Obtusaquinone is a cysteine modifying compound that targets Keap1 for degradation
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Bakhos Tannous
PROVIDER: MSV000084647 | MassIVE | Mon Dec 02 20:53:00 GMT 2019
REPOSITORIES: MassIVE
Similar Datasets
Project description:We used mass spectrometry-based proteomics to perform a phosphoproteomics analysis of selinexor-treated ex vivo AML patient samples (n=20) and 4 AML cell lines (PL-21, NOMO-1, GDM-1 and MV4-11). For quantitative phosphoproteomics, we used a tandem mass tag (TMT)-based approach. Conditions for the TMT 11-plex (Ex vivo samples) and TMT 8-plex (AML cell lines) setups are specified below. Cells were treated with 1 M selinexor (also known as KPT-330) or 0.1% DMSO for 6 hours. The experimental treatment conditions and TMT11-plex (ex vivo samples) and TMT8-plex (cell lines) labeling schemes are specified below: TMT-11-plex TMT channel Patient no Treatment Set 1 126 Ex_24 DMSO Set 1 127N Ex_24 Selinexor Set 1 127C Ex_25 DMSO Set 1 128N Ex_25 Selinexor Set 1 128C Ex_34 DMSO Set 1 129N Ex_34 Selinexor Set 1 129C Ex_41 DMSO Set 1 130N Ex_41 Selinexor Set 1 130C Ex_44 DMSO Set 1 131N Ex_44 Selinexor Set 1 131C Mix pool Mix pool Set 2 126 Ex_9 DMSO Set 2 127N Ex_9 Selinexor Set 2 127C Ex_18 DMSO Set 2 128N Ex_18 Selinexor Set 2 128C Ex_27 DMSO Set 2 129N Ex_27 Selinexor Set 2 129C Ex_29 DMSO Set 2 130N Ex_29 Selinexor Set 2 130C Ex_36 DMSO Set 2 131N Ex_36 Selinexor Set 2 131C Mix pool Mix pool Set 3 126 Ex_8 DMSO Set 3 127N Ex_8 Selinexor Set 3 127C Ex_13 DMSO Set 3 128N Ex_13 Selinexor Set 3 128C Ex_14 DMSO Set 3 129N Ex_14 Selinexor Set 3 129C Ex_19 DMSO Set 3 130N Ex_19 Selinexor Set 3 130C Ex_40 DMSO Set 3 131N Ex_40 Selinexor Set 3 131C Mix pool Mix pool Set 4 126 Ex_6 DMSO Set 4 127N Ex_6 Selinexor Set 4 127C Ex_15 DMSO Set 4 128N Ex_15 Selinexor Set 4 128C Ex_28 DMSO Set 4 129N Ex_28 Selinexor Set 4 129C Ex_39 DMSO Set 4 130N Ex_39 Selinexor Set 4 130C Ex_42 DMSO Set 4 131N Ex_42 Selinexor Set 4 131C Mix pool Mix pool AML cell lines: TMT-8-plex TMT channel Treatment Replicate GDM-1 126 DMSO 1 GDM-1 127N DMSO 2 GDM-1 127C DMSO 3 GDM-1 128N DMSO 4 GDM-1 128C Selinexor 1 GDM-1 129N Selinexor 2 GDM-1 129C Selinexor 3 GDM-1 130N Selinexor 4 MV4-11 126 DMSO 1 MV4-11 127N DMSO 2 MV4-11 127C DMSO 3 MV4-11 128N DMSO 4 MV4-11 128C Selinexor 1 MV4-11 129N Selinexor 2 MV4-11 129C Selinexor 3 MV4-11 130N Selinexor 4 NOMO-1 126 DMSO 1 NOMO-1 127N DMSO 2 NOMO-1 127C DMSO 3 NOMO-1 128N DMSO 4 NOMO-1 128C Selinexor 1 NOMO-1 129N Selinexor 2 NOMO-1 129C Selinexor 3 NOMO-1 130N Selinexor 4 PL-21 126 DMSO 1 PL-21 127N DMSO 2 PL-21 127C DMSO 3 PL-21 128N DMSO 4 PL-21 128C Selinexor 1 PL-21 129N Selinexor 2 PL-21 129C Selinexor 3 PL-21 130N Selinexor 4
2022-08-07 | PXD017660 | Pride
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:Bovine catalase: This is an experiment to use differential cysteine alkylation to map the nature of binding of a cysteine-targeting small molecule OBT (for details of the method, please see the Method Section of the manuscript). The alkylating reagents uses besides the studied drug were iodoacetamide (IAA) and N-ethylmaleimide (NEM). As described in the manuscript the experiment includes three routes of serial alkylation experiments termed OBT, IAA, and NEM. Samples were prepared in triplicate and TMT10-plex reagents were used for labeling as follows: OBT replicate 1 (OBT1), 129c; OBT2, 130n; OBT3, 130c; IAA1, 126; IAA2, 127n; IAA3, 127c; NEM1, 128n; NEM2, 128c; NEM3, 129n. An SPS-MS3 method was used for data acquisition on an Orbitrap Fusion Lumos mass spectrometer.
The RAW file for these data is catalase_diffAlk.RAW.
A differential alkylation experiment was also performed as described above for bovine catalase but using recombinant human KEAP1 as substrate. One set of experiments (OBT, IAA, NEM) was performed. TMT10-plex labeling was performed as follows: OBT, 129n; IAA, 128c; NEM, 128n. An SPS-MS3 method was used for data acquisition on an Orbitrap Fusion mass spectrometer.
The RAW file for these data is RAW_file: keap1_diffAlk.RAW.
2019-11-30 | MSV000084638 | MassIVE
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.
2020-12-09 | PXD016605 | Pride
Project description:We applied quantitative mass spectrometry (MS)-based proteomics to study the roles of Cbl and Cbl-b in long-term signaling responses related to neurite outgrowth and differentiation of SH-SY5Y neuroblastoma cells. Using stable isotope labeling by amino acids in cell culture (SILAC) and tandem mass tag (TMT)-labeling in combination with off-line high-pH reversed-phase fractionation and LC-MS/MS we analyzed how Cbl and Cbl-b depletion by siRNA affected the proteome, phosphoproteome and ubiquitylome of the neuroblastoma cells. SILAC proteome SILAC (Light Arg0/Lys0, medium Arg6/Lys4, heavy Arg10/Lys8) SH-SY5Y cells were treated with Cbl and Cbl-b or control (GFP) siRNA for 72 hours. For combined stimulation with ligand cocktail (FGF-2, IGF-1 PDGF-BB, TGFα) cells were treated with ligands for 48 h. Samples were analyzed in triplicates with set-up as described below: Set-up 1, 3 replicates (R1-3): Light: siGFP, Heavy: siCbl/siCbl-b Set-up 2, 3 replicates (E1-3): Light: siGFP + ligand cocktail, Medium: siCbl/siCbl-b, Heavy: siCbl/siCbl-b + ligand cocktail TMT phosphoproteome and proteome SH-SY5Y cells were treated with Cbl and Cbl-b siRNA, control (GFP) siRNA or Retinoic acid (RA) for 24 hours. Samples were prepared in triplicates and labelled with TMT10-plex reagents according to the set-up below: TMT10-126: siGFP E1 TMT10-127N: siCbl/siCbl-b E1 TMT10-127C: Retinoic acid E1 TMT10-128N: siGFP E2 TMT10-128C: siCbl/siCbl-b E2 TMT10-129N: Retinoic acid E2 TMT10-129C: siGFP E3 TMT10-130N: siCbl/siCbl-b E3 TMT10-130C: Retinoic acid E3 TMT10-131: Mix of the 9 samples SILAC Ubiquitin pulldown SILAC (Light Arg0/Lys0, heavy Arg10/Lys8) SH-SY5Y cells were treated with Cbl and Cbl-b or control (GFP) siRNA for 24 hours. Samples were analyzed in duplicates with set-up as described below: Light: siGFP, Heavy: siCbl/siCbl-b
2021-03-30 | PXD020389 | Pride
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: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.
2019-11-13 | PXD013284 | Pride
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-/-)
| MSV000095763 | MassIVE
Project description:Mass spectrometry-based proteomics was applied to unravel Erk signaling in mouse embryonic stem cells (ESCs). A previously described engineered ESCs system for Erk induction via a drug-inducible cRAF-ErT2 fusion (Hamilton, W. B. & Brickman, J. M., Cell Rep 2014) was used in two different setups measuring the phosphoproteome in an 11-plex tandem mass tag (TMT)-based approach as described below. Fgf4 stimulation and MEK inhibition: ESCs were stimulated with Fgf4 (40 nM, recombinant, mouse, 5 minutes) following pretreatment (30 minutes) with either DMSO (1:10000) or MEK inhibition (MEKi: 1 microM PD0325901): The experimental treatment conditions and TMT11-plex labeling are specified below: 126: DMSO, unstimulated control replicate 1 127N: DMSO, unstimulated control replicate 2 127C: DMSO, unstimulated control replicate 3 128N: DMSO + Fgf4 replicate 1 128C: DMSO + Fgf4 replicate 2 129N: DMSO + Fgf4 replicate 3 129C: MEKi + Fgf4 replicate 1 130N: MEKi + Fgf4 replicate 2 130C: MEKi + Fgf4 replicate 3 131N: MEKi replicate 1 131C: MEKi replicate 2 Analog sensitive Erk2 setup: In the ESC system the ERK2-/- ESCs (Hamilton et al., PloS ONE, 2013) were engineered to stably express an inducible cRAF-ErT2 fusion protein expressed from the same transgene as a FLAG-tagged analogue sensitive Erk2Q103A. Erk1 was subsequently removed by CRISPR-Cas9 mutagenesis using sgRNAs flanking exon 2. Cells were pre-treated for 30 minutes with either the ATP-mimetic compound 1-NM-PP1 (2 microM) (Endo et al., Biochem Biophys Res Commun 2006), the Mek1 inhibitor PD0325901 (1 microM), or DMSO (0.01%), followed by induction or not of the cRAF-ErT2 fusion by (Z)-4-Hydroxytamoxifen (4OHT) (250 nM) for 2 hours as indicated. The experimental treatment conditions and TMT11-plex labeling are specified below: 126: DMSO pretreatment, non-induced control, replicate 1 127N: DMSO pretreatment, non-induced control, replicate 2 127C: DMSO pretreatment, non-induced control, replicate 3 128N: DMSO pretreatment, 4OHT-induction, replicate 1 128C: DMSO pretreatment, 4OHT-induction, replicate 2 129N: DMSO pretreatment, 4OHT-induction, replicate 3 129C: PP1 pretreatment, 4OHT-induction, replicate 1 130N: PP1 pretreatment, 4OHT-induction, replicate 2 130C: PP1 pretreatment, 4OHT-induction, replicate 3 131N: MEKi pretreatment, 4OHT-induction, replicate 1 131C: MEKi pretreatment, 4OHT-induction, replicate 2
2019-08-12 | PXD012573 | Pride
Project description:Recent genetic evidence has revealed microRNA-137 (miR-137) as a risk gene in schizophrenia and autism spectrum disorder (ASD), and the following cellular studies have demonstrated the importance of miR-137 in regulating neurogenesis. We have generated miR-137 knockout mice which display behaviors that resemble some symptoms of these two diseases. To investigate the underlying molecular mechanism, we performed comprehensive analyses of the entire RNA and protein molecules of the miR-137 mouse brains. The dataset uploaded here is the raw data of the mass spectrometry-based whole proteome analysis of the six miR-137 mouse brains: wild-type, heterozygous (miR-137+/–) and homozygous (miR-137–/–) from two different litters. The tandem mass tag (TMT) methodology was employed in this proteomics analysis for the quantitation. The sample channels are: 128C (miR-137+/+, litter 1), 129N (miR-137+/–, litter 1), 129C (miR-137–/–, litter 1), 130N (miR-137+/+, litter 2), 130C (miR-137+/–, litter 2), and 131N (miR-137–/–, litter 2).
2018-10-17 | PXD003874 | Pride