PXD004799-2

PXD004799 is an original dataset announced via ProteomeXchange.

Title	Detection of Low Abundance Ocean Bacterial Peptides DDA
Description	Bacteria transform nutrients and degrade organic matter, making them an essential part of healthy ecosystems. By assaying bacterial physiology within a complex system, the status of the whole ecosystem can be investigated. Proteins are the dynamic molecules that control essential bacterial physiological responses and those of every organism; characterizing an organism's proteome can therefore provide information on its interaction with the environment. Data dependen proteomic analysis (DDA) is a global approach to assay the entire proteome, but sample complexity and the stochastic nature of mass spectrometry can make it difficult to detect low abundance proteins. We explored the development of targeted proteomic (selected reaction monitoring, SRM) assays in complex ocean samples in order to detect specific bacterial proteins of interest and to assess new tools for mixed community metaproteomic exploration. A mixed community was created from a dilution series of isolated culture of bacteria (Ruegeria pomoeroyi) and phytoplankton (Thalassiosira pseudonana). Using SRM, we were able to detect bacterial peptides from the community that were undetectable with the standard DDA approach. We demonstrate benefits and drawbacks of different proteomic approaches that can be used to probe for and resolve nuances of bacterial physiological processes in complex environmental systems.
HostingRepository	PRIDE
AnnounceDate	2017-06-20
AnnouncementXML	Submission_2017-06-20_05:44:38.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Emma Timmins-Schiffman
SpeciesList	scientific name: Thalassiosira pseudonana; NCBI TaxID: 35128; scientific name: Ruegeria pomeroyi; NCBI TaxID: 89184;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-08-15 02:36:43	ID requested
1	2017-02-01 11:47:31	announced
⏵ 2	2017-06-20 05:44:38	announced	Updated project metadata.
3	2018-06-25 05:53:59	announced	Updated project metadata.
4	2024-10-22 04:32:21	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

curator keyword: Biological

submitter keyword: Ruegeria pomeroyi, ocean bacteria, proteomics, DDA, Thalassiosira pseudonana

Brook L. Nunn
contact affiliation	University of Washington, Department of Genome Sciences
contact email	brookh@uw.edu
lab head
Emma Timmins-Schiffman
contact affiliation	University of Washington
contact email	emsie25@gmail.com
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/2017/02/PXD004799

PRIDE project URI

• PRIDE
  1. PXD004799
     1. Label: PRIDE project
     2. Name: Detection of Low Abundance Ocean Bacterial Peptides DDA