Dataset: Trichodesmium field metaproteomes - single colony metaproteomes

Name: Single colony metaproteomes of Trichodesmium from samples collected in North Atlantic surface waters during the R/V Atlantis cruise AT39-05 in March of 2018
Published: 2020-01-10
Keywords: Trichodesmium, metaproteomics, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.786694.1

Spatial Extent: N:17.02 E:65.22 S:17.02 W:65.22

Temporal Extent: 2018-03-11

Project:

Collaborative Research: Iron and phosphorus balanced limitation of nitrogen fixation in the oligotrophic ocean (TriCoLim)

Collaborative Research: Evolutionary, biochemical and biogeochemical responses of marine cyanobacteria to warming and iron limitation interactions (Cyanobacteria Warming Responses)

Marine Microbial Investigator Award: Investigator Mak Saito (MM Saito)

New technology for high resolution analysis of proteins and other organic materials produced by marine microorganisms (MM Proteins and Organics Tech)

Program:

Marine Microbiology Initiative (MMI)

Principal Investigator:

Mak A. Saito (Woods Hole Oceanographic Institution, WHOI)

Student:

Noelle Held (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2020-01-10

Restricted:

Release Date:

2020-10-07

Validated:

Yes

Current State:

Final no updates expected

Single colony metaproteomes of Trichodesmium from samples collected in North Atlantic surface waters during the R/V Atlantis cruise AT39-05 in March of 2018

Abstract:

Single colony metaproteomes of Trichodesmium from samples collected in North Atlantic surface waters during the R/V Atlantis cruise AT39-05 in March of 2018.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2020-01-10	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.786694.1	2020-10-08

Description

Single colony metaproteomes of Trichodesmium from samples collected in North Atlantic surface waters during the R/V Atlantis cruise AT39-05 in March of 2018. These data were published in Held et al. (2020).

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE [1] partner repository with the dataset identifier PXD016330 and 10.6019/PXD016330 but are not yet public.
* Project Name: Trichodesmium single colony metaproteomes field station Tricolim_19
* Project accession: PXD016330
* Project DOI: 10.6019/PXD016330

Methods & Sampling

A 200mm plankton net was deployed to ~20m depth, then recovered to just below surface, repeating five times. Trichodesmium colonies were hand-picked into 0.2mm filtered surface seawater, rinsed twice in 0.2mm filtered surface seawater, and decanted onto a 0.2-4mm Supor filter (indicated in sample provenance table, see dataset https://www.bco-dmo.org/dataset/787093).

Proteins were extracted and trypsin digested in-gel following Saito et al., 2014 (Science) with the following modifications: organic precipitation was skipped, benzonase nuclease treatment was performed instead to dissolve DNA/RNA material. Peptides were analyzed by LC-MS/MS in data discovery mode on a Thermo Orbitrap Fusion. Full details will be reported in Held et al. (in prep)

Location: North Atlantic surface waters 65.22 W 17.02 N

Data Processing Description

Thermo proteome discoverer 2.2 was used to search the data with the SEQUEST algorithm. Statistical validation was performed in Scaffold (Proteome Software) at the 1% protein and peptide false discovery rate (FDR) levels.

The sequence database was a trimmed set of Trichodesmium sequences which had been previously identified at this field station.

BCO-DMO Data Manager Processing Notes:

* originally submitted file TrichoSingleColony_dataset_TableS1.xlsx" converted to csv

* modified parameter names to conform with BCO-DMO naming conventions. "Product Name" changed to "Product_Name"

Data Files

File
Single colony metaproteomes of Trichodesmium filename: singlecolony.csv (Comma Separated Values (.csv), 3.46 MB) MD5:05329123d1ee52317c4618b694eaf849 Single colony metaproteomes of Trichodesmium. See Parameters section for column names, descriptions, and units in this file.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1657766
NSF Division of Ocean Sciences	OCE-1850719
Gordon and Betty Moore Foundation: Marine Microbiology Initiative	GBMF3934
Gordon and Betty Moore Foundation: Marine Microbiology Initiative	GBMF3782

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AT39-05	TriCoLim	2018-02-11	R/V Atlantis	David A. Hutchins (Chief Scientist)	data info

Instruments

Mass Spectrometer

Supplied Name: Thermo Orbitrap Fusion mass spectrometer

Supplied Description:

