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 (NCEI Accession 0278803)

This dataset contains biological and survey - biological data collected on R/V Falkor during cruise FK160115 in the North Pacific Ocean and South Pacific Ocean from 2016-01-17 to 2016-02-05. These data include depth, family, genus, order, phylum, species, taxon, and taxon_code. The instruments used to collect these data include McLane Pump. These data were collected by Jaci Saunders and Mak A. Saito of Woods Hole Oceanographic Institution as part of the "Marine Microbial Investigator Award: Investigator Mak Saito (MM Saito)" and "The ProteOMZ Expedition: Investigating Life Without Oxygen in the Pacific Ocean (ProteOMZ (Proteomics in an Oxygen Minimum Zone))" projects and "Marine Microbiology Initiative (MMI)" program. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2022-01-20.

The following is the text of the dataset description provided by BCO-DMO:

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