http://lod.bco-dmo.org/id/dataset/628718
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2015-12-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Proteins from Inferno hydrothermal vent plume meta-proteome - replicate Av2
2015-12-08
publication
2015-12-08
revision
BCO-DMO Linked Data URI
2015-12-08
creation
http://lod.bco-dmo.org/id/dataset/628718
Robert Morris
University of Washington
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Morris, R. (2015) Proteins from Inferno hydrothermal vent plume meta-proteome - replicate Av2. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version final) Version Date 2015-12-08 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/628718 [access date]
proteins from Inferno hydrothermal vent plume meta-proteome - replicate Av2 Dataset Description: <p>Proteins identified in the Inferno hydrothermal vent plume meta-proteome (replicate Av2).&nbsp; Only proteins identified by peptides with a protein probability &gt;0.9 are listed.&nbsp;</p>
<p>These data are reported as Supplementary Table 4 and discussed in <a href="http://dmoserv3.bco-dmo.org/data_docs/SulfurOxidizers/Mattes_2013_PlumeProt.pdf" target="_blank">Mattes et al., 2013</a>. (doi:10.1038/ismej.2013.113)</p>
<p>The FASTA information in the data was expanded to include the metadata when those FASTA headers were linked to GenBank.&nbsp;</p>
<p><em>Proteins that were identified in biological replicate AV2 that were not identified in biological replicate Av1. (GSO: Gamma Sulfur Oxidizer)</em></p>
<p><img alt="" src="https://datadocs.bco-dmo.org/d3/data_docs/SulfurOxidizers/Table5.png" style="float:left; height:174px; width:637px" /><br />
&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p><strong>DMO notes:</strong><br />
Put multiple FASTA entries on separate lines<br />
Split out one number in FASTA header for linking<br />
Sorted by entry number<br />
Added linkage column<br />
Removed commas in 'consensus annotation' column (signals database to put in new column)<br />
Reordered columns to put KEGG last -- much longer than any other column<br />
Changed ' to P within field because system won't take unmatched quotes. Means 'prime'.</p> Methods and Sampling: <p>Seawater (~180 L) was collected from the stable hydrothermal vent plume issuing from the black smoker chimney Inferno (CTD17, 1 450 m). Whole water was transferred to clean 50 L polystyrene reservoirs and concentrated to ~230 ml with a Pellicon 2 tangential flow filtration system equipped with a 30 kDa Biomax Polyethersulfone cassette (Millipore Corporation, Billerica, MA) as described previously (Morris et al 2010). Cells were collected and concentrated in approximately 2 hours. Concentrated cells were flash frozen in liquid nitrogen and stored at -80 ºC until further processing at the University of Washington.Cell counts before and after filtration (6.9 x 1010 and 2.9 x 1010, respectively) indicate that we recovered 42% of the cells present in 180 L of hydrothermal vent plume water. Cells in the concentrated sample were divided into replicate samples (Av1 and Av2, ~115 ml each) and harvested by centrifuging at 4°C for 60 min (17,000 x g). The supernatant was discarded and cell pellets were rinsed with 100 uL of 20 mM Tris buffer pH 7.4 and stored -80°C.</p>
<p>Cells were lysed using a titanium sonicating micro-probe (20 sec, 10 repetitions) in a 6M urea and 50 μM ammonium bicarbonate solution. Disulfide bonds were reduced with dithiothreitol and alkylated with iodo-acetic acid. After additions of ammonium bicarbonate and methanol, 2 μg of sequence grade trypsin (Promega, Madison, WI) were added to each sample. Enzymatic digestions were incubated for 12 h at 37 oC. Resulting peptides were desalted using a macro-spin C18 column (NestGroup) following the manufacturers guidelines prior to analysis by mass spectrometry (MS).</p>
