Abstract: To better understand health and disease, one must go beyond the study of the 20,000 genes within the human genome and obtain a deep understanding of the functional proteins that they encode. Most proteomics relies on the digestion of intact proteins into smaller peptides with trypsin. However, a newer approach called “Top-Down Proteomics” directly analyzes intact proteins. Analysis of whole protein molecules provides the ability to examine protein sequences, mutations, and modifications in unprecedented detail. These mature, modified proteins are now called “proteoforms” (Smith and Kelleher, Science, 2018, 359 (6380), 1106-1107). New technology to accelerate top-down proteomics will be described in both “denatured” and “native” modes. Within “denatured” mode, we have mapped 11 proteoforms from the oncogene KRAS in the context of colorectal cancer (Ntai et al., PNAS, 2018, in press). Here we begin to understand how driving mutations in the KRAS gene affect post-translational modifications elsewhere on the expressed protein in a low-bias and isoform-specific manner (i.e., KRAS4b vs. KRAS 4a). Finally in native mode, analysis of whole protein complexes present natively within human cells will be showcased with uses cases drawn from cancer biology and primary metabolism (Skinner et al., Nat Chem Biol 2018, 14 (1), 36-41).