PXD000065-1
PXD000065 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | HiRIEF deep proteomics of A431 human vulvar cancer cell line and N2A mouse neuroblastoma cell line |
| Description | Here we present high resolution data from two cancer cell lines. A human cell line, A431 was treated with a drug at different time points and then fractionated into its different subcellular compartments (nuclear, organellar, soluble, whole cell). Protein extracts were trypsinized, peptides separated by HiRIEF (high resolution isoelectric focusing) and analysed by LC-MS. From the mouse cell line N2A proteins were extracted and subjected to the same HiRIEF-LC-MS procedure. All MS/MS spectra were searched by Sequest/Percolator under the software platform Proteome Discoverer (PD, v1.3.0.339, Thermo Scientific) using a target-decoy strategy. The reference databases used were the human protein subset of Ensembl 63 and the mouse protein subset of Ensembl 64. Precursor mass tolerance of 10 ppm and product mass tolerances of 0.02 Da for HCD-FTMS and 0.8 Da for CID-ITMS were used. Additional settings were: trypsin with 1 missed cleavage; Lys-Pro and Arg-Pro not considered as cleavage sites; carbamidomethylation on cysteine and iTRAQ-8plex on lysine and N-terminal as fixed modifications; and oxidation of methionine and phosphorylation on serine, threonine or tyrosine as variable modifications. Quantitation of iTRAQ-8plex reporter ions was done using an integration window tolerance of 20ppm. Peptides found at 1% FDR (false discovery rate) were used by the protein grouping algorithm in PD to infer protein identities. |
| HostingRepository | PRIDE |
| AnnounceDate | 2013-09-27 |
| AnnouncementXML | Submission_2013-09-27_15:10:12.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Rui Branca |
| SpeciesList | scientific name: Homo Sapiens (Human); NCBI TaxID: 9606; scientific name: Mus musculus; NCBI TaxID: 10090; |
| ModificationList | monohydroxylated residue; iodoacetamide derivatized residue; phosphorylated residue; iTRAQ8plex-116 reporter+balance reagent acylated residue; iTRAQ8plex-115 reporter+balance reagent acylated residue |
| Instrument | LTQ Orbitrap |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2012-11-06 05:29:06 | ID requested | |
| ⏵ 1 | 2013-09-27 15:10:12 | announced | |
| ⏵ 1 | 2013-11-21 02:16:33 | announced | |
| 2 | 2014-07-25 00:44:03 | announced | Updated project metadata. |
| 3 | 2015-01-23 03:37:57 | announced | Updated project metadata. |
Publication List
| Dataset with its publication pending |
Keyword List
| submitter keyword: A431,N2A,human,mouse,LC-MS,HiRIEF,isoelectric focusing,cancer |
Contact List
| Rui Branca | |
|---|---|
| contact affiliation | Karolinska Institutet |
| contact email | rui.mamede-branca@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/2013/09/PXD000065 |
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