PXD006118

PXD006118 is an original dataset announced via ProteomeXchange.

Title	Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics
Description	In this study we developed metaproteomics based methods for quantifying taxonomic composition of microbiomes (microbial communities). We also compared metaproteomics based quantification to other quantification methods, namely metagenomics and 16S rRNA gene amplicon sequencing. The metagenomic and 16S rRNA data can be found in the European Nucleotide Archive (Study number: PRJEB19901). For the method development and comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing and metaproteomics. Three replicates of each community type were analyzed with metagenomics. The "C" type communities have same cell/phage particle number for all community members (C1 to C4). The "P" type communities have the same protein content for all community members (P1 to P4). The "U" (UNEVEN) type communities cover a large range of protein amounts and cell numbers (U1 to U4). We also generated proteomic data for four pure cultures to test the specificity of the protein inference method. This data is also included in this submission.
HostingRepository	PRIDE
AnnounceDate	2017-05-12
AnnouncementXML	Submission_2019-02-18_07:40:27.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manuel Kleiner
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	2017-03-20 03:09:39	ID requested
1	2017-05-12 00:43:22	announced
2	2017-11-22 08:34:24	announced	Updated publication reference for PubMed record(s): 29146960.
⏵ 3	2019-02-18 07:40:29	announced	Updated publication reference for PubMed record(s): 29146960.

Kleiner M, Dong X, Hinzke T, Wippler J, Thorson E, Mayer B, Strous M, Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities. Proc Natl Acad Sci U S A, 115(24):E5576-E5584(2018) [pubmed]

Kleiner M, Thorson E, Sharp CE, Dong X, Liu D, Li C, Strous M, Assessing species biomass contributions in microbial communities via metaproteomics. Nat Commun, 8(1):1558(2017) [pubmed]

curator keyword: Metaproteomics, Biological

submitter keyword: 1D-LC, 2D-LC, metaproteomics, metaproteome, mock community, metagenomics, biomass assessment, microbiome

Manuel Kleiner
contact affiliation	North Carolina State University, NC, USA
contact email	manuel_kleiner@ncsu.edu
lab head
Manuel Kleiner
contact affiliation	University of Calgary
contact email	manuel.kleiner@ucalgary.ca
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/2017/05/PXD006118

PRIDE project URI

• PRIDE
  1. PXD006118
     1. Label: PRIDE project
     2. Name: Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics