Dataset Information

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.

ABSTRACT: Environmental meta-omics is rapidly expanding as sequencing capabilities improve, computing technologies become more accessible, and associated costs are reduced. The in situ snapshots of marine microbial life afforded by these data provide a growing knowledge of the functional roles of communities in ecosystem processes. Metaproteomics allows for the characterization of the dynamic proteome of a complex microbial community. It has the potential to reveal impacts of microbial metabolism on biogeochemical transport, storage and cycling (for example, Hawley et al., 2014), while additionally clarifying which taxonomic groups perform these roles. Previous work illuminated many of the important functions and interactions within marine microbial communities (for example, Morris et al., 2010), but a review of ocean metaproteomics literature revealed little standardization in bioinformatics pipelines for detecting peptides and inferring and annotating proteins. As prevalence of these data sets grows, there is a critical need to develop standardized approaches for mass spectrometry (MS) proteomic spectrum identification and annotation to maximize the scientific value of the data obtained. Here, we demonstrate that bioinformatics decisions made throughout the peptide identification process are as important for data interpretation as choices of sampling protocol and bacterial community manipulation experimental design. Our analysis offers a best practices guide for environmental metaproteomics.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Marine Metagenome

SUBMITTER: Brook Nunn

LAB HEAD: Brook L. Nunn

PROVIDER: PXD006688 | Pride | 2019-01-25

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	2014_Sept_08_BeringSea08.pep.xml	Pepxml
	2014_Sept_08_BeringSea08.raw	Raw

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Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.

Timmins-Schiffman Emma E May Damon H DH Mikan Molly M Riffle Michael M Frazar Chris C Harvey H R HR Noble William S WS Nunn Brook L BL

The ISME journal 20161108 2

PMID: 27824341

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Dataset Information

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.

Dataset's files

Publications

Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.

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