Dataset: Trichodesmium field metaproteomes - protein spectral counts in alternative format

Name: Metaproteomes of Trichodesmium from samples collected in North Atlantic surface waters, station BATS, and station ALOHA between 2000 and 2018
Published: 2020-01-10
Keywords: Trichodesmium, metaproteomics, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.787078.1

Spatial Extent: N:23.22 E:-21.59 S:0.17 W:-158

Temporal Extent: 2000-07-27 - 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:

Validated:

Yes

Current State:

Final no updates expected

Metaproteomes of Trichodesmium from samples collected in North Atlantic surface waters, station BATS, and station ALOHA between 2000 and 2018

Abstract:

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2020-01-10	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.787078.1	2020-04-29

Description

Metaproteomes of Trichodesmium from samples collected in North Atlantic surface waters, at station BATS (Bermuda Atlantic Time-series Study), and station ALOHA (A Long-Term Oligotrophic Habitat Assessment) between 2000 and 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 PXD016225 and 10.6019/PXD016225 but are not yet public.

Project Name: Trichodesmium field metaproteomes

Project accession: PXD016225

Project DOI: 10.6019/PXD016225

An alternative form of these data are available as dataset:
"Trichodesmium field metaproteomes - protein spectral counts" https://www.bco-dmo.org/dataset/787147

Related Dataset:
Trichodesmium sample provenance: https://www.bco-dmo.org/dataset/787093 - Sample provenance file, which includes sample locations, filter sizes

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 and peptides were analyzed by LC-MS/MS in data discovery mode on a Thermo Orbitrap Fusion. Full details can be found in Held et al., 2020 (https://doi.org/10.5194/bg-2019-493).

Values are reported as summed top 3 total precursor intensity, normalized to equalize total sample intensities.

Values reported have a 0.1% peptide FDR and 1.9% protein FDR; decoy hits have been filtered out.
Taxonomic and functional annotations are reported as provided by the original sequencing project (JGI genome ID 2156126005)

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.

A publicly available Trichodesium metagenome was used in this search (IMG ID 2821474806) as well as the contents of the CyanoGEBA project (Shih et al, 2013).

BCO-DMO Processing

* Originally submitted file "richodesmiumfieldproteomes.xlsx" converted to csv
* Comment lines in original file extracted from data file and added to Methods & Sampling section.
* modified parameter names to conform with BCO-DMO naming conventions (spaces, +, and - changed to underscores).
* removed last two lines of table that contained a second header line and color names:
"location,Tricolim_14,Tricolim_15,Tricolim_16,Tricolim_16,Tricolim_15,Tricolim_15,Tricolim_15,Tricolim_18,Tricolim_18,Tricolim_18,JC150_02,JC150_02,Tricolim_03,Tricolim_03,Tricolim_13,Tricolim_19,Tricolim_19,Tricolim_19,JC150_03,JC150_03,JC150_03,JC150_04,JC150_05,JC150_05,JC150_05,JC150_06,JC150_07,JC150_07,JC150_07,BATS_01,BATS_01,JC150_01,JC150_01,JC150_01,HOT_01,HOT_01,BATS_01,,,,
color,cyan,blue,paleturquoise,paleturquoise,blue,blue,blue,darkturquoise,darkturquoise,darkturquoise,lightpink,lightpink,dodgerblue,dodgerblue,midnightblue,steelblue,steelblue,steelblue,navajowhite,navajowhite,navajowhite,red,darksalmon,darksalmon,darksalmon,coral,peru,peru,peru,dimgrey,dimgrey,crimson,crimson,crimson,lightgrey,lightgrey,dimgrey,,,,

Data Files

File

Trichodesmium field metaproteomes, protein spectral counts
filename: field.csv

(Comma Separated Values (.csv), 1.40 MB)
MD5:0adc64eae883c2228ed7e10052c47206

Metaproteomes of Trichodesmium from samples collected in North Atlantic surface waters, station BATS, and station ALOHA between 2000 and 2018. See "Parameter Description" section for column names, descriptions, and units in this comma delimited 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
JC150	Ziploc	2017-06-26	RRS James Cook	Claire Mahaffey (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 - protein spectral counts in alternative format