PXD024287 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Mixing of Escherichia coli cells labeled with 13C glucose with unlabeled E. coli cells 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 cultures were labeled with different percentages (1% or 10%) of either single-carbon 13C glucose (13C2) or fully-labeled 13C glucose (13C1-6). Labeled cells were subsequently mixed with unlabeled E. coli cells in fixed ratios (50%, 90%, 95%, 99%). Cultures of E. coli were grown in M9 minimal medium in which a percentage of the glucose was replaced with 13C2 or 13C1-6 glucose for >10 generations to achieve close to complete labeling of cells. 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_09:05:34.324.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; |
ModificationList | acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Q Exactive Plus |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-02-22 01:44:34 | ID requested | |
1 | 2023-01-03 05:46:11 | announced | |
2 | 2023-09-28 03:32:25 | announced | 2023-09-28: Updated project metadata. |
3 | 2023-11-14 08:52:00 | announced | 2023-11-14: Updated project metadata. |
⏵ 4 | 2023-11-14 09:05:35 | 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, metaproteomics, LC-MS/MS |
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
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD024287
- Label: PRIDE project
- Name: Mixing of Escherichia coli cells labeled with 13C glucose with unlabeled E. coli cells for benchmarking of protein-based stable isotope probing proteomics (Protein-SIP)