PXD000065

PXD000065 is an original dataset announced via ProteomeXchange.

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	2024-10-22
AnnouncementXML	Submission_2024-10-22_03:58:50.472.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rui Branca
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; iTRAQ8plex-115 reporter+balance reagent acylated residue; iTRAQ8plex-116 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

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.
⏵ 4	2024-10-22 03:58:58	announced	2024-10-22: Updated project metadata.

10.1038/nmeth.2732;

Branca RM, Orre LM, Johansson HJ, Granholm V, Huss M, P, é, rez-Bercoff Å, Forshed J, K, ä, ll L, Lehti, ö J, HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nat Methods, 11(1):59-62(2014) [pubmed]

curator keyword: Technical, Biomedical

submitter keyword: mouse,LC-MS,HiRIEF,isoelectric focusing,cancer,N2A,human,A431

Rui Branca
contact affiliation	Clinical Proteomics Unit, Dep. of Oncology-Pathology
contact email	rui.mamede-branca@ki.se
lab head
Rui Branca
contact affiliation	Clinical Proteomics Unit, Dep. of Oncology-Pathology
contact email	rui.mamede-branca@ki.se
dataset submitter

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/2013/09/PXD000065

PRIDE project URI

• PRIDE
  1. PXD000065
     1. Label: PRIDE project
     2. Name: HiRIEF deep proteomics of A431 human vulvar cancer cell line and N2A mouse neuroblastoma cell line