Effect of ATG5 depletion on virus infection
Proteome analysis of wild-type and atg5-/- mouse embryonic fibroblasts infected with Japanese encephalitis virus
Sample Processing Protocol
Digestion was performed using LysC and trypsin, 75ug of peptides of each sample were labelled with TMT reagent. 12 fractions were analyzed on Orbitrap Fusion mass spectrometer. Peptides were detected MS1 and quantified MS3 in the Orbitrap. Peptides were sequences MS2 in the ion trap.
Data Processing Protocol
MS2 spectra were searched using SEQUEST alogrithm using a Uniprot composite database from the Mus musculus proteome. Peptide spectral matches were filtered to a 1% FDA using the target decoy strategy combined with linear discriminant analysis. Proteins were quantified only from peptides with a summed SN threshold of >=200 and isolation specificity of 0.5
Sharma KB, Sharma M, Aggarwal S, Yadav AK, Bhatnagar S, Vrati S, Kalia M. Quantitative Proteome Analysis of Atg5-Deficient Mouse Embryonic Fibroblasts Reveals the Range of the Autophagy-Modulated Basal Cellular Proteome. mSystems. 2019 4(6) PubMed: 31690592