http://lod.bco-dmo.org/id/dataset/868030
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2022-01-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Relative protein abundance from scaled and corrected exclusive peptide spectral counts from the ProteOMZ R/V Falkor expedition cruise FK160115 in the Pelagic central Pacific Ocean in 2016
2022-01-13
publication
2022-01-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-01-20
publication
https://doi.org/10.26008/1912/bco-dmo.868030.1
Mak A. Saito
Woods Hole Oceanographic Institution
principalInvestigator
Jaci Saunders
Woods Hole Oceanographic Institution
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Saito, M. A., Saunders, J. (2022) Relative protein abundance from scaled and corrected exclusive peptide spectral counts from the ProteOMZ R/V Falkor expedition cruise FK160115 in the Pelagic central Pacific Ocean in 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-01-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.868030.1 [access date]
Methods and Sampling: <p>Methods &amp; Sampling:<br />
<br />
Samples were handled as described in (Saunders et al., submitted) and (McIlvin et al., 2021). There are a total of 107,579 unique peptide sequences from 56,543 protein groups (88,251 proteins). Proteins were extracted from biomass collected on a quarter section of a 142 mm 0.2 µm Supor filter (Pall Corporation) after pre-filtration through a 3.0 µm Supor filter. Proteins were extracted using a modified SP3 magnetic bead method (Hughes et al., 2014). Extracted proteins were quatified using the bicinchoninic acid method (Thermo Scientific Micro BCA protein assay kit) with an albumin protein reference standard. Extracted protein was purified and digested with trypsin. Purified and digested protein was then injected into an online nanoflow 2D active modulation liquid chromatography separation (McIlvin et al., 2021). Eluent flowed inline into the ion source of a Thermo Fusion quadrupole-Orbitrap mass spectrometer (Thermo Scientific). MS/MS spectra (and mass spec methods) are available at the PRIDE repository under accession PXD030684. Peptide to spectrum matching (PSM) on the MS/MS data was conducted with SEQUEST HT using Thermo Proteome Discoverer v 2.1 software against a database of predicted proteins from an assembled metagenome from the central Pacific Ocean. Additional protein inference and FDR calculations were conducted with Scaffold v 4.8.7. Identification was conducted with decoy false discovery rates (FDR) with a threshold of 95% minimum for peptides (FDR=0.1%) and a threshold of 99% (1 peptide minimum) for proteins (FDR=1.6%). Protein level inference for parsimony-based assignments of specific proteins was conducted using experiment-wide grouping with binary peptide-protein weights in Scaffold. All PSM and protein quantification in Scaffold was conducted using Exclusive Counts (not double-counted, PSM assignment to protein groups using parsimony).&nbsp;<br />
<br />
Location: Pelagic central Pacific Ocean from 20 – 1250 m depth</p>
Funding provided by Gordon and Betty Moore Foundation: Marine Microbiology Initiative (MMI) Award Number: GBMF3782 Award URL: https://www.moore.org/grant-detail?grantId=GBMF3782
Funding provided by Schmidt Ocean Institute (SOI) Award Number: R/V Falkor 160115 SOI ProteOMZ Expedition
completed
Mak A. Saito
Woods Hole Oceanographic Institution
508-289-2393
266 Woods Hole Rd. MS #51 Watson Lab
Woods Hole
MA
02543
USA
msaito@whoi.edu
pointOfContact
Jaci Saunders
Woods Hole Oceanographic Institution
jsaunders@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
MSMS_sample_name
Stn
Depth
Longitude
Latitude
DepthGroup
Region
Peptide_sequence
Protein_name
Exclusive_Sum_PSM
Scaling_Factor
Calculated_Total_Protein
Scaled_Corrected_Exclusive_Sum
blast_accession
blast_best_hit_taxon_id
KO
Group
Domain
Phylum
Class
Order
Family
Genus
Species
LCA_Group
LCA_Domain
LCA_Phylum
LCA_Class
LCA_Order
LCA_Family
LCA_Genus
LCA_Level
LCA_taxon
Combo_Group
Combo_Domain
Combo_Phylum
Combo_Class
Combo_Order
Combo_Family
Combo_Genus
Combo_KO
Combo_KO_Orthology
Combo_KO_Class
Combo_KO_Path
Combo_Gene_Name
Combo_Gene_Description
Combo_EC
Best_Peptide_identification_probability
Best_Sequest_XCorr_Only_deltaCn
Best_Sequest_XCorr_Only_XCorr
Number_of_identified_plus2H_spectra
Number_of_identified_plus3H_spectra
Number_of_identified_plus4H_spectra
Median_Retention_Time
Total_TIC
SOM_Label
SOM_Label_Flag
All_Other_Proteins
McLane in situ filtration pump
theme
None, User defined
No BCO-DMO term
station
depth
longitude
latitude
protein concentration
spectral counts
accession number
taxon
kingdom
phylum
taxonomic class
order
family
genus
species scientific name (binomial)
taxon_code
brief description
featureType
BCO-DMO Standard Parameters
McLane Pump
instrument
BCO-DMO Standard Instruments
FK160115
service
Deployment Activity
Central Pacific
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Marine Microbiology Initiative
https://www.moore.org/initiative-strategy-detail?initiativeId=marine-microbiology-initiative
Marine Microbiology Initiative
A Gordon and Betty Moore Foundation Program.
