PXD001548

PXD001548 is an original dataset announced via ProteomeXchange.

Title	Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling
Description	Membrane proteins are crucial targets for cancer biomarker discovery and drug development. However, in addition to the inherent challenges of hydrophobicity and low abundance, complete membrane proteome coverage of clinical specimen is usually hindered by the requirement of large amount of starting materials. Towards comprehensive membrane proteomic profiling for small amounts of samples (< 10 µg), we developed high-pH reverse phase (Hp-RP) combined with stop-and-go extraction tip (StageTip) technique, as a fast (~ 15 mins.), sensitive, reproducible, high-resolution and multiplexed fractionation method suitable for accurate quantification of the membrane proteome. This approach provided almost 2-fold enhanced detection of peptides within transmembrane helix domains compared with strong anion exchange (SAX) and strong cation exchange (SCX) StageTip techniques. More than 5000 proteins (63% membrane proteins) can be identified in only 10 µg of membrane protein digests, showing the superior sensitivity of the Hp-RP StageTip approach. The Hp-RP StageTip method enabled in-depth membrane proteome profiling of 11 lung cancer cell lines harboring different EGFR mutation status, which resulted in the identification of 3983 annotated membrane proteins. This provides the largest collection of reference peptide spectral data for lung cancer membrane sub-proteome. Finally, relative quantification of membrane proteins between Gefitinib-resistant and -sensitive lung cancer cell lines revealed several upregulated membrane proteins with key roles in lung cancer progression.
HostingRepository	PRIDE
AnnounceDate	2015-11-16
AnnouncementXML	Submission_2015-11-16_13:39:12.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Baby Rorielyn Dimayacyac-Esleta
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Rattus rattus (Black rat); NCBI TaxID: 10117;
ModificationList	deamidated residue; monohydroxylated residue; methylthiolated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2014-11-27 06:51:48	ID requested
⏵ 1	2015-11-16 13:39:13	announced

Dimayacyac-Esleta BR, Tsai CF, Kitata RB, Lin PY, Choong WK, Lin TD, Wang YT, Weng SH, Yang PC, Arco SD, Sung TY, Chen YJ, Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling. Anal Chem, 87(24):12016-23(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: high-pH reverse phase StageTip, membrane proteins, lung cancer

Yu-Ju Chen
contact affiliation	Institute of Chemistry, Academia Sinica
contact email	yujuchen@gate.sinica.edu.tw
lab head
Baby Rorielyn Dimayacyac-Esleta
contact affiliation	Academia Sinica
contact email	babyrorielyn@gmail.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/2015/11/PXD001548

PRIDE project URI

• PRIDE
  1. PXD001548
     1. Label: PRIDE project
     2. Name: Rapid High-pH Reverse Phase StageTip for Sensitive Small-Scale Membrane Proteomic Profiling