PXD000309
PXD000309 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Proteomic portrait of human breast cancer progression identifies novel prognostic markers |
| Description | Triplicate analysis of eleven breast cancer cell lines, each separated to 12 offgel fractions. Proteomes were quantified relative to heavy SILAC-labeled MCF7 cells that served as a spike-in standard. In this study, we used system-wide analysis of breast cancer proteomes to identify proteins that are associated with the progression of ER(-) tumors. Our two-step approach included an initial deep analysis of cultured cells that were obtained from tumors of defined breast cancer stages, followed by a validation set using human breast tumors. Using high-resolution mass spectrometry and quantification by Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC), we identified 8,750 proteins and quantified 7,800 of them. A stage-specific signature was extracted and validated by mass spectrometry and immunohistochemistry on tissue microarrays. Data analysis: Raw MS files from the LTQ-Orbitrap were analyzed by MaxQuant (version 1.1.1.9). MS/MS spectra were searched against the decoy IPI-human database version 3.68 containing both forward and reverse protein sequences by the Andromeda search engine. For identification, the false discovery rate (FDR) was set to 0.01 on the protein and on the peptide levels. |
| HostingRepository | PRIDE |
| AnnounceDate | 2013-07-02 |
| AnnouncementXML | Submission_2013-07-02_05:30:02.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Mario Oroshi |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
| ModificationList | monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue |
| Instrument | LTQ Orbitrap |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2013-07-01 04:55:23 | ID requested | |
| 1 | 2013-07-02 05:27:23 | announced | |
| 1 | 2014-07-25 01:17:36 | announced | |
| ⏵ 2 | 2013-07-02 05:30:02 | announced | Add reference |
Publication List
| Geiger T, Madden SF, Gallagher WM, Cox J, Mann M, Proteomic portrait of human breast cancer progression identifies novel prognostic markers. Cancer Res, 72(9):2428-39(2012) [pubmed] |
Keyword List
| submitter keyword: proteomics, mass spectrometry, breast cancer |
Contact List
| Mario Oroshi | |
|---|---|
| contact affiliation | Proteomics |
| contact email | oroshi@biochem.mpg.de |
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/2013/07/PXD000309 |
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