PXD000218-3

PXD000218 is an original dataset announced via ProteomeXchange.

Title	System-level analysis of cancer and stomal cell specific proteomes reveals extensive reprogramming of phosphorylation networks by tumor microenvironment
Description	DLD-1 cells and mouse were treated with DMSO, GDC0941 and CAL101 for 2 hours. Proteins were digested with trypsin and phospho peptides were enriched using TiO2. Enriched phosphopeptides and peptides were analysed by LTQ Orbitrap Velos mass spectrometer. (MS/MS data were converted to mgf files using Mascot Distiller (version 2.2) and searched against the UniProt-TrEMBL and UniProt SwissProt databases (release March 2012) and a decoy database using the Mascot search engine (version 2.2). The data was searched twice, restricting searches against human or mouse specific sequences in each separate search. For phosphoproteomics, tolerance windows were 3 p.p.m. and 600 mmu for parent and fragment ions, respectively. For proteomics, these were 5 p.p.m. and 50 mmu for parent and fragment ions, respectively. Allowed variable modifications were methionine oxidation, pyroglutamate at the N-terminus and phosphorylation of serine, threonine and tyrosine residues. Significance of peptide identification was assessed by comparing results returned by searches against random and forward databases. The probability of correct phosphorylation site assignment was determined by the Mascot delta score approach. Ambiguous phosphorylation site assignments are reported as gene name followed by start and end of the amino acid sequence
HostingRepository	PRIDE
AnnounceDate	2014-07-28
AnnouncementXML	Submission_2014-07-28_00:35:24.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000218
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Vinothini Rajeeve
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue; phosphorylated residue; deaminated residue
Instrument	LTQ Orbitrap; instrument model: LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-04-19 02:56:02	ID requested
1	2014-04-02 02:13:08	announced
2	2014-06-02 05:02:43	announced	Updated publication reference for PubMed record(s): 24648465.
⏵ 3	2014-07-28 00:35:24	announced	Updated project metadata.

Rajeeve V, Vendrell I, Wilkes E, Torbett N, Cutillas PR, Cross-species proteomics reveals specific modulation of signaling in cancer and stromal cells by phosphoinositide 3-kinase (PI3K) inhibitors. Mol Cell Proteomics, 13(6):1457-70(2014) [pubmed]

submitter keyword: proteomics, phosphoproteomics, DLD-1 cells

Vinothini Rajeeve
contact affiliation	Centre for Cell Signalling
contact email	v.rajeeve@qmul.ac.uk
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/2014/04/PXD000218

PRIDE project URI

• PRIDE
  1. PXD000218
     1. Label: PRIDE project
     2. Name: System-level analysis of cancer and stomal cell specific proteomes reveals extensive reprogramming of phosphorylation networks by tumor microenvironment