PXD004039

PXD004039 is an original dataset announced via ProteomeXchange.

Title	Sequence database choice significantly affects taxonomic and functional metaproteomic results in gut microbiota studies
Description	Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics (the study of the whole protein complement of a microbial community) can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Here we present a systematic investigation of variables concerning database construction and annotation, and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. Taxonomic and functional results were revealed to be strongly database-dependent, especially when dealing with mouse samples. As a striking example, in mouse the Firmicutes/Bacteroidetes ratio varied up to 10-fold depending on the database used. Finally, we provide recommendations regarding metagenomic sequence processing aimed at maximizing gut metaproteome characterization, and contribute to identify an optimized pipeline for metaproteomic data analysis.
HostingRepository	PRIDE
AnnounceDate	2016-10-10
AnnouncementXML	Submission_2016-10-10_10:38:10.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alessandro Tanca
SpeciesList	scientific name: human gut metagenome; NCBI TaxID: 408170;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-24 23:39:06	ID requested
⏵ 1	2016-10-10 10:38:11	announced

Tanca A, Palomba A, Fraumene C, Pagnozzi D, Manghina V, Deligios M, Muth T, Rapp E, Martens L, Addis MF, Uzzau S, The impact of sequence database choice on metaproteomic results in gut microbiota studies. Microbiome, 4(1):51(2016) [pubmed]

curator keyword: Technical, Biological

submitter keyword: bioinformatics, gut microbiota, metagenomics, metaproteomics

Sergio Uzzau
contact affiliation	Porto Conte Ricerche, Science and Technology Park of Sardinia, Tramariglio, Alghero, Italy
contact email	uzzau@portocontericerche.it
lab head
Alessandro Tanca
contact affiliation	Proteomics Laboratory, Porto Conte Ricerche, Alghero, Italy
contact email	tanca@portocontericerche.it
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD004039
     1. Label: PRIDE project
     2. Name: Sequence database choice significantly affects taxonomic and functional metaproteomic results in gut microbiota studies