Kultz et al. (2015) Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks. Proteomics

Kultz et al. (2015) Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks. Proteomics
Clustergrammer Heatmap
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tfreedman_brian023_20190605_17363_LMWstim_2019-07-11_11-35-04.sky.zip (834 KB)2019-07-1515101006
tfreedman_brian023_20190605_17363_LMWnostim_2019-07-11_11-34-30.sky.zip (814 KB)2019-07-1515101006
tfreedman_brian023_20190605_17363_HMWstim_2019-07-11_11-34-02.sky.zip (843 KB)2019-07-1515101006
tfreedman_brian023_20190605_17363_HMWnostim_2019-07-11_11-33-22.sky.zip (834 KB)2019-07-15158806
tfreedman_brian023_20190605_17363_Calibration_2019-07-09_12-03-07.sky.zip (2 MB)2019-07-151144024
calcurve_pY32_unmodifiedY32_2019-07-09_11-44-05.sky.zip (2 MB)2019-07-151267834
Round2_S26_110515_Controls5_2019-07-08_13-48-30.sky.zip (1 MB)2019-07-0811254516814
Round2_S26_missing_Controls10_2019-07-08_13-47-57.sky.zip (431 KB)2019-07-081125451683
Round2_S26_113015_Controls9_2019-07-08_13-47-03.sky.zip (2 MB)2019-07-0811254516820
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Round2_S26_111115_Controls7_2019-07-08_13-45-14.sky.zip (1 MB)2019-07-0811254516814
Round2_S26_110715_Controls6_2019-07-08_13-44-11.sky.zip (2 MB)2019-07-0811254516823
Round2_S26_110315_Controls4_2019-07-08_13-43-07.sky.zip (2 MB)2019-07-0811254516823
Round2_S26_110215_Controls3_2019-07-08_13-42-11.sky.zip (2 MB)2019-07-0811254516824
Round2_S26_101815_Controls2_2019-07-08_13-39-51.sky.zip (2 MB)2019-07-0811254516820
Round2_S26_033116_missing_Controls1_2019-07-08_13-38-37.sky.zip (21 MB)2019-07-081125451686
032115_S26_Results_Controls7_2019-07-08_13-30-46.sky.zip (3 MB)2019-07-0820294918224
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031715_S26_Results_Controls5_2019-07-08_13-29-40.sky.zip (2 MB)2019-07-0820294918218
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031115_S26_Results_Controls1_2019-07-08_13-26-51.sky.zip (2 MB)2019-07-0820294918223
CUL5_HIV_interactors_quant_2018-02-16_10-51-21.sky.zip (12 MB)2019-06-281062752751,07116
CBFB_HIV_CUL2_CUL5_interactors_quant_2018-02-16_10-59-32.sky.zip (5 MB)2019-06-2820878734118
ELOB_HIV_interactors_quant_2018-02-16_11-00-53.sky.zip (33 MB)2019-06-281906636632,63520
CBFB_HIV_interactors_quant_2018-02-16_10-55-27.sky.zip (12 MB)2019-06-28972812811,08316
Healthy_controls_round2_042617_2019-06-27_16-10-07.sky.zip (1 MB)2019-06-2710204015414
Healthy_controls_round1_042617_2019-06-27_16-09-16.sky.zip (1 MB)2019-06-2711204015620
103015_LewinsohnNegatives_round2_2019-06-27_16-02-00.sky.zip (1 MB)2019-06-2710204015415
103015_LewinsohnNegatives_round1_2019-06-27_15-31-23.sky.zip (1 MB)2019-06-2711204015615
LINCS_P100_DIA_Plate80_annotated_minimized_2019-06-13_12-13-28.sky.zip (121 MB)2019-06-1390961922,76496
LINCS_GCP_Plate71b_annotated_minimized_2019-06-10_18-12-11.sky.zip (12 MB)2019-06-10818116283018
LINCS_GCP_Plate71a_annotated_minimized_2019-06-10_18-10-31.sky.zip (5 MB)2019-06-1081811628548
LINCS_P100_DIA_Plate77_annotated_minimized_2019-06-10_16-17-36.sky.zip (81 MB)2019-06-1090961922,76266
