PXD024291

PXD024291 is an original dataset announced via ProteomeXchange.

Title	Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities using protein-based stable isotope probing proteomics (Protein-SIP)
Description	This dataset was obtained from the authors of Starke et al. (2020, Journal of Proteomics 222: 103791, https://doi.org/10.1016/j.jprot.2020.103791). Sample labels: 1 - High fiber diet inoculum 2 - High protein diet inoculum 3,4,5 - High fiber + unlabeled water 6,7,8 - High protein + unlabeled water 9,10,11 - High fiber + 25% of 99.9 atom% D2O 12,13,14 - High protein + 25% of 99.9 atom% D2O 15,16,17 - High fiber + 25% of 99.0 atom% H218O 18,19,20 - High protein + 25% of 99.0 atom% H218O Direct quote from the original article describing the dataset. “…the impact of specific diets on a defined microbial community derived from a human fecal sample was to be determined. The defined community was chosen to provide a stable in vitro setup that could be useful for future microbiome research. Briefly, the microbial community was grown in a heavy fiber and a heavy protein diet in addition to 25% heavy water, either as D2O or H218O. A dosage of 25% isotopically labeled water was chosen by trial-and-error to yield sufficient incorporation into protein but avoid the reduction of activity of individual organisms. A difference in growth medium formulation, representing a high-fiber diet and a high-protein diet, was utilized to evaluate shifts in microbial activity. We chose to assess these diets because high-protein, low-carbohydrate interventions represent a popular weight-loss strategy and because we expected a strong effect on the synthesis of amino acids by this comparison. After an incubation time of 12 h, the proteins were analyzed for label-free quantitation (metaproteomics) and incorporation of isotopes (protein-SIP), each in triplicates….”
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:51:36.403.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Manuel Kleiner
SpeciesList	scientific name: Bacteria; NCBI TaxID: 2;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-22 01:44:51	ID requested
1	2022-12-30 07:44:24	announced
2	2023-11-14 07:12:29	announced	2023-11-14: Updated project metadata.
⏵ 3	2023-11-14 08:51:41	announced	2023-11-14: Updated project metadata.

Starke R, Oliphant K, Jehmlich N, Sch, ä, pe SS, Sachsenberg T, Kohlbacher O, Allen-Vercoe E, von Bergen M, Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities. J Proteomics, 222():103791(2020) [pubmed]

submitter keyword: deuterium, stable isotope probing, 18O, Protein-SIP, D2O, metaproteomics, LC-MS/MS,Heavy water, 2H, Oxygen 18, H218O, stable isotope, 1D-LC

Martin von Bergen
contact affiliation	Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
contact email	martin.vonbergen@ufz.de
lab head
Manuel Kleiner
contact affiliation	North Carolina State University
contact email	manuel_kleiner@ncsu.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/2022/12/PXD024291

PRIDE project URI

• PRIDE
  1. PXD024291
     1. Label: PRIDE project
     2. Name: Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities using protein-based stable isotope probing proteomics (Protein-SIP)