ERDDAP > info > bcodmo_dataset_627835

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
	set	data	graph		files	public	Proteins identified from the black smoker chimney Inferno hydrothermal vent plume meta- proteome - replicate Av1 - on the Axial seamount off the coast of Washington in 2011.		I   M	background			BCO-DMO	bcodmo_dataset_627835

The Dataset's Variables and Attributes

Row Type	Variable Name	Attribute Name	Data Type	Value
attribute	NC_GLOBAL	access_formats	String	.htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson
attribute	NC_GLOBAL	acquisition_description	String	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 \u00baC 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\u00b0C 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\u00b0C. Cells were lysed using a titanium sonicating micro-probe (20 sec, 10 repetitions) in a 6M urea and 50 \u03bcM ammonium bicarbonate solution. Disulfide bonds were reduced with dithiothreitol and alkylated with iodo- acetic acid. After additions of ammonium bicarbonate and methanol, 2 \u03bcg 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). 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 \u03bcg 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 \u03bcm i.d. fused silica capillary column packed with C18 particles (Magic C18AQ, 100 \u00c5, 5 \u03bcm; Michrom, Bioresources, Inc., CA) fitted with a 2 cm long, 100 \u03bcm i.d. pre-column (Magic C18AQ, 200 \u00c5, 5\u03bcm; 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. Mass spectrometry was performed on replicates Av1 and Av2 independently using the Thermo Fisher (San Jose, Ca) linear ion trap \u2013Orbitrap (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.
attribute	NC_GLOBAL	awards_0_award_nid	String	529021
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1232840
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1232840
attribute	NC_GLOBAL	awards_0_funder_name	String	NSF Division of Ocean Sciences
attribute	NC_GLOBAL	awards_0_funding_acronym	String	NSF OCE
attribute	NC_GLOBAL	awards_0_funding_source_nid	String	355
attribute	NC_GLOBAL	awards_0_program_manager	String	David L. Garrison
attribute	NC_GLOBAL	awards_0_program_manager_nid	String	50534
attribute	NC_GLOBAL	cdm_data_type	String	Other
attribute	NC_GLOBAL	comment	String	Inferno Plume Proteins replicate Av1 (Supplementary Table 3) only protein probability > .9 reported location and depth added by DMO R.Morris, PI
attribute	NC_GLOBAL	Conventions	String	COARDS, CF-1.6, ACDD-1.3
attribute	NC_GLOBAL	creator_email	String	info at bco-dmo.org
attribute	NC_GLOBAL	creator_name	String	BCO-DMO
attribute	NC_GLOBAL	creator_type	String	institution
attribute	NC_GLOBAL	creator_url	String	https://www.bco-dmo.org/
attribute	NC_GLOBAL	data_source	String	extract_data_as_tsv version 2.3 19 Dec 2019
attribute	NC_GLOBAL	date_created	String	2015-11-25T16:24:25Z
attribute	NC_GLOBAL	date_modified	String	2017-11-12T19:58:17Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.1575/1912/bco-dmo.643630
attribute	NC_GLOBAL	Easternmost_Easting	double	-130.0138
attribute	NC_GLOBAL	geospatial_lat_max	double	45.934
attribute	NC_GLOBAL	geospatial_lat_min	double	45.934
attribute	NC_GLOBAL	geospatial_lat_units	String	degrees_north
attribute	NC_GLOBAL	geospatial_lon_max	double	-130.0138
attribute	NC_GLOBAL	geospatial_lon_min	double	-130.0138
attribute	NC_GLOBAL	geospatial_lon_units	String	degrees_east
attribute	NC_GLOBAL	geospatial_vertical_max	double	1450.0
attribute	NC_GLOBAL	geospatial_vertical_min	double	1450.0
attribute	NC_GLOBAL	geospatial_vertical_positive	String	down
attribute	NC_GLOBAL	geospatial_vertical_units	String	m
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/627835
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	CTD SBE 9
attribute	NC_GLOBAL	instruments_0_dataset_instrument_description	String	Seabird 9plus CTD with temperature and conductivity sensors.
