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NCI60 proteome by PCT-SWATH - Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

ABSTRACT: We obtained quantitative analysis of the NCI-60 cell panels using pressure cycling technology (PCT) and SWATH-MS. Each cell was analyzed in duplicate. The data were analyzed using a cell line SWATH assay library and OpenSWATH, followed by SWATH-expert refinement.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Ruedi Aebersold

PROVIDER: MSV000085848 | MassIVE | Wed Jul 29 14:53:00 BST 2020

SECONDARY ACCESSION(S): PXD003539

REPOSITORIES: MassIVE

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Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.

Guo Tiannan T Luna Augustin A Rajapakse Vinodh N VN Koh Ching Chiek CC Wu Zhicheng Z Liu Wei W Sun Yaoting Y Gao Huanhuan H Menden Michael P MP Xu Chao C Calzone Laurence L Martignetti Loredana L Auwerx Chiara C Buljan Marija M Banaei-Esfahani Amir A Ori Alessandro A Iskar Murat M Gillet Ludovic L Bi Ran R Zhang Jiangnan J Zhang Huanhuan H Yu Chenhuan C Zhong Qing Q Varma Sudhir S Schmitt Uwe U Qiu Peng P Zhang Qiushi Q Zhu Yi Y Wild Peter J PJ Garnett Mathew J MJ Bork Peer P Beck Martin M Liu Kexin K Saez-Rodriguez Julio J Elloumi Fathi F Reinhold William C WC Sander Chris C Pommier Yves Y Aebersold Ruedi R

iScience 20191031

Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry. We developed the DIA-expert software to curate and visualize the SWATH data, leading to reproducible detection of over 3,100 SwissProt proteotypic proteins and systematic quantification of pathway activities. Stoichiometric relationships of interacting proteins for DNA replication, repair, the chromatin remodeling NuRD complex, β-catenin, RNA metabolism, and ...[more]

PMID: 31733513

Similar Datasets

NCI60 proteome by PCT-SWATH - Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines

Project description:We obtained quantitative analysis of the NCI-60 cell panels using pressure cycling technology (PCT) and SWATH-MS. Each cell was analyzed in duplicate. The data were analyzed using a cell line SWATH assay library and OpenSWATH, followed by SWATH-expert refinement.

2020-06-01 | PXD003539 | Pride

DDA files of human cancer cells for the NCI-60 SWATH project PXD003539

Project description:This is the raw files for the DDA library used for intepreting the NCI-60 SWATH project PXD003539

2019-10-21 | PXD009597 | Pride

NCI-60 Cancer Cell Line

Project description:NCI-60 cancer cell lines were profiled with their genome-wide gene expression patterns using Affymetrix HG-U133A chips. Keywords: NCI-60 cancer cell line expression profiling

2009-08-26 | GSE5846 | GEO

Global Proteome Analysis of the NCI-60 Cell Line Panel

Project description: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).

2017-03-31 | PXD005940 | Pride

NCI 60 Cell Lines - Proteome Profiles

Project description: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.

2016-05-02 | MSV000079694 | MassIVE

Transcription profiling of human NCI-60 Cancer Cell Line

Project description:NCI-60 cancer cell lines were profiled with their genome-wide gene expression patterns using Affymetrix HG-U133A chips. Experiment Overall Design: Total RNA sample of each of the NCI-60 cell lines was obtained before the treatment of any anticancer compound.

2009-09-15 | E-GEOD-5846 | biostudies-arrayexpress

Global Proteome Analysis of the NCI-60 Cell Line Panel, part 3

2017-09-25 | PXD005946 | Pride

Global Proteome Analysis of the NCI-60 Cell Line Panel, part 2

2017-03-31 | PXD005942 | Pride

Proteomic profiling of NCI60 cell lines from Cancer Cell Line Encyclopedia

Project description:This ArrayExpress record contains meta-data and results of quantitative analysis of cell lines from the NCI-60 panel using pressure cycling technology (PCT) and SWATH-mass spectrometry. Each cell line was analyzed in duplicate. Raw data files are available at the EMBL-EBI protemics data archive (PRIDE) at accession PXD003539 (http://www.ebi.ac.uk/pride/archive/projects/PXD003539). Since the record here does not include the raw data files and hence there is no need to explicitly link individual replicate to a raw file, each sample is only listed once in the ArrayExpress samples table for clarity.

2017-01-27 | E-PROT-2 | biostudies-arrayexpress

The NCI-60 Methylome and Its Integration into CellMiner

Project description:Methylation assay of cell lines from 9 different cancer tissue of origin types (Breast, Central Nervous System, Colon, Leukemia, Melanoma, Non-Small Cell Lung, Ovarian, Prostate, Renal) from NCI-60 panel

2017-03-31 | GSE79185 | GEO

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