Top-down proteomics provides information closely connected to complex disease phenotypes. Many protein molecules can be encoded by a single gene locus, owing to modifications such as methylation (Me) and phosphorylation (P). These different forms, which can be present simultaneously in the proteome, are called proteoforms . In this example, the expression of one protein-coding gene leads to four distinct proteoforms, owing to different combinations of Me and P modifications (top left). Top-down proteomic analysis preserves the proteoforms and yields 'proteoform-resolved' data; mock mass-spectrometry (MS) data are presented for this example (top right). Bottom-up analysis depends on the enzymatic digestion of proteins: the four distinct proteoforms form a mixture of five MS-compatible peptides (bottom left); mock MS data are presented (bottom right). The bottom-up analysis clearly shows an increase in the abundance of methylated and phosphorylated peptides, but it cannot link this information to the expression levels of the intact proteoforms, leading to an ambiguous result. The top-down analysis, by contrast, indicates that the doubly modified proteoform is upregulated compared with the other three forms. In a complementary approach, the full protein characterization afforded by top-down proteomics can be used to develop multiple reaction monitoring (MRM) assays that reliably report on distinct intact protein molecules. In the future, most clinical translational proteomic strategies are likely to take a combination approach, taking advantage of the sensitivity and high-throughput capacity of MRM and the high molecular precision of top-down proteomics.