An integrated ten-pump, eight-channel parallel LC/MS system for automated high-throughput analysis of proteins

An integrated 10-pump eight-channel LC/MS system has been developed for automated high-throughput analysis of intact proteins in recombinant protein purification processes. The key features of the system include (1) a compact 10-pump HPLC module that uses two pumps to generate a binary gradient and 8 pumps to deliver the mixed gradient to eight independent flow channels; (2) a TOF mass spectrometer with an eight-channel multiplexed ESI interface, which records separate data for all eight channels over each HPLC run cycle; and (3) highly automated data processing software that allows unattended calculation of protein molecular weight (in Da) from original mass spectral data (in m/z). This system was used in the routine screening of fractions from preparative scale chromatography to monitor the purification process with the required mass accuracy and throughput. As an example, the production and purification of an acylated protein with a molecular weight of 9 kDa is described. Using this off-line approach, it is practical to fully characterize protein-containing fractions from column chromatography with an overall analytical throughput of 1 min/protein sample with minimum operator involvement.