LINCS_P100_DIA_Plate70_annotated_minimized_2019-06-03_13-47-33.sky.zip (140 MB)2019-06-0890961922,76496
LINCS_P100_DIA_Plate82_annotated_minimized_2019-06-03_16-03-24.sky.zip (110 MB)2019-06-0890961922,76491
LINCS_P100_DIA_Plate76_annotated_minimized_2019-06-07_15-29-16.sky.zip (100 MB)2019-06-0790961922,75866
LINCS_P100_QC_Plate80_annotated_minimized_2019-06-04_16-27-57.sky.zip (7 MB)2019-06-04882417496
LINCS_P100_QC_Plate82_annotated_minimized_2019-06-04_15-46-59.sky.zip (8 MB)2019-06-04882418396
LINCS_P100_QC_Plate78_annotated_minimized_2019-06-03_15-57-25.sky.zip (7 MB)2019-06-03882316196
LINCS_P100_DIA_Plate70_annotated_minimized_2019-06-03_13-47-33.sky.zip (140 MB)2019-06-0390961922,76496
LINCS_P100_QC_Plate70_annotated_minimized_2019-06-03_13-48-35.sky.zip (7 MB)2019-06-03882416596
all combined_2019-03-21_20-40-14.sky.zip (46 MB)2019-05-31133575268,5337
20180518 multiplex quantification - APOA4 only samples_2018-05-18_12-13-20.sky.zip (265 MB)2019-05-311364864
20180518 multiplex quantification only samples_2018-05-18_11-58-07.sky.zip (380 MB)2019-05-3128357050268
20180509_prest-kinetics_2018-05-09_18-52-06.sky.zip (120 MB)2019-05-311613628684820
500 µE (PG-500uE_2ul_2019-05-16_15-23-09).sky.zip (7 MB)2019-05-292710510555811
Huidan-LHCSR3-Trypsin-PRM_FINAL2_2019-05-16_17-33-35.sky.zip (3 MB)2019-05-2920611225758
Huidan-LHCSR3-LysC-selected-tSIM-PRM_FINAL_2019-05-16_17-31-57.sky.zip (13 MB)2019-05-2931681366528
200µE (R5-8_V2_2019-05-16_15-31-29).sky.zip (8 MB)2019-05-2928979751616
matchedmatrixcalcurve_yeasthela_2019-05-28_13-23-23.sky.zip (1 GB)2019-05-283,22827,28927,28985,17542
matchedmatrixcalcurve_yeastwater_2019-05-24_12-06-14.sky.zip (1 GB)2019-05-243,73136,39336,39395,63942
20150514_Plasma_remove_points_2019-05-22_18-51-25.sky.zip (162 MB)2019-05-2220989862412
matchedmatrixcalcurve_csf_2019-05-22_14-34-12.sky.zip (531 MB)2019-05-224,00716,22916,22947,85630
matchedmatrixcalcurve_yeastyeast_2019-05-22_12-49-50.sky.zip (1 GB)2019-05-223,48230,60230,60290,48842
Janschitz et al_PRM_results_Panorama upload_2019-05-06_18-03-18.sky.zip (611 MB)2019-05-094475833712
LINCS_GCP_Plate76_annotated_minimized_2019-04-29_15-46-06.sky.zip (16 MB)2019-04-29818116287833
LINCS_P100_DIA_Plate51_annotated_minimized_2017-08-02_16-21-22.sky.zip (43 MB)2019-04-26909619292496
LINCS_P100_DIA_Plate41_annotated_minimized_2017-02-16_14-31-38.sky.zip (128 MB)2019-04-2690961921,00296
LINCS_P100_DIA_PlateAD2_annotated_minimized_2019-04-18_11-17-21.sky.zip (52 MB)2019-04-18909619278892
LINCS_P100_QC_PlateAD2_annotated_minimized_2019-04-18_11-15-52.sky.zip (6 MB)2019-04-18882413292
LINCS_GCP_Plate77_annotated_minimized_2019-04-17_09-22-00.sky.zip (19 MB)2019-04-17818116291233
LINCS_GCP_Plate75_annotated_minimized_2019-04-16_13-40-09.sky.zip (26 MB)2019-04-16818116291233
LINCS_GCP_Plate74_annotated_minimized_2019-04-16_13-21-11.sky.zip (24 MB)2019-04-16808016080533
LINCS_GCP_Plate73_annotated_minimized_2019-04-16_11-45-08.sky.zip (24 MB)2019-04-16818116289433
LINCS_P100_QC_Plate75_annotated_minimized_2019-04-08_16-33-18.sky.zip (4 MB)2019-04-08882415666
LINCS_P100_DIA_Plate75_annotated_minimized_2019-04-08_16-26-05.sky.zip (72 MB)2019-04-0890961922,76466
