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Sénécaut N, Poulain P, Lignières L, Terrier S, Legros V, Chevreux G, Lelandais G, Camadro JM. Quantitative Proteomics in Yeast : From bSLIM and Proteome Discoverer Outputs to Graphical Assessment of the Significance of Protein Quantification Scores. Methods Mol Biol 2022; 2477:275-292. [PMID: 35524123 DOI: 10.1007/978-1-0716-2257-5_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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.
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Affiliation(s)
- Nicolas Sénécaut
- Mitochondria, Metals, and Oxidative Stress Group, Institut Jacques Monod, Université de Paris-CNRS, Paris, France
| | - Pierre Poulain
- Mitochondria, Metals, and Oxidative Stress Group, Institut Jacques Monod, Université de Paris-CNRS, Paris, France
| | - Laurent Lignières
- ProteoSeine@IJM, Institut Jacques Monod, Université de Paris-CNRS, Paris, France
| | - Samuel Terrier
- ProteoSeine@IJM, Institut Jacques Monod, Université de Paris-CNRS, Paris, France
| | - Véronique Legros
- ProteoSeine@IJM, Institut Jacques Monod, Université de Paris-CNRS, Paris, France
| | - Guillaume Chevreux
- ProteoSeine@IJM, Institut Jacques Monod, Université de Paris-CNRS, Paris, France
| | - Gaëlle Lelandais
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jean-Michel Camadro
- Mitochondria, Metals, and Oxidative Stress Group, Institut Jacques Monod, Université de Paris-CNRS, Paris, France.
- ProteoSeine@IJM, Institut Jacques Monod, Université de Paris-CNRS, Paris, France.
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