 · 2013: 4
- FWCI
- 14.07
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- mediaTUM – the media and publications repository of the Technical University Munich (Technical University Munich) (submittedVersion)
- OPUS (Augsburg University) (submittedVersion, cc-by)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- NCI-60 cell lines, tumor proteome, differentially regulated proteins, tumor markers, drug sensitivity, drug resistance, mRNA-protein expression correlation, proteomics database
- MeSH terms
- Humans, Neoplasm Proteins, Neoplasms, Cluster Analysis, Proteome, Gene Expression Profiling, Cell Line, Tumor
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