PXD008952-2

PXD008952 is an original dataset announced via ProteomeXchange.

Title	Evaluation of NCI-7 Cell Line Panel
Description	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 PDX-derived comparative reference (CompRef) materials for the longitudinal assessment of proteomic performance, however, inherent drawbacks of PDX-derived material has 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 the human proteome. Our results showed that not only is the NCI-7 material suitable for benchmarking laboratory sample preparation methods, but 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:43:02.158.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008952
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	David Clark
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	Phospho; TMT6plex; Oxidation; Carbamidomethyl
Instrument	Orbitrap Fusion Lumos; Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-14 01:34:02	ID requested
1	2018-05-14 03:29:49	announced
⏵ 2	2024-10-22 04:43:07	announced	2024-10-22: Updated project metadata.

Clark DJ, Hu Y, Bocik W, Chen L, Schnaubelt M, Roberts R, Shah P, Whiteley G, Zhang H, Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics. J Proteome Res, 17(6):2205-2215(2018) [pubmed]

10.1021/acs.jproteome.8b00165;

10.6019/PXD008952;

ProteomeXchange project tag: Reference, CPTAC Consortium

curator keyword: Biological

submitter keyword: NCI-60, proteomics reference standard, NCI-7,CPTAC

Hui Zhang
contact affiliation	Clinical Chemistry Division, Department of Pathology, The Johns Hopkins University, Baltimore, MD, USA
contact email	huizhang@jhu.edu
lab head
David Clark
contact affiliation	The Johns Hopkins University
contact email	dclark71@jhmi.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008952

PRIDE project URI

• PRIDE
  1. PXD008952
     1. Label: PRIDE project
     2. Name: Evaluation of NCI-7 Cell Line Panel