PXD024288

PXD024288 is an original dataset announced via ProteomeXchange.

Title	Labeling Escherichia coli to saturation with 2.5 % of 15N ammonium in two conditions (aerobic and anaerobic) for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)
Description	This dataset is part of a study aimed at developing algorithms for the quantification of stable isotope content in microorganisms after labeling them with stable isotope-labeled substrates. For this dataset Escherichia coli cultures were labeled with 2.5 % of 15N-labeled NH4Cl and grown either anaerobically or aerobically. Cultures of E. coli were grown in M9 minimal medium in which 2.5 % of the ammonium was replaced with 15N-labeled NH4Cl for >10 generations to achieve close to complete labeling of cells. Triplicate cultures were grown. Please note that the unlabeled ammonium that was used of course had a natural content of 15N of around 0.4 %, thus the 0% added label samples have an actual 15N content of 0.4 % and all added label is on top of this value. We included a tab delimited table with this submission providing details on all raw files.
HostingRepository	PRIDE
AnnounceDate	2023-09-28
AnnouncementXML	Submission_2023-09-28_03:32:50.816.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	ManuelKleiner
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-22 01:44:38	ID requested
1	2022-02-16 15:52:43	announced
⏵ 2	2023-09-28 03:32:53	announced	2023-09-28: Updated project metadata.

Jensen M, Wippler J, Kleiner M, as a Field-Compatible Preservation Method for Metaproteomic Analyses of Bacterium-Animal Symbioses. Microbiol Spectr, 9(2):e0142921(2021) [pubmed]

Kleiner M, Kouris A, Violette M, D'Angelo G, Liu Y, Korenek A, Toli, ć N, Sachsenberg T, McCalder J, Lipton MS, Strous M, Ultra-sensitive isotope probing to quantify activity and substrate assimilation in microbiomes. Microbiome, 11(1):24(2023) [pubmed]

submitter keyword: nitrogen 15, stable isotope probing, stable isotope,15N, Protein-SIP, 1D-LC, metaproteomics, LC-MS/MS

ManuelKleiner
contact affiliation	North Carolina State University
contact email	manuel_kleiner@ncsu.edu
lab head
ManuelKleiner
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/2022/02/PXD024288

PRIDE project URI

• PRIDE
  1. PXD024288
     1. Label: PRIDE project
     2. Name: Labeling Escherichia coli to saturation with 2.5 % of 15N ammonium in two conditions (aerobic and anaerobic) for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)