Bruce - PRM_XL_manuscript

Bruce - PRM_XL_manuscript
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FL_MAL_PsbO_band_SRM_v4.sky.zip2021-07-23 06:10:3630371724
DDRpanel2_LCL_time_2021-07-16_11-50-45.sky.zip2021-07-19 08:33:2632011884730
DDRpanel2_PBMC_2021-07-16_11-50-34.sky.zip2021-07-19 08:33:2632011884125
DDRpanel1_PBMC_2021-07-16_11-50-24.sky.zip2021-07-19 08:33:2637014054226
DDRpanel2_LCL_dose_2021-07-16_11-50-14.sky.zip2021-07-19 08:33:2632011884715
20180731_UPR_ARoos_H&L_paper_Lumos_RT.sky.zip2021-07-16 07:57:13804214228
Nrxn3 HA IP splice segment analysis2021-07-13 08:24:0940147011
Nrxn3 AS5 knock-out analysis2021-07-13 08:17:39103216631
Nrxn3 Exon 25 Titration Curve2021-07-13 08:15:0510169214
Figure 5.sky.zip2021-07-10 09:08:06903410230
Figure 4.sky.zip2021-07-10 09:08:06903410222
Figure 3D.sky.zip2021-07-10 09:08:05903410227
Figure 3C.sky.zip2021-07-10 09:08:05903410227
Figure 3B.sky.zip2021-07-10 09:08:05903410222
Figure 3A.sky.zip2021-07-10 09:08:05903410222
PRM Splice Assays2021-06-24 08:36:073901659900
DDR2_response curve_2021-06-17_11-52-03.sky.zip2021-06-24 08:35:552709264434
210429to210501_ApoE_5x5_Precision.sky2021-06-22 12:52:48101024139
DDR2_chromatogram8_2021-06-21_13-22-59.sky.zip2021-06-22 08:22:184010801
DDR2_chromatogram8_2021-06-21_13-22-59.sky.zip2021-06-21 13:23:364010801
DDR2_response curve_2021-06-17_11-52-03.sky.zip2021-06-17 11:52:482709264434
Bruderer.sky.zip2021-06-11 09:20:413,866029,238175,3950
Selevsek.sky.zip2021-06-08 13:46:483,597050,764304,5840
BSA-QC_68fmol_Apr2021_Impact-II_2021-05-20_15-45-54.sky.zip2021-05-20 15:46:2110402164
210512_Trypsin_P100_upload_2021-05-12_13-19-24.sky.zip2021-05-12 04:19:429005792,8570
210512_Lysarginase_P100_upload_2021-05-12_13-17-23.sky.zip2021-05-12 04:17:397403411,6630
20200704_ITvOT_plasma_final_2021-04-28_13-32-15.sky.zip2021-04-28 20:58:3815404342,98414
qLITvsqOT_matrix_matched_originaltransitions_LIT_2021-04-27_14-24-59.sky.zip2021-04-28 20:58:3812404232,95933
qLITvsqOT_matrix_matched_originaltransitions_OT_2021-04-27_14-23-49.sky.zip2021-04-28 20:58:3812404232,95933
qLITvsqOT_matrix_matched_alltransitions_OT_2021-04-27_14-18-08.sky.zip2021-04-28 20:58:3812404236,20233
qLITvsqOT_matrix_matched_alltransitions_LIT_2021-04-27_14-13-12.sky.zip2021-04-28 20:58:3812404236,20233
qLITvsqOT_precision_final_2020-12-30_07-35-14.sky.zip2021-04-28 20:58:3812804603,01420
LINCS_GCP_Plate70_annotated_minimized_2019-12-16_17-22-40.sky.zip2021-04-21 20:21:5681016280285
LINCS_GCP_Plate94_annotated_minimized_2020-04-03_16-19-23.sky.zip2021-04-18 11:14:2481016285096
BSA-QC_68fmol_Jan-Feb2021_Impact-II_2021-04-16_07-04-15.sky.zip2021-04-16 07:04:3310402164
MRM Brain_2021-02-24_11-23-27.sky.zip2021-04-13 15:28:282209026841
MRM Heart_2021-02-26_13-08-25.sky.zip2021-04-13 15:28:282208625638
MRM Cerebelum_2021-02-24_13-23-28.sky.zip2021-04-13 15:28:282208625640
DDR2_chromatogram5.sky.zip2021-04-08 06:02:52102141
DDR2_chromatogram1.sky.zip2021-04-07 18:04:17270765261
DDR2_chromatogram2.sky.zip2021-04-07 18:03:1070161101
DDR2_chromatogram4.sky.zip2021-04-07 18:02:2010281
DDR2_chromatogram3.sky.zip2021-04-07 18:01:31102141
ARP_Plasma_0.2_vs_2.0_mg_2021-02-24_18-55-48.sky.zip2021-04-02 14:46:324004891,40511
ARP-OxHSA-PlasmaMatrix_DilSeries_2021-02-25_11-31-34.sky.zip2021-04-02 14:46:322029686218
Plasma-OxHSA_2021-02-25_11-37-12.sky.zip2021-04-02 14:46:326030991811
3cm_preliminary_data_2021-03-26_18-17-25.sky.zip2021-03-31 10:24:111071312
20190927 PIP extraction efficiency.sky.zip2021-03-29 06:45:27111114122
20190928 Donor 6-7 PIPs MRM 190926.sky.zip2021-03-29 06:45:26111114130
20190929 Extraction efficiency.sky.zip2021-03-29 06:45:26111114120
