Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores - CNRS - Centre national de la recherche scientifique Accéder directement au contenu
Chapitre D'ouvrage Année : 2022

Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores

Résumé

Abstract Simple light isotope metabolic labeling (bSLIM) is an innovative method to accurately quantify differences in protein abundance at the proteome level in standard bottom-up experiments. The quantification process requires computation of the ratio of intensity of several isotopologs in the isotopic cluster of every identified peptide. Thus, appropriate bioinformatic workflows are required to extract the signals from the instrument files and calculate the required ratio to infer peptide/protein abundance. In a previous study (Sénécaut et al., J Proteome Res 20:1476–1487, 2021), we developed original open-source workflows based on OpenMS nodes implemented in a KNIME working environment. Here, we extend the use of the bSLIM labeling strategy in quantitative proteomics by presenting an alternative procedure to extract isotopolog intensities and process them by taking advantage of new functionalities integrated into the Minora node of Proteome Discoverer 2.4 software. We also present a graphical strategy to evaluate the statistical robustness of protein quantification scores and calculate the associated false discovery rates (FDR). We validated these approaches in a case study in which we compared the differences between the proteomes of two closely related yeast strains.

Dates et versions

hal-03858134 , version 1 (17-11-2022)

Identifiants

Citer

Nicolas Sénécaut, Pierre Poulain, Laurent Lignières, Samuel Terrier, Véronique Legros, et al.. Quantitative Proteomics in Yeast: From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores. Yeast Functional Genomics, 2477, Springer US, pp.275-292, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-2257-5_16⟩. ⟨hal-03858134⟩
10 Consultations
0 Téléchargements

Altmetric

Partager

Gmail Facebook X LinkedIn More