PXD006688

PXD006688 is an original dataset announced via ProteomeXchange.

Title	Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.
Description	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.
HostingRepository	PRIDE
AnnounceDate	2017-07-10
AnnouncementXML	Submission_2017-07-10_00:18:50.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Brook Nunn
SpeciesList	scientific name: marine metagenome; NCBI TaxID: 408172;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-06-09 03:52:08	ID requested
⏵ 1	2017-07-10 00:18:51	announced

Timmins-Schiffman E, May DH, Mikan M, Riffle M, Frazar C, Harvey HR, Noble WS, Nunn BL, Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns. ISME J, 11(2):309-314(2017) [pubmed]

curator keyword: Metaproteomics, Biological

submitter keyword: metaproteomics

ocean metaproteomics

Brook L. Nuun
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

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/2017/07/PXD006688

PRIDE project URI

• PRIDE
  1. PXD006688
     1. Label: PRIDE project
     2. Name: Critical decisions in metaproteomics: achieving high confidence protein annotations in a sea of unknowns.