20191002 Brain samples.sky.zip2021-03-29 06:45:26111114113
20191003 Donor 6-7 + calibration curve.sky.zip2021-03-29 06:45:26111114136
20191105 Calibration curve.sky.zip2021-03-29 06:45:26111114130
20191108 Gradient.sky.zip2021-03-29 06:45:2611111413
D2 15 CRP.sky.zip2021-03-29 06:45:26111114120
20191114 Extraction efficiency.sky.zip2021-03-29 06:45:26111114119
PIPs MRM 191001 Donor 45.sky.zip2021-03-29 06:45:26111114124
PIPs MRM 190930 OP9.sky.zip2021-03-29 06:45:26111114111
LINCS_P100_DIA_Plate15_annotated_minimized_2018-05-02_19-32-22.sky.zip2021-03-19 20:17:489001921,20296
LINCS_P100_DIA_Plate16_annotated_minimized_2018-05-02_19-43-10.sky.zip2021-03-19 20:17:489001921,12295
LINCS_P100_DIA_Plate17_annotated_minimized_2018-05-02_17-35-29.sky.zip2021-03-19 20:17:489001921,05495
LINCS_P100_DIA_Plate19_annotated_minimized_2018-05-02_17-18-22.sky.zip2021-03-19 20:17:489001921,16096
LINCS_P100_DIA_Plate20_annotated_minimized_2018-05-02_21-04-33.sky.zip2021-03-19 20:17:489001921,07496
LINCS_P100_DIA_Plate22_annotated_minimized_2018-05-02_22-33-32.sky.zip2021-03-19 20:17:489001921,09695
LINCS_P100_DIA_Plate23_annotated_minimized_2018-05-02_18-13-55.sky.zip2021-03-19 20:17:4890019296096
LINCS_P100_DIA_Plate24_annotated_minimized_2018-05-02_19-07-44.sky.zip2021-03-19 20:17:4890019273296
LINCS_P100_DIA_Plate27_annotated_minimized_2018-05-02_19-16-47.sky.zip2021-03-19 20:17:489001921,06496
LINCS_P100_DIA_Plate30_annotated_minimized_2018-05-02_18-33-32.sky.zip2021-03-19 20:17:4890019278596
LINCS_P100_DIA_Plate33_annotated_minimized_2018-05-02_17-47-07.sky.zip2021-03-19 20:17:4890019279696
LINCS_P100_DIA_Plate34_annotated_minimized_2019-08-30_17-25-21.sky.zip2021-03-19 20:17:4890019275296
LINCS_P100_DIA_Plate58_annotated_minimized_2017-11-28_11-50-08.sky.zip2021-03-19 20:17:4890019283495
LINCS_P100_DIA_Plate59a_annotated_minimized_2018-11-30_14-13-58.sky.zip2021-03-19 20:17:489001922,76494
LINCS_P100_DIA_Plate60_annotated_minimized_2017-11-29_16-22-26.sky.zip2021-03-19 20:17:4890019297895
LINCS_P100_DIA_Plate61_annotated_minimized_2018-02-06_17-09-06.sky.zip2021-03-19 20:17:4890019299095
LINCS_P100_DIA_Plate62_annotated_minimized_2018-04-20_15-55-05.sky.zip2021-03-19 20:17:4890019298696
LINCS_P100_DIA_Plate63a_annotated_minimized_2019-11-14_15-28-26.sky.zip2021-03-19 20:17:489001922,76494
LINCS_P100_DIA_Plate64_annotated_minimized_2018-05-02_20-34-19.sky.zip2021-03-19 20:17:4890019298295
LINCS_P100_DIA_Plate66_annotated_minimized_2018-08-31_10-36-13.sky.zip2021-03-19 20:17:479001922,76496
LINCS_P100_PRM_Plate25_annotated_minimized_2018-05-02_18-24-10.sky.zip2021-03-19 20:17:479001921,24296
LINCS_P100_DIA_Plate67_annotated_minimized_2018-08-02_13-56-24.sky.zip2021-03-19 20:17:479001922,75496
LINCS_P100_PRM_Plate18_annotated_minimized_2020-01-08_17-11-19.sky.zip2021-03-19 20:17:479001921,53896
LINCS_P100_PRM_Plate28_annotated_minimized_2018-05-02_18-51-02.sky.zip2021-03-19 20:17:479001921,15896
LINCS_P100_PRM_Plate29_03H_annotated_minimized_2018-05-02_21-16-28.sky.zip2021-03-19 20:17:479001921,53696
LINCS_P100_DIA_Plate65_annotated_minimized_2019-10-21_16-54-32.sky.zip2021-03-19 20:17:479001921,58694
LINCS_P100_PRM_Plate31_annotated_minimized_2018-05-02_18-00-17.sky.zip2021-03-19 20:17:4790019299684
LINCS_P100_PRM_Plate32_annotated_minimized_2018-05-02_20-45-26.sky.zip2021-03-19 20:17:479001921,14696
ZaharaN_MM_Final_SkylineReport_2020-07-30_12-54-33.sky.zip2021-03-18 16:36:23902321832
Martinez et al_PRM Replicates 5-7_MCP_2021-01-28_10-13-34.sky.zip2021-03-18 16:36:2390192378
DDR2_repeatability2.sky.zip2021-03-18 07:29:152065057
DDR2_repeatability1.sky.zip2021-03-18 07:29:093109868857
DDR2_response curve2.sky.zip2021-03-18 07:22:231042827
