Dataset Information

Proteome characterization of Breast Cancer Cell lines

ABSTRACT: Protein profiling of 18 breast cancer cell lines in triplicates using TMT10-plex.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Janne Lehtiö

PROVIDER: PXD013276 | JPOST Repository | Sat Jul 04 00:00:00 BST 2020

REPOSITORIES: jPOST

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Dataset's files

Source:

			Action	DRS
	HJYZ_QEHF1_20150904_BC-Cell-lines_TMT10_set1_250ug_IPG3-10_7of15ul_fr01.raw	Raw
	HJYZ_QEHF1_20150904_BC-Cell-lines_TMT10_set1_250ug_IPG3-10_7of15ul_fr02.raw	Raw
	HJYZ_QEHF1_20150904_BC-Cell-lines_TMT10_set1_250ug_IPG3-10_7of15ul_fr03.raw	Raw
	HJYZ_QEHF1_20150904_BC-Cell-lines_TMT10_set1_250ug_IPG3-10_7of15ul_fr04.raw	Raw
	HJYZ_QEHF1_20150904_BC-Cell-lines_TMT10_set1_250ug_IPG3-10_7of15ul_fr05.raw	Raw

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Publications

PTEN and DNA-PK determine sensitivity and recovery in response to WEE1 inhibition in human breast cancer.

Brunner Andrä A Suryo Rahmanto Aldwin A Johansson Henrik H Franco Marcela M Viiliäinen Johanna J Gazi Mohiuddin M Frings Oliver O Fredlund Erik E Spruck Charles C Lehtiö Janne J Rantala Juha K JK Larsson Lars-Gunnar LG Sangfelt Olle O

eLife 20200706

Inhibition of WEE1 kinase by AZD1775 has shown promising results in clinical cancer trials, but markers predicting AZD1775 response are lacking. Here we analysed AZD1775 response in a panel of human breast cancer (BC) cell lines by global proteome/transcriptome profiling and identified two groups of basal-like BC (BLBCs): 'PTEN low' BLBCs were highly sensitive to AZD1775 and failed to recover following removal of AZD1775, while 'PTEN high' BLBCs recovered. AZD1775 induced phosphorylation of DNA- ...[more]

PMID: 32628111

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Project description:<p>Tissue for this CPTAC study was collected and characterized for a confirmatory cohort of 125 individuals with breast cancer. Quantitative mass-spectrometry-based proteomic, phosphoproteomic, and acetylome analyses were performed on breast tumors (125 participants) and adjacent normal breast tissue (18 participants). The analyses of this CPTAC cohort were conducted in order to more extensively characterize the proteogenomic landscape of breast cancer initially described in the publication by <a href="https://www.ncbi.nlm.nih.gov/pubmed/27251275" target="_blank">Mertins et al., (Nature 2016)</a>. Data were generated with TMT10plex quantification and each 10-plex experiment contained a common reference sample composed of a pooled mixture of 40 tumor samples. There are 17 global proteomic 10-plex datasets each with 25 fractions, 17 phosphoproteomic 10-plex datasets each with 13 fractions, and 17 acetylome 10-plex datasets each with 6 fractions. Raw LC-MS/MS (level 1 data) provided below are from investigators at the Proteome Characterization Center located at the Broad Institute of MIT and Harvard. Raw data were processed through the CPTAC Common Data Analysis Pipeline (CDAP) to produce peptide spectrum match reports (level 2 data) and protein summary reports (level 3 data), which are also provided below.</p><p>TMT phosphoproteome data were generated twice for plex #2 ,02CPTAC_BCProspective_Phosphoproteome_BI. The first replicate (20160928) had an uncharacteristically low phosphopeptide enrichment rate of 72%, typical values are > 90%. Hence, the IMAC flow thru was re-enriched to generate a second dataset (20170303). However, the second replicate yielded only 60% as many phosphopeptides and the phospho-enrichment rate was worse, 62%. Consequently, only the "20160928" dataset will be used in the final analyses, the second dataset (20170303) is labeled "deprecated."</p> ' <ul><li>Dataset imported into MassIVE from <a href="https://cptac-data-portal.georgetown.edu/study-summary/S039">https://cptac-data-portal.georgetown.edu/study-summary/S039</a> on 01/25/21</li></ul>