PXD000578-1
PXD000578 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Mass spectrometry-based quantitative proteomics of whole cell lysate from breast cancer cell line MCF7 spiked with 57 protein standards |
| Description | Here we present quantitative proteomics data used in the evaluation of quantitative accuracy. A human cell line, MCF7 was split into 9 aliquotes that were spiked with a dilution series of 57 protein standards of known amounts spanning 5 orders of magnitude. The protein extracts were trypsinized, and the peptides were analysed by LC-MS using either a label-free or a label-based (TMT 6-plex and iTRAQ 8-plex) quantification approach. The iTRAQ- and TMT-labelled samples were co-analysed and separated by HiRIEF (high resolution isoelectric focusing) prior LC-MS. Raw MS data was identified and quantified under the software platform Proteome Discoverer 1.3.0.339 (Thermo Fisher Scientific Inc.) or MaxQuant software (version 1.2.0.18) (label-free data). For both protein identification and quantification at least 1 unique (i.e. a peptide that occurs in not more than one database entry) peptide was required. The false discovery rate (FDR) for peptide identification was set to 5% in all analyses. For the iTRAQ and TMT labeled samples, all MS/MS spectra were searched by SEQUEST combined with the Percolator algorithm (version 2.0) for PSM search optimization. Searches were performed against a custom made database consisting of SwissProt human sequences(uniprot.org 2012-01-17, 20242 entries), and the spiked in protein standards (57 protein sequences). Peptide FDR was calculated by a target – decoy approach. |
| HostingRepository | PRIDE |
| AnnounceDate | 2013-12-03 |
| AnnouncementXML | Submission_2013-12-03_07:20:06.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | AnnSofi Sandberg |
| SpeciesList | scientific name: Homo Sapiens (Human); NCBI TaxID: 9606; |
| ModificationList | monohydroxylated residue; iodoacetamide derivatized residue; iTRAQ8plex; iTRAQ8plex:13C(6)15N(2); TMT6plex |
| Instrument | LTQ Orbitrap |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2013-11-13 01:22:24 | ID requested | |
| ⏵ 1 | 2013-12-03 07:20:18 | announced | |
| ⏵ 1 | 2013-12-03 07:21:14 | announced | |
| 2 | 2014-07-25 01:46:57 | announced | Updated project metadata. |
Publication List
| Dataset with its publication pending |
Keyword List
| submitter keyword: iTRAQ,TMT,quantification,MCF7,LC-MS,precursor mixing,isoelectric focusing |
Contact List
| AnnSofi Sandberg | |
|---|---|
| contact affiliation | Karolinska Institutet |
| contact email | annsofi.sandberg@ki.se |
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/2013/12/PXD000578 |
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