Mass spectrometry(MS)has become a crucial technique for the analysis of protein complexes.Native MS has traditionally examined protein subunit arrangements,while proteomics MS has focused on sequence identification.These two techniques are usually performed separately without harvesting the synergies between them.Here we describe the development of an integrated native MS and top-down proteomics method using Fourier transform ion cyclotron resonance(FTICR)to analyze macromolecular protein complexes in a single experiment.We address the challenges of employing top-down MS to directly fragment large macromolecular complexes in their native state in the gas phase,and we demonstrate the efficacy of this technique for direct acquirement of sequence to higher order structural information with several large complexes.We then summarize the unique functionalities of different activation/dissociation techniques.The platform expands the ability of MS to integrate proteomics and structural biology to provide insights into protein structure,function and regulation.