PXD002811 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Peptide recovery from acid-precipitated sodium deoxycholate pellet |
Description | Sodium deoxycholate (SDC) is MS-compatible ionic detergent which is compatible with in-solution tryptic digestion. SDC is removed from tryptic digested mixtures easily by acid precipitation and it has been demonstrated its capacity to increase trypsin activity. Additionally, and on the contrary to urea, SDC does not generate carbamylation side-products. Here, we report an optimized SDC-based shotgun proteomics sample preparation methods for blood-based protein biomarker research applied to human plasma. We show that an important subset of peptides was co-precipitated with the SDC salts and was recovered by a sequencial extraction of the SDC pellet by re-solubilization and precipitation. |
HostingRepository | PRIDE |
AnnounceDate | 2016-02-04 |
AnnouncementXML | Submission_2016-02-04_00:19:14.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Aida Serra |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | deamidated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | LTQ FT |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2015-08-28 01:43:28 | ID requested | |
⏵ 1 | 2016-02-04 00:19:15 | announced | |
Publication List
Serra A, Zhu H, Gallart-Palau X, Park JE, Ho HH, Tam JP, Sze SK, Plasma proteome coverage is increased by unique peptide recovery from sodium deoxycholate precipitate. Anal Bioanal Chem, 408(7):1963-73(2016) [pubmed] |
Keyword List
curator keyword: Technical |
submitter keyword: human plasma / mass spectrometry / shotgun proteomics / sodium deoxycholate / trypsin digestion. |
Contact List
Siu Kwan Sze |
contact affiliation | School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551. |
contact email | SKSze@ntu.edu.sg |
lab head | |
Aida Serra |
contact affiliation | School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551. |
contact email | aserramaq@ntu.edu.sg |
dataset submitter | |
Full Dataset Link List
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/2016/02/PXD002811 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD002811
- Label: PRIDE project
- Name: Peptide recovery from acid-precipitated sodium deoxycholate pellet