U of Geneva Loewith Lab - 20191004_AGC_kinases

U of Geneva Loewith Lab - 20191004_AGC_kinases
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variance-plate-skyline_2021-10-15_14-20-51.sky.zip2021-10-15 14:33:331,2156,5256,52547,07469
prtc_EEVsamples-forChris_2021-10-14_21-49-16.sky.zip2021-10-14 21:49:252202016942
UW_Cpep_Linearity_Imprecision_NoAnnotations.sky.zip2021-10-13 17:22:221261625
P155_06_WT_Pto_treatment_Panorama_2021-10-08_15-31-38.sky.zip2021-10-13 12:31:12211116014
P155_04_WT_GLV2_flg22_treatment_Panorama_2021-10-08_15-29-12.sky.zip2021-10-13 12:31:12211116022
04April2021_batch_2_88m_3x4_2021-10-12_16-35-30.sky.zip2021-10-12 16:41:512,43912,24812,24873,4884
06April2021_batch_3_44min_3x4_2021-10-12_12-57-28.sky.zip2021-10-12 13:03:152,63513,53513,53581,2104
04April2021_batch_2_44min_3x4_2021-10-12_12-51-06.sky.zip2021-10-12 12:56:452,58014,16014,16084,9604
all-44_2021-10-12_12-40-06.sky.zip2021-10-12 12:48:102,72514,88814,888105,89512
Smoke_Inhalation_BALF_(+)_2021-10-08_12-49-38.sky.zip2021-10-08 17:36:551101881,18523
Smoke_Inhalation_BALF_(-)_2021-10-08_12-47-55.sky.zip2021-10-08 17:36:471302722,22025
Smoke_Inhalation_Plasma_(+)_2021-10-08_12-45-31.sky.zip2021-10-08 17:36:331102271,38922
Smoke_Inhalation_Plasma_(-)_2021-10-08_12-42-24.sky.zip2021-10-08 17:36:241403352,81822
Plasma_Lipid_Library_(-)_NIST_SRM_2021-10-08_12-22-12.sky.zip2021-10-08 17:35:571503713,1323
Plasma_Lipid_Library_(+)_NIST_SRM_2021-10-08_12-21-23.sky.zip2021-10-08 17:35:461304462,7983
Rpl3_LysC_071021.sky.zip2021-10-07 08:37:351281912
WUSTL IDG 47 Peptide Set Repeatability.sky.zip2021-10-02 18:46:1933479428245
WUSTL IDG 2 Peptide Set Repeatability.sky.zip2021-10-02 18:46:082241245
WUSTL IDG 17 Peptide Set Repeatability.sky.zip2021-10-02 18:46:0511173410245
WUSTL IDG 47 Peptide Set Chromatograms.sky.zip2021-10-02 18:30:583347942821
WUSTL IDG 2 Peptide Set Chromatograms.sky.zip2021-10-02 18:30:50224121
WUSTL IDG 17 Peptide Set Chromatogram.sky.zip2021-10-02 18:30:461117341021
SigPath_TitrationCurve_IMAC_04282021_2021-06-11_11-37-39.sky.zip2021-09-21 20:44:231321863761,57215
SigPath_TitrationCurve_pY_04262021_2021-06-11_11-28-15.sky.zip2021-09-21 20:44:2375911827086
SigPath_Medulloblastoma_IMAC_02282021_2021-09-21_21-00-06.sky.zip2021-09-21 20:43:251602274581,90639
SigPathAssay_PerturbagenStudy_IMAC_05042021_2021-09-21_21-14-52.sky.zip2021-09-21 20:42:101562274641,88216
SigPathAssay_PerturbagenStudy_pY_05042021_2021-06-09_09-39-53.sky.zip2021-09-21 20:42:10729018270616
SigPath_PDXsamples_pY_03152021_2021-06-08_20-47-33.sky.zip2021-09-21 20:40:01688316664830
SigPath_PDXsamples_IMAC_03152021_2021-06-08_20-00-50.sky.zip2021-09-21 20:40:011492184481,80830
SigPath_250plex_10cellLines_pY_05282021_2021-06-08_18-21-24.sky.zip2021-09-21 20:38:57688717467610
SigPath_250plex_10cellLines_IMAC_05282021_2021-06-08_18-14-00.sky.zip2021-09-21 20:38:578111223088210
BSA-QC_68fmol_Jun2021_Impact-II_minPanorama_2021-09-09_16-33-00.sky.zip2021-09-09 16:33:19131402166
Aging_Run_1_Analysis_Use_no_precursor_32247_Removed_2021-06-14_15-09-39.sky.zip2021-09-03 18:47:003110310347155
Calibration peptide TPLTATLSK.sky.zip2021-08-17 20:18:281121033
Calibration, peptide SAVQGPPER.sky.zip2021-08-17 20:18:281121254
Calibration peptide VVLEGGIDPILR.sky.zip2021-08-17 20:18:28112630
Calibration peptide LGHPDTLNQGEFK.sky.zip2021-08-17 20:18:28112824
Calibration peptide NQNTFLR.sky.zip2021-08-17 20:18:28112830
Calibration, peptide DPPQYPVVPVHLDR.sky.zip2021-08-17 20:18:281121026
Calibration peptide DLQNFLK.sky.zip2021-08-17 20:18:281121030
