Transcriptional-translational conflict is a barrier to cellular transformation and cancer progression
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Eclipse
ORGANISM(S): Mus Musculus (ncbitaxon:10090)
SUBMITTER: 
Andrew C. Hsieh, MD
PROVIDER: MSV000089875 | MassIVE | Tue Jul 12 15:23:00 BST 2022
REPOSITORIES: MassIVE
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Project description:We aimed to identify the response mechanism to EGFR tyrosine kinase inhibition. A431 cells were transfected with mock siRNA or BCL6 siRNA. Cells were then treated with gefitinib. Harvesting was done at 0h, at 24h and at 48h. Two TMT10plex sets were organized as follows: TMT set1: mock 0h (3x, channels 126, 127N and 127C), mock 24h (3x, 128N, 128C and 129N), mock 48h (3x, 129C, 130N, 130C) and internal pooled standard (131) composed from equal aliquots of all samples (mock siRNA and BCL6 siRNA). TMT set2: siBCL6 0h (3x, channels 126, 127N and 127C), siBCL6 24h (3x, 128N, 128C and 129N), siBCL6 48h (3x, 129C, 130N, 130C) and the same internal pooled standard (131) as for set 1.
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Project description:High Resolution Isoelectric Focusing (HiRIEF) LC-MS was used to analyze samples from the human A431 cell line and also samples of histologically normal tissues. The high analytical depth afforded by HiRIEF permitted proteogenomics on these two sample sets (A431 cells and normal tissues). The A431 data was obtained from a time course experiment upon Gefitinib treatment (EGFR inhibition) of A431 cells with harvests at 2h, 6h and 24h after treatment as well of untreated cells. Isobaric tag labelling of peptide samples with TMT10plex was used. Biological triplicate controls (TMT channels 126, 127N, 127C), duplicate 2h (128N, 128C), duplicate 6h (129N, 129C) and triplicate 24h (130N, 130C, 131) samples were employed. The normal tissues data was obtained from two separate TMT10plex sets. TMT set1 was composed of 9 samples, all from different individuals, including three placenta samples (126, 127N, 127C) two liver samples (128N, 128C), two kidney samples (129N, 129C), two tonsil samples (130N, 130C), plus an internal pooled standard (131). TMT set2 was composed of 8 samples, all from different individuals, including one tonsil sample (126), two liver samples (127C, 128N), two kidney samples (128C, 129N), three testis samples (129C, 130N, 130C), plus an internal pooled standard (131). The internal pooled standard was made by combining equal aliquots of the tryptic peptide mixtures from each of the 17 tissue samples.
2018-01-19 | PXD006291 | Pride
Project description:The raw data for chemoproteomic experiment of multiple concentrations of IDRB-Probe-2 in Hela. Each concentration includes two measurements taken from distinct samples. 127N and 127C represent the data of 0 μM IDRB-Probe-2. 128N and 128C represent the data of 0.5 μM IDRB-Probe-2. 129N and 129C represent the data of 1.5 μM IDRB-Probe-2. 130N and 130C represent the data of 5 μM IDRB-Probe-2. 131N and 131C represent the data of 15 μM IDRB-Probe-2. 132N and 132C represent the data of 50 μM IDRB-Probe-2. 133N and 133C represent the data of 1000 μM IDRB-Probe-2.
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Project description:Proteome maps of biochemically enriched synaptic tissue from human Alzheimers Disease (AD) and control angular gyrus samples to highlight the synapse as a site of integration for pathophysiological processes active in AD. The samples were combined into eleven TMTpools (01 to 11). Samples pools were fractionated using basic pH reversed-phase chromatography (bRPLC) and at least 12 fractions were analyzed by LC-MS2/MS3 per pool.
