SAFER, an Analysis Method of Quantitative Proteomic Data, Reveals New Interactors of the C. elegans Autophagic Protein LGG-1.
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.
['Yi|Zhou|Z|', 'Manil-Ségalen|Marion|M|', 'Sago|Laila|L|', 'Glatigny|Annie|A|', 'Redeker|Virginie|V|', 'Legouis|Renaud|R|', 'Mucchielli-Giorgi|Marie-Hélène|MH|']
D000465:Algorithms D000818:Animals D001343:Autophagy D017173:Caenorhabditis elegans D029742:Caenorhabditis elegans Proteins D003627:Data Interpretation, Statistical D030562:Databases, Protein D008869:Microtubule-Associated Proteins D011485:Protein Binding D040901:Proteomics D015203:Reproducibility of Results D053719:Tandem Mass Spectrometry
proteomics C. elegans autophagy atg-8/LC3 label free mass spectrometry statistical methodology