Dataset Information

Metaproteomic analysis using the Galaxy framework

ABSTRACT: Metaproteomics characterizes proteins expressed by microorganism communities (microbiome) present in environmental samples or a host organism (e.g. human), revealing insights into the molecular functions conferred by these communities. Compared to conventional proteomics, metaproteomics presents unique data analysis challenges, including the use large protein databases derived from hundreds of organisms, as well as numerous processing steps to ensure data quality. This data analysis complexity limits the use of metaproteomics for many researchers. In response, we have developed an accessible and flexible metaproteomics workflow within the Galaxy bioinformatics framework. Via analysis of human oral tissue exudate samples, we have established a modular Galaxy-based workflow that automates a reduction method for searching large sequence databases, enabling comprehensive identification of host proteins (human) as well as meta-proteins from the non-host organisms. Downstream, automated processing steps enable BLASTP analysis and evaluation/visualization of peptide sequence match quality, maximizing confidence in results. Outputted results are compatible with tools for taxonomic and functional characterization (e.g. Unipept, MEGAN5). Galaxy also allows for the sharing of complete workflows with others, promoting reproducibility and also providing a template for further modification and improvement. Our results provide a blueprint for establishing Galaxy as a solution for metaproteomic data analysis.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Saliva

DISEASE(S): Oral Squamous Cell Carcinoma

SUBMITTER: Pratik Jagtap

LAB HEAD: Timothy J. Griffin

PROVIDER: PXD001655 | Pride | 2015-07-02

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	3-Frame-translated-cDNA-Homo_sapiens.GRCh37.75.fasta	Fasta
	CONTROL_ProteinPilot_methods_xml.xml	Xml
	Control__HOMD-EnSEMBL_Peptide_Summary.tabular	Other
	Galaxy1-tgriffin_koore004_040511_patient4_control_CA_Fr1.RAW.raw	Raw
	Galaxy10-tgriffin_koore004_040511_patient4_lesion_LC_Fr3.RAW.raw	Raw

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Publications

Metaproteomic analysis using the Galaxy framework.

Jagtap Pratik D PD Blakely Alan A Murray Kevin K Stewart Shaun S Kooren Joel J Johnson James E JE Rhodus Nelson L NL Rudney Joel J Griffin Timothy J TJ

Proteomics 20150724 20

Metaproteomics characterizes proteins expressed by microorganism communities (microbiome) present in environmental samples or a host organism (e.g. human), revealing insights into the molecular functions conferred by these communities. Compared to conventional proteomics, metaproteomics presents unique data analysis challenges, including the use of large protein databases derived from hundreds or thousands of organisms, as well as numerous processing steps to ensure high data quality. These chal ...[more]

PMID: 26058579

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