The RAW files are:
Carlyle_TMTpool_01_fraction_01 to Carlyle_TMTpool_01_fraction_12
Carlyle_TMTpool_02_fraction_01 to Carlyle_TMTpool_02_fraction_12
Carlyle_TMTpool_03_fraction_01 to Carlyle_TMTpool_03_fraction_12
Carlyle_TMTpool_04_fraction_01 to Carlyle_TMTpool_04_fraction_12
Carlyle_TMTpool_05_fraction_01 to Carlyle_TMTpool_05_fraction_12
Carlyle_TMTpool_06_fraction_01 to Carlyle_TMTpool_06_fraction_12
Carlyle_TMTpool_07_fraction_01 to Carlyle_TMTpool_07_fraction_12
Carlyle_TMTpool_08_fraction_01 to Carlyle_TMTpool_08_fraction_08, Carlyle_TMTpool_08_fraction_09A, Carlyle_TMTpool_08_fraction_09B, Carlyle_TMTpool_08_fraction_10 to Carlyle_TMTpool_08_fraction_12
Carlyle_TMTpool_09_fraction_01 to Carlyle_TMTpool_09_fraction_12
Carlyle_TMTpool_10_fraction_01 to Carlyle_TMTpool_10_fraction_12
Carlyle_TMTpool_11_fraction_01 to Carlyle_TMTpool_11_fraction_12
The labeling scheme is:
TMTpool_01: RUSH_0592 (126), RUSH_0034 (127n), RUSH_0755 (127c), RUSH_0143 (128n), RUSH_1442 (128c), RUSH_0570 (129n), Pooled_sample (129c), Pooled_sample (130n), RUSH_0992 (130c), RUSH_0857 (131n), bridge (131c).
TMTpool_02: RUSH_0974 (126), RUSH_1440 (127n), RUSH_0240 (127c), RUSH_0032 (128n), RUSH_0406 (128c), RUSH_0065 (129n), RUSH_1376 (129c), RUSH_0684 (130n), RUSH_0269 (130c), RUSH_1159 (131n), bridge (131c).
TMTpool_03: RUSH_0136 (126), Pooled_sample (127n), RUSH_0537 (127c), RUSH_1250 (128n), RUSH_0795 (128c), RUSH_0001 (129n), RUSH_0404 (129c), RUSH_0606 (130n), RUSH_0229 (130c), RUSH_0465 (131n), bridge (131c).
TMTpool_04: RUSH_0734 (126), RUSH_0873 (127n), RUSH_0743 (127c), Pooled_sample (128n), RUSH_0712 (128c), RUSH_0751 (129n), RUSH_0302 (129c), RUSH_0499 (130n), RUSH_1218 (130c), RUSH_1421 (131n), bridge (131c).
TMTpool_05: RUSH_1392 (126), RUSH_0890 (127n), RUSH_1006 (127c), RUSH_1063 (128n), RUSH_0128 (128c), RUSH_0590 (129n), RUSH_0674 (129c), RUSH_0572 (130n), RUSH_0413 (130c), RUSH_1288 (131n), bridge (131c).
TMTpool_06: RUSH_1487 (126), RUSH_1348 (127n), RUSH_0007 (127c), RUSH_1323 (128n), RUSH_1498 (128c), RUSH_0976 (129n), RUSH_0859 (129c), RUSH_0544 (130n), RUSH_0067 (130c), RUSH_1384 (131n), bridge (131c).
TMTpool_07: RUSH_0212 (126), RUSH_1474 (127n), Pooled_sample (127c), RUSH_0010 (128n), RUSH_0931 (128c), RUSH_1205 (129n), RUSH_1200 (129c), RUSH_0206 (130n), RUSH_0376 (130c), RUSH_0460 (131n), bridge (131c).
TMTpool_08: RUSH_0927 (126), RUSH_0963 (127n), RUSH_0055 (127c), RUSH_0085 (128n), RUSH_0780 (128c), RUSH_0327 (129n), RUSH_0354 (129c), RUSH_0123 (130n), RUSH_1358 (130c), RUSH_1424 (131n), bridge (131c).
TMTpool_09: RUSH_1334 (126), RUSH_0921 (127n), Pooled_sample (127c), RUSH_1093 (128n), RUSH_1499 (128c), RUSH_1419 (129n), Pooled_sample (129c), RUSH_0555 (130n), RUSH_0618 (130c), RUSH_0732 (131n), bridge (131c).
TMTpool_10: RUSH_1176 (126), Pooled_sample (127n), RUSH_0958 (127c), RUSH_0447 (128n), RUSH_1485 (128c), RUSH_0158 (129n), RUSH_0252 (129c), RUSH_0078 (130n), RUSH_0415 (130c), Pooled_sample (131n), bridge (131c).
TMTpool_11: RUSH_1313 (126), RUSH_0989 (127n), RUSH_0295 (127c), RUSH_0177 (128n), RUSH_0064 (128c), RUSH_0919 (129n), RUSH_0847 (129c), RUSH_0266 (130n), RUSH_0933 (130c), Pooled_sample (131n), bridge (131c).
2020-02-17 | MSV000084959 | MassIVE
Project description:LUM1_969842: Brown adipocyte lipid droplet proteomics (Figure 4d):
126, 127N, 127C, 128N: WT
128C, 129N, 129C, 130N: KO (clstn3b-/-)
LUM1_997681: White adipocyte lipid droplet proteomics (Figure 4e):
126, 127C, 127N, 128C, 128N: WT
129C, 129N, 130C, 130N, 131N: KO (clstn3b-/-)
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CCLP (ICCL_TMT2:129c, ICCL_TMT6:127n), CCSW1(ICCL_TMT2:128c, ICCL_TMT7:130c), AOVC1 (ICCL_TMT9:129n, ICCL_TMT10:129c), EGI1(ICCL_TMT16:126, ICCL_TMT16:127n), ETK1 (ICCL_TMT16:127c, ICCL_TMT16:128n), G415 (ICCL_TMT11:129c, ICCLTMT12:130n), GB2 (ICCL_TMT1:127n, ICCL_TMT5:128n), HKGZCC (ICCL_TMT4:129n, ICCL_TMT8:128c), HUCCT1 (ICCL_TMT1:127c, ICCL_TMT6:129n), HUH28 (ICCL_TMT4:130n, ICCL_TMT8:128n), GB3 (ICCL_TMT3:131n, ICCL_TMT7:131n), ICC10 (ICCL_TMT1:128c, ICCL_TMT7:126), ICC10-6 (ICCL_TMT4:128n, ICCL_TMT7:127n), ICC10-8 (ICCL_TMT2:131n, ICCL_TMT7:127c), ICC11 (ICCL_TMT4:128c, ICCL_TMT5:129n), ICC12 (ICCL_TMT4:130c, ICCL_TMT6:129c), ICC13-7 (ICCL_TMT2:126, ICCL_TMT8:127c, ICCL_TMT11:129n, ICCL_TMT12:131n), ECC3 (ICCL_TMT1:128n, ICCL_TMT5:127c), ICC16 (ICCL_TMT11:128n, ICCL_TMT12:128c), ICC17 (ICCL_TMT3:129c, ICCL_TMT7:129n), ICC18 (ICCL_TMT13:127c, ICCL_TMT13:128n), ICC19 (ICCL_TMT11:128c, ICCL_TMT12:127c), ICC2 (ICCL_TMT4:127c, ICCL_TMT5:126), ICC20 (ICCL_TMT13:128c, ICCL_TMT13:129n), ICC21 (ICCL_TMT14:131n, ICCL_TMT14:131c), ICC24 (ICCL_TMT13:129c, ICCL_TMT13:130n), ICC25 (ICCL_TMT13:130c, ICCL_TMT13:131n), ICC26 (ICCL_TMT15:128c, ICCL_TMT15:129n), ECC4 (ICCL_TMT4:127n, ICCL_TMT6:131n, ICCL_TMT13:126, ICCL_TMT13:127n), ICC4 (ICCL_TMT9:128n, ICCL_TMT10:130n), ICC5 (ICCL_TMT3:127c, ICCL_TMT6:130n), ICC8 (ICCL_TMT2:127n, ICCL_TMT7:129c), ICC9 (ICCL_TMT2:127c, ICCL_TMT7:128c), KKU100 (ICCL_TMT9:127n, ICCL_TMT10:131n), KKU312 (ICCL_TMT9:129c, ICCL_TMT10:127n), GB4 (ICCL_TMT15:127n, ICCL_TMT15:128n), NOZ (ICCL_TMT16:132c, ICCL_TMT16:133n), OCUG1 (ICCL_TMT16:129n), RBE (ICCL_TMT1:126, ICCL_TMT7:128n), SG231 (ICCL_TMT9:126, ICCL_TMT10:127c), SNU1079 (ICCL_TMT9:130c, ICCL_TMT10:128n), SNU1196 (ICCL_TMT1:130n, ICCL_TMT8:130n), SNU245 (ICCL_TMT17:128n, ICCL_TMT17:129c), SNU308 (ICCL_TMT4:131n, ICCL_TMT8:131n), SNU478 (ICCL_TMT2:128n, ICCL_TMT6:130c), SNU869 (ICCL_TMT4:129c, ICCL_TMT5:130n), SSP25 (ICCL_TMT2:130c, ICCL_TMT5, 131n), TFK1 (ICCL_TMT17:126, ICCL_TMT17:130c) TGC1TKB (ICCL_TMT17:127c, ICCL_TMT17:129n), TGBC52TKB (ICCL_TMT11:130c, ICCL_TMT12:128n), TKKK (ICCL_TMT9:128c, ICCL_TTM10:129n), YSCCC (ICCL_TMT9:127c, ICCL_TMT10:126), ICC7 (ICCL_TMT3:128c, ICCL_TMT5:129c), OZ (ICCL_TMT11:127n, ICCL_TMT12:129n), KMCH1 (ICCL_TMT1:129n, ICCL_TMT8:129c), KKU055 (ICCL_TMT16:131c), ICC28 (ICCL_TMT2:132n, ICCL_TMT3:126), TGBC14TKB (ICCL_TMT11:131n, ICCL_TMT12:130c), PLCPRF5 (ICCL_TMT14:129n, ICCL_TMT14:129c) TONG (ICCL_TMT14:127n, ICCL_TMT14:127c), HUH7 (ICCL_TMT15:129c, ICCL_TMT14:130n, ICCL_TMT14:130c), SNU449 (ICCL_TMT15:131n), SNU387 (ICCL_TMT17:126, ICCL_TMT17:128c), JHH7 (ICCL_TMT15:130n, ICCL_TMT1:130c), SNU475 (ICCL_TMT17:130n, ICCL_TMT17:132n), HEPG2 (ICCL_TMT13:131c, ICCL_TMT13:132n), SNU423 (ICCL_TMT17:131n, ICC_TMT17:131c)
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Project description:Subcellular proteomics analysis of human T-cells in response to T-cell receptor stimulation. High Resolution Isoelectric Focusing (HiRIEF) LC-MS/MS and relative quantification by TMT 10-plex was used to analyze subcellular fractions (Cytosol, Nuclear and Mitochondria-Small Organelle-Membrane) of Human T-cells from 3 separate donors stimulated with T-cell receptor stimulation for 0, 15 minutes or 60 minutes. The data was obtained from 3 separate TMT10 plex sets which included: 126 – Cytosol, unstimulated; 127N – Cyto, 15 min; 127C – Cyto, 60 min; 128N – Mitochondrion-Small Organelle-Membrane, unstimulated; 128C – Mito-SmO-Mem, 15 min; 129N – Mito-SmO-Mem, 60 min; 129C – Nuclear, unstimulated; 130N – Nuc, 15 min; 130C– Nuc, 60 min; 131 – pooled internal control of all samples.
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Project description:Associated to PXD009877 which contains Part I and Part II. Part III – Pevonedistat/MLN4924 and Bortezomib treatment of the SI-NET (small intestinal – neuroendocrine tumor) cell line CNDT2. High Resolution Isoelectric Focusing (HiRIEF) LC-MS and relative quantification by TMT 10-plex was used to analyze cellular response to the proteasome inhibitor Bortezomib alone or in combination with the neddylation inhibitor pevonedistat (MLN4924) at 12h after treatment in the CNDT2 cell line. The data was obtained from one TMT 10-plex experiment which included 4 untreated controls (TMT channels 126, 127N, 127C and 128N), 3 samples treated with 500 nM Bortezomib for 12 hours (TMT channels 128C, 129N and 129C) as well as 3 samples treated with both Bortezomib and Pevonedistat at 500 nM respectively for 12 hours (TMT channels 130N, 130C and 131).
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Project description:Proteome maps were generated for mouse KGC pancreatic tumor organoid lines expressing doxycycline-inducible constitutively-active mutant GNAS (GNASR201C). The organoids were analyzed in the absence (ctrl) or presence (induced) of doxycycline. Two models, KGC Line-1 (line1) and Line-2 (line2), were analyzed in two separate experiments, 1 and 2. Proteome maps were generated using multiplexed proteomics using TMT10plex technology. Mass spectrometry was done on an Orbitrap Fusion using the SPS-MS3 method. TMT labeling was done as follows: experiment 1, line1_induced_replicate1 (126), line1_ctrl_replicate1 (127n), line2_induced_replicate1 (127c), line2_ctrl_replicate1 (128n), line1_induced_replicate2 (128c), line1_ctrl_replicate2 (129n), line2_induced_replicate2 (129c), line2_ctrl_replicate2 (130c); experiment 2, line1_induced_replicate1 (126), line1_induced_replicate2 (127n), line1_induced_replicate3 (127c), line1_ctrl_replicate1 (128n), line1_ctrl_replicate2 (128c), line1_ctrl_replicate3 (129n), line2_induced_replicate1 (129c), line2_induced_replicate2 (130n), line2_ctrl_replicate1 (130c), line2_ctrl_replicate2 (131).
2018-04-23 | MSV000082305 | MassIVE