Dataset Information

System-level analysis of cancer and stomal cell specific proteomes reveals extensive reprogramming of phosphorylation networks by tumor microenvironment

ABSTRACT: 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

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Epithelial Cell, Colon

SUBMITTER: Vinothini Rajeeve

LAB HEAD: Vinothini Rajeeve

PROVIDER: PXD000218 | Pride | 2014-04-02

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_29354.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_29354.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_29354.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_29355.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_29355.pride.mztab.gz	Mztab

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Publications

Cross-species proteomics reveals specific modulation of signaling in cancer and stromal cells by phosphoinositide 3-kinase (PI3K) inhibitors.

Rajeeve Vinothini V Vendrell Iolanda I Wilkes Edmund E Torbett Neil N Cutillas Pedro R PR

Molecular & cellular proteomics : MCP 20140319 6

The tumor microenvironment plays key roles in cancer biology, but its impact on the regulation of signaling pathway activity in cancer cells has not been systemically investigated. We designed an analytical strategy that allows differential analysis of signaling between cancer and stromal cells present in tumor xenografts. We used this approach to investigate how in vivo growth conditions and PI3K inhibitors regulate pathway activities in both cancer and stromal cell populations. We found that, ...[more]

PMID: 24648465

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