Dataset: ProteOMZ Exclusive Peptide Level Spectral Counts
Deployment: FK160115

View Data: For data, See Dataset Metadata Page: https://osprey.bco-dmo.org/dataset/868030

Principal Investigator:

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

Scientist:

Jaci Saunders (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

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

Project:

Marine Microbial Investigator Award: Investigator Mak Saito (MM Saito)

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

Version:

Deployment Synonyms:

ProteOMZ

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Description

Methods & Sampling

Dataset acquisition description

Methods & Sampling:

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).

Location: Pelagic central Pacific Ocean from 20 – 1250 m depth

Data Processing Description

Dataset Processing Description

Data Processing:
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.

BCO-DMO data manager processing notes:
* Un-named first data column with row index removed (verified with submitter).

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

McLane Pump

Supplied Name: McLane in situ filtration pump

Supplied Description:

Instrument Type

Generic Name: McLane Pump

Generic 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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
MSMS_sample_name	RAW file name; crossreferences to proteomexchange or OPP repository	unitless	no_bcodmo_term
Stn	Station number	unitless	station
Depth	Depth of sampling	meters	depth
Longitude	Longitude	decimal degrees	lon
Latitude	Latitude	decimal degrees	lat
DepthGroup	K-means cluster of depths across transect	unitless	no_bcodmo_term
Region	Hierarchical cluster of stations across transect	unitless	no_bcodmo_term
Peptide_sequence	Unique Peptide sequence; this is the most unique identifier	unitless	no_bcodmo_term
Protein_name	Metagenome ID of best inferred protein from Scaffold protein inference; needed to map to protein IDs.	unitless	proteins
Exclusive_Sum_PSM	Exclusive Sum of +2 +3 +4 data = total unnormalized spectral counts; Quantitative Value	count	spectral_counts
Scaling_Factor	Scaling factor used to normalize samples across experiment to control for identification bias of PSMs	unitless	no_bcodmo_term
Calculated_Total_Protein	Concentration of protein per L of seawater passed through filter	ug/L	proteins
Scaled_Corrected_Exclusive_Sum	Scaled and normalized exclusive sum of spectral counts	sc/L	no_bcodmo_term
blast_accession	Accession number in NCBI of best blast hit for query of ORF from protein name identified	unitless	accession_number
blast_best_hit_taxon_id	best NCBI taxon ID for best blast hit in NCBI for query of ORF from protein name identified	unitless	accession_number
KO	accession number of KEGG Orthology (KO) identifier for ORF from protein name	unitless	accession_number
Group	NCBI taxonomic group for ORF from protein name	unitless	taxon
Domain	NCBI taxonomic domain for ORF from protein name	unitless	kingdom
Phylum	NCBI taxonomic phylum for ORF from protein name	unitless	phylum
Class	NCBI taxonomic class for ORF from protein name	unitless	class
Order	NCBI taxonomic order for ORF from protein name	unitless	order
Family	NCBI taxonomic family for ORF from protein name	unitless	family
Genus	NCBI taxonomic genus for ORF from protein name	unitless	genus
Species	NCBI taxonomic species for ORF from protein name	unitless	species
LCA_Group	Lowest Common Ancestor for groups of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	taxon
LCA_Domain	Lowest Common Ancestor for domains of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	kingdom
LCA_Phylum	Lowest Common Ancestor for phyla of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	phylum
LCA_Class	Lowest Common Ancestor for classes of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	class
LCA_Order	Lowest Common Ancestor for orders of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	order
LCA_Family	Lowest Common Ancestor for families of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	family
LCA_Genus	Lowest Common Ancestor for genuses of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	genus
LCA_Level	lowest taxonomic level of the Lowest Common Ancestor of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	no_bcodmo_term
LCA_taxon	lowest taxonomic identification of the Lowest Common Ancestor of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	taxon_code
Combo_Group	All groups of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	taxon
Combo_Domain	All domains of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	kingdom
Combo_Phylum	All phyla of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	phylum
Combo_Class	All classes of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	class
Combo_Order	All orders of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	order
Combo_Family	All families of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	family
Combo_Genus	All genuses of all NCBI taxons from ORFs containing peptide sequence in the entire metagenome	unitless	genus
Combo_KO	All KEGG Orthology (KO) identifiers from ORFs containing peptide sequence in the entire metagenome	unitless	accession_number
Combo_KO_Orthology	All KEGG Orthology (KO) orthologies from ORFs containing peptide sequence in the entire metagenome	unitless	no_bcodmo_term
Combo_KO_Class	All KEGG Orthology (KO) classes from ORFs containing peptide sequence in the entire metagenome	unitless	no_bcodmo_term
Combo_KO_Path	All KEGG Orthology (KO) paths from ORFs containing peptide sequence in the entire metagenome	unitless	no_bcodmo_term
Combo_Gene_Name	All KEGG Orthology (KO) gene names form ORFs containing peptide sequence in the entire metagenome	unitless	no_bcodmo_term
Combo_Gene_Description	All KEGG Orthology (KO) gene descriptions containing peptide sequence in the entire metagenome	unitless	brief_desc
Combo_EC	All Enzyme Commission (E.C.) numbers from ORFs from ORFs containing peptide sequence in the entire metagenome	unitless	accession_number
Best_Peptide_identification_probability	Metric of peptide quality	unitless	no_bcodmo_term
Best_Sequest_XCorr_Only_deltaCn	Metric of peptide quality	unitless	no_bcodmo_term
Best_Sequest_XCorr_Only_XCorr	Metric of peptide quality	unitless	no_bcodmo_term
Number_of_identified_plus2H_spectra	Count of +2H spectra	count	spectral_counts
Number_of_identified_plus3H_spectra	Count of +3H spectra	count	spectral_counts
Number_of_identified_plus4H_spectra	Count of +4H spectra	count	spectral_counts
Median_Retention_Time	Median retention time	minutes	no_bcodmo_term
Total_TIC	Total Ion Current	unitless	no_bcodmo_term
SOM_Label	Taxon and KO grouping label for SOM neural net	unitless	no_bcodmo_term
SOM_Label_Flag	Flag for SOM neural net that indicates whether more than one group listed condensed into SOM Label	unitless	no_bcodmo_term
All_Other_Proteins	All other ORFs in metagenome that contain the peptide sequences. Used to calculate LCA and Combos for taxonomy and KO annotations.	unitless	no_bcodmo_term

Database

Contribute Data

Dataset: ProteOMZ Exclusive Peptide Level Spectral Counts
Deployment: FK160115

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: ProteOMZ Exclusive Peptide Level Spectral CountsDeployment: FK160115

Dataset acquisition description

Dataset Processing Description

Dataset: ProteOMZ Exclusive Peptide Level Spectral Counts
Deployment: FK160115