Nunn - Detection of Low Abundance Ocean Bacteria Peptides

Nunn - Detection of Low Abundance Ocean Bacteria Peptides
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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
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
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
sasp_panel_atazanavir_2019-02-26_11-45-06.sky.zip (27 MB)2019-02-2637615,60123,172301,0320
sasp_panel_all_inducers_2019-02-26_11-18-00.sky.zip (17 MB)2019-02-261729,62414,598189,6470
QEPlus_2019-02-05_05-55-27.sky.zip (23 MB)2019-02-0419192414469
QEPlus_2019-02-03_11-26-48.sky.zip (23 MB)2019-02-0319192414469
Gigas-6-10-DIA.sky.zip (1 GB)2019-01-309,04732,31233,292348,20120
2017-09-06-GigasDilutionCurve.sky.zip (118 MB)2019-01-301851511728
2017-09-06-Gigas-SRM-ReplicatesOnly-PostDilutionCurve-emma.sky.zip (244 MB)2019-01-3017474713795
WB_PK_bi_scFv_2019-01-18_23-49-08.sky.zip (2 MB)2019-01-2215107062
Plasma_PK_bi_scFv_2019-01-18_23-51-46.sky.zip (2 MB)2019-01-2215107058
Plasma_PK_bi_scFv_2019-01-18_23-51-46.sky.zip (2 MB)2019-01-1815107058
WB_PK_bi_scFv_2019-01-18_23-49-08.sky.zip (2 MB)2019-01-1815107062
PlasmaExp2B4-5_5x_Chromatogram_2019-01-17_08-10-03.sky.zip (815 KB)2019-01-1897971949311
PlasmaExp2B4-5_5x_Chromatogram_2_20180117_2019-01-17_12-35-37.sky.zip (815 KB)2019-01-1897971949311
MousePlasma_Exp2B7_Chromatogram_5x_2019-01-16_16-21-58.sky.zip (758 KB)2019-01-162121422021
20160309_MouseV2B12M6&7_refined_2019-01-16_16-20-54.sky.zip (15 MB)2019-01-16465110239039
20160914_Batch6results_refined_2019-01-16_16-20-19.sky.zip (13 MB)2019-01-16535410851045
20170215_Exp2B6.5_Chromatogram_5x_2019-01-16_16-19-40.sky.zip (294 KB)2019-01-161717341661
20170215_Exp2B6.5_Chromatogram_2.5x_2019-01-16_16-17-36.sky.zip (334 KB)2019-01-1649501004831
PlasmaExp2B4-5_5x_refined_2019-01-16_16-15-55.sky.zip (32 MB)2019-01-16979719496345
MousePlasmaExp2B4-5_Refined_2019-01-16_16-13-46.sky.zip (62 MB)2019-01-161661703401,69045
20160620_Plasma_Exp1_B4_M1_refined_2019-01-16_16-13-15.sky.zip (17 MB)2019-01-16676713462845
MousePlasmaExp2B4-5_Chromatogram_2019-01-16_16-11-35.sky.zip (1 MB)2019-01-161661703401,6501
20160620_Plasma_Exp1_B4_M2_refined_2019-01-16_16-10-19.sky.zip (19 MB)2019-01-16717114269845
MousePlasma_Exp2B7_Chromatogram_2.5x_2019-01-16_16-10-16.sky.zip (929 KB)2019-01-161631603201,5481
MousePlasmaExp2B3_Chromatogram_2019-01-16_16-03-45.sky.zip (305 KB)2019-01-163946924561
20160720_MousePlasmaExp1Batch5_refined_2019-01-16_15-45-10.sky.zip (31 MB)2019-01-161311332661,26045
MousePlasma_Exp2B7_refined_2.5x_2019-01-16_14-55-31.sky.zip (34 MB)2019-01-161591603201,58445
MousePlasma_Exp1B9_Results_refined1_2019-01-16_14-41-33.sky.zip (71 MB)2019-01-161131142281,06239
20190110 - Ajinomoto Complete_2019-01-10_13-31-48.sky.zip (23 MB)2019-01-1163434161238
20180801_UPR_paper_celllines.zip (451 KB)2019-01-10819381369
20180406_180307CN1_Heavy&Light_paper_QExHF02_calcurve3.zip (2 MB)2019-01-108214214427
20180401_180307CN1_Heavy&Light_paper_QExHF02_calcurve1.zip (1 MB)2019-01-108214215027
20180329_180307CN1_Heavy&Light_paper_QExHF02_24hr.zip (558 KB)2019-01-10821421569
Detection of Low Abundance Ocean Bacteria Peptides

  • Organism: Ruegeria pomeroyi
  • Instrument: Thermo Vantage
  • SpikeIn: No
Abstract
Bacteria transform nutrients and degrade organic matter, making them an essential part of healthy ecosystems. By assaying bacterial physiology within a complex system, the status of the whole ecosystem can be investigated. Proteins are the dynamic molecules that control essential bacterial physiological responses and those of every organism; characterizing an organism’s proteome can therefore provide information on its interaction with the environment. Data dependent proteomic analysis (DDA) is a global approach to assay the entire proteome, but sample complexity and the stochastic nature of mass spectrometry can make it difficult to detect low abundance proteins. We explored the development of targeted proteomic (selected reaction monitoring, SRM) assays in complex ocean samples in order to detect specific bacterial proteins of interest and to assess new tools for mixed community metaproteomic exploration. A mixed community was created from a dilution series of an isolated cultures of bacteria (Reugeria pomeroyi) and phytoplankton (Thalassiosira pseudonana). Using SRM, we were able to select and detect bacterial peptides from the community that were undetectable with the standard DDA approach. We demonstrate benefits and drawbacks of different proteomic approaches that can be used to probe for and resolve nuances of bacterial physiological processes in complex environmental systems.
Sample Description
To mimic a complex marine sample, a dilution series of R. pomeroyi and Thalasiosira pseudonana was created at different cellular ratios. These Rpom:Thaps mixtures were filtered onto 47 mm, 0.2 um Nucleopore polycarbonate filters from which proteins were extracted and digested. Samples were prepared so that 1 µg of protein (sample + QC mix) was injected per 3 µl injection. A C18 trap (2 cm) and C18 analytical columns (27.5 cm) were used and each sample was analyzed in 2 MS experiments to cover the entire peptide transition list (n=334). Raw data can be accessed in the PeptideAtlas (http://www.peptideatlas.org/PASS/PASS00917) under accession PASS00917.
Created on 8/8/16, 4:14 PM