Frontal cortex - proteomics in a mouse model of chronic heart failure

Bottom-up proteomic analysis of frontal cortex was performed using a Thermo Scientific Q Exactive Plus Orbitrap Mass Spectrometer and TOP-10 Data Dependent Acquisition (DDA).

Data were processed using Thermo Proteome Discoverer (version 2.3) in conjunction with SEQUEST using default settings. SEQUEST used a curated database consisting of FASTA sequences extracted from UniProt (Mus musculus taxon identifier 10090). Parameters were set as follows: MS1 tolerance of 10 ppm; MS2 mass tolerance of 0.02 Da for Orbitrap detection; enzyme specificity was set as trypsin with two missed cleavages allowed; carbamidomethylation of cysteine was set as a fixed modification; and oxidation of methionine was set as a variable modification. The minimum peptide length was set to six amino acids. Peptide-spectrum-matches (PSMs) and protein identifications were filtered at 1% false discovery rate (FDR) threshold. For protein quantification and comparative analysis, we used the peak integration feature of the Proteome Discoverer software. For each identified protein, the average ion intensity of the unique peptides was used for protein abundance. The sham group was the control group.