PXD021329

PXD021329 is an original dataset announced via ProteomeXchange.

Title	Novel insights into quantitative proteomics from an innovative bottom-up Simple Light Isotope Metabolic (bSLIM) labeling data processing strategy
Description	The Simple Light Isotope Metabolic labeling (SLIM-labeling) is an inovative method to quantify proteome variations based on an original in vivo labeling strategy. Heterotrophic cells grown on a U-[12C] sole source of carbon synthesize U-[12C]-amino acids which are incorporated into proteins giving rise ultimately to U-[12C]-proteins. This results in a large increase of the intensity of the monoisotope ion of peptides and proteins, and therefore allows higher identification scores and protein sequence coverage in mass spectrometry experiments. The method initially developed for signal processing and quantification of the rate of incorporation of 12C into peptides was based on a multistep process that was found difficult to implement by many laboratories. To overcome these limitations, we developed a new theoretical background to analyze the bottom-up proteomics data using SLIM-labeling (bSLIM) and set simple procedures based on open source software, using dedicated OpenMS modules, and embedded R scripts to process the bSLIM experimental data. These new tools allow both the computation of the 12C abundance in peptides to follow kinetics of protein labeling, and of the molar fraction of unlabeled and 12C-labeled peptides in multiplexing experiments to determine the relative abun-dance of proteins extracted from different biological conditions. The tools also allow us to take into account incomplete 12C labeling as observed in cells with nutritional requirements for non-labeled amino acids. These tools were validated on experimental dataset produced using various yeast strains of Saccharomyces cerevisiae and growth conditions. The workflows are built on the implemen-tation of appropriate calculus modules in a KNIME working environment. These new integrated tools provide a convenient frame-work for a wider use of the SLIM-labeling strategy.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:32:14.014.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nicolas SENECAUT
SpeciesList	scientific name: Saccharomyces cerevisiae (Baker's yeast); NCBI TaxID: 4932;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-07 00:52:23	ID requested
1	2022-02-16 04:06:15	announced
⏵ 2	2024-10-22 05:32:15	announced	2024-10-22: Updated project metadata.

10.1021/acs.jproteome.0c00478;

S, é, n, é, caut N, Alves G, Weisser H, Ligni, è, res L, Terrier S, Yang-Crosson L, Poulain P, Lelandais G, Yu YK, Camadro JM, Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy. J Proteome Res, 20(3):1476-1487(2021) [pubmed]

submitter keyword: OpenMS, data processing workflow, Yeast,In vivo metabolic labeling, light carbon isotope, quantitative proteomics, 12C, KNIME

Jean-Michel CAMADRO
contact affiliation	Jean-Michel CAMADRO, PhD DR1 CNRS "Mitochondria, Metals and Oxidative Stress" group leader Head "Mass Spectrometry Lab and Proteomics core Facility" Jacques Monod Institute UMR7592 CNRS - Paris University 15 rue Hélène Brion 75205 Paris Cedex 13, FRANCE
contact email	jean-michel.camadro@ijm.fr
lab head
Nicolas SENECAUT
contact affiliation	Institut Jacques-Monod UMR7592
contact email	nicolas.senecaut@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/2022/02/PXD021329

PRIDE project URI

• PRIDE
  1. PXD021329
     1. Label: PRIDE project
     2. Name: Novel insights into quantitative proteomics from an innovative bottom-up Simple Light Isotope Metabolic (bSLIM) labeling data processing strategy