PXD001655-2

PXD001655 is an original dataset announced via ProteomeXchange.

Title	Metaproteomic analysis using the Galaxy framework
Description	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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:22:25.931.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Pratik Jagtap
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-01-06 06:22:50	ID requested
1	2015-07-02 01:51:59	announced
⏵ 2	2024-10-22 04:22:26	announced	2024-10-22: Updated project metadata.

Jagtap PD, Blakely A, Murray K, Stewart S, Kooren J, Johnson JE, Rhodus NL, Rudney J, Griffin TJ, Metaproteomic analysis using the Galaxy framework. Proteomics, 15(20):3553-65(2015) [pubmed]

10.1002/pmic.201500074;

curator keyword: Metaproteomics

submitter keyword: Metaproteomics

Workflows.

Timothy J. Griffin
contact affiliation	Associate Professor, BMBB, University of Minnesota, Minneapolis, MN
contact email	tgriffin@umn.edu
lab head
Pratik Jagtap
contact affiliation	Center for Mass Spectrometry and Proteomics
contact email	pjagtap@umn.edu
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/2015/07/PXD001655

PRIDE project URI

• PRIDE
  1. PXD001655
     1. Label: PRIDE project
     2. Name: Metaproteomic analysis using the Galaxy framework