PXD011735

PXD011735 is an original dataset announced via ProteomeXchange.

Title	Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic
Description	Quantitative metaproteomics is a relatively new research field by applying proteomics technique to study microbial proteins of microbiome, and holds the great potential to truly quantify the functional proteins actually expressed by microbes in the biological environment such as gastrointestinal tract. The significant association between arsenic exposure and gut microbiome perturbations has been reported; however, metaproteomics has not yet been applied to study arsenic induced proteome changes of microbiome. Most importantly, to our knowledge, isobaric-labeling based large-scale metaproteomics has not been reported using the advanced database search approaches such as MetaPro-IQ and matched metagenome database search strategies to provide high quantification accuracy and less missing quantification values. In the present study, a new experimental workflow coupled with isobaric labeling and MetaPro-IQ was demonstrated for metaproteomics study of arsenic induced gut microbiome perturbations. The advantages of this workflow were also discussed. For all 18 fecal samples analyzed, 7,611 protein groups were quantified without any missing values. The consistent results of expression profiles were observed between 16S rRNA gene sequencing and metaproteomics. This isobaric labeling based workflow demonstrated the significant improvement of quantitative metaproteomics for gut microbiome study.
HostingRepository	PRIDE
AnnounceDate	2018-12-17
AnnouncementXML	Submission_2018-12-21_01:32:16.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Chih-Wei Liu
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-19 08:16:31	ID requested
1	2018-12-17 08:38:59	announced
⏵ 2	2018-12-21 01:32:18	announced	Updated publication reference for PubMed record(s): 30545218.

Liu CW, Chi L, Tu P, Xue J, Ru H, Lu K, Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic. J Proteome Res, 18(3):970-981(2019) [pubmed]

curator keyword: Metaproteomics, Biomedical

submitter keyword: Metaproteomics, gut microbiome, arsenic, isobaric labeling, tandem mass tags, label free, MetaPro-IQ

Kun Lu
contact affiliation	University of North Carolina at Chapel Hill
contact email	kunlu@unc.edu
lab head
Chih-Wei Liu
contact affiliation	University of North Carolina at Chapel Hill
contact email	ericleah@email.unc.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/2018/12/PXD011735

PRIDE project URI

• PRIDE
  1. PXD011735
     1. Label: PRIDE project
     2. Name: Isobaric Labeling Quantitative Metaproteomics for the Study of Gut Microbiome Response to Arsenic