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Re-analysis of an ultra-deep and quantitative saliva proteome

ABSTRACT: This is a re-analysis of the saliva metaproteome dataset by Grassl et al. (Grassl et al. 2016 Genome Med, 8(1):44 DOI: 10.1186/s13073-016-0293-0) available on ProteomeXchange PXD003028. The data was used as a case study for a method development study in which we developed metaproteomics based methods for quantifying taxonomic composition of microbiomes (microbial communities). We used the fraction data from the original study for individuals 1 (female1), 3 (female3), 5 (male1), and 7 (male3).

OTHER RELATED OMICS DATASETS IN: PRJEB19901

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Bacteria

TISSUE(S): Saliva

SUBMITTER: Manuel Kleiner

LAB HEAD: Marc Strous

PROVIDER: PXD006366 | Pride | 2017-05-12

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	1_fractionated.msf	Msf
	1_fractionated.pep.xml	Pepxml
	20150414_QEp1_LC7_NiGr_SA_Saliva_1_fractionated1.raw	Raw
	20150414_QEp1_LC7_NiGr_SA_Saliva_1_fractionated2.raw	Raw
	20150414_QEp1_LC7_NiGr_SA_Saliva_1_fractionated3.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]

PMID: 29146960

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