title: SAFER, an Analysis Method of Quantitative Proteomic Data, Reveals New Interactors of the C. elegans Autophagic Protein LGG-1.
abstract: Affinity purifications followed by mass spectrometric analysis are used to identify protein-protein interactions. Because quantitative proteomic data are noisy, it is necessary to develop statistical methods to eliminate false-positives and identify true partners. We present here a novel approach for filtering false interactors, named "SAFER" for mass Spectrometry data Analysis by Filtering of Experimental Replicates, which is based on the reproducibility of the replicates and the fold-change of the protein intensities between bait and control. To identify regulators or targets of autophagy, we characterized the interactors of LGG1, a ubiquitin-like protein involved in autophagosome formation in C. elegans. LGG-1 partners were purified by affinity, analyzed by nanoLC-MS/MS mass spectrometry, and quantified by a label-free proteomic approach based on the mass spectrometric signal intensity of peptide precursor ions. Because the selection of confident interactions depends on the method used for statistical analysis, we compared SAFER with several statistical tests and different scoring algorithms on this set of data. We show that SAFER recovers high-confidence interactors that have been ignored by the other methods and identified new candidates involved in the autophagy process. We further validated our method on a public data set and conclude that SAFER notably improves the identification of protein interactors.
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Yi
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
authors.forename: Marion
authors.initials: M
authors.lastname: Manil-Ségalen
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.|Service d'Identification et de Caractérisation des Protéines par Spectrométrie de masse (SICaPS), CNRS, 91198 Gif-sur-Yvette, France.
authors.forename: Laila
authors.initials: L
authors.lastname: Sago
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
authors.forename: Annie
authors.initials: A
authors.lastname: Glatigny
authors.affiliation: Service d'Identification et de Caractérisation des Protéines par Spectrométrie de masse (SICaPS), CNRS, 91198 Gif-sur-Yvette, France.|Paris-Saclay Institute of Neuroscience (Neuro-PSI), CNRS, 91198 Gif-sur-Yvette cedex, France.
authors.forename: Virginie
authors.initials: V
authors.lastname: Redeker
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.
authors.forename: Renaud
authors.initials: R
authors.lastname: Legouis
authors.affiliation: Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette cedex, France.|Sorbonne Universités , UPMC Univ Paris 06, UFR927, F-75005, Paris, France.
authors.forename: Marie-Hélène
authors.initials: MH
authors.lastname: Mucchielli-Giorgi
mesh_terms: D000465:Algorithms; D000818:Animals; D001343:Autophagy; D017173:Caenorhabditis elegans / Q000737:chemistry*; D029742:Caenorhabditis elegans Proteins / Q000032:analysis / Q000378:metabolism*; D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D008869:Microtubule-Associated Proteins / Q000032:analysis / Q000378:metabolism*; D011485:Protein Binding; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D053719:Tandem Mass Spectrometry
chemical_list: D029742:Caenorhabditis elegans Proteins; C587195:LGG-1 protein, C elegans; D008869:Microtubule-Associated Proteins
keywords: C. elegans; atg-8/LC3; autophagy; label free mass spectrometry; proteomics; statistical methodology