1) The document describes a method for analyzing proteoforms (protein complexes with different post-translational modifications) in membrane protein complexes using top-down proteomics. 2) Native gel electrophoresis was used to isolate two protein complexes, Complex IV and Complex V, from bovine heart mitochondria. 3) Using an unbiased extraction method and high-resolution mass spectrometry, 120 proteoforms were identified between the two complexes, including various post-translational modifications like phosphorylation and acetylation.