PXD004131

PXD004131 is an original dataset announced via ProteomeXchange.

Title	Human_MCF7_membrane
Description	MCF7 cell was an important stabilized breast cancer cell in cancer research. A membrane proteomic method was developed and compared in this study. A membrane protein enrichment method composed of ultra-centrifugation and detergent-based extraction was first developed. Then in-solution digestion with detergents and eFASP (enhanced filter aided sample preparation) with detergents were compared with the time consuming in-gel digestion method. Our data indicated that ultra-centrifugation combined detergent-based extraction can effectively enrich membrane proteins with higher purity. Among the in-solution digestion methods, the eFASP combined with RapiGest method identified 1125 membrane proteins. Similarly, the eFASP combined with SDC identified 1069 membrane proteins, however, the in-gel digestion characterized 1091 membrane proteins. Totally, with the 5 digestion methods, 1390 membrane proteins were identified with ≥1 unique peptides, among which 1345 membrane proteins contain unique peptides ≥2. This is the biggest membrane protein datasets for MCF7 cell line and even breast cancer tissue samples. Interestingly, we realized that 9 missing proteins (MPs) present with one or more unique peptides. After verification, 4 of them were validated by synthesized peptide with amino acids larger than 9.
HostingRepository	PRIDE
AnnounceDate	2016-10-07
AnnouncementXML	Submission_2016-10-07_02:18:50.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD004131
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Wei Wei
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-05-11 05:21:47	ID requested
⏵ 1	2016-10-07 02:18:51	announced

Zhao M, Wei W, Cheng L, Zhang Y, Wu F, He F, Xu P, Searching Missing Proteins Based on the Optimization of Membrane Protein Enrichment and Digestion Process. J Proteome Res, 15(11):4020-4029(2016) [pubmed]

ProteomeXchange project tag: Chromosome-centric Human Proteome Project (C-HPP), Human Proteome Project

curator keyword: Biological

submitter keyword: Human, MCF7, membrane

Ping Xu
contact affiliation	State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing 102206, China
contact email	xuping_bprc@126.com
lab head
Wei Wei
contact affiliation	BPRC
contact email	powerweiwei@163.com
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/2016/10/PXD004131

PRIDE project URI

• PRIDE
  1. PXD004131
     1. Label: PRIDE project
     2. Name: Human_MCF7_membrane