PXD000185

PXD000185 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Kinase Substrate Enrichment Analysis Provides Insights into the Heterogeneity of Signaling Pathway Activation in Leukemia Cells
Description	Experiments were performed in AML (Acute Myeloid Leukemia) cell lines and in primary cells coming from patients with AML and healthy donors. The AML cell lines P31/Fuj and Kasumi-1 were treated with vehicle (DMSO), 100 nM or 1000 nM of the PI3K/mTOR inhibitor AZ123 or the mTOR inhibitor Ku0063794 for 2h. Both cell lines were treated also with vehicle and 1000 nM of the PI3K/mTOR inhibitor PI103. 6 replicates per condition were done. AML primary cells and GMPBs (G-CSF-mobilized peripheral blood cell) from patients and healthy donors respectively were treated or untreated with 100 mM sodium pervanadate for 30 min. Samples 45-46 correspond to the GMPBs and the rest correspond to AML patients. All samples were digested with trypsin and subjected to phosphoenrichment usin TiO2. 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	2013-04-11
AnnouncementXML	Submission_2013-04-11_08:29:37.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000185
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: 79.966331; monohydroxylated residue: 15.994915; iodoacetamide -site C: 57.021464; 2-pyrrolidone-5-carboxylic acid (Gln): -17.026549; N-formylated residue: 27.994915
Instrument	LTQ Orbitrap

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2013-03-18 05:52:55	ID requested
1	2013-04-09 09:11:39	announced
1	2014-07-28 00:31:11	announced
⏵ 2	2013-04-11 08:29:37	announced	Add reference

Publication List

Casado P, Rodriguez-Prados JC, Cosulich SC, Guichard S, Vanhaesebroeck B, Joel S, Cutillas PR, Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells. Sci Signal, 6(268):rs6(2013) [pubmed]

Casado P, Rodriguez-Prados JC, Cosulich SC, Guichard S, Vanhaesebroeck B, Joel S, Cutillas PR, Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells. Sci Signal, 6(268):rs6(2013) [pubmed]

Keyword List

submitter keyword: PI3K/mTOR inhibitors, AML Primary Cells, Label Free Quantification, TiO2 phosphoenrichment

submitter keyword: PI3K/mTOR inhibitors, AML Primary Cells, Label Free Quantification, TiO2 phosphoenrichment

Contact List

Pedro R. Cutillas
contact attribute	pedro.cutillas@csc.mrc.ac.uk
contact affiliation	Medical Researh Council Clinical Sciences Centre, Imperial Collegel
contact email	pedro.cutillas@csc.mrc.ac.uk
Pedro Casado-Izquierdo
contact affiliation	Cell Signalling
contact email	p.m.casado-izquierdo@qmul.ac.uk

Full Dataset Link List

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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/2013/04/PXD000185

Repository Record List

[ + ]

