PXD023187

PXD023187 is an original dataset announced via ProteomeXchange.

Title	Protein cycling in the eastern tropical North Pacific oxygen deficient zone: a de novo-discovery peptidomic approach
Description	Peptides and proteins were identified using a novel de novo-discovery approach in suspended and sinking organic particles from the eastern tropical North Pacific and in a culture of a dominant autotroph from the region, the cyanobacterium Prochlorococcus. De novo peptide sequencing, where the sequence of amino acids is determined directly from mass spectra rather than from comparison to theoretical spectra from a selected sequence database, was found to be a useful tool for discovery of peptides present in a sample but not initially included in the search database. Iterative de novo-informed database search results suggested the presence of fungal peptides and proteins in deep sinking particles, consistent with growing evidence that fungi play an important role in degradation of sinking material in the ocean. The de novo-discovery approach also allowed the tracking of modified autotrophic cyanobacterial peptides to the deep sea, where they contributed 0.63% of the phylum-level identifiable peptide pool in a bathymetric sediment trap sample. Overall, the amino acid composition of the peptides in the sinking material showed little change with depth, consistent with earlier observations of bulk organic matter and/or amino acid composition during the early stages of degradation. However, we identified an abundance of modified amino acids in sinking and suspended particles, including high levels of deamidation, suggesting that partial degradation of protein could potentially fuel observed anammox and contribute to observed pool of refractory organic nitrogen. We also observe methylation of arginine, which has previously been shown to slow degradation of peptides in seawater. Our results demonstrate several examples how de novo-discovery allows for a deeper evaluation of proteins and peptides in environmental systems undergoing degradation.
HostingRepository	PRIDE
AnnounceDate	2022-01-10
AnnouncementXML	Submission_2022-01-10_07:54:37.485.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Richard Keil
SpeciesList	scientific name: environmental samples
ModificationList	methylated residue; monohydroxylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2020-12-17 02:40:51	ID requested
⏵ 1	2022-01-10 07:54:37	announced

Dataset with its publication pending

submitter keyword: Metaproteomics, Eastern tropical North Pacific, De novo peptide sequencing, Marine organic matter, Particulate organic matter, Protein and peptide cycling, Oxygen deficient zones

Richard Keil
contact affiliation	Oceanography, University of Washington, USA
contact email	rickkeil@uw.edu
lab head
Richard Keil
contact affiliation	University of Washington
contact email	keillab@uw.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2022/01/PXD023187

PRIDE project URI

• PRIDE
  1. PXD023187
     1. Label: PRIDE project
     2. Name: Protein cycling in the eastern tropical North Pacific oxygen deficient zone: a de novo-discovery peptidomic approach