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	637597
attribute	NC_GLOBAL	instruments_0_description	String	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
attribute	NC_GLOBAL	instruments_0_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/130/
attribute	NC_GLOBAL	instruments_0_instrument_name	String	CTD Sea-Bird 9
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	488
attribute	NC_GLOBAL	instruments_0_supplied_name	String	CTD Seabird 9 plus
attribute	NC_GLOBAL	instruments_1_acronym	String	Mass Spec
attribute	NC_GLOBAL	instruments_1_dataset_instrument_description	String	"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)
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	627987
attribute	NC_GLOBAL	instruments_1_description	String	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.
attribute	NC_GLOBAL	instruments_1_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB16/
attribute	NC_GLOBAL	instruments_1_instrument_name	String	Mass Spectrometer
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	685
attribute	NC_GLOBAL	instruments_1_supplied_name	String	Thermo Fisher (San Jose, Ca) linear ion trap –Orbitrap (LTQ-OT) hybrid tandem mass spectrometer
attribute	NC_GLOBAL	instruments_2_acronym	String	Spectrophotometer
attribute	NC_GLOBAL	instruments_2_dataset_instrument_description	String	Measured peptide bond absorbance at wavelength 205nm
attribute	NC_GLOBAL	instruments_2_dataset_instrument_nid	String	637598
attribute	NC_GLOBAL	instruments_2_description	String	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.
attribute	NC_GLOBAL	instruments_2_instrument_external_identifier	String	https://vocab.nerc.ac.uk/collection/L05/current/LAB20/
attribute	NC_GLOBAL	instruments_2_instrument_name	String	Spectrophotometer
attribute	NC_GLOBAL	instruments_2_instrument_nid	String	707
attribute	NC_GLOBAL	instruments_2_supplied_name	String	Thermo Scientific Nanodrop 2000/2000c Spectrophotometer
attribute	NC_GLOBAL	keywords	String	annotation, bco, bco-dmo, biological, category, chemical, consensus, consensus_annotation, data, dataset, depth, dmo, entry, erddap, fasta, indep, indep_spectra_tot, kegg, KEGG_category, latitude, link, longitude, management, ncbi, NCBI_FASTA_link, num, num_unique_peptide, oceanography, office, peptide, peptide_seq, preliminary, probability, protein, protein_probability, seq, spectra, tot, unique
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/627835/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/627835
attribute	NC_GLOBAL	Northernmost_Northing	double	45.934
attribute	NC_GLOBAL	param_mapping	String	{'627835': {'lat': 'master - latitude', 'depth': 'flag - depth', 'lon': 'master - longitude'}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/627835/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of Washington
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UW
attribute	NC_GLOBAL	people_0_person_name	String	Robert Morris
attribute	NC_GLOBAL	people_0_person_nid	String	51295
attribute	NC_GLOBAL	people_0_role	String	Principal Investigator
attribute	NC_GLOBAL	people_0_role_type	String	originator
attribute	NC_GLOBAL	people_1_affiliation	String	University of Washington
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	UW
attribute	NC_GLOBAL	people_1_person_name	String	Robert Morris
attribute	NC_GLOBAL	people_1_person_nid	String	51295
attribute	NC_GLOBAL	people_1_role	String	Contact
attribute	NC_GLOBAL	people_1_role_type	String	related
attribute	NC_GLOBAL	people_2_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_2_person_name	String	Ms Dicky Allison
attribute	NC_GLOBAL	people_2_person_nid	String	50382
attribute	NC_GLOBAL	people_2_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	project	String	Sulfur Oxidizers
attribute	NC_GLOBAL	projects_0_acronym	String	Sulfur Oxidizers
attribute	NC_GLOBAL	projects_0_description	String	Description from NSF award abstract: 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. Three specific hypotheses will be tested. 1. Arctic96BD-19 cells assimilate either organic carbon or fixes inorganic carbon, depending on environmental conditions. 2. Arctic96BD-19 cells oxidize thiosulfate via formation of a tetrathionate intermediate, or using the branched thiosulfate oxidation pathway. 3. Arctic96BD-19 cells are ubiquitous sulfur oxidizers that assimilate organic and inorganic carbon through the Pacific Northwest. 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. 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.
