Proteomic profiles of myocardial tissue in two different etiologies of heart failure were investigated using right atrial appendages samples representative for the aortic valve disease and coronary heart disease using a quadrupole/hexapole FT-ICR MS that allowed collision induced dissociation (CID) of selected classifier masses. For comparison and further validation, classifier masses were also fragmented and analyzed using HPLC/Matrix assisted laser desorption ionization (MALDI) time-of-flight/time-of-flight (TOF/TOF) mass spectrometry.