NCI-60 proteome resource

NCI60 proteome resource is a web application that facilitates comprehensive proteome analysis of the NCI-60 cell line panel. The NCI-60 is a set of 60 (now 59) human cancer cell lines from nine different tissues introduced in 1990 by the US National Cancer Institute (NCI) to screen for new anticancer agents.
The current database comprises a very high proteome coverage (more than half of human genome) and serves as a reference expression profiles of NCI-60 cell line panel. As such it contains details about protein and peptide identifications together with the corresponding fragment spectra and quantitative information. It also contains chromosome-centric view to identify the abundance and distribution of proteins whose genes are co-located on the same chromosome. In addition, a simple interface allows to query for differential protein expression either by protein names or attributes such as ontology terms. The protein queries return the cell lines where protein expression has been reported.

To cite this resource, the primary reference is (Gholami AM., et al., CELL reports, 2013) (pdf)

How to find information

work flow

Protein explorer
You can search for protein/gene name, synonym, GO category, experiment and etc. Start typing and autosuggest will help you narrow your search.
work flow

Global expression analysis
A simple interface allows you query for differential protein expression. The protein queries return the cell lines where protein expression has been reported.
work flow

Chromosome explorer
Chromosome-centric view provide the ability to identify the abundance and distribution of proteins whose genes are co-located on the same chromosome.
work flow

Annotation viewer
Annotation viewer provides a one-page summary of information for a given protein, its peptides and summaries of quantification from different experiments.
work flow

Spectrum viewer
This plug-in allows to view MS/MS spectra annotated with fragment ions.

Statistics

Number of proteins: 10,350
Number of genes: 8,739
Number of peptides: 225,687
Number of ms/ms spectra: 6,894,688
Mean chromosome coverage: 44%

Proteomics of the NCI-60 panel

work flow