attribute	NC_GLOBAL	projects_0_end_date	String	2015-09
attribute	NC_GLOBAL	projects_0_geolocation	String	North Pacific Ocean
attribute	NC_GLOBAL	projects_0_name	String	Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade
attribute	NC_GLOBAL	projects_0_project_nid	String	529022
attribute	NC_GLOBAL	projects_0_project_website	String	http://morrislab.ocean.washington.edu/
attribute	NC_GLOBAL	projects_0_start_date	String	2012-10
attribute	NC_GLOBAL	publisher_name	String	Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute	NC_GLOBAL	publisher_type	String	institution
attribute	NC_GLOBAL	sourceUrl	String	(local files)
attribute	NC_GLOBAL	Southernmost_Northing	double	45.934
attribute	NC_GLOBAL	standard_name_vocabulary	String	CF Standard Name Table v55
attribute	NC_GLOBAL	subsetVariables	String	latitude,longitude,depth
attribute	NC_GLOBAL	summary	String	Proteins identified in the Inferno hydrothermal vent plume meta-proteome (replicate Av1).\u00a0 Only proteins identified by peptides with a protein probability >0.9 are listed.\u00a0 These data are reported as Supplementary Table 3 and discussed in [Mattes et al., 2013](\\http://dmoserv3.bco- dmo.org/data_docs/SulfurOxidizers/Mattes_2013_PlumeProt.pdf\\). (doi:10.1038/ismej.2013.113) The FASTA information in the data was expanded to include the metadata when those FASTA headers were linked to GenBank.\u00a0 Proteins that were identified in biological replicate Av2 that were not identified in biological replicate Av1. (GSO: Gamma Sulfur Oxidizer) \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \Although fewer proteins were identified in Av2, nearly all (94%) of the proteins identified in Av2 were also identified in Av1.\u00a0 Differences in the total number of proteins identified in replicate samples may result from differences in the amount of biomass obtained during sample processing.\ DMO notes: Put multiple FASTA entries on separate lines Split out one number in FASTA header for linking Left it sorted by Total Independent Spectra column Added linkage column Removed commas in 'consensus annotation' column (signals database to put in new column) Reordered columns to put KEGG last -- much longer than any other column
attribute	NC_GLOBAL	title	String	Proteins identified from the black smoker chimney Inferno hydrothermal vent plume meta-proteome - replicate Av1 - on the Axial seamount off the coast of Washington in 2011.
