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
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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).
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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: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: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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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: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.
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