Dataset: Deep-DOM Metaproteome

Name: Deep-DOM Metaproteome
Published: 2022-06-13
Keywords: biota, oceans

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Spatial Extent: N:-38 E:-45 S:-38 W:-45

Temporal Extent: 2013-03-27 - 2013-03-29

Project:

Deep Dissolved Organic Matter Multi-omics Analyses (DeepDom Multi-omics)

Dissolved Organic Matter Composition in the Deep Atlantic Ocean (Deep Atlantic DOM)

Program:

Ocean Carbon and Biogeochemistry (OCB)

Center for Chemical Currencies of a Microbial Planet (C-CoMP)

Principal Investigator:

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

Co-Principal Investigator:

Matthew R. McIlvin (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Danie Kinkade (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-06-13

Restricted:

Validated:

Current State:

Preliminary and in progress

Metaproteomic dataset from DeepDOM Station 2

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Description

The dataset includes total spectral counts for Proteins and Peptides. Four files and a link to raw data at the domain repository are included:

1) Sample metadata file with station locations, depth, time of collection and sample IDs. DeepDOM_sample_metadata_for_OPP.csv

2)Raw mass spectral data files are available on PRIDE and ProteomXchange.

ProteomeXchange title: Microbial Metaproteome from the Western Atlantic Ocean DeepDOM KN210-04 Expedition

ProteomeXchange accession: PXD034035

Project Webpage: http://www.ebi.ac.uk/pride/archive/projects/PXD034035

FTP Download: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/05/PXD034035

Acquisition Description

Samples were collected by McLane Pump and filtered onto GFF and GF75 glass filters and frozen at -80C until analysis.

Filters were extracted using SDS detergent and tube gel purification followed by trypsin digestion alkylation and reduction. Analysis was conducted by 2D active modulation Orbitrap mass spectrometry as described in McIlvin and Saito 2021.

Data was collected with a Thermo Fusion Orbitrap mass spectrometer interfaced with a Dionex nano-HPLC configured with 2D active modulation chromatography using the methods of McIlvin and Saito 2021.

Processing Description

The raw mass spectra files were searched against SEQUEST high thread database within Proteome Discoverer software (v2.4). Processed files were then loaded into Proteome Software (Scaffold v5) and filtered to False Discovery rates less than 1% using Percolator. Protein and Peptide reports as well as discovered proteins fasta files will be generated. The files will be modified slightly to map to the Ocean Protein Portal data model for submission to BCO-DMO.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2019589

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
KN210-04	DeepDOM	2013-03-25	R/V Knorr	Elizabeth Kujawinski (Chief Scientist)	data info

Instruments

High-Performance Liquid Chromatograph

Supplied Name: nano-HPLC

Supplied Description:

Nano-HPLC configured with 2D active modulation chromatography.

Instrument Type

Generic Name: High-Performance Liquid Chromatograph

Acronym: HPLC

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/

Generic Description:

A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase.

Thermal Ionization Mass Spectrometer

Supplied Name: Thermo Fusion Orbitrap mass spectrometer

Supplied Description:

Thermo Fusion Orbitrap mass spectrometer interfaced with a Dionex nano-HPLC configured with 2D active modulation chromatography.

Instrument Type

Generic Name: Thermal Ionization Mass Spectrometer

Acronym: TI Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

A Thermal Ionization Mass Spectrometer (TIMS) is an instrument that measures isotopic ratios after electrical excitation of a sample causes ionization of the isotopes.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_id	sample identifier	unitless	sample
ms_ms_sample_name	additional sample identifier that includes date of analysis run, method (2D), total amount of protein injected, cruise name, station number, pump cast number, filter type, and sample depth	unitless	sample
station_id	station identifier	unitless	station
depth_m	Sample depth	meters	depth
latitude_dd	latitude of sampling location with positive values indicating North	decimal degrees	lat
longitude_dd	longitude of sampling location with positive values indicating West	decimal degrees	lon
date_y_m_d	date of sample collection	unitless	date
date_ISO	date of sample collection in ISO format Format: %Y-%m-%d	unitless	date
time_h_m_s	time of sample collection	unitless	time
minimum_filter_size_microns	minimum filter sized used reported in microns	microns	filter_size
maximum_filter_size_microns	maximum filter sized used reported in microns	microns	filter_size
cruise_id	cruise identifier	unitless	cruise_id
event_number	event identification number which includes sampling date in year-month-day format. This ID corresponds to the DeepDOM event log 'event' parameter.	unitless	event

Database

Geospatial Access

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Dataset: Deep-DOM Metaproteome