Calibration peptide DASGATFTWTPSSGK.sky.zip2021-08-17 20:18:281121027
Calibration peptide AVLTIDEK.sky.zip2021-08-17 20:18:281121430
Calibration peptide ALNSIIDVYHK.sky.zip2021-08-17 20:18:281121024
Proteomic analysis of 134 newborn samples.sky.zip2021-08-17 20:18:289102093134
Trypsin digestion time lapse.sky.zip2021-08-17 20:18:28910209321
Matrix effect on protein quantification.sky.zip2021-08-17 20:18:28910209821
Initial screening_SRMatlas method.sky.zip2021-08-17 12:40:4011313651
Initial screening_Skyline method.sky.zip2021-08-17 12:40:4012424751
Quantitative performance of SIL-TCT and SIL-ExC5 dissolved in water and SDC buffer.sky.zip2021-08-17 12:40:40110209612
SiL-Ex peptides solubility testing.sky.zip2021-08-17 12:40:40110209636
Incubation time optimization-additional measurement for SIL-ExC3N3 peptide YLYEIAR.sky.zip2021-08-17 12:40:401121018
Optimization of incubation time for trypsin digestion.sky.zip2021-08-17 12:40:39110209672
Comparison of all types of internal standards.sky.zip2021-08-17 12:40:39110209615
Repeatability.sky.zip2021-08-17 12:40:39110209636
SPE recovery.sky.zip2021-08-17 12:40:3911020966
PFAS_Pine_Temporal_ArchivedSamples_2021-08-16_11-55-53.sky.zip2021-08-16 13:59:2490565620
PFAS_Pine_Spatial_FieldSamples_2021-08-16_11-52-29.sky.zip2021-08-16 13:59:2490888850
20210603_ISPRM_spleen_dasatinib_2021-06-19_09-14-10.sky.zip2021-08-12 08:07:143030606018
FL_MAL_PsbO_band_SRM_v4.sky.zip2021-07-23 06:10:36328371724
DDRpanel2_LCL_time_2021-07-16_11-50-45.sky.zip2021-07-19 08:33:26325911884730
DDRpanel2_PBMC_2021-07-16_11-50-34.sky.zip2021-07-19 08:33:26325911884125
DDRpanel1_PBMC_2021-07-16_11-50-24.sky.zip2021-07-19 08:33:26377014054226
DDRpanel2_LCL_dose_2021-07-16_11-50-14.sky.zip2021-07-19 08:33:26325911884715
20180731_UPR_ARoos_H&L_paper_Lumos_RT.sky.zip2021-07-16 07:57:138214214228
Nrxn3 HA IP splice segment analysis2021-07-13 08:24:0947147011
Nrxn3 AS5 knock-out analysis2021-07-13 08:17:391153216631
Nrxn3 Exon 25 Titration Curve2021-07-13 08:15:0518169214
Figure 5.sky.zip2021-07-10 09:08:069203410230
Figure 4.sky.zip2021-07-10 09:08:069203410222
Figure 3D.sky.zip2021-07-10 09:08:059203410227
Figure 3C.sky.zip2021-07-10 09:08:059203410227
Figure 3B.sky.zip2021-07-10 09:08:059203410222
Figure 3A.sky.zip2021-07-10 09:08:059203410222
HLA_NeoAntg_HL_Mel6_PeptideYIH_2021-07-08_17-37-20.sky.zip2021-07-09 07:13:4711245
PRM Splice Assays2021-06-24 08:36:0739841659900
DDR2_response curve_2021-06-17_11-52-03.sky.zip2021-06-24 08:35:5527469264434
210429to210501_ApoE_5x5_Precision.sky2021-06-22 12:52:48151024139
DDR2_chromatogram8_2021-06-21_13-22-59.sky.zip2021-06-22 08:22:184510801
DDR2_chromatogram8_2021-06-21_13-22-59.sky.zip2021-06-21 13:23:364510801
02April2021_batch1_88min_3x4_2021-06-18_13-47-57.sky.zip2021-06-18 14:04:322,75014,30914,30985,8544
02April2021_batch1_44min_3x4_2021-06-18_13-20-11.sky.zip2021-06-18 13:37:032,78715,39815,39892,3884
DDR2_response curve_2021-06-17_11-52-03.sky.zip2021-06-17 11:52:4827469264434
Bruderer.sky.zip2021-06-11 09:20:413,86625,31129,238175,3950
Selevsek.sky.zip2021-06-08 13:46:483,59738,88950,764304,5840
test-plate-sky_2021-06-06_14-23-49.sky.zip2021-06-06 16:52:452,36613,01113,01194,94396
AutoQC-lumos-PRTC-15NAPOA1-Enolase-CSF-EvoSep-ADC1-testplate_2021-06-06_16-02-39.sky.zip2021-06-06 16:05:492141417396
BSA-QC_68fmol_Apr2021_Impact-II_2021-05-20_15-45-54.sky.zip2021-05-20 15:46:21131402164
210512_Trypsin_P100_upload_2021-05-12_13-19-24.sky.zip2021-05-12 04:19:42902765792,8570
210512_Lysarginase_P100_upload_2021-05-12_13-17-23.sky.zip2021-05-12 04:17:39741633411,6630
191224_FOSL1_IP_2021-04-30_11-40-54.sky.zip2021-05-06 08:15:4419569997610
191224_FOSL2_IP_ts_2021-04-30_11-39-08.sky.zip2021-05-06 08:15:441944746756
20200704_ITvOT_plasma_final_2021-04-28_13-32-15.sky.zip2021-04-28 20:58:381544344342,98414
qLITvsqOT_matrix_matched_originaltransitions_LIT_2021-04-27_14-24-59.sky.zip2021-04-28 20:58:381244234232,95933
qLITvsqOT_matrix_matched_originaltransitions_OT_2021-04-27_14-23-49.sky.zip2021-04-28 20:58:381244234232,95933
qLITvsqOT_matrix_matched_alltransitions_OT_2021-04-27_14-18-08.sky.zip2021-04-28 20:58:381244234236,20233
qLITvsqOT_matrix_matched_alltransitions_LIT_2021-04-27_14-13-12.sky.zip2021-04-28 20:58:381244234236,20233
qLITvsqOT_precision_final_2020-12-30_07-35-14.sky.zip2021-04-28 20:58:381284604603,01420
LINCS_GCP_Plate70_annotated_minimized_2019-12-16_17-22-40.sky.zip2021-04-21 20:21:56818116280285
LINCS_GCP_Plate94_annotated_minimized_2020-04-03_16-19-23.sky.zip2021-04-18 11:14:24818116285096
BSA-QC_68fmol_Jan-Feb2021_Impact-II_2021-04-16_07-04-15.sky.zip2021-04-16 07:04:33131402164
PRM of Nth1 phospho-peptides in response to AGC-kinase inhibition
Data License: CC BY 4.0 | ProteomeXchange: PXD015760
  • Organism: Saccharomyces cerevisiae
  • Instrument: Orbitrap Fusion ETD
  • SpikeIn: No
  • Keywords: AGC-kinases, Sch9, Ypk1, PKA, chemical genetics
  • Lab head: Michael Plank Submitter: Michael Plank
Abstract
Protein phosphorylation cascades play a central role in the regulation of cell growth and protein kinases PKA, Sch9 and Ypk1 take centre stage in regulating this process in S. cerevisiae. To understand how these kinases co-ordinately regulate cellular functions we compared the phospho-proteome of exponentially growing cells without and with acute chemical inhibition of PKA, Sch9 and Ypk1. Reduced phosphorylation of Nth1 S83 upon PKA- and Ypk1-inhibition was validated by Western blotting and PRM.
Experiment Description
Samples for targeted proteomics by PRM were prepared from 250 µg of protein of yeast cultures (wt, PKA-, Ypk1- or PKA+Ypk1- analog sensitive) treated with 500 nM 1NM-PP1 or DMSO for 15 min. Proteins were digested with LysC and trypsin and a mixture of magnetic TiO2, ZrO2 and Ti(IV)-IMAC beads (15 µl each; ReSyn Biosciences) were used for phospho-peptide enrichment, essentially following the manufacturer`s instructions. Data acquisition was performed on an Orbitrap Fusion Tribrid mass spectrometer coupled to an nLC1000 uHPLC without use of internal standard peptides (Tier 3). Peptides were separated on a 25 cm EASY-spray column (Thermo Scientific) with a 30 min gradient from 3 to 25% acetonitrile, 0.1% formic acid vs. 0.1% formic acid in water. MS-scans were acquired at 60 000 resolution, with an ion target of 4x 105 and maximum injection time of 118 ms. Targeted MS/MS employing higher energy collisional dissociation on 9 selected precursors representing Nth1 phospho-peptides and targeted single ion monitoring on two precursors were each acquired at a resolution of 60 000 with an ion target of 4x 105 and maximum injection time of 200 ms. For data analysis in Skyline 4.2.0.19072 we employed spectral libraries from previously generated data-dependent acquisition and filtered for seven b- or y-ions from ion 3 to last ion.
Sample Description
Three replicates each of 250 µg of protein of yeast cultures (wt, PKA-, Ypk1- or PKA+Ypk1- analog sensitive) treated with 500 nM 1NM-PP1 or DMSO for 15 min.
Created on 10/9/19, 9:14 AM

This data is available under the CC BY 4.0 license.