LINCS_P100_QC_Plate76_annotated_minimized_2019-04-08_15-34-30.sky.zip (5 MB)2019-04-08882415066
Dee Dee Luu et. al_The immunogenic microbial peptide RaxX represents an unclassified group of sulfated ribosomally synthesized and post-translationally modified peptides_2019-04-02_12-44-12.sky.zip (1 MB)2019-04-062221318
LINCS_P100_DIA_Plate73_annotated_minimized_2019-04-02_12-31-00.sky.zip (75 MB)2019-04-0290961922,76466
LINCS_P100_QC_Plate74a_annotated_minimized_2019-04-01_16-25-26.sky.zip (2 MB)2019-04-01882417436
LINCS_P100_DIA_Plate74a_annotated_minimized_2019-04-01_16-19-30.sky.zip (39 MB)2019-04-0190961922,76236
20181129_HFF1mut_IP_PRM_2019-03-15_14-54-27.sky.zip (4 MB)2019-04-0172020935
LINCS_P100_QC_Plate73_annotated_minimized_2019-03-28_10-49-18.sky.zip (5 MB)2019-03-28882416266
LINCS_P100_QC_Plate74_annotated_minimized_2019-03-27_16-36-40.sky.zip (6 MB)2019-03-27882417182
LINCS_P100_DIA_Plate74_annotated_minimized_2019-03-27_16-18-55.sky.zip (98 MB)2019-03-2790961922,76284
PRM_final_quantification_non-normalized_2019-03-18_10-30-44.sky.zip (148 MB)2019-03-265353514748
LINCS_P100_QC_Plate70_annotated_minimized_2019-03-13_14-12-46.sky.zip (7 MB)2019-03-13882416596
HLF with ladder_GUnames_2018-08-15_19-59-17.sky.zip (176 KB)2019-03-086045451
U87MG with ladder_GUnames_2018-08-15_20-02-38.sky.zip (429 KB)2019-03-08901181181
IgA with ladder_GUnames_2018-08-15_20-00-17.sky.zip (358 KB)2019-03-08801251251
HNE with ladder_GUnames_2018-08-15_19-59-46.sky.zip (174 KB)2019-03-086038381
PGM OG with ladder_GUnames_2018-08-15_20-01-34.sky.zip (370 KB)2019-03-08201061061
IgG with ladder_GUnames_2018-08-15_20-01-05.sky.zip (228 KB)2019-03-087061611
Fet NG with ladder_GUnames_2018-08-15_19-58-42.sky.zip (229 KB)2019-03-087063631
CBHI OG with ladder_GUnames_2018-08-15_19-58-20.sky.zip (93 KB)2019-03-082020201
CBHI NG with ladder_GUnames_2018-08-15_19-57-24.sky.zip (109 KB)2019-03-083028281
BLF with ladder_GUnames_2018-08-15_19-55-59.sky.zip (302 KB)2019-03-088085851
Fig3_U87MG_iRT_ladder_2018-08-15_19-50-07.sky.zip (429 KB)2019-03-08901191191
Fig5_SupFig3_Dextran_Spectral_Library_2018-08-15_19-53-02.sky.zip (40 KB)2019-03-08103181
Fig1_SupFig1_Ladder_tech_reps_2018-08-15_19-48-46.sky.zip (797 KB)2019-03-0810151510
Fig6_2019-01-26_23-48-44.sky.zip (63 MB)2019-03-088011634212
Fig2_SupFig2_iRT_linear.sky.zip (6 MB)2019-03-0820183216
PRM-Identifying the N-terminal amino acid for a TAG start codon_2019-03-04.sky.zip (3 MB)2019-03-05266583
PRM-Identifying the N-terminal amino acid for an ATG start codon_2019-03-04.sky.zip (1 MB)2019-03-05266563
Cortex_50_targets_PRM_finaL_20181212_2019-01-15_15-55-34.sky.zip (5 MB)2019-03-01551332582,2633
Pancreas_50_targets_PRM_final_20181210_2019-01-15_15-52-49.sky.zip (5 MB)2019-03-01631342602,0613
sasp_panel_ras_2019-02-26_13-24-23.sky.zip (51 MB)2019-02-2674730,02544,411576,8660
sasp_panel_irradiation_2019-02-26_13-00-53.sky.zip (17 MB)2019-02-261729,62414,598189,6470
Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks

  • Organism: Gasterosteus aculeatus
  • Instrument: ImpactHD (Bruker)
  • SpikeIn: No
Abstract