Forging a new paradigm in marine microbial ecology:
Microbes in the ocean produce half of the oxygen on the planet and remove vast amounts of carbon dioxide, a greenhouse gas, from the atmosphere. Yet, we have known surprisingly little about these microscopic organisms. As we discover answers to some long-standing puzzles about the roles that marine microorganisms play in supporting the ocean’s food webs and driving global elemental cycles, we realized that we still need to learn much more about what these organisms do and how they do it—including how they evolved and contribute to our ocean's health and productivity.
The Marine Microbiology Initiative seeks to gain a comprehensive understanding of marine microbial communities, including their diversity, functions and behaviors; their ecological roles; and their origins and evolution. Our focus has been to enable researchers to uncover the principles that govern the interactions among microbes and that govern microbially mediated nutrient flow in the sea. To address these opportunities, we support leaders in the field through investigator awards, multidisciplinary team research projects, and efforts to create resources of broad use to the research community. We also support development of new instrumentation, tools, technologies and genetic approaches.
Through the efforts of many scientists from around the world, the initiative has been catalyzing new science through advances in methods and technology, and to reduce interdisciplinary barriers slowing progress. With our support, researchers are quantifying nutrient pools in the ocean, deciphering the genetic and biochemical bases of microbial metabolism, and understanding how microbes interact with one another. The initiative has five grant portfolios:
Individual investigator awards for current and emerging leaders in the field.
Multidisciplinary projects that support collaboration across disciplines.
New instrumentation, tools and technology that enable scientists to ask new questions in ways previously not possible.
Community resource efforts that fund the creation and sharing of data and the development of tools, methods and infrastructure of widespread utility.
Projects that advance genetic tools to enable development of experimental model systems in marine microbial ecology.
We also bring together scientists to discuss timely subjects and to facilitate scientific exchange.
Our path to marine microbial ecology was a confluence of new technology that could accelerate science and an opportunity to support a field that was not well funded relative to potential impact. Around the time we began this work in 2004, the life sciences were entering a new era of DNA sequencing and genomics, expanding possibilities for scientific research – including the nascent field of marine microbial ecology. Through conversations with pioneers inside and outside the field, an opportunity was identified: to apply these new sequencing tools to advance knowledge of marine microbial communities and reveal how they support and influence ocean systems.
After many years of success, we will wind down this effort and close the initiative in 2021. We will have invested more than $250 million over 17 years to deepen understanding of the diversity, ecological activities and evolution of marine microbial communities. Thanks to the work of hundreds of scientists and others involved with the initiative, the goals have been achieved and the field has been profoundly enriched; it is now positioned to address new scientific questions using innovative technologies and methods.
