PXD023693 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Labeling of Bacillus subtilis and Escherichia coli to saturation with different percentages of fully 13C labeled glucose 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. In this dataset Escherichia coli and Bacillus subtilis cultures were labeled with different percentages of fully labeled 13C glucose (13C6). Cultures of B. subtilis and E. coli were grown in Bacillus minimal medium or M9 minimal medium (E. coli) in which a percentage of the glucose was replaced with 13C6 glucose for >10 generations to achieve close to complete labeling of cells. The following percentages of 13C6 glucose were added 0, 0.01, 0.025, 0.1, 0.25, 1, 5 and 10%. Triplicate cultures were grown for each percentage. Please note that the unlabeled glucose that was used of course had a natural content of 13C of around 1.1%, thus the 0% added label samples have an actual 13C content of 1.1% 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 | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_09:05:23.221.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Manuel Kleiner |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Bacillus subtilis subsp. subtilis; NCBI TaxID: 135461; |
ModificationList | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive HF |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-01-20 01:36:42 | ID requested | |
1 | 2023-01-04 03:45:57 | announced | |
2 | 2023-09-28 03:32:14 | announced | 2023-09-28: Updated project metadata. |
3 | 2023-11-14 08:51:42 | announced | 2023-11-14: Updated project metadata. |
⏵ 4 | 2023-11-14 09:05:30 | announced | 2023-11-14: Updated project metadata. |
Publication List
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] |
Keyword List
submitter keyword: 13C, carbon 13, stable isotope probing, stable isotope, Protein-SIP, 1D-LC |
Contact List
Manuel Kleiner |
contact affiliation | North Carolina State University |
contact email | manuel_kleiner@ncsu.edu |
lab head | |
Manuel Kleiner |
contact affiliation | North Carolina State University |
contact email | manuel_kleiner@ncsu.edu |
dataset submitter | |
Full Dataset Link List
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/PXD023693 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD023693
- Label: PRIDE project
- Name: Labeling of Bacillus subtilis and Escherichia coli to saturation with different percentages of fully 13C labeled glucose for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)