Project PXD000217

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Summary

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.

Sample Processing Protocol

See details in reference(s) : 23628362

Data Processing Protocol

See details in reference(s) : 23628362

Contact

Pedro Casado-Izquierdo, Cell Signalling

Submission Date

19/04/2013

Publication Date

26/04/2013

Tissue

Not available

Cell Type

B cell
blood cell

Experiment Type

Bottom-up proteomics

Assay count

75

Publication

    Casado P, Alcolea MP, Iorio F, Rodríguez-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, 2013 Apr 29, 14, 4, R37, PubMed: 23628362

Assay

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# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 29279 AML Cell Lines Experiment AML Replicate 1 160 228 154 3811 143
2 29280 AML Cell Lines Experiment AML Replicate 2 214 298 210 4436 194
3 29281 AML Cell Lines Experiment AML Replicate 3 180 268 179 3497 176
4 29282 AML Cell Lines Experiment CMK Replicate 2 200 293 215 5740 218
5 29283 AML Cell Lines Experiment CMK Replicate 3 182 215 165 4810 155
6 29284 AML Cell Lines Experiment CMK Replicate 1 270 429 321 6052 319
7 29285 AML Cell Lines Experiment Hel Replicate1 266 418 298 5012 303
8 29286 AML Cell Lines Experiment Hel Replicate2 167 211 156 4600 141
9 29287 AML Cell Lines Experiment Hel Replicate3 231 318 234 4718 216
10 29288 AML Cell Lines Experiment Kasumi1 Replicate 1 154 180 136 4316 123