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	Westernmost_Easting	double	-130.0138
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.3
variable	entry		String
attribute	entry	bcodmo_name	String	sample
attribute	entry	description	String	data entry number; each entry number is a unit and all columns of information with the same entry number should be considered together
attribute	entry	long_name	String	Entry
attribute	entry	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P02/current/ACYC/
attribute	entry	units	String	number
variable	latitude		double
attribute	latitude	_CoordinateAxisType	String	Lat
attribute	latitude	_FillValue	double	NaN
attribute	latitude	actual_range	double	45.934, 45.934
attribute	latitude	axis	String	Y
attribute	latitude	bcodmo_name	String	latitude
attribute	latitude	colorBarMaximum	double	90.0
attribute	latitude	colorBarMinimum	double	-90.0
attribute	latitude	description	String	latitude of sample collection
attribute	latitude	ioos_category	String	Location
attribute	latitude	long_name	String	Latitude
attribute	latitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LATX/
attribute	latitude	standard_name	String	latitude
attribute	latitude	units	String	degrees_north
variable	longitude		double
attribute	longitude	_CoordinateAxisType	String	Lon
attribute	longitude	_FillValue	double	NaN
attribute	longitude	actual_range	double	-130.0138, -130.0138
attribute	longitude	axis	String	X
attribute	longitude	bcodmo_name	String	longitude
attribute	longitude	colorBarMaximum	double	180.0
attribute	longitude	colorBarMinimum	double	-180.0
attribute	longitude	description	String	longitude of sample collection; West is negative
attribute	longitude	ioos_category	String	Location
attribute	longitude	long_name	String	Longitude
attribute	longitude	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/LONX/
attribute	longitude	standard_name	String	longitude
attribute	longitude	units	String	degrees_east
variable	depth		double
attribute	depth	_CoordinateAxisType	String	Height
attribute	depth	_CoordinateZisPositive	String	down
attribute	depth	_FillValue	double	NaN
attribute	depth	actual_range	double	1450.0, 1450.0
attribute	depth	axis	String	Z
attribute	depth	bcodmo_name	String	depth
attribute	depth	colorBarMaximum	double	8000.0
attribute	depth	colorBarMinimum	double	-8000.0
attribute	depth	colorBarPalette	String	TopographyDepth
attribute	depth	description	String	depth of sample collection
attribute	depth	ioos_category	String	Location
attribute	depth	long_name	String	Depth
attribute	depth	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P09/current/DEPH/
attribute	depth	positive	String	down
attribute	depth	standard_name	String	depth
attribute	depth	units	String	m
variable	NCBI_FASTA_link		String
attribute	NCBI_FASTA_link	bcodmo_name	String	external_link
attribute	NCBI_FASTA_link	description	String	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
attribute	NCBI_FASTA_link	long_name	String	NCBI FASTA Link
attribute	NCBI_FASTA_link	units	String	link
variable	protein_probability		float
attribute	protein_probability	_FillValue	float	NaN
attribute	protein_probability	actual_range	float	0.9052, 1.0
attribute	protein_probability	bcodmo_name	String	unknown
attribute	protein_probability	description	String	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
attribute	protein_probability	long_name	String	Protein Probability
attribute	protein_probability	units	String	decimal number
variable	num_unique_peptide		byte
attribute	num_unique_peptide	_FillValue	byte	127
attribute	num_unique_peptide	actual_range	byte	1, 20
attribute	num_unique_peptide	bcodmo_name	String	unknown
attribute	num_unique_peptide	description	String	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
attribute	num_unique_peptide	long_name	String	Num Unique Peptide
attribute	num_unique_peptide	units	String	number
variable	indep_spectra_tot		short
attribute	indep_spectra_tot	_FillValue	short	32767
attribute	indep_spectra_tot	actual_range	short	1, 218
attribute	indep_spectra_tot	bcodmo_name	String	unknown
attribute	indep_spectra_tot	description	String	number of identifying peaks from the tandem mass spectrometer
attribute	indep_spectra_tot	long_name	String	Indep Spectra Tot
attribute	indep_spectra_tot	units	String	number
variable	peptide_seq		String
attribute	peptide_seq	bcodmo_name	String	unknown
attribute	peptide_seq	description	String	amino acids identified in the peptide; A=Alanine; G=Glycine; etc
attribute	peptide_seq	long_name	String	Peptide Seq
attribute	peptide_seq	units	String	text
variable	consensus_annotation		String
attribute	consensus_annotation	bcodmo_name	String	unknown
attribute	consensus_annotation	description	String	describing protein X in terms of topic Y; these dominant active bacterial groups are determined by consensus annotation of identified proteins
attribute	consensus_annotation	long_name	String	Consensus Annotation
attribute	consensus_annotation	units	String	text
variable	KEGG_category		String
attribute	KEGG_category	bcodmo_name	String	unknown
attribute	KEGG_category	description	String	Kyoto Encyclopedia of Genes and Genomes; used to identify dominant functional classifications like metabolism or genetic information processing
attribute	KEGG_category	long_name	String	KEGG Category
attribute	KEGG_category	units	String	text

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.