Protein identification by top-down mass spectrometry based methods yield intact mass of the proteins and indicate the presence of post-translational modifications (PTMs) and/or isoforms. Currently, the methods employed for top-down protein identification are performed using instruments with dual mass analyzers and are based on fragmenting isolated charge states, which greatly reduces the duty cycle of the instrument. High throughput top-down methods are required for protein identification in complex sample mixtures. We demonstrate the capability to perform intact protein identifications in a single-stage time-of-flight mass spectrometer during protein elution from a liquid chromatography (LC) column. In addition, we have developed a new data-independent fragmentation method known as `Continuous Accumulation of Selected Ions-Collisionally Activated Dissociation' (CASI-CAD) to fragment multiple charge states of the protein simultaneously for the purpose of identification in the LC timescale. CASI-CAD is performed without any precursor selection and thus, the duty-cycle of the instrument is not lowered. Both these methods unambiguously identified all the proteins in the human proteasome complex used for method development. The presence of PTMs and N-terminal modifications were also characterized for the proteins in this complex.

Supercharging reagents are known for their ability to enhance the multiple charging of proteins during electrospray ionization (ESI). This improves the mass measurement accuracy and fragmentation efficiency of proteins during ESI-MS. Currently, the mechanism behind supercharging is unknown. We have analyzed different supercharging reagents under a variety of solvent conditions to probe the mechanisms behind supercharging. In addition, the supercharging ability of sulfolane was utilized for proteins eluting from a column by adding the reagent to the LC solvents. Furthermore, reagent introduction in the vapor phase increased the signal intensity for intact proteins eluting from a column when compared to experiments performed without the reagent. These methods presented here are efficient top-down means to address complex samples in the chromatographic timescale.