Dataset: Ross Sea metaproteome peptide spectral counts

Name: Ross Sea metaproteome peptide spectral counts searched against Phaeocystis strain transcriptome from net tows during RVIB Nathaniel B. Palmer cruise NBP0601 in December of 2015
Published: 2024-05-24
Keywords: metaproteomics, Ross Sea, Phaeocystis antarctica, Antartica, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.768259.2

Spatial Extent: N:-76.82 E:170.76 S:-76.82 W:170.76

Ross Sea

Temporal Extent: 2005-12-30

Project:

Controls of Ross Sea Algal Community Structure (CORSACS)

Program:

Ocean Carbon and Biogeochemistry (OCB)

Principal Investigator:

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

Contact:

Sara Bender (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

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

Version:

Version Date:

2024-05-24

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Ross Sea metaproteome peptide spectral counts searched against Phaeocystis strain transcriptome from net tows during RVIB Nathaniel B. Palmer cruise NBP0601 in December of 2015

Abstract:

A net tow metaproteome of a Phaeocystis antarctica bloom in the Ross Sea, mapped here to Phaeocystis metatranscriptomes analyzed by 2D LCMS, in units of peptide spectral counts.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2024-05-24	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.768259.2	2024-05-24
2024-04-29	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.768259.1	2024-05-23

Description

These data are part of the Ocean Protein Portal "Ross Sea Net Tow (Bender)" dataset version 1 (https://proteinportal.whoi.edu/; Saito et al., 2020).

Methods & Sampling

Sampling was conducted with a 20 micron plankton net on 12/30/2005 at about 1am (local time), near station 137, was extracted for total protein using an SDS detergent method followed by tube gel purification, reduction, alkylation, and tryptic digestion and analyzed on a Thermo Orbitrap Fusion using 2-dimensional separation scheme to maximize metaproteome depth. Detailed methods available in Bender et al. 2018.

Organism identifier (LifeSciences Identifier, LSID):
Phaeocystis antarctica, urn:lsid:marinespecies.org:taxname:341585

Data Processing Description

Mass spectra from 2D LC-MS was peptide-to-spectrum matched using the SEQUEST algorithm within Proteome Discoverer software, followed by spectral counting with Proteome Software's Scaffold software using the FASTA sequence file generated from Phaeocystis culture transcriptome study. Data processing documented in Bender et al. 2018.

BCO-DMO Processing

Data version 1: 2024-04-29
* Data file "peptides_V2.csv" was imported into the BCO-DMO data system for this dataset. This was the file imported into Ocean Protein Portal version 1 of the Bender Ross Sea dataset.
** Missing data values are displayed differently based on the file format you download. They are blank in csv files, "NaN" in MatLab files, etc.

* Column name "absolute_unites_fmol_L" corrected to "absolute_units_fmol_L"

* Date converted to ISO 8601 format

* several columns ( median_retention_time,total_precursor_intensity,TIC,absolute_units_fmol_L) contain no values but were not removed since these are named columns in the Ocean Protein Portal template, though optional columns.

Data version 2: 2024-05-24 fixes issue in version 1 peptide data where the Z was removed from timestamp values.
This version 2 matches the data at the Ocean Protein Portal "Ross Sea Net Tow (Bender)" dataset version 1 (https://proteinportal.whoi.edu/; Saito et al., 2019).

Data Files

File
768259_v2_bender-ross-sea-peptides.csv (Comma Separated Values (.csv), 1.09 MB) MD5:48b12c83f351f9b14f5a2142dc533fb5 Primary data file for dataset ID 768259, version 2. Corresponds to Ocean Protein Portal Bender-Ross Sea data (version 1) .

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Office of Polar Programs (formerly NSF PLR)	OPP-0338097

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
NBP0601	CORSACS I	2005-12-17	RVIB Nathaniel B. Palmer	Giacomo DiTullio (Chief Scientist)	data info

Instruments

Mass Spectrometer

Supplied Name: Thermo Scientific Q-Exactive Orbitrap mass spectrometer with a Michrom Advance CaptiveSpray source

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
sample_id	Sample identifier. Identifies the sample associated with this annotation	unitless	sample
cruise_id	Cruise identifier	unitless	cruise_id
station_id	Station identifier where sample was taken	unitless	station
latitude_dd	Station latitude	decimal degrees (DD)	lat
longitude_dd	Station longitude	decimal degrees (DD)	lon
depth_m	Sample depth	meters (m)	depth
date_local	Date (local) of sample collection in format YYYY-mm-dd. Time zone is Antarctica/McMurdo (NZST/NZDT, UTC+12/UTC+13) Format: %Y-%m-%d	unitless	date_local
time_local	Time (local) of sample collection in format HH:MM:SS. Time zone is Antarctica/McMurdo (NZST/NZDT, UTC+12/UTC+13) Format: %H:%M:%S	unitless	time_local
minimum_filter_size_microns	Minimum size of the collection filter	microns (um)	filter_size
maximum_filter_size_microns	Maximum size of the collection filter	microns (um)	filter_size
peptide_sequence	Peptide genomic sequence	unitless	sequence
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
protein_molecular_weight_kDa	Molecular weight in kilo-Daltons of the related protein	kilo-Daltons (kDa)	weight
protein_id	Identification parameter for protein sequence, typically shared with metagenomic database	unitless	no_bcodmo_term
spectral_count_sum	Sum of spectral counts (+2, +3, +4 ions)	unitless	spectral_counts
other_protein_ids	Additional IDs from similar proteins that share peptide sequences	unitless	sample_descrip
best_protein_id_probability	A percentage identifying the quality of the protein identification	unitless	sample_descrip
best_sequest_DCn_score	Sequest DCn score	unitless	sample_descrip
best_sequest_Xcorr_score	Sequest Xcorr	unitless	sample_descrip
plus2H_spectra_count	Spectral counts of +2 ions	unitless	sample_descrip
plus3H_spectra_count	Spectral counts of +3 ions	unitless	sample_descrip
plus4H_spectra_count	Spectral counts of +4 ions	unitless	sample_descrip
median_retention_time	Median retention time of peptide	unitless	no_bcodmo_term
total_precursor_intensity	Total precursor intensity (ms1) of peptide	unitless	no_bcodmo_term
TIC	Total ion current (TIC) value of peptide	unitless	no_bcodmo_term
absolute_units_fmol_L	Concentration of peptide in calibrated absolute units (fmol / L)	femtomoles per liter (fmol/L)	no_bcodmo_term
ISO_DateTime_UTC	Timestamp (UTC) in standard ISO 8601:2004(E) format YYYY-mm-ddTHH:MM:SSZ Format: %Y-%m-%dT%H:%M:%SZ	unitless	ISO_DateTime_UTC