Dataset Information

Phosphoproteomics data classify haematological cancer cell lines according to tumour type and sensitivity to kinase inhibitors

ABSTRACT: Acute myeloid leukemia, lymphoma and multiple myeloma cell lines were grown for 24h in RPMI medium and cells were harvested by centrifugation. Samples were digested with trypsin and subjected to phosphoenrichment using IMAC. Phosphopeptides were run in a LTQ-Orbitrap-XL. Peaks lists were generated with Mascot Distiller (version 2.3) in MGF format and Database searches were with Mascot Server (version 2.3) against the SwissProt database restricted to human sequences (release December 2011) and trypsin cleavage. Restrictions were 7ppm for parent ions and 600 mmu for fragment masses. Allowed modifications were phosphorylation of Ser/Thr/Tyr, pyro-Glu (N-term) and methionine oxidation and one miss-cleavage allowed. Quantification was by label-free using peak heights of extracted ion chromatograms (XICs) constructed with narrow mass windows (7ppm) and time windows (1.5 minutes). Pescal, a computer program written in house, was used to automate the generation of XICs and to calculate peak heights.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Blood Cell

SUBMITTER: Pedro Casado-Izquierdo

LAB HEAD: Pedro Casado-Izquierdo

PROVIDER: PXD000217 | Pride | 2013-04-26

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

			Action	DRS
	PRIDE_Exp_Complete_Ac_29279.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_29279.pride.mztab.gz	Mztab
	PRIDE_Exp_Complete_Ac_29279.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_29280.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_29280.pride.mztab.gz	Mztab

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Publications

Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors.

Casado Pedro P Alcolea Maria P MP Iorio Francesco F Rodríguez-Prados Juan-Carlos JC Rodríguez-Prados Juan-Carlos JC Vanhaesebroeck Bart B Saez-Rodriguez Julio J Joel Simon S Cutillas Pedro R PR

Genome biology 20130429 4

<h4>Background</h4>Tumor classification based on their predicted responses to kinase inhibitors is a major goal for advancing targeted personalized therapies. Here, we used a phosphoproteomic approach to investigate biological heterogeneity across hematological cancer cell lines including acute myeloid leukemia, lymphoma, and multiple myeloma.<h4>Results</h4>Mass spectrometry was used to quantify 2,000 phosphorylation sites across three acute myeloid leukemia, three lymphoma, and three multiple ...[more]

PMID: 23628362

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