<p>Peptide concentrations from Axial volcano hydrothermal vent plume proteome replicates Av1 and Av2 were measured using the Thermo Scientific Nanodrop 2000/2000c, which measures the peptide bond absorbance at wavelength of 205 nm. Approximately 1 μg of peptide digest was used for each injection into the mass spectrometer. Each sample consisted of a complex mixture of peptides that were introduced into the mass spectrometer by reverse-phase chromatography using a brand new 15 cm long, 75 μm i.d. fused silica capillary column packed with C18 particles (Magic C18AQ, 100 Å, 5 μm; Michrom, Bioresources, Inc., CA) fitted with a 2 cm long, 100 μm i.d. pre-column (Magic C18AQ, 200 Å, 5μm; Michrom). Peptides were first trapped on the pre-column (5% ACN; 4 ml min-1; 7 min). Chromatographic separations were performed using an acidified (formic acid, 0.1% v/v) water-acetonitrile gradient (5-35% acetonitrile in 60 min) with a total run-time of 95 minutes.</p>
<p>Mass spectrometry was performed on replicates Av1 and Av2 independently using the Thermo Fisher (San Jose, Ca) linear ion trap –Orbitrap (LTQ-OT) hybrid tandem mass spectrometer. Peptides were analyzed using the data-independent Precursor Acquisition Independent from Ion Count (PAcIFIC) method (Panchaud et al 2009). Rather than requiring the mass spectrometer to select ions for fragmentation based on MS1 data, the PAcIFIC method systematically fragments ions at all m/z channels (Panchaud et al 2011). Each method file includes the full 95 minute linear HPLC gradient of 5-35% ACN over 60 minutes (see above) and covers a 21.5 m/z range using 14 contiguous, unique channels that span 2.5 m/z in the mass spectrometer. This results in a total of 45 method files per PAcIFIC analytical cycle to cover a full m/z range of 400-1400.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1232840 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1232840
completed
Robert Morris
University of Washington
206-221-7228
School of Oceanography Box 357940
Seattle
WA
98195-7940
USA
morrisrm@uw.edu
pointOfContact
asNeeded
Dataset Version: final
Unknown
entry
lat
lon
depth
NCBI_FASTA_link
protein_probability
num_unique_peptide
indep_spectra_tot
peptide_seq
consensus_annotation
KEGG_category
CTD Seabird 9 plus
Thermo Fisher (San Jose, Ca) linear ion trap –Orbitrap (LTQ-OT) hybrid tandem mass spectrometer
Thermo Scientific Nanodrop 2000/2000c Spectrophotometer
theme
None, User defined
sample identification
latitude
longitude
depth
external_link
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird 9
Mass Spectrometer
Spectrophotometer
instrument
BCO-DMO Standard Instruments
TN268
service
Deployment Activity
North Pacific
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade
http://morrislab.ocean.washington.edu/
Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade
<p><em>Description from NSF award abstract:</em><br />
The ocean serves an immense reservoir of carbon, nitrogen, phosphorus, sulfur, and other elements required for all life. The active and diverse microbial populations that inhabit the oceans are responsible for mediating nutrient transformations that maintain the chemistry of seawater. A recent study identified a ubiquitous group of marine bacteria from the Arctic96BD-19 gamma-proteobacterial sulfur oxidizer (GSO) lineage that is closely related to known sulfur oxidizing species that fix inorganic carbon and oxidize sulfide in low-oxygen waters. The potential for GSOs to use reduced forms of sulfur in oxygenated waters suggests that they are a keystone species that link the marine carbon and sulfur cycles. The only known isolates from the Arctic96BD-19 lineage of GSOs are now in culture, allowing fundamental questions about their roles in carbon and sulfur cycling to be investigated. Preliminary data suggest that they use energy from the oxidation of sulfur to assimilate carbon. This project seek to address the overarching hypothesis that sulfur transformations provide the Arctic96BD- 19 lineage of GSOs with energy for organic and inorganic carbon cycling throughout the water column.</p>
<p>Three specific hypotheses will be tested.<br />
