PXD000948

PXD000948 is an original dataset announced via ProteomeXchange.

Title	Macro-porous Reversed Phase Separation of Proteins Combined with Reversed Phase Separation of Phosphopeptides and Tandem Mass Spectrometry for Profiling the Phosphoproteome of MDA-MB-231 cells
Description	A new method of combining macro-porous reversed phase (mRP) protein fractionation with reversed phase liquid chromatography (RPLC) peptide separation tandem mass spectrometry (MS/MS) is reported for profiling the phosphoproteome of a complex sample. In this method, an mRP-C18 column was used to fractionate the proteins from a whole cell lysate of a breast cancer cell line, MDA-MB-231, into 38 fractions. Each fraction was subjected to tryptic digestion, sequential phosphopeptide enrichment by immobilized metal ion affinity chromatography (IMAC) and titanium dioxide (TiO2), followed by capillary RPLC-MS/MS analysis. For comparison, the conventional method of using strong cation exchange (SCX)-RPLC separation of peptides combined with MS/MS was also used for analyzing the phosphoproteome. Replicate experiments by the mRP-RPLC method identified 1585 distinct phosphoproteins with 4519 phosphopeptides, compared to 1585 phosphoproteins with 4297 phosphopeptides by SCX-RPLC, with a total of 1947 phosphoproteins and 6278 phosphopeptides identified from the combined results. While the two methods have similar ability in the identification of the phosphoproteome, they produce complementary information. The phosphoproteins identified in this study, including 67 novel phosphorylation sites from 56 breast cancer related proteins, can serve as the entry point for future validation with biological implications in breast cancer.
HostingRepository	PRIDE
AnnounceDate	2017-08-03
AnnouncementXML	Submission_2017-08-03_01:46:03.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000948
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Xiaoxia Ye
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Waters instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2014-05-02 01:19:00	ID requested
1	2014-06-06 07:52:44	announced
2	2014-07-24 05:17:54	announced	Updated project metadata.
⏵ 3	2017-08-03 01:46:04	announced	Updated project metadata.

Ye X, Li L, Macroporous reversed-phase separation of proteins combined with reversed-phase separation of phosphopeptides and tandem mass spectrometry for profiling the phosphoproteome of MDA-MB-231 cells. Electrophoresis, 35(24):3479-86(2014) [pubmed]

curator keyword: Biomedical

submitter keyword: mass spectrometry, MDA-MB-231, mRP-RPLC, phosphoproteome, SCX-RPLC

Xiaoxia Ye
contact affiliation	Chemistry Department, University of Alberta
contact email	xiaoxia@ualberta.ca
lab head
Xiaoxia Ye
contact affiliation	University of Alberta
contact email	xiaoxia@ualberta.ca
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/2014/07/PXD000948

PRIDE project URI

• PRIDE
  1. PXD000948
     1. Label: PRIDE project
     2. Name: Macro-porous Reversed Phase Separation of Proteins Combined with Reversed Phase Separation of Phosphopeptides and Tandem Mass Spectrometry for Profiling the Phosphoproteome of MDA-MB-231 cells