Dataset: ProteOMZ Peptide Level Spectral Counts

Name: Total spectral counts of peptides from the R/V Falkor cruise 160115 in the Central Pacific for the ProteOMZ expedition in 2016
Published: 2022-06-03
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.737596.1

Spatial Extent: N:17.4465 E:-139.1089 S:-0.4708 W:-157.3022

Central Pacific

Temporal Extent: 2016-01-19 - 2016-01-28

Project:

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

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)

Version:

Version Date:

2022-06-03

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

Relative protein abundance data of the upper 1000m water column from the ProteOMZ R/V Falkor expedition. There are 109952 unique peptides, each with spectral counts associated with each of the 102 samples, for 10 million data points.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2022-06-03	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.737596.1	2024-11-06

Description

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

Data 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.

BCO-DMO Processing

Preprocessing:
-Date, time, filter min, filter max, lat, lon, and cruise columns added based on information from the Falkor 160115 Event log and CTD log.
-Column names reformatted to comply with BCO-DMO standards.

Dataset Version 1: This file version (2022-06-03) replaces a previous revision of dataset version 1 from 2019-02-24.
* Data from source file "ProteOMZ_peptides_for_OPP.csv" was imported into the BCO-DMO data system for this dataset. This file "ProteOMZ_peptides_for_OPP.csv" is from Ocean Protein Portal "ProteOMZ" dataset v3 (file version 2022-06-03)
** In the BCO-DMO data system missing data identifiers are displayed according to the format of data you access. For example, in csv files it will be blank (null) values. In Matlab .mat files it will be NaN values. When viewing data online at BCO-DMO, the missing value will be shown as blank (null) values.

* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number] e.g. date_y-m-d changed to date_ymd

* ISO DateTime with timezone (UTC) column added in ISO 8601 format from local date and times in HST.

* Data table attached to dataset as Data File:"737596_v1_proteomz-peptides.csv"

Data Files

File
737596_v1_proteomz-peptides.csv (Comma Separated Values (.csv), 775.75 MB) MD5:2a69f9ed3937e0384f9d9b453108dd63 Primary data file for dataset ID 737596, version 1

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
FK160115	ProteOMZ	2016-01-16	R/V Falkor	Mak A. Saito (Chief Scientist)	data info

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

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

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) Format: %Y-%m-%d	unitless	date
time_hms	Time of sampling; (local time zone HST) Format: %H:%M:%S	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 Format: %Y-%m-%dT%H:%MZ	unitless	ISO_DateTime_UTC

Status message

Database

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Dataset: ProteOMZ Peptide Level Spectral Counts