Dataset: Trichodesmium field metaproteomes - peptide spectral counts

Name: Net tow metaproteoome of Trichodesmium species mapped to a Trichodesmium metagenome plus cyanoGEBA species genomes in units of normalized peptide spectral counts from samples collected in the Atlantic and Pacific Ocean between 2000 and 2018
Published: 2020-04-30
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.787168.1

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

Temporal Extent: 2000-07-27 - 2018-03-18

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:

2020-04-30

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Net tow metaproteoome of Trichodesmium species mapped to a Trichodesmium metagenome plus cyanoGEBA species genomes in units of normalized peptide spectral counts from samples collected in the Atlantic and Pacific Ocean between 2000 and 2018

Abstract:

Net tow metaproteoome of Trichodesmium species mapped to a Trichodesmium metagenome plus cyanoGEBA species genomes, analyzed by 2D LC-MS/MS in units of normalized peptide spectral counts. Samples were 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.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2020-04-30	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.787168.1	2020-05-01

Description

Related datasets:
Trichodesmium field metaproteomes - sequence fasta: https://www.bco-dmo.org/dataset/787181
Trichodesmium field metaproteomes - protein spectral counts: https://www.bco-dmo.org/dataset/787147
Trichodesmium sample provenance: https://www.bco-dmo.org/dataset/787093 - Sample provenance file, which includes sample locations, filter sizes

Methods & Sampling

A 200um plankton net net was deployed to ~20m depth, then recovered to just below surface, repeating five times. Trichodesmium colonies were hand picked into 0.2um filtered surface seawater, rinsed twice in 0.2um filtered surface seawater, and decanted onto a 0.2-4um 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). Peptides were analyzed by LC-MS/MS in data discovery mode on a Thermo Orbitrap Fusion.

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. This file represents the peptide identifications made as normalized spectral counts. Peptides may be assigned to more than one protein.

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 Data Manager Processing Notes:
* prefix "20" added to year values to change format from yy-mm-dd to ISO 8601 format yyyy-mm-dd
* Time values "00009" changed to 09:00 after checking the sample log.
* Delimiter for multiple IDs in the other_protein_ids column changed from comma to semicolon.
* Rows with missing date,time, cruise, station, and location information missing were removed (filtered to remove all rows with time value "00nan" )
* Commas removed from number values in columns median_retention_time, total_precursor_intensity,TIC so they could be correctly typed as numbers not strings.

Data Files

File

Trichodesmium field metaproteomes - peptide spectral counts
filename: peptides.csv

(Comma Separated Values (.csv), 43.72 MB)
MD5:bd1a6d484f598281daff452c63f69d6b

Net tow metaproteoome of Trichodesmium species mapped to a Trichodesmium metagenome plus cyanoGEBA species genomes in units of normalized peptide spectral counts from samples collected in the Atlantic and Pacific Ocean between 2000 and 2018.

Parameters in this comma delimited file are included in the Parameter section of the Dataset Landing Page "Trichodesmium field metaproteomes - peptide spectral counts" https://www.bco-dmo.org/dataset/787168.

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_id	Unique protein peptide belongs to	unitless	sample_descrip
protein_molecular_weight_kDa	Molecular weight of the sample (no data, column included to comply with Ocean Protein Portal template)	kilo-Daltons (kDa)	weight
peptide_sequence	Peptide genomic sequence	unitless	sequence
best_peptide_id_probability	Probability (0-1) the peptide belongs to this protein.	unitless	sample_descrip
best_sequest_DCn_score	delta Cn score	unitless	sample_descrip
best_sequest_Xcorr_score	Xcorr score	unitless	sample_descrip
plus_2H_spectra_count	Peptide in the 2+ state spectral count	unitless	spectral_counts
plus_3H_spectra_count	Peptide in the 3+ state spectral count	unitless	spectral_counts
plus_4H_spectra_count	Peptide in the 4+ state spectral count	unitless	spectral_counts
spectral_count_sum	Sum of spectral counts (+2, +3, +4 ions)	unitless	spectral_counts
median_retention_time	Median retention time of peptide	seconds (s)	time_elapsed
total_precursor_intensity	Total precursor intensity at the MS1 stage of the peptide	unitless	no_bcodmo_term
TIC	Total ion current (TIC) value of peptide	unitless	no_bcodmo_term
peptide_start_index	Start location of peptide within protein sequence	unitless	sample_descrip
peptide_stop_index	Stop location of peptide within protein sequence	unitless	sample_descrip
other_protein_ids	Additional proteins the peptide may belong to. Multiple identifiers delimited with a semicolon.	unitless	sample_descrip
sample_id	Unique sample location ID	unitless	station
cruise_id	Cruise name	unitless	cruise_id
station_id	Station name	unitless	no_bcodmo_term
cruise_station	Station identifier where sample was taken	unitless	station
time_h-m-s	Time (Local ship time) of sampling in format HH:MM (various time zones, see sample provenance dataset http://lod.bco-dmo.org/id/dataset/787093)	unitless	time_local
date_y-m-d	Date (Local ship time) in format yyyy-mm-dd (various time zones, see sample provenance dataset http://lod.bco-dmo.org/id/dataset/787093)	unitless	date_local
maximum_filter_size_microns	Minimum size of the collection filter	microns (?m)	filter_size
minimum_filter_size_microns	Maximum size of the collection filter	microns (?m)	filter_size
latitude_dd	Latitude (South is negative)	decimal degrees (DD)	lat
longitude_dd	Longitude (West is negative)	decimal degrees (DD)	lon
depth_m	Sample depth	meters (m)	depth
sample_type	Sample type "Trichodesmium net tow"	unitless	sample_descrip

Status message

Database

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Dataset: Trichodesmium field metaproteomes - peptide spectral counts