Computational protocol: Acetylome Analysis Identifies SIRT1 Targets in mRNA-Processing and Chromatin-Remodeling in Mouse Liver

Similar protocols

Protocol publication

[…] Proteins were identified and quantified through the Proteome Discoverer 1.4 platform (thermo) by using Sequest HT searching engine and the mouse database. Sequest parameters were used as follow: Carbamidomethylation of cysteine and acetylation of lysine were set as fixed modifications and oxidation of methionine and deamination of asparagine (D) and glutamine (Q) were set as variable modifications. Trypsin was the protease selected and up to two missed cleavages was used. Mass tolerance for the precursor ions was 10 ppm and for the MS/MS 0.2 Da. Only peptides with minimal length of four amino acids were considered and peptides were filtered for maximum false discovery rate of 1%. Acetylated peptides were further manually confirmed by comparing their detected fragmentation ions with theoretic counterparts and guaranteeing the appearance of m/z 126.0914 corresponding to acetylated lysine. […]

Pipeline specifications

Software tools Proteome Discoverer, Comet
Application MS-based untargeted proteomics
Organisms Mus musculus