PXD003941

PXD003941 is an original dataset announced via ProteomeXchange.

Title	Automated SDS depletion for mass spectrometry of membrane proteins through transmembrane electrophoresis
Description	Membrane proteins are underrepresented in proteome analysis platforms because of their hydrophobic character, contributing to decreased solubility. Sodium dodecyl sulfate is a favored denaturant in proteomic workflows, facilitating cell lysis and protein dissolution. However, SDS impedes MS detection and therefore must be removed prior to analysis. Though strategies exist for SDS removal, they provide low recovery, purity, or reproducibility. Here we present a simple automated device, termed transmembrane electrophoresis (TME), incorporating the principles of membrane filtration, but with an applied electric current to ensure near complete (99.9 %) removal of the surfactant, including protein-bound SDS. Intact proteins are recovered in solution phase in high yield (90-100%), within 1 hour of operation. They strategy is applied to protein standards and proteome mixtures, including E. coli membrane fractions, resulting in quality MS spectra free of SDS adducts. The TME platform is applicable to both bottom-up MS/MS, as well as LC-ESI-MS analysis of intact proteins. SDS depleted fractions reveal a similar number of protein identifications (285) compared to a non-SDS control (280), being highly correlated in terms of protein spectral counts. This fully automated approach to SDS removal presents a viable tool for proteome sample processing ahead of MS analysis.
HostingRepository	PRIDE
AnnounceDate	2017-07-10
AnnouncementXML	Submission_2017-07-10_00:09:05.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD003941
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Carolyn Kachuk
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	No PTMs are included in the dataset
Instrument	LTQ

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-12 02:38:38	ID requested
⏵ 1	2017-07-10 00:09:07	announced

Kachuk C, Faulkner M, Liu F, Doucette AA, Automated SDS Depletion for Mass Spectrometry of Intact Membrane Proteins though Transmembrane Electrophoresis. J Proteome Res, 15(8):2634-42(2016) [pubmed]

curator keyword: Technical

submitter keyword: E.coli, membrane proteins, LTQ,

Alan A Doucette
contact affiliation	Chemistry Department Dalhousie University Halifax, NS, Canada
contact email	alan.doucette@dal.ca
lab head
Carolyn Kachuk
contact affiliation	Dalhousie University
contact email	carolynkachuk@hotmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD003941
     1. Label: PRIDE project
     2. Name: Automated SDS depletion for mass spectrometry of membrane proteins through transmembrane electrophoresis