Development of native mass spectrometry with nanoelectrospray ionization coupled to size exclusion chromatography for proteins

Rationale Native mass spectrometry (MS) is an analytical technique used to determine the molecular mass of protein complexes without cross‐linking. Size exclusion chromatography (SEC) coupled with native MS using conventional electrospray ionization (ESI) has been reported to allow online buffer exchange. To detect a wide variety of protein complexes without a collapse in the ionization process, it is important to build an online system that enables robust analysis with a low flow rate. Methods We created an online native MS system equipped with nanoESI connected to the SEC component (online SEC/nanoESI system) and optimized several parameters for SEC separation and ionization. The constructed system was used to measure a solution consisting of a protein mixture of various molecular masses (10–300 kDa) to verify characteristics such as the measurable molecular mass range, reproducibility, and online buffer exchange. Results The optimal flow rates for SEC separation and nanoESI analysis using this system were 200 and 1 μL/min, respectively. This system was able to analyze proteins in the ranges of 10–300 and 20–300 kDa for protein samples in ammonium acetate and nonvolatile buffer, respectively. Furthermore, the results of consecutive measurements showed that the relative standard deviations of the retention times and observed masses for each protein were sufficiently small. Conclusions We created an online SEC/nanoESI system and evaluated its utility for the analysis of various proteins in conventional measurement solvent and nonvolatile buffer. As a result, the structural stability and resolution of the proteins were found to be sufficient when using online buffer exchange. Therefore, this online SEC/nanoESI system would be a useful technique for obtaining mass spectra of various proteins automatically with good resolution, simply by loading samples into an autosampler.