PRIDE
1. 28869
  1. InstrumentRef: INSTRUMENT_1
  2. Label: PI103 P31 Exp1
  3. ModificationList: phosphorylated residue, monohydroxylated residue, iodoacetamide -site C, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of PI103 in P31 Cells File 1 of 2
  5. PublicationRef: PMID23532336
2. 28864
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Ku Kas Exp2
  3. ModificationList: phosphorylated residue, monohydroxylated residue, iodoacetamide -site C, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of Ku in Kas Cells File 2 of 2
  5. PublicationRef: PMID23532336
3. 28863
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Ku Kas Exp1
  3. ModificationList: phosphorylated residue, monohydroxylated residue, iodoacetamide -site C, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of Ku in Kas Cells File 1 of 2
  5. PublicationRef: PMID23532336
4. 28860
  1. InstrumentRef: INSTRUMENT_1
  2. Label: AZ123 Kas Exp2
  3. ModificationList: phosphorylated residue, iodoacetamide -site C, monohydroxylated residue, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of AZ123 in Kas Cells File 2 of 2
  5. PublicationRef: PMID23532336
5. 28874
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Primary Cells 4 of 5
  3. ModificationList: phosphorylated residue, monohydroxylated residue, N-formylated residue, iodoacetamide -site C, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Phosphoproteome of AML primary cells and GMPB 4 of 5
  5. PublicationRef: PMID23532336
6. 28875
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Primary Cells 5 of 5
  3. ModificationList: N-formylated residue, monohydroxylated residue, phosphorylated residue, iodoacetamide -site C, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Phosphoproteome of AML primary cells and GMPB 4 of 5
  5. PublicationRef: PMID23532336
7. 28867
  1. InstrumentRef: INSTRUMENT_1
  2. Label: PI103 Kas Exp1
  3. ModificationList: phosphorylated residue, monohydroxylated residue, iodoacetamide -site C, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of PI103 in Kas Cells File 1 of 2
  5. PublicationRef: PMID23532336
8. 28868
  1. InstrumentRef: INSTRUMENT_1
  2. Label: PI103 Kas Exp2
  3. ModificationList: phosphorylated residue, iodoacetamide -site C, monohydroxylated residue,
  4. Name: Effects of PI103 in Kas Cells File 2 of 2
  5. PublicationRef: PMID23532336
9. 28866
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Ku P31 Exp2
  3. ModificationList: phosphorylated residue, iodoacetamide -site C, monohydroxylated residue, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of Ku in P31 Cells File 2 of 2
  5. PublicationRef: PMID23532336
10. 28859
  1. InstrumentRef: INSTRUMENT_1
  2. Label: AZ123 Kas Exp1
  3. ModificationList: phosphorylated residue, monohydroxylated residue, iodoacetamide -site C, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of AZ123 in Kas Cells File 1 of 2
  5. PublicationRef: PMID23532336
11. 28865
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Ku P31 Exp1
  3. ModificationList: phosphorylated residue, iodoacetamide -site C, monohydroxylated residue, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of Ku in P31 Cells File 1 of 2
  5. PublicationRef: PMID23532336
12. 28862
  1. InstrumentRef: INSTRUMENT_1
  2. Label: AZ123 P31 Exp2
  3. ModificationList: phosphorylated residue, iodoacetamide -site C, monohydroxylated residue, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of AZ123 in P31 Cells File 2 of 2
  5. PublicationRef: PMID23532336
13. 28872
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Primary Cells 2 of 5
  3. ModificationList: phosphorylated residue, N-formylated residue, monohydroxylated residue, iodoacetamide -site C, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Phosphoproteome of AML primary cells and GMPB 2 of 5
  5. PublicationRef: PMID23532336
14. 28871
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Primary Cells 1 of 5
  3. ModificationList: monohydroxylated residue, phosphorylated residue, N-formylated residue, iodoacetamide -site C, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Phosphoproteome of AML primary cells and GMPB 1 of 5
  5. PublicationRef: PMID23532336
15. 28873
  1. InstrumentRef: INSTRUMENT_1
  2. Label: Primary Cells 3 of 5
  3. ModificationList: phosphorylated residue, N-formylated residue, monohydroxylated residue, 2-pyrrolidone-5-carboxylic acid (Gln), iodoacetamide -site C,
  4. Name: Phosphoproteome of AML primary cells and GMPB 3 of 5
  5. PublicationRef: PMID23532336
16. 28870
  1. InstrumentRef: INSTRUMENT_1
  2. Label: PI103 P31 Exp2
  3. ModificationList: monohydroxylated residue, phosphorylated residue, iodoacetamide -site C, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of PI103 in P31 Cells File 2 of 2
  5. PublicationRef: PMID23532336
17. 28861
  1. InstrumentRef: INSTRUMENT_1
  2. Label: AZ123 P31 Exp1
  3. ModificationList: iodoacetamide -site C, phosphorylated residue, monohydroxylated residue, 2-pyrrolidone-5-carboxylic acid (Gln),
  4. Name: Effects of AZ123 in P31 Cells File 1 of 2
  5. PublicationRef: PMID23532336