1. Arctic96BD-19 cells assimilate either organic carbon or fixes inorganic carbon, depending on environmental conditions.<br />
2. Arctic96BD-19 cells oxidize thiosulfate via formation of a tetrathionate intermediate, or using the branched thiosulfate oxidation pathway.<br />
3. Arctic96BD-19 cells are ubiquitous sulfur oxidizers that assimilate organic and inorganic carbon through the Pacific Northwest.</p>
<p>A combination of laboratory growth studies of the investigator's pure cultures and comparative genomic analyses will be used. The genomic data will be used to determine whether the Arctic96BD-19 cultures possess the genetic potential to oxidize reduced sulfur to sulfate (based on possession of known core and ancillary sulfur oxidation genes), which potential oxidation pathways are used, and whether they can fix inorganic carbon. These data will help guide the physiology studies by determining the most likely forms of inorganic and organic compounds that can be utilized.</p>
<p>Marine bacteria are critical players in global nutrient cycles, but many of their individual and community functions in the ecosystem are not well understood. Future oceanographers will need to use cultivation-dependent and cultivation-independent methods to identify metabolic process that shape microbial communities and impact biogeochemical cycles. Student education, scientific advancement, and public awareness are all important components of this project.</p>
Sulfur Oxidizers
largerWorkCitation
project
eng; USA
biota
oceans
North Pacific
-130.0138
-130.0138
45.934
45.934
2011-08-29
2011-08-29
North Pacific Ocean
0
BCO-DMO catalogue of parameters from Proteins from Inferno hydrothermal vent plume meta-proteome - replicate Av2
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/637585.rdf
Name: entry
Units: number
Description: <p>data entry number; each entry number is a unit and all columns of information with the same entry number should be considered together</p>
http://lod.bco-dmo.org/id/dataset-parameter/637586.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/637587.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude of sample collection; West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/637588.rdf
Name: depth
Units: meters
Description: <p>depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/637589.rdf
Name: NCBI_FASTA_link
Units: link
Description: <p>FASTA header with embedded NCBI reference number; link is to protein page in that database; several entries with multiple links separated by commas had to be put on separate lines to enable multiple links</p>
http://lod.bco-dmo.org/id/dataset-parameter/637590.rdf
Name: protein_probability
Units: decimal number
Description: <p>the probability that the protein identified from the peptide sequences is correct. Only proteins identified by peptides with a protein probability of >0.9 are listed</p>
http://lod.bco-dmo.org/id/dataset-parameter/637591.rdf
Name: num_unique_peptide
Units: number
Description: <p>the number of unique peptide sequences identified; unique peptide is defined as a peptide -- irrespective of its length -- that exists only in one protein of a proteome of interest. The peptide sequences themselves are in the peptide sequence column</p>
http://lod.bco-dmo.org/id/dataset-parameter/637592.rdf
Name: indep_spectra_tot
Units: number
Description: <p>number of identifying peaks from the tandem mass spectrometer</p>
http://lod.bco-dmo.org/id/dataset-parameter/637593.rdf
Name: peptide_seq
Units: text
Description: <p>amino acids identified in the peptide; A=Alanine; G=Glycine; etc</p>
http://lod.bco-dmo.org/id/dataset-parameter/637594.rdf
Name: consensus_annotation
Units: text
Description: <p>describing protein X in terms of topic Y; these dominant active bacterial groups are determined by consensus annotation of identified proteins</p>
http://lod.bco-dmo.org/id/dataset-parameter/637595.rdf
Name: KEGG_category
Units: text
Description: <p>Kyoto Encyclopedia of Genes and Genomes; used to identify dominant functional classifications like metabolism or genetic information processing</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
