Top-down mass spectrometry for protein molecular diagnostics, structure analysis, and biomarker discovery

Top-down mass spectrometry (TDMS) differs from the traditional bottom-up approach in that proteins are analyzed directly, rather than enzymatically digested prior to analysis. While bottom-up tends to be faster and more readily implemented, top-down has improved selectivity, enabling simultaneous characterization of dynamic and hard-to-predict events such as coding polymorphisms, alternative splicing, and posttranslational modifications. Thus, TDMS promises to provide a clearer picture of the biological variation that exists beyond gene translation. With the maturation of multidimensional sample processing procedures, data analysis tools, and “online” liquid chromatography and mass spectrometry technologies, top-down for proteomics investigations has achieved the sensitivity and dynamic range typically associated with peptide workflows. Plus, further advancements in native MS technologies have enabled TDMS to complement modern structural biology research by providing information on intact protein complexes such as subunit composition, stoichiometry, modifications, and interactions with various ligands and cofactors.