PXD001573

PXD001573 is an original dataset announced via ProteomeXchange.

Title	Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota
Description	Up to date, most metaproteomic studies of the gut microbiota describe the use of stool sample pretreatment methods to enrich for microbial components. However, a specific investigation aimed at assessing if, how and to what extent this may impact on the final taxonomic and functional results is still lacking. Here, stool replicates were either pretreated by differential centrifugation (DC) or not centrifuged (NC). Protein extracts were then processed by filter-aided sample preparation, single-run LC and high-resolution MS, and the metaproteomic data were compared by spectral counting. DC led to a higher number of identifications, a significantly richer microbial diversity, as well as to reduced information on the non-microbial components (host and food) when compared to NC. Nevertheless, dramatic differences in the relative abundance of many gut microbial taxa were also observed, including a significant change in the Firmicutes/Bacteroidetes ratio. Furthermore, several microbial functional categories, including cell surface enzymes, membrane-associate proteins, and flagella, were significant reduced after DC. In conclusion, this work underlines that a critical evaluation is needed when selecting the appropriate stool sample processing protocol in the context of a metaproteomic study, depending on the specific target to which the research is aimed.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:21:46.262.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Alessandro Tanca
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2014-12-05 00:56:56	ID requested
1	2015-02-25 08:20:48	announced
⏵ 2	2024-10-22 04:21:50	announced	2024-10-22: Updated project metadata.

10.1002/pmic.201400573;

Tanca A, Palomba A, Pisanu S, Addis MF, Uzzau S, Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota. Proteomics, 15(20):3474-85(2015) [pubmed]

curator keyword: Biomedical

submitter keyword: differential centrifugation

gut microbiome

host

metaproteomics

sample preparation

Maria Filippa Addis
contact affiliation	Proteomics Laboratory, Porto Conte Ricerche, Alghero, Italy
contact email	addis@portocontericerche.it
lab head
Alessandro Tanca
contact affiliation	Proteomics Laboratory, Porto Conte Ricerche, Alghero, Italy
contact email	tanca@portocontericerche.it
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/2015/02/PXD001573

PRIDE project URI

• PRIDE
  1. PXD001573
     1. Label: PRIDE project
     2. Name: Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota