PXD028880-2

PXD028880 is an original dataset announced via ProteomeXchange.

Title	Extending the range of SLIM-labeling applications: from human cell lines in culture to Caenorhabditis elegans whole-organism labeling
Description	The simple light isotope metabolic-labeling technique relies on the in-vivo biosynthesis of amino acids from U-[12C]-labeled molecules provided as the sole carbon source. The incorporation of the resulting U-[12C]-amino acids into proteins presents several key advantages for mass-spectrometry-based proteomics analysis, as it results in more intense monoisotopic ions, with a better signal-to-noise ratio in bottom-up analysis. In our initial studies, we developed the SLIM-labeling strategy using prototrophic eukaryotic microorganisms, the yeasts Candida albicans and Saccharomyces cerevisiae, as well as strains with genetic markers that lead to amino-acid auxotrophy. To extend the range of SLIM-Labeling applications, we evaluated (i) the incorporation of U-[12C]-glucose into proteins of human cells grown in a complex RPMI-based medium containing the labelled molecule, considering that human cell lines require a large number of essential amino-acids to support their growth, and (ii) an indirect labeling strategy in which the nematode Caenorhabditis elegans grown on plates was fed U-[12C]-labelled bacteria (Eschericha coli) and the worm proteome analyzed for 12C incorporation into proteins. In both cases, we were able to demonstrate efficient incorporation of 12C into the newly synthesized proteins, opening the way for original approaches in quantitative proteomics.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:50:18.639.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Laurent Lignières
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Caenorhabditis elegans; NCBI TaxID: 6239; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-10-01 01:30:24	ID requested
1	2023-06-23 08:05:51	announced
⏵ 2	2024-10-22 05:50:19	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: auxin, mass spectrometry, bottom-up proteomics, human cell line, essential amino acids,SLIM metabolic labeling, Caenorhabditis elegans

Jean-Michel Camadro
contact affiliation	Team Mitochondria, metals and oxidative stress, Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris France
contact email	jean-michel.camadro@ijm.fr
lab head
Laurent Lignières
contact affiliation	Proteomic facility of Institut Jacques Monod (UMR7592) - CNRS & Université de Paris
contact email	laurent.lignieres@ijm.fr
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/2023/06/PXD028880

PRIDE project URI

• PRIDE
  1. PXD028880
     1. Label: PRIDE project
     2. Name: Extending the range of SLIM-labeling applications: from human cell lines in culture to Caenorhabditis elegans whole-organism labeling