MMI
largerWorkCitation
program
The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean
https://schmidtocean.org/cruise/investigating-life-without-oxygen-in-the-tropical-pacific/#team
The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean
<p>From Schmidt Ocean Institute's ProteOMZ Project page:</p>
<p>Rising temperatures, ocean acidification, and overfishing have now gained widespread notoriety as human-caused phenomena that are changing our seas. In recent years, scientists have increasingly recognized that there is yet another ingredient in that deleterious mix: a process called deoxygenation that results in less oxygen available in our seas.</p>
<p>Large-scale ocean circulation naturally results in low-oxygen areas of the ocean called oxygen deficient zones (ODZs). The cycling of carbon and nutrients – the foundation of marine life, called biogeochemistry – is fundamentally different in ODZs than in oxygen-rich areas. Because researchers think deoxygenation will greatly expand the total area of ODZs over the next 100 years, studying how these areas function now is important in predicting and understanding the oceans of the future. This first expedition of 2016 led by Dr. Mak Saito from the Woods Hole Oceanographic Institution (WHOI) along with scientists from University of Maryland Center for Environmental Science, University of California Santa Cruz, and University of Washington aimed to do just that, investigate ODZs.</p>
<p>During the 28 day voyage named “ProteOMZ,” researchers aboard R/V <em>Falkor </em>traveled from Honolulu, Hawaii to Tahiti to describe the biogeochemical processes that occur within this particular swath of the ocean’s ODZs. By doing so, they contributed to our greater understanding of ODZs, gathered a database of baseline measurements to which future measurements can be compared, and established a new methodology that could be used in future research on these expanding ODZs.</p>
ProteOMZ (Proteomics in an Oxygen Minimum Zone)
largerWorkCitation
project
Marine Microbial Investigator Award: Investigator Mak Saito
https://osprey.bco-dmo.org/project/786672
Marine Microbial Investigator Award: Investigator Mak Saito
<p>In support of obtaining deeper knowledge of major biogeochemically relevant proteins to inform a mechanistic understanding of global marine biogeochemical cycles.</p>
MM Saito
largerWorkCitation
project
eng; USA
oceans
Central Pacific
-156
-139.8
-10.6
10
2016-01-17
2016-02-05
Central Pacific Ocean (Hawaii to Tahiti)
0
BCO-DMO catalogue of parameters from Relative protein abundance from scaled and corrected exclusive peptide spectral counts from the ProteOMZ R/V Falkor expedition cruise FK160115 in the Pelagic central Pacific Ocean in 2016
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/868624.rdf
Name: MSMS_sample_name
Units: unitless
Description: <p>RAW file name; crossreferences to proteomexchange or OPP repository</p>
http://lod.bco-dmo.org/id/dataset-parameter/868625.rdf
Name: Stn
Units: unitless
Description: <p>Station number</p>
http://lod.bco-dmo.org/id/dataset-parameter/868626.rdf
Name: Depth
Units: meters
Description: <p>Depth of sampling</p>
http://lod.bco-dmo.org/id/dataset-parameter/868627.rdf
Name: Longitude
Units: decimal degrees
Description: <p>Longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/868628.rdf
Name: Latitude
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/868629.rdf
Name: DepthGroup
Units: unitless
Description: <p>K-means cluster of depths across transect</p>
http://lod.bco-dmo.org/id/dataset-parameter/868630.rdf
Name: Region
Units: unitless
Description: <p>Hierarchical cluster of stations across transect</p>
http://lod.bco-dmo.org/id/dataset-parameter/868631.rdf
Name: Peptide_sequence
Units: unitless
Description: <p>Unique Peptide sequence; this is the most unique identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/868632.rdf
Name: Protein_name
Units: unitless
Description: <p>Metagenome ID of best inferred protein from Scaffold protein inference; needed to map to protein IDs.</p>
http://lod.bco-dmo.org/id/dataset-parameter/868633.rdf
Name: Exclusive_Sum_PSM
Units: count
Description: <p>Exclusive Sum of +2 +3 +4 data = total unnormalized spectral counts; Quantitative Value</p>
http://lod.bco-dmo.org/id/dataset-parameter/868634.rdf
Name: Scaling_Factor
Units: unitless
Description: <p>Scaling factor used to normalize samples across experiment to control for identification bias of PSMs</p>
http://lod.bco-dmo.org/id/dataset-parameter/868635.rdf
Name: Calculated_Total_Protein
Units: ug/L
Description: <p>Concentration of protein per L of seawater passed through filter</p>
http://lod.bco-dmo.org/id/dataset-parameter/868636.rdf
Name: Scaled_Corrected_Exclusive_Sum
Units: sc/L
Description: <p>Scaled and normalized exclusive sum of spectral counts</p>
http://lod.bco-dmo.org/id/dataset-parameter/868637.rdf
Name: blast_accession
Units: unitless
Description: <p>Accession number in NCBI of best blast hit for query of ORF from protein name identified</p>
http://lod.bco-dmo.org/id/dataset-parameter/868638.rdf
Name: blast_best_hit_taxon_id
Units: unitless
Description: <p>best NCBI taxon ID for best blast hit in NCBI for query of ORF from protein name identified</p>
http://lod.bco-dmo.org/id/dataset-parameter/868639.rdf
Name: KO
Units: unitless
Description: <p>accession number of KEGG Orthology (KO) identifier for ORF from protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/868640.rdf
Name: Group
Units: unitless
Description: <p>NCBI taxonomic group for ORF from protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/868641.rdf
Name: Domain
Units: unitless
Description: <p>NCBI taxonomic domain for ORF from protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/868642.rdf
Name: Phylum
Units: unitless
Description: <p>NCBI taxonomic phylum for ORF from protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/868643.rdf
Name: Class
Units: unitless
Description: <p>NCBI taxonomic class for ORF from protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/868644.rdf
Name: Order
Units: unitless
Description: <p>NCBI taxonomic order for ORF from protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/868645.rdf
Name: Family
Units: unitless
Description: <p>NCBI taxonomic family for ORF from protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/868646.rdf
Name: Genus
Units: unitless
Description: <p>NCBI taxonomic genus for ORF from protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/868647.rdf
Name: Species
Units: unitless
Description: <p>NCBI taxonomic species for ORF from protein name</p>
http://lod.bco-dmo.org/id/dataset-parameter/868648.rdf
Name: LCA_Group
Units: unitless
Description: <p>Lowest Common Ancestor for groups of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868649.rdf
Name: LCA_Domain
Units: unitless
Description: <p>Lowest Common Ancestor for domains of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868650.rdf
Name: LCA_Phylum
Units: unitless
Description: <p>Lowest Common Ancestor for phyla of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868651.rdf
Name: LCA_Class
Units: unitless
Description: <p>Lowest Common Ancestor for classes of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868652.rdf
Name: LCA_Order
Units: unitless
Description: <p>Lowest Common Ancestor for orders of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868653.rdf
Name: LCA_Family
Units: unitless
Description: <p>Lowest Common Ancestor for families of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868654.rdf
Name: LCA_Genus
Units: unitless
Description: <p>Lowest Common Ancestor for genuses of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868655.rdf
Name: LCA_Level
Units: unitless
Description: <p>lowest taxonomic level of the Lowest Common Ancestor of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868656.rdf
Name: LCA_taxon
Units: unitless
Description: <p>lowest taxonomic identification of the Lowest Common Ancestor of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868657.rdf
Name: Combo_Group
Units: unitless
Description: <p>All groups of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868658.rdf
Name: Combo_Domain
Units: unitless
Description: <p>All domains of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868659.rdf
Name: Combo_Phylum
Units: unitless
Description: <p>All phyla of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868660.rdf
Name: Combo_Class
Units: unitless
Description: <p>All classes of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868661.rdf
Name: Combo_Order
Units: unitless
Description: <p>All orders of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868662.rdf
Name: Combo_Family
Units: unitless
Description: <p>All families of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868663.rdf
Name: Combo_Genus
Units: unitless
Description: <p>All genuses of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868664.rdf
Name: Combo_KO
Units: unitless
Description: <p>All KEGG Orthology (KO) identifiers from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868665.rdf
Name: Combo_KO_Orthology
Units: unitless
Description: <p>All KEGG Orthology (KO) orthologies from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868666.rdf
Name: Combo_KO_Class
Units: unitless
Description: <p>All KEGG Orthology (KO) classes from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868667.rdf
Name: Combo_KO_Path
Units: unitless
Description: <p>All KEGG Orthology (KO) paths from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868668.rdf
Name: Combo_Gene_Name
Units: unitless
Description: <p>All KEGG Orthology (KO) gene names form ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868669.rdf
Name: Combo_Gene_Description
Units: unitless
Description: <p>All KEGG Orthology (KO) gene descriptions containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868670.rdf
Name: Combo_EC
Units: unitless
Description: <p>All Enzyme Commission (E.C.) numbers from ORFs from ORFs containing peptide sequence in the entire metagenome</p>
http://lod.bco-dmo.org/id/dataset-parameter/868671.rdf
Name: Best_Peptide_identification_probability
Units: unitless
Description: <p>Metric of peptide quality</p>
http://lod.bco-dmo.org/id/dataset-parameter/868672.rdf
Name: Best_Sequest_XCorr_Only_deltaCn
Units: unitless
Description: <p>Metric of peptide quality</p>
http://lod.bco-dmo.org/id/dataset-parameter/868673.rdf
Name: Best_Sequest_XCorr_Only_XCorr
Units: unitless
Description: <p>Metric of peptide quality</p>
http://lod.bco-dmo.org/id/dataset-parameter/868674.rdf
Name: Number_of_identified_plus2H_spectra
