Proteomics

Dataset Information

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Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics


ABSTRACT: 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.

OTHER RELATED OMICS DATASETS IN: PRJEB19901

INSTRUMENT(S): Q Exactive

ORGANISM(S): Archaea Bacteria Viruses Eukaryota (eucaryotes)

SUBMITTER: Manuel Kleiner  

LAB HEAD: Manuel Kleiner

PROVIDER: PXD006118 | Pride | 2017-05-12

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
C1_run3.msf Msf
C1_run3.pep.xml Pepxml
C1_run3_1000mM.raw Raw
C1_run3_100mM.raw Raw
C1_run3_10mM.raw Raw
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Publications

Assessing species biomass contributions in microbial communities via metaproteomics.

Kleiner Manuel M   Thorson Erin E   Sharp Christine E CE   Dong Xiaoli X   Liu Dan D   Li Carmen C   Strous Marc M  

Nature communications 20171116 1


Microbial community structure can be analyzed by quantifying cell numbers or by quantifying biomass for individual populations. Methods for quantifying cell numbers are already available (e.g., fluorescence in situ hybridization, 16-S rRNA gene amplicon sequencing), yet high-throughput methods for assessing community structure in terms of biomass are lacking. Here we present metaproteomics-based methods for assessing microbial community structure using protein abundance as a measure for biomass  ...[more]

Publication: 1/2

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