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Trifluoroacetic acid (TFA) is often used as a mobile phase modifier to enhance reversed phase chromatographic performance. TFA adjusts solution pH and is an ion-pairing agent, but it is not typically suitable for electrospray ionization-mass spectrometry (ESI-MS) and liquid chromatography/MS (LC/MS) because of its significant signal suppression. Supercharging agents elevate peptide and protein charge states in ESI, increasing tandem MS (MS/MS) efficiency. Here, LC/MS protein supercharging was effected by adding agents to LC mobile phase solvents. Significantly, the ionization suppression generally observed with TFA was, for the most part, rescued by supercharging agents, with improved separation efficiency (higher number of theoretical plates) and lowered detection limits.

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 f

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 f

Understanding the charging mechanism of electrospray ionization is central to overcoming shortcomings such as ion suppression or limited dynamic range, and explaining phenomena such as supercharging. Towards that end, we explore what accumulated observations reveal about the mechanism of electrospray. We introduce the idea of an intermediate region for electrospray ionization (and other ionization methods) to account for the facts that solution charge state distributions (CSDs) do not correlate with those observed by ESI-MS (the latter bear more charge) and that gas phase reactions can reduce, but not increase, the extent of charging. This region incorporates properties (e.g., basicities) intermediate between solution and gas phase. Assuming that droplet species polarize within the high electric field leads to equations describing ion emission resembling those from the equilibrium partitioning model. The equations predict many trends successfully, including CSD shifts to higher m/z for concentrated analytes and shifts to lower m/z for sprays employing smaller emitter opening diameters. From this view, a single mechanism can be formulated to explain how reagents that promote analyte charging ("supercharging") such as m-NBA, sulfolane, and 3-nitrobenzonitrile increase analyte charge from "denaturing" and "native" solvent systems. It is suggested that additives' Brønsted basicities are inversely correlated to their ability to shift CSDs to lower m/z in positive ESI, as are Brønsted acidities for negative ESI. Because supercharging agents reduce an analyte's solution ionization, excess spray charge is bestowed on evaporating ions carrying fewer opposing charges. Brønsted basicity (or acidity) determines how much ESI charge is lost to the agent (unavailable to evaporating analyte).