PXD011005

PXD011005 is an original dataset announced via ProteomeXchange.

Title	Detection of Low Abundance Ocean Bacterial Peptides SRM (Noga et al. 2016)
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 organismÂ?s proteome can therefore provide information on its interaction with the environment. Data dependent 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 an isolated cultures of bacteria (Reugeria pomeroyi) and phytoplankton (Thalassiosira pseudonana). Using SRM, we were able to select and 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	PeptideAtlas
AnnounceDate	2018-09-04
AnnouncementXML	Submission_2018-09-04_09:05:36.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Emma Timmins-Schiffman
SpeciesList	scientific name: Ruegeria pomeroyi; NCBI TaxID: 89184;
ModificationList	No PTMs are included in the dataset
Instrument	TSQ Vantage

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-04 09:01:32	ID requested
⏵ 1	2018-09-04 09:05:37	announced

Timmins-Schiffman E, Mikan MP, Ting YS, Harvey HR, Nunn BL, MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides. Sci Rep, 8(1):9276(2018) [pubmed]

curator keyword: selected reaction monitoring, SRM, targeted

Emma Timmins-Schiffman
contact affiliation	University of Washington
contact email	emmats@uw.edu
dataset submitter
Brook Nunn
contact affiliation	University of Washington
contact email	brookh@uw.edu
lab head

PeptideAtlas dataset URI

PASSEL experiment URI

PASSEL transition group browser URI