Dataset Information

Detection of Low Abundance Ocean Bacterial Peptides DDA

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Ruegeria Pomeroyi Thalassiosira Pseudonana

SUBMITTER: Emma Timmins-Schiffman

LAB HEAD: Brook L. Nunn

PROVIDER: PXD004799 | Pride | 2017-02-01

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	2015_June_9_BactDetection22.raw	Raw
	2015_June_9_BactDetection25.raw	Raw
	2015_June_9_BactDetection26.raw	Raw
	2015_June_9_BactDetection27.raw	Raw
	2015_June_9_BactDetection28.raw	Raw

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Publications

MS analysis of a dilution series of bacteria:phytoplankton to improve detection of low abundance bacterial peptides.

Timmins-Schiffman Emma E Mikan Molly P MP Ting Ying Sonia YS Harvey H Rodger HR Nunn Brook L BL

Scientific reports 20180618 1

Assigning links between microbial activity and biogeochemical cycles in the ocean is a primary objective for ecologists and oceanographers. Bacteria represent a small ecosystem component by mass, but act as the nexus for both nutrient transformation and organic matter recycling. There are limited methods to explore the full suite of active bacterial proteins largely responsible for degradation. Mass spectrometry (MS)-based proteomics now has the potential to document bacterial physiology within ...[more]

PMID: 29915279

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