Diab_tear_SRM_2021-03-18_13-32-33.sky.zip2021-03-18 05:33:4518049102112
BSA_method_dev.sky.zip2021-03-14 13:29:5810545443
BSA_and_PRTC.sky.zip2021-03-14 13:29:53601171,1683
Meningioma_CSF_MRM_2021-02-17_13-51-29.sky.zip2021-03-11 11:32:285015627
Glioma_CSF_MRM_2021-02-17_13-57-43.sky.zip2021-03-11 11:32:2850156410
Medulloblastoma_MRM_2021-02-17_14-29-27.sky.zip2021-03-11 11:32:283010539
MCF-7_QC_Analysed_2021-02-17_14-54-14.sky.zip2021-03-11 11:32:28206675
BSA_QC_Analysed_2021-02-17_14-56-13.sky.zip2021-03-11 11:32:28107655
BSA_QC_standard curve_2021-02-17_14-57-03.sky.zip2021-03-11 11:32:28107655
A general method for targeted quantitative cross-linking mass spectrometry
  • Organism: Bovine, Human
  • Instrument: Q-Exactive Plus, Q-Exactive Plus HF
  • SpikeIn: No
Abstract
Chemical cross-linking mass spectrometry (XL-MS) provides protein structural information by identifying covalently linked proximal amino acid residues on protein surfaces. The information gained by this technique is complementary to other structural biology methods such as x-ray crystallography, NMR and cryo-electron microscopy. The extension of traditional quantitative proteomics methods with chemical cross-linking can provide information on the structural dynamics of protein structures and protein complexes. The identification and quantitation of cross-linked peptides remains challenging for the general community, requiring specialized expertise ultimately limiting more widespread adoption of the technique. We describe a general method for targeted quantitative mass spectrometric analysis of cross-linked peptide pairs utilizing PRM and Skyline for analysis. We demonstrate the utility and robustness of the method with a cross-laboratory study analyzing cross-linked bovine serum albumin (BSA) samples and cross-linked SILAC labeled cultured cells treated with varying concentrations of the Hsp90 inhibitor 17-AAG. This advance provides an easy to use resource so that any lab with access to a LC-MS system capable of performing targeted quantitative analysis can quickly and accurately measure dynamic changes in protein structure and protein interactions.
Experiment Description
Varying amounts (50-1000 ng) of cross-linked BSA peptides were analyzed by LC-MS using a PRM method targeting 30 cross-linked peptide pairs. Cross-linked peptide pairs enriched from in vivo cross-linking of cultured human cells cultured in SILAC media and treated with varying concentrations of the Hsp90 inhibitor 17-AAG were analyzed by LC-MS using a PRM method to target at total of 12 precursor ions (light and heavy isotope versions for 6 cross-linked peptide pairs). Data was collected in the Bruce Laboratory at UW as well as at Cold Spring Harbor Laboratory (CSHL) during the 2016 Proteomics Course.
Sample Description
BSA was cross-linked with the protein interaction reporter cross-linker BDP-NHP. The protein was reduced, alkylated and digested with trypsin. The resulting peptide mixture was desalted with reversed phase solid phase extraction before LC-MS analysis. HeLa cells were cultured in SILAC media containing either isotopically light or heavy Lys and Arg. The cells were treated with varying concentrations of 17-AAG (100, 250, 500, 1000 nM) or a DMSO control for 18 h. The cells were harvested and mixed with a counterpart SILAC label DMSO control cell sample. The cells were then cross-linked with BDP-NHP followed by protein extraction with 8M urea. The protein was reduced, alkylated and digested with trypsin. Cross-linked peptides were enriched using a combination of strong cation exchange chromatography followed by avidin affinity chromatography before LC-MS analysis.
Created on 9/21/16, 3:45 PM