Instrument Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic 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.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Protein_Accession	Protein accession, unique protein identifier.	unitless	sample_descrip
Tricolim_14b	Relative protein abundance data for sample Tricolim_14b. Normalized MS1 Intensity.	unitless	abundance
Tricolim_15a	Relative protein abundance data for sample Tricolim_15a. Normalized MS1 Intensity.	unitless	abundance
Tricolim_16a	Relative protein abundance data for sample Tricolim_16a. Normalized MS1 Intensity.	unitless	abundance
Tricolim_16b	Relative protein abundance data for sample Tricolim_16b. Normalized MS1 Intensity.	unitless	abundance
Tricolim_15b	Relative protein abundance data for sample Tricolim_15b. Normalized MS1 Intensity.	unitless	abundance
Tricolim_15c	Relative protein abundance data for sample Tricolim_15c. Normalized MS1 Intensity.	unitless	abundance
Tricolim_15d	Relative protein abundance data for sample Tricolim_15d. Normalized MS1 Intensity.	unitless	abundance
Tricolim_18a	Relative protein abundance data for sample Tricolim_18a. Normalized MS1 Intensity.	unitless	abundance
Tricolim_18b	Relative protein abundance data for sample Tricolim_18b. Normalized MS1 Intensity.	unitless	abundance
Tricolim_18c	Relative protein abundance data for sample Tricolim_18c. Normalized MS1 Intensity.	unitless	abundance
JC150_02a	Relative protein abundance data for sample JC150_02a. Normalized MS1 Intensity.	unitless	abundance
JC150_02b	Relative protein abundance data for sample JC150_02b. Normalized MS1 Intensity.	unitless	abundance
Tricolim_03a	Relative protein abundance data for sample Tricolim_03a. Normalized MS1 Intensity.	unitless	abundance
Tricolim_03b	Relative protein abundance data for sample Tricolim_03b. Normalized MS1 Intensity.	unitless	abundance
Tricolim_13a	Relative protein abundance data for sample Tricolim_13a. Normalized MS1 Intensity.	unitless	abundance
Tricolim_19a	Relative protein abundance data for sample Tricolim_19a. Normalized MS1 Intensity.	unitless	abundance
Tricolim_19b	Relative protein abundance data for sample Tricolim_19b. Normalized MS1 Intensity.	unitless	abundance
Tricolim_19c	Relative protein abundance data for sample Tricolim_19c. Normalized MS1 Intensity.	unitless	abundance
JC150_03a	Relative protein abundance data for sample JC150_03a. Normalized MS1 Intensity.	unitless	abundance
JC150_03b	Relative protein abundance data for sample JC150_03b. Normalized MS1 Intensity.	unitless	abundance
JC150_03c	Relative protein abundance data for sample JC150_03c. Normalized MS1 Intensity.	unitless	abundance
JC150_04a	Relative protein abundance data for sample JC150_04a. Normalized MS1 Intensity.	unitless	abundance
JC150_05a	Relative protein abundance data for sample JC150_05a. Normalized MS1 Intensity.	unitless	abundance
JC150_05b	Relative protein abundance data for sample JC150_05b. Normalized MS1 Intensity.	unitless	abundance
JC150_05c	Relative protein abundance data for sample JC150_05c. Normalized MS1 Intensity.	unitless	abundance
JC150_06a	Relative protein abundance data for sample JC150_06a. Normalized MS1 Intensity.	unitless	abundance
JC150_07a	Relative protein abundance data for sample JC150_07a. Normalized MS1 Intensity.	unitless	abundance
JC150_07b	Relative protein abundance data for sample JC150_07b. Normalized MS1 Intensity.	unitless	abundance
JC150_07c	Relative protein abundance data for sample JC150_07c. Normalized MS1 Intensity.	unitless	abundance
BATS_01b	Relative protein abundance data for sample BATS_01b. Normalized MS1 Intensity.	unitless	abundance
BATS_01c	Relative protein abundance data for sample BATS_01c. Normalized MS1 Intensity.	unitless	abundance
JC150_01a	Relative protein abundance data for sample JC150_01a. Normalized MS1 Intensity.	unitless	abundance
JC150_01b	Relative protein abundance data for sample JC150_01b. Normalized MS1 Intensity.	unitless	abundance
JC150_01c	Relative protein abundance data for sample JC150_01c. Normalized MS1 Intensity.	unitless	abundance
HOT_01a	Relative protein abundance data for sample HOT_01a. Normalized MS1 Intensity.	unitless	abundance
HOT_01b	Relative protein abundance data for sample HOT_01b. Normalized MS1 Intensity.	unitless	abundance
BATS_01d	Relative protein abundance data for sample BATS_01d. Normalized MS1 Intensity.	unitless	abundance
Taxonomy	Taxanomic description. Taxonomy with semicolon as the delimiter (e.g. "Bacteria;Cyanobacteria;unclassified;Nostocales;Nostocaceae;Raphidiopsis;brookii;Raphidiopsis brookii D9")	unitless	taxon
Protein_Product_Name	Protein description	unitless	sample_descrip
KO_Annotation	Kegg Ontology annotation	unitless	sample_descrip
Pfam_Annotation	Pfam protein family annotation	unitless	sample_descrip

Status message

Database

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Dataset: Trichodesmium field metaproteomes - single colony metaproteomes