Plasma proteins of marine (Bodega Harbor) and landlocked freshwater (FW, Lake Solano) three-spined sticklebacks were quantified by targeted proteomics. Proteins to be targeted were selected based on a PEAKS label-free quantitative survey of the entire identified plasma proteome. Forty-five plasma proteins were confirmed as highly population-specific with regard to their abundance in stickleback plasma. Proteins with functions in cell adhesion, tissue remodeling, proteolytic processing, defense signaling, and bone morphogenesis are more abundant in marine sticklebacks. Proteins involved in translation, heme biosynthesis, and lipid transport, which may be localized in plasma microparticles are more abundant in FW sticklebacks. Several uncharacterized proteins with unknown functions also show highly population-specific abundance profiles in three-spined stickleback plasma. The molecular phenotypes identified in this study provide insight into targets of selection and molecular mechanisms of adaptation during FW invasion of three-spined sticklebacks.
Experiment Description
Tryptic peptides from each sample (200 ng on column) were injected with a nanoAcquity sample manager (Waters), trapped for 1 min at 15 µL/min on a Symmetry trap column (Waters 186003514), and separated on a 1.7µm particle size BEH C18 column (250mm x 75µm, Waters) by reversed phase LC using a nanoAcquity binary solvent manager (Waters). A 125 min linear gradient ranging from 3% to 35% acetonitrile was used. Peptides were ionized by nano-ESI using a pico-emitter tip (New Objective) and analyzed by an ImpactHD UHR-QTOF mass spectrometer (Bruker). Batch-processing of samples was controlled with Hystar 3.2 (Bruker). The mass range was set to 490 – 910 m/z at 25 Hz scan rate with an isolation width of 11 m/z (1 m/z overlap). Spectral libraries were created from prior precursor-dependent MS1 data (< 20 ppm mass error) that were analyzed by unbiased PEAKSQ quantitative profiling (BSI) to identify protein targets that differ in abundance between stickleback populations. DIA data for targeted proteins were statistically analyzed using Skyline 3.1 (MacCossLab, UW).
Sample Description
Adult sticklebacks were collected by seining from Bodega Harbor (34 g/kg salinity SW) and by unbaited minnow traps from Lake Solano (FW) in August 2014 using California Department of Fish and Wildlife scientific collecting permit SCP12637. They were sacrificed under protocols approved by the University of California Davis (IACUC number 18010, AALAC number A3433-01) and blood collected from the dorsal aorta using EDTA-coated hematocrit capillary tubes (Thermo Fisher, Waltham, MA, USA) within 2 h of capture. Plasma was prepared by centrifugation of blood at 2000×g, 4_C for 10 min followed by collection of supernatant and storage at −80_C until processed for protein extraction (e.g. from exosomes), protein assay, and in solution trypsin digestion as previously described [1]. 1. Kültz D. et al. (2013) Quantitative molecular phenotyping of gill remodeling in a cichlid fish responding to salinity stress. Molecular & Cellular Proteomics 12 (12), 3962-3975.
Created on 8/7/15, 4:07 PM