PXD000217

PXD000217 is an original dataset announced via ProteomeXchange.

Title	Phosphoproteomics data classify haematological cancer cell lines according to tumour type and sensitivity to kinase inhibitors
Description	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.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_08:53:45.265.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000217
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Pedro Casado-Izquierdo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; deaminated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-04-19 02:20:03	ID requested
1	2013-04-26 06:58:28	announced
1	2014-07-28 00:35:06	announced
2	2013-05-01 04:46:38	announced	Add reference
⏵ 3	2024-10-07 08:53:46	announced	2024-10-07: Updated project metadata.

10.1186/gb-2013-14-4-r37;

10.6019/PXD000217;

Casado P, Alcolea MP, Iorio F, Rodr, í, guez-Prados JC, Vanhaesebroeck B, Saez-Rodriguez J, Joel S, Cutillas PR, Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors. Genome Biol, 14(4):R37(2013) [pubmed]

submitter keyword: Kinase inhibitor, Drug sensitivity, IMAC,Phosphoproteomics, Hierarchical Clustering Analysis, Blood Malignancies, Acute Myeloid Leukemia

Pedro Casado-Izquierdo
contact affiliation	Cell Signalling
contact email	p.m.casado-izquierdo@qmul.ac.uk
lab head
Pedro Casado-Izquierdo
contact affiliation	Cell Signalling
contact email	p.m.casado-izquierdo@qmul.ac.uk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000217
     1. Label: PRIDE project
     2. Name: Phosphoproteomics data classify haematological cancer cell lines according to tumour type and sensitivity to kinase inhibitors