PXD006417

PXD006417 is an original dataset announced via ProteomeXchange.

Title	Protein recycling in Bering Sea Algal incubations
Description	Protein present in phytoplankton represents a large fraction of the organic nitrogen and carbon transported from its synthesis in surface waters to marine sediments. Yet relatively little is known about the longevity of identifiable protein in situ, or the potential modifications to proteins that occur during bloom termination, protein recycling and degradation. To address this knowledge gap, diatom-dominated phytoplankton was collected during the Bering Sea spring blooms of 2009 and 2010, and incubated under darkness in separate shipboard degradation ex periments spanning 11 and 53 d, respectively. In each experiment, the protein distribution was monited over time using shotgun proteomics, along with total hydrolyzable amino acids (THAAs), total protein, particulate organic carbon (POC) and nitrogen (PN), and bacterial cell abundance. Identifiable proteins, total protein and THAAs were rapidly lost during the first 5 d of enclosure in darkness in both incubations. Thereafter the loss rate was slower, and it declined further after 22 d. The initial loss of identifiable biosynthetic, glycolysis, metabolism and translation proteins after 12 h may represent shutdown of cellular activity among algal cells. Additional peptides with glycan modifications were identified in early incubation time points, suggesting that such protein modifications could be used as a marker for internal recycling processes and possibly cell death. Protein recycling was not uniform, with a subset of algal proteins including fucoxanthin chlorophyll binding proteins and RuBisCO identified after 53 d of degradation. Non-metric multidimensional scaling was used to compare the incubations with previous environmental results. The results confirmed recent observations that some fraction of algal proteins can survive water column recycling and undergo transport to marine sediments, thus contributing organic nitrogen to the benthos.
HostingRepository	PRIDE
AnnounceDate	2019-10-10
AnnouncementXML	Submission_2019-10-10_10:23:20.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Brook Nunn
SpeciesList	scientific name: Thalassiosira pseudonana; NCBI TaxID: 35128;
ModificationList	No PTMs are included in the dataset
Instrument	Finnigan MAT instrument model

Revision	Datetime	Status	ChangeLog Entry
0	2017-05-02 01:47:19	ID requested
1	2017-05-19 02:21:41	announced
⏵ 2	2019-10-10 10:23:21	announced	2019-10-10: Updated project metadata.

Dataset with its publication pending

curator keyword: Metaproteomics, Biological

submitter keyword: Protein recycling, Bering Sea, Amino acid, Nitrogen cycle, Tandem mass spectrometry, Diatom, Cell death, Preservation

Brook L. Nunn
contact affiliation	University of Washington, Department of Genome Sciences
contact email	brookh@uw.edu
lab head
Brook Nunn
contact affiliation	University of Washington
contact email	brookh@uw.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD006417
     1. Label: PRIDE project
     2. Name: Protein recycling in Bering Sea Algal incubations