200265
https://datadocs.bco-dmo.org/file/xooy0Qxsx8lyE3/vent_proteins2.csv
vent_proteins2.csv
Primary data file for dataset ID 628718
download
https://osprey.bco-dmo.org/dataset/628718/data/download
download
onLine
dataset
<p>Seawater (~180 L) was collected from the stable hydrothermal vent plume issuing from the black smoker chimney Inferno (CTD17, 1 450 m). Whole water was transferred to clean 50 L polystyrene reservoirs and concentrated to ~230 ml with a Pellicon 2 tangential flow filtration system equipped with a 30 kDa Biomax Polyethersulfone cassette (Millipore Corporation, Billerica, MA) as described previously (Morris et al 2010). Cells were collected and concentrated in approximately 2 hours. Concentrated cells were flash frozen in liquid nitrogen and stored at -80 ºC until further processing at the University of Washington.Cell counts before and after filtration (6.9 x 1010 and 2.9 x 1010, respectively) indicate that we recovered 42% of the cells present in 180 L of hydrothermal vent plume water. Cells in the concentrated sample were divided into replicate samples (Av1 and Av2, ~115 ml each) and harvested by centrifuging at 4°C for 60 min (17,000 x g). The supernatant was discarded and cell pellets were rinsed with 100 uL of 20 mM Tris buffer pH 7.4 and stored -80°C.</p>
<p>Cells were lysed using a titanium sonicating micro-probe (20 sec, 10 repetitions) in a 6M urea and 50 μM ammonium bicarbonate solution. Disulfide bonds were reduced with dithiothreitol and alkylated with iodo-acetic acid. After additions of ammonium bicarbonate and methanol, 2 μg of sequence grade trypsin (Promega, Madison, WI) were added to each sample. Enzymatic digestions were incubated for 12 h at 37 oC. Resulting peptides were desalted using a macro-spin C18 column (NestGroup) following the manufacturers guidelines prior to analysis by mass spectrometry (MS).</p>
<p>Peptide concentrations from Axial volcano hydrothermal vent plume proteome replicates Av1 and Av2 were measured using the Thermo Scientific Nanodrop 2000/2000c, which measures the peptide bond absorbance at wavelength of 205 nm. Approximately 1 μg of peptide digest was used for each injection into the mass spectrometer. Each sample consisted of a complex mixture of peptides that were introduced into the mass spectrometer by reverse-phase chromatography using a brand new 15 cm long, 75 μm i.d. fused silica capillary column packed with C18 particles (Magic C18AQ, 100 Å, 5 μm; Michrom, Bioresources, Inc., CA) fitted with a 2 cm long, 100 μm i.d. pre-column (Magic C18AQ, 200 Å, 5μm; Michrom). Peptides were first trapped on the pre-column (5% ACN; 4 ml min-1; 7 min). Chromatographic separations were performed using an acidified (formic acid, 0.1% v/v) water-acetonitrile gradient (5-35% acetonitrile in 60 min) with a total run-time of 95 minutes.</p>
<p>Mass spectrometry was performed on replicates Av1 and Av2 independently using the Thermo Fisher (San Jose, Ca) linear ion trap –Orbitrap (LTQ-OT) hybrid tandem mass spectrometer. Peptides were analyzed using the data-independent Precursor Acquisition Independent from Ion Count (PAcIFIC) method (Panchaud et al 2009). Rather than requiring the mass spectrometer to select ions for fragmentation based on MS1 data, the PAcIFIC method systematically fragments ions at all m/z channels (Panchaud et al 2011). Each method file includes the full 95 minute linear HPLC gradient of 5-35% ACN over 60 minutes (see above) and covers a 21.5 m/z range using 14 contiguous, unique channels that span 2.5 m/z in the mass spectrometer. This results in a total of 45 method files per PAcIFIC analytical cycle to cover a full m/z range of 400-1400.</p>
Specified by the Principal Investigator(s)
<p>Protein identifications</p>
