Protein cycling in the eastern tropical North Pacific oxygen‐deficient zone: A de novo‐discovery peptidomic approach

Peptides are identified using a de novo‐discovery approach in suspended and sinking particles from the eastern tropical North Pacific oxygen‐deficient zone (ODZ) and in a culture of a dominant autotroph from the region, the cyanobacterium Prochlorococcus. The benchmarking experiment with Prochlorococcus shows de novo peptides to be taxonomically specific, and thus of value in augmenting database‐driven approaches. Analysis of the suspended and sinking particles using the de novo‐discovery approach reveals the presence of fungal proteins in deep sinking particles that were not in our original search database, contributing to growing recognition that fungi may play important roles in marine organic matter cycling. Cyanobacterial peptides that have been post‐translationally modified were tracked to depth, where they contribute ~ 1% of the phylum‐level identifiable peptide pool in the sediment trap sample. The majority of peptides found at depth in the detrital pool are associated with membranes, indicating that cellular location is associated with early preservation within the detrital pool. Modified amino acids in sinking and suspended particles include high levels of deamidation, suggesting that partial extracellular degradation of protein could fuel observed anammox and contribute to pools of refractory organic nitrogen.