PXD008017

PXD008017 is an original dataset announced via ProteomeXchange.

Title	More is not always better: Evaluation of 1D- and 2D-LC-MS2 methods for metaproteomics
Description	Metaproteomics is a powerful tool to characterize the structure of microbial communities and the physiology, metabolism and interactions of the species in these communities. Metaproteomics seeks to identify and quantify proteins from microbial communities on a large scale using gel electrophoresis or advanced liquid chromatography (LC) combined with high-resolution, accurate-mass mass spectrometry. To achieve extensive coverage of a metaproteome using shotgun proteomics, the sample complexity has to be decreased, for which a main approach is the on-line separation of peptides using one or more LC dimensions. The aim of this study is to test different 1D- and 2D-LC methods, also in comparison with the standard GeLC (pre-separation of proteins via gel electrophoresis) to find the best approach for analyzing metaproteome samples, using a mock community with 32 species in different abundances.
HostingRepository	PRIDE
AnnounceDate	2019-02-13
AnnouncementXML	Submission_2019-03-11_14:37:12.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tjorven Hinzke
SpeciesList	scientific name: Archaea; NCBI TaxID: 2157; scientific name: Eukaryota (eucaryotes); NCBI TaxID: 2759; scientific name: Viruses; NCBI TaxID: 10239; scientific name: Bacteria; NCBI TaxID: 2;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-10-23 02:18:43	ID requested
1	2019-02-13 06:07:45	announced
⏵ 2	2019-03-11 14:37:13	announced	Updated publication reference for PubMed record(s): 30837968.

Hinzke T, Kouris A, Hughes RA, Strous M, Kleiner M, More Is Not Always Better: Evaluation of 1D and 2D-LC-MS/MS Methods for Metaproteomics. Front Microbiol, 10():238(2019) [pubmed]

curator keyword: Metaproteomics, Technical

submitter keyword: microbial community

microbiota

microbiome

mock community

method evaluation

microbial ecology

Q Exactive

liquid chromatography

GeLC

Manuel Kleiner
contact affiliation	Department of Geoscience, University of Calgary, Calgary, AB, Canada; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
contact email	manuel_kleiner@ncsu.edu
lab head
Tjorven Hinzke
contact affiliation	University of Greifswald, Greifswald Intitute of Marine Biotechnology
contact email	tjorven.hinzke@stud.uni-greifswald.de
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/2019/02/PXD008017

PRIDE project URI

• PRIDE
  1. PXD008017
     1. Label: PRIDE project
     2. Name: More is not always better: Evaluation of 1D- and 2D-LC-MS2 methods for metaproteomics