Dataset: ProteOMZ Peptide Level Spectral Counts
Deployment: FK160115

Total spectral counts of peptides from the R/V Falkor cruise 160115 in the Central Pacific for the ProteOMZ expedition in 2016.

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/737596

Principal Investigator:

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

BCO-DMO Data Manager:

Hannah Ake (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

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

Project:

The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean (ProteOMZ (Proteomics in an Oxygen Minimum Zone))

Current State:

Final no updates expected

Version:

Deployment Synonyms:

ProteOMZ

Version Date:

2018-05-25

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Description

These data are part of the Ocean Protein Portal "ProteOMZ" dataset v3 (https://proteinportal.whoi.edu/; Saito et al., 2019).

Methods & Sampling

Dataset acquisition description

Data Processing Description

Dataset Processing Description

The raw mass spectra files were searched against SEQUEST within Proteome Discoverer v2.2 software. Processed files were then loaded into Proteome Software and protein and peptide reports as well as and fasta files were exported. The files were modified slightly to map to the Protein Portal data model for submission to BCO-DMO. The peptide report was too large to work with within Excel and was modified in Pandas/Python to produce a CSV file.

More information about this dataset deployment

Funding

Award Number	Funding Source
GBMF3782	Gordon and Betty Moore Foundation: Marine Microbiology Initiative
R/V Falkor 160115 SOI ProteOMZ Expedition	Schmidt Ocean Institute

Instruments

Alpkem RFA300

Supplied Name: Alpkem Autosampler

Supplied Description:

Used in nutrient analysis

Instrument Type

Generic Name: Alpkem RFA300

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0414/

Generic Description:

A rapid flow analyser (RFA) that may be used to measure nutrient concentrations in seawater. It is an air-segmented, continuous flow instrument comprising a sampler, a peristaltic pump which simultaneously pumps samples, reagents and air bubbles through the system, analytical cartridge, heating bath, colorimeter, data station, and printer. The RFA-300 was a precursor to the smaller Alpkem RFA/2 (also RFA II or RFA-2).

CTD Sea-Bird

Supplied Name: SeaBird SBE19 CTD

Supplied Description:

Used for water sampling

Instrument Type

Generic Name: CTD Sea-Bird

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.

Technicon AutoAnalyzer II

Supplied Description:

Used to measure phosphate and ammonium

Instrument Type

Generic Name: Technicon AutoAnalyzer II

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0291/

Generic Description:

A rapid flow analyzer that may be used to measure nutrient concentrations in seawater. It is a continuous segmented flow instrument consisting of a sampler, peristaltic pump, analytical cartridge, heating bath, and colorimeter. See more information about this instrument from the manufacturer.

Trace Metal Bottle

Supplied Name: Trace Metal Rosette

Supplied Description:

Used for nutrient sampling

Instrument Type

Generic Name: Trace Metal Bottle

Acronym: TM Bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/30/

Generic Description:

Trace metal (TM) clean rosette bottle used for collecting trace metal clean seawater samples.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_id	Unique sample name for the specific filter collected (station/depth/version if applicable)	unitless	sample
MS_MS_sample_name	Unique name for the mass spec sample and run	unitless	no_bcodmo_term
protein_id	The specific name of the full protein length sequence assembled in the metagenome that was used for peptide identification	unitless	protein_ID
protein_molecular_weight_kDa	Molecular weight of the full length protein sequences	kDa	weight
best_protein_id_probability	Probability of the protein assignment for the peptide	unitless	no_bcodmo_term
peptide_sequence	Amino acid sequence of the identified peptide. Unique Peptide sequence; this is the most unique identifier	unitless	sequence
peptide_start_index	Starting amino acid in the full length protein sequence for the identified peptide	unitless	no_bcodmo_term
peptide_stop_index	Stopping amino acid in the full length protein sequence for the identified peptide	unitless	no_bcodmo_term
plus2H_spectra_count	Number of identified spectral counts for a peptide of the +2 charge state	count	spectral_counts
plus3H_spectra_count	Number of identified spectral counts for a peptide of the +3 charge state	count	spectral_counts
plus4H_spectra_count	Number of identified spectral counts for a peptide of the +4 charge state	count	spectral_counts
best_sequest_DCn_score	Delta CN score for peptide spectrum match (PSM). Metric of peptide quality	unitless	no_bcodmo_term
best_sequest_Xcorr_score	XCorr score for peptide spectrum match (PSM). Metric of peptide quality	unitless	no_bcodmo_term
median_retention_time	Median amount of time for a peptide in LC before it was identified via MS/MS	minutes	no_bcodmo_term
total_precursor_intensity	Total precursor intensity.	unitless	no_bcodmo_term
TIC	Total Ion Chromatogram (TIC).	unitless	no_bcodmo_term
spectral_count_sum	The sum of spectral counts for all peptide proton ionzation states. Sum of +2 +3 +4 data = total unnormalized spectral counts; Quantitative Value	count	spectral_counts
other_protein_ids	All other possible proteins in the metagenome that contain the same peptide as the protein assigned. Other protein IDs from the FASTA file (see Related Datasets)	unitless	no_bcodmo_term
station_id	Station number	unitless	station
depth_m	Depth of sampling	meters	depth
latitude_dd	Latitude of station	decimal degrees	lat
longitude_dd	Longitude of station	decimal degrees	lon
date_ymd	Date of sampling; (local time zone HST)	unitless	date
time_hms	Time of sampling; (local time zone HST)	unitless	time
minimum_filter_size_microns	Minimum filter size	microns	filter_size
maximum_filter_size_microns	Maximum filter size	microns	filter_size
cruise_id	The unique cruise identifier	unitless	cruise_id
ISO_DateTime_UTC	DateTime with timezone (UTC)of sampling in ISO 8601 format	unitless	ISO_DateTime_UTC

Database

Contribute Data

Dataset: ProteOMZ Peptide Level Spectral Counts
Deployment: FK160115

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: ProteOMZ Peptide Level Spectral CountsDeployment: FK160115

Dataset acquisition description

Dataset Processing Description

Dataset: ProteOMZ Peptide Level Spectral Counts
Deployment: FK160115