Proteoform Specific Process Validation

A continuous process validation (CPV) system for assessing the concentration of proteoforms in a family of protein variants contained within complex biological compositions obtained from a fermentor, the CPV system comprising:

• a sampling system associated with the fermentor and operable to extract a sample of the biological composition from the fermentor;
• a top-down (TD) sector including a plurality of distinct TD analysis columns that are each configured and operable for intact proteoform resolution, for detection of specific analyte proteoforms in the sample and for generating data that identifies and quantifies the proteoforms;
• a TD multi-channel selection (TD mcsv) valve disposed between the sampling system and the plurality of TD analysis columns, the TD mcsv valve operable to selectively direct the sample to one or more of the columns of the plurality of TD analysis columns and then to an output of the TD sector;
• a bottom-up (BU) sector including a plurality of distinct BU analysis columns configured and operable for affinity purification, proteolysis of proteoforms during transport into the BU sector to generate proteoform specific signature peptides and generating data that identifies and quantifies the signature peptides;
• a sector coupling valve configured to selectively connect the output of the TD sector to an input of the BU sector for passage of the sample from the TD sector to the BU sector;
• a BU multi-channel selection (BU mcsv) valve disposed between the sector coupling valve and the plurality of BU analysis columns, the BU mcsv valve operable to direct the sample to one or more of the plurality of BU analysis columns and then to an output of the BU sector;
• and
• a controller configured and operable to selectively actuate the sampling system, the TD mcsv valve, the sector coupling valve and the BU mcsv valve to control the flow of the sample through the plurality of TD analysis columns and through the plurality of BU analysis columns according to a protocol adapted to validate the manufacturing process for the production of the complex biological compositions, the controller further configured to receive and evaluate the data from the TD and the BU sectors according to the protocol.