The evolution of technology to determine the composition of protein molecules with complete molecular specificity continues. As we move forward, one can frame the use of mass spectrometry and associated methods into a three-level enterprise: bottom up, top down and native proteomics. Native TDMS requires robust solutions to the challenges that arise when shifting to analyze proteins when ionized by electrospray at approximately neutral pH. Such a simple change creates many ripple effects in the separations, mass spectrometry and informatics that have been demonstrated by many over the past years to be of high value. Therefore, given the proven ability of native mass spectrometry to preserve high-value compositional information, we must begin to address the technical challenges associated with performing on-line and off-line LC-MS/MS with native-mode electrospray with high-resolution tandem mass spectrometry.