Dataset: 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

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