Raw data from each fraction were searched using SEQUEST (v28) against a mouse SwissProt/trEMBL database (release of 09/09/2011), concatenated with a decoy database with all the protein sequences in reverse order. Searches were performed using a 15 p.p.m. mass tolerance for precursor ions and 0.02 Da window for fragment ions, allowing up to two missed trypsin cleavage sites. Six-plex TMT tags on lysine residues and peptide N termini (+229.162932 Da) and oxidation of methionine residues (+15.99492 Da) were used for dynamic modification, and carbamidomethylation of cysteine residues (+57.021 Da) was used for static modifications.
