Nunn - Detection of Low Abundance Ocean Bacteria Peptides

Nunn - Detection of Low Abundance Ocean Bacteria Peptides
Clustergrammer Heatmap
Flag FileDownloadCreatedProteinsPeptidesPrecursorsTransitionsReplicates (121 MB)2019-06-1390961922,76496 (12 MB)2019-06-10818116283018 (5 MB)2019-06-1081811628548 (81 MB)2019-06-1090961922,76266 (140 MB)2019-06-0890961922,76496 (110 MB)2019-06-0890961922,76491 (100 MB)2019-06-0790961922,75866 (7 MB)2019-06-04882417496 (8 MB)2019-06-04882418396 (7 MB)2019-06-03882316196 (140 MB)2019-06-0390961922,76496 (7 MB)2019-06-03882416596
all (46 MB)2019-05-31133575268,5337
20180518 multiplex quantification - APOA4 only (265 MB)2019-05-311364864
20180518 multiplex quantification only (380 MB)2019-05-3128357050268 (120 MB)2019-05-311613628684820
500 µE (PG-500uE_2ul_2019-05-16_15-23-09) (7 MB)2019-05-292710510555811 (3 MB)2019-05-2920611225758 (13 MB)2019-05-2931681366528
200µE (R5-8_V2_2019-05-16_15-31-29) (8 MB)2019-05-2928979751616 (1 GB)2019-05-283,22827,28927,28985,17542 (1 GB)2019-05-243,73136,39336,39395,63942 (162 MB)2019-05-2220989862412 (531 MB)2019-05-224,00716,22916,22947,85630 (1 GB)2019-05-223,48230,60230,60290,48842
Janschitz et al_PRM_results_Panorama (611 MB)2019-05-094475833712 (16 MB)2019-04-29818116287833 (43 MB)2019-04-26909619292496 (128 MB)2019-04-2690961921,00296 (52 MB)2019-04-18909619278892 (6 MB)2019-04-18882413292 (19 MB)2019-04-17818116291233 (26 MB)2019-04-16818116291233 (24 MB)2019-04-16808016080533 (24 MB)2019-04-16818116289433 (4 MB)2019-04-08882415666 (72 MB)2019-04-0890961922,76466 (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 (1 MB)2019-04-062221318 (75 MB)2019-04-0290961922,76466 (2 MB)2019-04-01882417436 (39 MB)2019-04-0190961922,76236 (5 MB)2019-03-28882416266 (6 MB)2019-03-27882417182 (98 MB)2019-03-2790961922,76284 (7 MB)2019-03-13882416596
HLF with (176 KB)2019-03-086045451
U87MG with (429 KB)2019-03-08901181181
IgA with (358 KB)2019-03-08801251251
HNE with (174 KB)2019-03-086038381
PGM OG with (370 KB)2019-03-08201061061
IgG with (228 KB)2019-03-087061611
Fet NG with (229 KB)2019-03-087063631
CBHI OG with (93 KB)2019-03-082020201
CBHI NG with (109 KB)2019-03-083028281
BLF with (302 KB)2019-03-088085851 (429 KB)2019-03-08901191191 (40 KB)2019-03-08103181 (797 KB)2019-03-0810151510 (63 MB)2019-03-088011634212 (6 MB)2019-03-0820183216
PRM-Identifying the N-terminal amino acid for a TAG start (3 MB)2019-03-05266583
PRM-Identifying the N-terminal amino acid for an ATG start (1 MB)2019-03-05266563 (5 MB)2019-03-01551332582,2633 (5 MB)2019-03-01631342602,0613 (51 MB)2019-02-2674730,02544,411576,8660 (17 MB)2019-02-261729,62414,598189,6470 (27 MB)2019-02-2637615,60123,172301,0320 (17 MB)2019-02-261729,62414,598189,6470 (23 MB)2019-02-0419192414469 (23 MB)2019-02-0319192414469 (1 GB)2019-01-309,04732,31233,292348,20120 (118 MB)2019-01-301851511728 (244 MB)2019-01-3017474713795 (2 MB)2019-01-2215107062 (2 MB)2019-01-2215107058 (2 MB)2019-01-1815107058 (2 MB)2019-01-1815107062 (815 KB)2019-01-1897971949311 (815 KB)2019-01-1897971949311 (758 KB)2019-01-162121422021
20160309_MouseV2B12M6& (15 MB)2019-01-16465110239039 (13 MB)2019-01-16535410851045 (294 KB)2019-01-161717341661 (334 KB)2019-01-1649501004831 (32 MB)2019-01-16979719496345 (62 MB)2019-01-161661703401,69045 (17 MB)2019-01-16676713462845 (1 MB)2019-01-161661703401,6501 (19 MB)2019-01-16717114269845 (929 KB)2019-01-161631603201,5481 (305 KB)2019-01-163946924561 (31 MB)2019-01-161311332661,26045 (34 MB)2019-01-161591603201,58445 (71 MB)2019-01-161131142281,06239
20190110 - Ajinomoto (23 MB)2019-01-1163434161238 (451 KB)2019-01-10819381369
20180406_180307CN1_Heavy& (2 MB)2019-01-108214214427
20180401_180307CN1_Heavy& (1 MB)2019-01-108214215027
20180329_180307CN1_Heavy& (558 KB)2019-01-10821421569
Detection of Low Abundance Ocean Bacteria Peptides

  • Organism: Ruegeria pomeroyi
  • Instrument: Thermo Vantage
  • SpikeIn: No
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 ( under accession PASS00917.
Created on 8/8/16, 4:14 PM