<p>Tandem mass spectra were interrogated against a composite database containing deduced protein sequences from lineages identified in the CTD17 clone library and lineages that are dominant in the deep ocean (background seawater). The database contained marine GSOs Candidatus Vesicomyosocius okutanii HA, Candidatus Ruthia magnifica Cm, the SUP05 metagenome (Walsh et al 2009), and SCGC AAA001-B15 (Arctic96BD-19 draft genome); the methylotrophs Methylobacter tundripaludum SV96 and Methylomicrobium alcaliphilum; iron-oxidizing bacteria Gallionella capsiferriformans ES-2 and Sideroxydans lithotrophicus ES-1; abundant lineages in seawater Candidatus Pelagibacter ubique HTCC1062; Candidatus Pelagibacter ubique HTCC1002; Ammonia-oxidizing archaea Nitrosopumilus maritimus SCM1, an uncultured marine group II (Iverson et al 2012); an incomplete hydrothermal vent metagenome (Xie et al 2011); and common contaminants. SEQUEST (v. UW2011.01.1) was used to correlate observed tandem mass spectra to peptide sequence via theoretical tandem mass spectra from the composite database described above (Eng et al 1994, Eng et al 2008). For a detailed discussion of database considerations in community proteomics see Morris et al. (2010). SEQUEST parameters included a 3.75 Da peptide mass tolerance on MS1 spectra, specifying trypsin as the enzyme, variable oxidation modification on methionine (15.9949 Da), and static modification on Cysteine residues (57.021464 Da) resulting from alkylation.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
CTD Seabird 9 plus
CTD Seabird 9 plus
PI Supplied Instrument Name: CTD Seabird 9 plus PI Supplied Instrument Description:Seabird 9plus CTD with temperature and conductivity sensors. Instrument Name: CTD Sea-Bird 9 Instrument Short Name:CTD SBE 9 Instrument Description: The Sea-Bird SBE 9 is a type of CTD instrument package. The SBE 9 is the Underwater Unit and is most often combined with the SBE 11 Deck Unit (for real-time readout using conductive wire) when deployed from a research vessel. The combination of the SBE 9 and SBE 11 is called a SBE 911. The SBE 9 uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 and SBE 4). The SBE 9 CTD can be configured with auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorometer, altimeter, etc.). Note that in most cases, it is more accurate to specify SBE 911 than SBE 9 since it is likely a SBE 11 deck unit was used. more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Thermo Fisher (San Jose, Ca) linear ion trap –Orbitrap (LTQ-OT) hybrid tandem mass spectrometer
Thermo Fisher (San Jose, Ca) linear ion trap –Orbitrap (LTQ-OT) hybrid tandem mass spectrometer
PI Supplied Instrument Name: Thermo Fisher (San Jose, Ca) linear ion trap –Orbitrap (LTQ-OT) hybrid tandem mass spectrometer PI Supplied Instrument Description:"The hybrid Fourier Transform (FT) mass spectrometer(MS) combines a linear ion trap
MS and the Orbitrap mass analyzer. Ions generated by API
are collected in the LTQ XL followed by axial ejection to the
C-shaped storage trap which is used to store and collisionally
cool ions before injection into the orbital trap. The ions
transferred from the C-Trap are captured in the orbital trap
by rapidly increasing the electric field and the detection of
the image current from coherent ion packets takes place
after the voltages have stabilized. Signals from each of the
orbital trap outer electrodes are amplified and transformed
into a frequency spectrum by fast Fourier transformation
which is finally converted into a mass spectrum." (From Fisher Scientific)
Instrument Name: Mass Spectrometer Instrument Short Name:Mass Spec Instrument Description: General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
Thermo Scientific Nanodrop 2000/2000c Spectrophotometer
Thermo Scientific Nanodrop 2000/2000c Spectrophotometer
PI Supplied Instrument Name: Thermo Scientific Nanodrop 2000/2000c Spectrophotometer PI Supplied Instrument Description:Measured peptide bond absorbance at wavelength 205nm Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
Cruise: TN268
TN268
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN268
Dr John R. Delaney
University of Washington
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel