Dataset: AE1913 Protein Identification FASTA

Name: Protein identification FASTA file (scaffold-derived metaproteomic proteins) from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019
Published: 2024-08-01
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.934727.1

Spatial Extent: N:38.527393 E:-64.165587 S:31.586387 W:-70.840703

Subtropical North Atlantic, beginning at the Bermuda Atlantic Time-series Station (BATS) of the Sargasso Sea (31.666888 N64.166293 W) and ending in coastal Northeast US shelf waters (39.31658 N 71.123208 W)

Temporal Extent: 2019-06-16 - 2019-06-27

Project:

Collaborative Research: Direct Characterization of Adaptive Nutrient Stress Responses in the Sargasso Sea using Protein Biomarkers and a Biogeochemical AUV (Nutrient Stress Responses and AUV Clio)

Principal Investigator:

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

Scientist:

Natalie Cohen (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

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

Version:

Version Date:

2024-08-01

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Protein identification FASTA file (scaffold-derived metaproteomic proteins) from samples taken during R/V Atlantic Explorer cruise AE1913 from the Sargasso Sea to Northeast US shelf waters in June of 2019

Abstract:

This is a FASTA file of protein identifications (scaffold-derived metaproteomic proteins). Samples were taken during R/V Atlantic Explorer cruise AE1913 in Subtropical North Atlantic, beginning at the Bermuda Atlantic Time-series Station (BATS) of the Sargasso Sea and ending in coastal Northeast US shelf waters in June of 2019.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2024-08-01	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.934727.1	2024-10-29

Description

Related data table and dataset descriptions:

Total spectral counts refer to the total number of spectra with peptide to spectrum matches (PSMs) that matches to each entry within the FASTA sequence database. This approach allows each peptide to map to multiple closely related sequences. In contrast, with exclusive spectral counts each peptide is only allowed to map to one sequence within the FASTA database, and when a peptide is found in multiple database sequences the one with the most peptides mapping (parsimony) to it is selected. There are pros and cons to each approach, where total spectral counts will double count peptides when two similar proteins are compared, and exclusive spectral counts will underrepresent less abundant proteins with shared peptides, favoring the most homolog with the most shared peptides. Considering protein groups with shared peptides or focusing on peptide-level analyses are alternative approaches that could be constructed from these results.

See "Related Datasets" section for:
* "AE1913 Protein Spectral Counts" which includes the exclusive and total spectral counts associated with proteins.
* "AE1913 Peptide Spectral Counts" which includes the individual peptides associated with these proteins (includes total spectral counts for each peptide).

CTD and other data from the same cruise are listed on deployment page AE1913: https://www.bco-dmo.org/deployment/916412

These data will become part of the Ocean Protein Portal (https://proteinportal.whoi.edu/; Saito et al., 2020).

The assembly, annotations, metatranscriptomic assembly products, the same exclusive protein spectral counts, and other useful information associated with this multi-omic analysis was published as a package at Zenodo (doi: 10.5281/zenodo.8287779).

Methods & Sampling

Methods are reported in Cohen et al. 2023 (biorxiv preprint doi: 10.1101/2023.11.20.567900) and are summarized below.
* This section describes how this and related datasets were generated (see "Related Datasets" section).

One half of the 142 mm filters (0.2-51 μm) collected by Clio were processed for metaproteomics. Proteins were extracted in an 1% SDS-based detergent in 50 mM HEPES at pH 8.5, reduced with dithiothreitol, alkylated with iodoacetamide, and purified using a polyacrylamide electrophoresis tube gel method. Protein quantification was performed using a BSA assay. Trypsin was added to the protein-bead mixture in a 1:20 trypsin:protein ratio. Peptides were purified using C18 tips and diluted to a concentration of 0.1 μg μL−1.

Approximately 2-5 µg of purified peptides were injected onto a Dionex UltiMate 3000 RSLCnano LC system with an additional RSLCnano pump, run in online 2D active modulation mode interfaced with a Thermo Fusion mass spectrometer. The mass spectrometer acquired MS1 scans from 380 to 1,580 m/z at 240K resolution in the Orbitrap. MS2 were collected in data dependent mode in the ion trap with a cycle time of 2 seconds between scans and acquisition of charge states 2 to 10. MS2 scans had 1.6 m/z isolation window, 50 ms maximum injection time and 5 s dynamic exclusion time.

Data Processing Description

The metatranscriptomic ORFs were used as the protein database, and peptide-spectrum matches were performed using Sequest algorithm within IseNode Proteome Discoverer 2.2.0.388 with a parent ion tolerance of 10 ppm and fragment tolerance of 0.6 Da, and 0 max missed cleavage. Identification criteria consisted of a peptide threshold of 98% (false discovery rate [FDR] = 0.1%) and protein threshold of 99% (1 peptide minimum, FDR = 1.5%) in Scaffold 5.1.2 (Proteome Software) resulting in 77,438 proteins and 3,155,061 exclusive spectral counts.

BCO-DMO Processing

No additional processing besides extracting from a package .zip and renaming filename .fasta for clarity. Confirmed with the author it is in FASTA format.
* Downloaded from part of Zenodo v2 package (doi: https://zenodo.org/records/8287779) file
merged.fasta.transdecoder.pep.zip and the filename was "merged.fasta.transdecoder.pep" renamed "merged_fasta_transdecoder_pep.fasta"

Data Files

File
Protein Identification FASTA file filename: merged_fasta_transdecoder_pep.fasta (FASTA, 4.47 GB) MD5:e220f99eda2cb487a3001d18c4ff3f26 Open reading frames of final assembly, predicted by Transdecoder.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1658030

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AE1913	Clio-BATS-WHOI AE1913	2019-06-16	R/V Atlantic Explorer	Mak A. Saito (Chief Scientist)	data info

Instruments

AUV Clio

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: AUV Clio

Generic Description:

Clio is an autonomous underwater vehicle (AUV) created to accomplish the dual goals of global ocean mapping and biochemistry sampling. The ability to sample dissolved and particulate seawater biochemistry across ocean basins while capturing fine-scale biogeochemical processes sets it apart from other AUVs. Clio is designed to efficiently and precisely move vertically through the ocean, drift laterally to observe water masses, and integrate with research vessel operations to map large horizontal scales up to a depth of 6,000 meters. More information is available at https://www2.whoi.edu/site/deepsubmergencelab/clio/

Mass Spectrometer

Supplied Name: Thermo 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.

Ultra high-performance liquid chromatography

Supplied Name: Dionex UltiMate 3000 RSLCnano LC system

Supplied Description:

Instrument Type

Generic Name: Ultra high-performance liquid chromatography

Acronym: UHPLC

Generic Description:

Ultra high-performance liquid chromatography: Column chromatography where the mobile phase is a liquid, the stationary phase consists of very small (< 2 microm) particles and the inlet pressure is relatively high.

Parameters

None available yet

Status message

Database

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Dataset: AE1913 Protein Identification FASTA