Units: count
Description: <p>Count of +2H spectra</p>
http://lod.bco-dmo.org/id/dataset-parameter/868675.rdf
Name: Number_of_identified_plus3H_spectra
Units: count
Description: <p>Count of +3H spectra</p>
http://lod.bco-dmo.org/id/dataset-parameter/868676.rdf
Name: Number_of_identified_plus4H_spectra
Units: count
Description: <p>Count of +4H spectra</p>
http://lod.bco-dmo.org/id/dataset-parameter/868677.rdf
Name: Median_Retention_Time
Units: minutes
Description: <p>Median retention time</p>
http://lod.bco-dmo.org/id/dataset-parameter/868678.rdf
Name: Total_TIC
Units: unitless
Description: <p>Total Ion Current</p>
http://lod.bco-dmo.org/id/dataset-parameter/868679.rdf
Name: SOM_Label
Units: unitless
Description: <p>Taxon and KO grouping label for SOM neural net</p>
http://lod.bco-dmo.org/id/dataset-parameter/868680.rdf
Name: SOM_Label_Flag
Units: unitless
Description: <p>Flag for SOM neural net that indicates whether more than one group listed condensed into SOM Label</p>
http://lod.bco-dmo.org/id/dataset-parameter/868681.rdf
Name: All_Other_Proteins
Units: unitless
Description: <p>All other ORFs in metagenome that contain the peptide sequences. Used to calculate LCA and Combos for taxonomy and KO annotations.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
1882078698
https://darchive.mblwhoilibrary.org/bitstream/1912/27948/1/proteomz_peptide_spec_counts.csv
download
https://doi.org/10.26008/1912/bco-dmo.868030.1
download
onLine
dataset
<p>Methods &amp; Sampling:<br />
<br />
Samples were handled as described in (Saunders et al., submitted) and (McIlvin et al., 2021). There are a total of 107,579 unique peptide sequences from 56,543 protein groups (88,251 proteins). Proteins were extracted from biomass collected on a quarter section of a 142 mm 0.2 µm Supor filter (Pall Corporation) after pre-filtration through a 3.0 µm Supor filter. Proteins were extracted using a modified SP3 magnetic bead method (Hughes et al., 2014). Extracted proteins were quatified using the bicinchoninic acid method (Thermo Scientific Micro BCA protein assay kit) with an albumin protein reference standard. Extracted protein was purified and digested with trypsin. Purified and digested protein was then injected into an online nanoflow 2D active modulation liquid chromatography separation (McIlvin et al., 2021). Eluent flowed inline into the ion source of a Thermo Fusion quadrupole-Orbitrap mass spectrometer (Thermo Scientific). MS/MS spectra (and mass spec methods) are available at the PRIDE repository under accession PXD030684. Peptide to spectrum matching (PSM) on the MS/MS data was conducted with SEQUEST HT using Thermo Proteome Discoverer v 2.1 software against a database of predicted proteins from an assembled metagenome from the central Pacific Ocean. Additional protein inference and FDR calculations were conducted with Scaffold v 4.8.7. Identification was conducted with decoy false discovery rates (FDR) with a threshold of 95% minimum for peptides (FDR=0.1%) and a threshold of 99% (1 peptide minimum) for proteins (FDR=1.6%). Protein level inference for parsimony-based assignments of specific proteins was conducted using experiment-wide grouping with binary peptide-protein weights in Scaffold. All PSM and protein quantification in Scaffold was conducted using Exclusive Counts (not double-counted, PSM assignment to protein groups using parsimony).&nbsp;<br />
<br />
Location: Pelagic central Pacific Ocean from 20 – 1250 m depth</p>
Specified by the Principal Investigator(s)
<p>Data Processing:<br />
The raw mass spectra files were searched against SEQUEST within Proteome Discoverer v2.2 software. Raw mass spectra files are available in ProteomeXchange via the PRIDE database with accession # PXD030684 and 10.6019/PXD030684. Processed files were then loaded into Proteome Software and exclusive peptide reports were exported. The files were modified to scale and normalize the spectral counts at across the entire dataset. The peptide report was too large to work within Excel and was modified in Pandas/Python to produce a CSV file. Lowest Common Ancestor (LCA) analysis was conducted with METATRYP v 2 (Saunders et al 2020). Grouping of taxonomic and KO levels was conducted with pandas in python.&nbsp;<br />
<br />
BCO-DMO data manager processing notes:<br />
* Un-named first data column with row index removed (verified with submitter).</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
McLane in situ filtration pump
McLane in situ filtration pump
PI Supplied Instrument Name: McLane in situ filtration pump Instrument Name: McLane Pump Instrument Short Name:McLane Pump Instrument Description: McLane pumps sample large volumes of seawater at depth. They are attached to a wire and lowered to different depths in the ocean. As the water is pumped through the filter, particles suspended in the ocean are collected on the filters. The pumps are then retrieved and the contents of the filters are analyzed in a lab.
Cruise: FK160115
FK160115
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK160115
Mak A. Saito
Woods Hole Oceanographic Institution
https://service.rvdata.us/data/cruise/FK160115/doc/FK160115_OfficialCruiseReport_Saito_v3.pdf
Report describing FK160115
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel