Integrated in vivo multi-omics identifies p21-activated kinase signaling as a driver of colitis
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Orbitrap Fusion
ORGANISM(S): Mouse
SUBMITTER: 
Kevin M. Haigis
PROVIDER: MSV000081198 | MassIVE | Sun Jun 25 17:29:00 BST 2017
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: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: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: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: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).
2021-06-10 | PXD013024 | Pride
Project description:Total proteome abundance measurement after 24h 6-MP treatment in WT or ATG5 KO HEK293T cells. Channels 128n, 128c, 129n, 129c are not used for this analysis.
2020-04-30 | PXD017859 | Pride
Project description:Part I - SI-NET tumors High Resolution Isoelectric Focusing (HiRIEF) LC-MS and relative quantification by iTRAQ 8-plex was used to analyze 14 small intestinal neuroendocrine tumors (SI-NETs). The data was obtained from two separate TMT10plex sets and linked by a single internal pooled standard. The internal pooled standard was made by combining equal aliquots of the tryptic peptide mixtures from each of the 14 tissue samples. iTRAQ set1 was composed of 7 SI-NET samples, all from different individuals, and internal pooled standard labelled as follows: Channel 113 (sample Screen-1 with liver metastasis), Channel 114 (sample Screen-8 with liver metastasis), Channel 115 (sample Screen-3 with liver metastasis), Channel 116 (sample Screen-2 with liver metastasis), Channel 117 (sample Screen-5 no liver metastasis), Channel 118 (sample Screen-4 no liver metastasis), Channel 119 (sample Screen-10 no liver metastasis), Channel 121 (internal pooled standard). iTRAQ set2 was composed of 7 SI-NET samples, all from different individuals, and internal pooled standard labelled as follows: Channel 113 (sample Screen-7 with liver metastasis), Channel 114 (sample Screen-11 with liver metastasis), Channel 115 (sample Screen-13 with liver metastasis), Channel 116 (sample Screen-6 no liver metastasis), Channel 117 (sample Screen-12 no liver metastasis), Channel 118 (sample Screen-9 no liver metastasis), Channel 119 (sample Screen-14 no liver metastasis), Channel 121 (internal pooled standard). Part II - time course profiling in cell lines High Resolution Isoelectric Focusing (HiRIEF) LC-MS and relative quantification by TMT 10-plex was used to analyze cellular response to the neddylation inhibitor pevonedistat (MLN4924) at different timepoints in two SI-NET (small intestinal neuroendocrine tumors) cell lines. The data was obtained from two separate TMT 10-plex experiments. TMT set1 includes a time course experiment upon pevonedistat treatment of CNDT2 cells with harvests at 2h, 6h, 12h and 24h after treatment as well as of untreated control cells. Isobaric tag labelling of peptide samples with TMT10plex was used as follows. Biological duplicate controls (TMT channels 126, 127N), duplicate 2h (127C, 128N), duplicate 6h (128C, 129N), duplicate 12h (129C, 130N) and duplicate 24h (130C, 131) samples were employed. TMT set2 includes a time course experiment upon pevonedistat treatment of HC45 cells with harvests at 2h, 6h, 12h and 24h after treatment as well as of untreated control cells. Isobaric tag labelling of peptide samples with TMT10plex was used as follows. Biological duplicate controls (TMT channels 126, 127N), duplicate 2h (127C, 128N), duplicate 6h (128C, 129N), duplicate 12h (129C, 130N) and duplicate 24h (130C, 131) samples were employed.
2020-12-09 | PXD009877 | 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:K562 cells were synchronized by cell size difference based Elutriation scheme into G1, S and G2 fractions. Three biological replicates were collected on different days, and assembled into a 2D-CETSA scheme with 6 different heating temperatures (37ºC, 47ºC, 50ºC, 52ºC,54ºC and 57ºC), (Figure 1A, Methods section of the associated paper), with each set of samples heated at one temperature included in the same isobaric TMT10 set and measured at the same time on Mass Spectrometer.
The labeling order of samples in the TMT10 channels is as follows:
37C/47C samples: Biorep1_G1(126), Biorep1_S(127N), Biorep1_G2(127C), Biorep2_G1(128N), Biorep2_S(128C), Biorep2_G2(129N), Biorep3_S(129C), Biorep3_G1(130N), Biorep3_G2(130C), mixed_control(131);
50C/52C/54C/57C samples: Biorep1_G1(126), Biorep1_S(127N), Biorep1_G2(127C), Biorep2_G1(128N), Biorep2_S(128C), Biorep2_G2(129N), Biorep3_G1(129C), Biorep3_S(130N), Biorep3_G2(130C), mixed_control(131);
2018-05-08 | PXD009171 | JPOST Repository
Project description:The data were acquired by performing multiplexed proteomics with TMT10-plex reagents using both and Orbitrap Fusion and an Orbitrap Lumos mass spectrometer and applying an SPS-supported LC-MS2/MS3 method. Samples were anti-FLAG immunoprecipitates of RB phospho-isoforms from human RPE1 cells. Samples were labeled with the specific TMT reagents as follows:
Sample pool 1: 126, Bridge; 127n, RB wild-type (replicate 1); 127c, RB_DELTA_cdk (replicate 1); 128n, FLAG-RB wild-type (replicate 1); 128c, FLAG-RB_DELTA_cdk (replicate 1); 129n, FLAG-RB_DELTA_cdk + S230 (replicate 1); 129c, FLAG-RB_delta_cdk + S249 (replicate 1); 130n, ,FLAG-RB_delta_cdk + T252 (replicate 1); 131, Bridge.
Sample pool 2: 126, Bridge; 127n, RB wild-type (replicate 2); 127c, RB_delta_cdk (replicate 2); 128n, FLAG-RB wild-type (replicate 2); 128c, FLAG-RB_delta_cdk (replicate 2); 129n, FLAG-RB_delta_cdk + S230 (replicate 2); 129c, FLAG-RB_delta_cdk + S249 (replicate 2), 130n, ,FLAG-RB_delta_cdk + T252 (replicate 2), 131, Bridge.
Sample pool 3: 126, Bridge; 127n, RB wild-type (replicate 3); 127c, RB_delta_cdk (replicate 3); 128n, FLAG-RB wild-type (replicate 3); 128c, FLAG-RB_delta_cdk (replicate 3); 129n, FLAG-RB_delta_cdk + S230 (replicate 3); 129c, FLAG-RB_delta_cdk + S249 (replicate 3); 130n, FLAG-RB_delta_cdk + T252 (replicate 3); 131, Bridge.
Sample pool 4: 126, Bridge; 127n, FLAG-RB_delta_cdk + T356 (replicate 1); 127c, FLAG-RB_delta_cdk + T373 (replicate 1); 128n, FLAG-RB_delta_cdk + S608 (replicate 1); 128c, FLAG-RB_delta_cdk + S612 (replicate 1); 129n, FLAG-RB_delta_cdk + S780 (replicate 1); 129c, FLAG-RB_delta_cdk + S788 (replicate 1); 130n, FLAG-RB_delta_cdk + S795 (replicate 1); 131, Bridge.
Sample pool 5: 126, Bridge; 127n, FLAG-RB_delta_cdk + T356 (replicate 2); 127c, FLAG-RB_delta_cdk + T373 (replicate 2); 128n, FLAG-RB_delta_cdk + S608 (replicate 2); 128c, FLAG-RB_delta_cdk + S612 (replicate 2); 129n, FLAG-RB_delta_cdk + S780 (replicate 2); 129c, FLAG-RB_delta_cdk + S788 (replicate 2); 130n, FLAG-RB_delta_cdk + S795 (replicate 2); 131, Bridge.
Sample pool 6: 126, Bridge; 127n, FLAG-RB_delta_cdk + T356 (replicate 3); 127c, FLAG-RB_delta_cdk + T373 (replicate 3); 128n, FLAG-RB_delta_cdk + S608 (replicate 3); 128c, FLAG-RB_delta_cdk + S612 (replicate 3); 129n, FLAG-RB_delta_cdk + S780 (replicate 3); 129c, FLAG-RB_delta_cdk + S788 (replicate 3); 130n, FLAG-RB_delta_cdk + S795 (replicate 3); 131, Bridge.
Sample pool 7: 126, Bridge; 127n, FLAG-RB_delta_cdk + S807 (replicate 1); 127c, FLAG-RB_delta_cdk + S811 (replicate 1); 128n, FLAG-RB_delta_cdk + T821 (replicate 1); 128c, FLAG-RB_delta_cdk + T826 (replicate 1); 131, Bridge.
Sample pool 8: 126, Bridge; 127n, FLAG-RB_delta_cdk + S807 (replicate 2); 127c, FLAG-RB_delta_cdk + S811 (replicate 2); 128n, FLAG-RB_delta_cdk + T821 (replicate 2); 128c, FLAG-RB_delta_cdk + T826 (replicate 2); 131, Bridge.
Sample pool 9: 126, Bridge; 127n, FLAG-RB_delta_cdk + S807 (replicate 3); 127c, FLAG-RB_delta_cdk + S811 (replicate 3); 128n, FLAG-RB_delta_cdk + T821 (replicate 3); 128c, FLAG-RB_delta_cdk + T826 (replicate 3); 131, Bridge.
2018-07-01 | MSV000082562 | MassIVE